@article{18904,
abstract = {The Planetary Transits and Oscillations of stars mission (PLATO) will allow us to measure surface rotation and monitor photometric activity of tens of thousands of main sequence solar-type and subgiant stars. This paper is the first of a series dedicated to the preparation of the analysis of stellar surface rotation and photospheric activity with the near-future PLATO data. We describe in this work the strategy that will be implemented in the PLATO pipeline to measure stellar surface rotation, photometric activity, and long-term modulations. The algorithms are applied on both noise-free and noisy simulations of solar-type stars, which include activity cycles, latitudinal differential rotation, and spot evolution. PLATO simulated systematics are included in the noisy light curves. We show that surface rotation periods can be recovered with confidence for most of the stars with only six months of observations and that the recovery rate of the analysis significantly improves as additional observations are collected. This means that the first PLATO data release will already provide a substantial set of measurements for this quantity, with a significant refinement on their quality as the instrument obtains longer light curves. Measuring the Schwabe-like magnetic activity cycle during the mission will require that the same field be observed over a significant timescale (more than four years). Nevertheless, PLATO will provide a vast and robust sample of solar-type stars with constraints on the activity-cycle length. Such a sample is lacking from previous missions dedicated to space photometry.},
author = {Breton, S. N. and Lanza, A. F. and Messina, S. and Pagano, I. and Bugnet, Lisa Annabelle and Corsaro, E. and García, R. A. and Mathur, S. and Santos, A. R. G. and Aigrain, S. and Amard, L. and Brun, A. S. and Degott, L. and Noraz, Q. and Palakkatharappil, D. B. and Panetier, E. and Strugarek, A. and Belkacem, K. and Goupil, M.-J and Ouazzani, R. M. and Philidet, J. and Renié, C. and Roth, O.},
issn = {1432-0746},
journal = {Astronomy and Astrophysics},
publisher = {EDP Sciences},
title = {{Measuring stellar surface rotation and activity with the PLATO mission. I. Strategy and application to simulated light curves}},
doi = {10.1051/0004-6361/202449893},
volume = {689},
year = {2024},
}
@inproceedings{18906,
abstract = {Expander decompositions of graphs have significantly advanced the understanding of many classical graph problems and led to numerous fundamental theoretical results. However, their adoption in practice has been hindered due to their inherent intricacies and large hidden factors in their asymptotic running times. Here, we introduce the first practically efficient algorithm for computing expander decompositions and their hierarchies and demonstrate its effectiveness and utility by incorporating it as the core component in a novel solver for the normalized cut graph clustering objective.
Our extensive experiments on a variety of large graphs show that our expander-based algorithm outperforms state-of-the-art solvers for normalized cut with respect to solution quality by a large margin on a variety of graph classes such as citation, e-mail, and social networks or web graphs while remaining competitive in running time.},
author = {Hanauer, Kathrin and Henzinger, Monika H and Münk, Robin and Räcke, Harald and Vötsch, Maximilian},
booktitle = {Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining},
isbn = {9798400704901},
location = {Barcelona, Spain},
pages = {1016--1027},
publisher = {ACM},
title = {{Expander hierarchies for normalized cuts on graphs}},
doi = {10.1145/3637528.3671978},
year = {2024},
}
@article{18908,
abstract = {Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for > 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.},
author = {Le Moan, Alan and Stankowski, Sean and Rafajlović, Marina and Ortega-Martinez, Olga and Faria, Rui and Butlin, Roger K and Johannesson, Kerstin},
issn = {2056-3744},
journal = {Evolution Letters},
number = {4},
pages = {575--586},
publisher = {Oxford University Press},
title = {{Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes}},
doi = {10.1093/evlett/qrae014},
volume = {8},
year = {2024},
}
@article{18910,
abstract = {Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.},
author = {Schanda, Paul and Haran, Gilad},
issn = {1936-1238},
journal = {Annual Review of Biophysics},
pages = {247--273},
publisher = {Annual Reviews},
title = {{NMR and single-molecule FRET insights into fast protein motions and their relation to function}},
doi = {10.1146/annurev-biophys-070323-022428},
volume = {53},
year = {2024},
}
@inproceedings{18912,
abstract = {This paper presents a computational method for automatically creating fabricable 3D wire sculptures from various input modalities, including 3D models, images, and even text. There are several challenges to wire art creation. For example, artists must express the desired visual as a sparse wire representation. It is also difficult to manually bend wires in the air without guidance to fabricate the designed 3D curves. Our workflow solves these challenges by using two core techniques. First, we present an algorithm that automatically generates a fabricable 3D curve representation of the target based on a loss function that measures the semantic distance between the rendered curve and the target. The loss function can be defined using different pre-trained vision-language neural networks to generate wire art from different input types. The loss function is then optimized using differentiable rendering specifically targeting 3D parametric curves. Our method can incorporate various fabrication constraints on the wire as additional regularization terms in the optimization process. Second, we present an algorithm to generate a 3D printable jig structure that can be used to fabricate the generated wire path. The major challenge in the jig generation stems from the design of an intersection-free surface mesh for 3D printing, which we address with our inflation algorithm. The experimental results indicate that our method can handle a wider range of input types and can produce physically fabricable wire shapes compared to previous wire generation methods. Various wire arts have been fabricated using our 3D-printed jig to demonstrate its effectiveness in 3D wire bending.},
author = {Tojo, Kenji and Shamir, Ariel and Bickel, Bernd and Umetani, Nobuyuki},
booktitle = {SIGGRAPH '24: ACM SIGGRAPH 2024 Conference Papers},
isbn = {9798400705250},
location = {Denver, CO, United States},
publisher = {ACM},
title = {{Fabricable 3D wire art}},
doi = {10.1145/3641519.3657453},
year = {2024},
}
@inproceedings{18913,
abstract = {With the proliferation of blockchain technology in high-value sectors, consensus protocols are becoming critical infrastructures. The rapid innovation cycle in Byzantine fault tolerant (BFT) consensus protocols has culminated in HotStuff, which provides linear message complexity in the partially synchronous setting. To achieve this, HotStuff leverages a leader that collects, aggregates, and broadcasts the messages of other validators. This paper analyzes the security implications of such approaches in practice, from the perspective of liveness and availability.
By implementing attacks in a globally-distributed testbed, we show that state-of-the-art leader-based protocols are vulnerable to denial-of-service (DoS) attacks on the leader. Our attacks, demonstrated on committees of up to 64 validators, manage to disrupt liveness within seconds, using only a few tens of Mbps of attack bandwidth per validator. Crucially, the cost and effectiveness of the attacks are independent of the committee size. Based on the outcome of these experiments, we then propose and test effective mitigations. Our findings show that advancements in both protocol design and network-layer defenses can greatly improve the practical resilience of BFT consensus protocols.},
author = {Giuliari, Giacomo and Sonnino, Alberto and Frei, Marc and Streun, Fabio and Kokoris Kogias, Eleftherios and Perrig, Adrian},
booktitle = {Proceedings of the 19th ACM Asia Conference on Computer and Communications Security},
isbn = {9798400704826},
location = {Singapore, Singapore},
pages = {1345--1360},
publisher = {ACM},
title = {{An empirical study of consensus protocols’ DoS resilience}},
doi = {10.1145/3634737.3656997},
year = {2024},
}
@inproceedings{18917,
abstract = {An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in ℝ³ consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in ℝ³ admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument.
We prove the following variant of this result: Any mass distribution (or point set) in ℝ³ admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction.
Moreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in ℝ³ (with prescribed normal direction of one of the planes) in time O^*(n^{5/2}).},
author = {Aronov, Boris and Basit, Abdul and Ramesh, Indu and Tasinato, Gianluca and Wagner, Uli},
booktitle = {40th International Symposium on Computational Geometry},
isbn = {9783959773164},
location = {Athens, Greece},
pages = {8:1--8:15},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Eight-partitioning points in 3D, and efficiently too}},
doi = {10.4230/LIPIcs.SoCG.2024.8},
volume = {293},
year = {2024},
}
@article{18919,
abstract = {The integration of theory and experiment makes possible tracking the slow evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic phase under the influence of electron-lattice coupling.},
author = {Baykusheva, Denitsa Rangelova},
issn = {1745-2481},
journal = {Nature Physics},
number = {5},
pages = {684--685},
publisher = {Springer Nature},
title = {{Through the slopes of a light-induced phase transition}},
doi = {10.1038/s41567-024-02401-7},
volume = {20},
year = {2024},
}
@article{18920,
abstract = {The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis.},
author = {Homola, Miroslav and Büttner, Renate Carina and Füzik, Tibor and Křepelka, Pavel and Holbová, Radka and Nováček, Jiří and Chaillet, Marten L. and Žák, Jakub and Grybchuk, Danyil and Förster, Friedrich and Wilson, William H. and Schroeder, Declan C. and Plevka, Pavel},
issn = {2375-2548},
journal = {Science Advances},
number = {15},
publisher = {American Association for the Advancement of Science},
title = {{Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi}},
doi = {10.1126/sciadv.adk1954},
volume = {10},
year = {2024},
}
@inproceedings{18922,
abstract = {Let G be a directed graph with m edges and n vertices. We present a deterministic linear-time algorithm for computing the 3-edge-connected components of G. This is a significant improvement over the previous best bound by Georgiadis et al. [SODA 2023], which is Õ(m√{m}) and randomized. Our result is based on a novel characterization of 2-edge cuts in directed graphs and on a new technique that exploits the concept of divergent spanning trees and 2-connectivity-light graphs, and requires a careful modification of the minset-poset technique of Gabow [TALG 2016]. As a side result, our new technique yields also an oracle for providing in constant time a minimum edge-cut for any two vertices that are not 3-edge-connected. The oracle uses space O(n) and can be built in O(mlog n) time: given two query vertices, it determines in constant time whether they are 3-edge-connected, or provides a k-edge cut, with k≤ 2, that separates them.},
author = {Georgiadis, Loukas and Italiano, Giuseppe F. and Kosinas, Evangelos},
booktitle = {65th Annual Symposium on Foundations of Computer Science},
isbn = {9798331516741},
location = {Chicago, IL, United States},
pages = {62--85},
publisher = {IEEE},
title = {{Computing the 3-edge-connected components of directed graphs in linear time}},
doi = {10.1109/focs61266.2024.00015},
year = {2024},
}
@article{18923,
abstract = {Combinatorial optimization is a challenging problem applicable in a wide range of fields from logistics to finance. Recently, quantum computing has been used to attempt to solve these problems using a range of algorithms, including parameterized quantum circuits, adiabatic protocols, and quantum annealing. These solutions typically have several challenges: 1) there is little to no performance gain over classical methods; 2) not all constraints and objectives may be efficiently encoded in the quantum ansatz; and 3) the solution domain of the objective function may not be the same as the bit strings of measurement outcomes. This work presents “nonnative hybrid algorithms”: a framework to overcome these challenges by integrating quantum and classical resources with a hybrid approach. By designing nonnative quantum variational anosatzes that inherit some but not all problem structure, measurement outcomes from the quantum computer can act as a resource to be used by classical routines to indirectly compute optimal solutions, partially overcoming the challenges of contemporary quantum optimization approaches. These methods are demonstrated using a publicly available neutral-atom quantum computer on two simple problems of Max k-Cut and maximum independent set. We find improvements in solution quality when comparing the hybrid algorithm to its “no quantum” version, a demonstration of a “comparative advantage.”},
author = {Wurtz, Jonathan and Sack, Stefan and Wang, Sheng-Tao},
issn = {2689-1808},
journal = {IEEE Transactions on Quantum Engineering},
pages = {1--14},
publisher = {Institute of Electrical and Electronics Engineers },
title = {{Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms}},
doi = {10.1109/tqe.2024.3443660},
volume = {5},
year = {2024},
}
@inproceedings{18925,
abstract = {Given the increasingly stringent requirements on the performance and efficiency of communication networks, over the last years, great efforts have been made to render networks more flexible and programmable. In particular, modern networks support a flexible rerouting of flows, e.g., depending on the dynamically changing traffic or network conditions. However, the underlying algorithmic problems are still not well-understood today.In this paper, we revisit the k-Network Flow Update problem that asks for a schedule to reroute k unsplittable flows from their current paths to the given new paths, in a congestion-free manner in a capacitated network. We show that the problem is already NP-hard for three acyclic flows on simple directed graphs. Our main contribution is an efficient algorithm for sparse networks; specifically the algorithm is fixed parameter tractable in the number of flows and the treewidth of a graph that is the union of all flows. Our results also settle the open complexity question in the literature.},
author = {Ceylan, Esra and Chatterjee, Krishnendu and Schmid, Stefan and Svoboda, Jakub},
booktitle = {NOMS 2024-2024 IEEE Network Operations and Management Symposium},
isbn = {9798350327946},
issn = {2374-9709},
location = {Seoul, Republic of Korea},
publisher = {IEEE},
title = {{Congestion-free rerouting of network flows: Hardness and an FPT algorithm}},
doi = {10.1109/noms59830.2024.10575579},
year = {2024},
}
@article{18926,
abstract = {We study weak solutions to mean curvature flow satisfying Young’s angle condition for general contact angles α ∈ (0, π). First, we construct BV solutions by using the Allen-Cahn approximation with boundary contact energy as proposed by Owen and Sternberg. Second, we prove the weak-strong uniqueness and stability for this solution concept. The main ingredient for both results is a relative energy, which can also be interpreted as a tilt excess. },
author = {Hensel, Sebastian and Laux, Tim},
issn = {0022-2518},
journal = {Indiana University Mathematics Journal},
number = {1},
pages = {111--148},
publisher = {Indiana University Mathematics Journal},
title = {{BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness}},
doi = {10.1512/iumj.2024.73.9701},
volume = {73},
year = {2024},
}
@inproceedings{18928,
abstract = {Algorithms with predictions is a new research direction that leverages machine learned predictions for algorithm design. So far a plethora of recent works have incorporated predictions to improve on worst-case bounds for online problems. In this paper, we initiate the study of complexity of dynamic data structures with predictions, including dynamic graph algorithms. Unlike online algorithms, the goal in dynamic data structures is to maintain the solution efficiently with every update.
We investigate three natural models of prediction: (1) δ-accurate predictions where each predicted request matches the true request with probability δ, (2) list-accurate predictions where a true request comes from a list of possible requests, and (3) bounded delay predictions where the true requests are a permutation of the predicted requests. We give general reductions among the prediction models, showing that bounded delay is the strongest prediction model, followed by list-accurate, and δ-accurate.
Further, we identify two broad problem classes based on lower bounds due to the Online Matrix Vector (OMv) conjecture. Specifically, we show that locally correctable dynamic problems have strong conditional lower bounds for list-accurate predictions that are equivalent to the non-prediction setting, unless list-accurate predictions are perfect. Moreover, we show that locally reducible dynamic problems have time complexity that degrades gracefully with the quality of bounded delay predictions. We categorize problems with known OMv lower bounds accordingly and give several upper bounds in the delay model that show that our lower bounds are almost tight.
We note that concurrent work by v.d.Brand et al. [SODA '24] and Liu and Srinivas [arXiv:2307.08890] independently study dynamic graph algorithms with predictions, but their work is mostly focused on showing upper bounds.},
author = {Henzinger, Monika H and Saha, Barna and Seybold, Martin P. and Ye, Christopher},
booktitle = {15th Innovations in Theoretical Computer Science Conference},
isbn = {9783959773096},
issn = {1868-8969},
location = {Berkeley, CA, United States},
pages = {62:1--62:25},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{On the complexity of algorithms with predictions for dynamic graph problems}},
doi = {10.4230/LIPIcs.ITCS.2024.62},
volume = {287},
year = {2024},
}
@article{18930,
abstract = {We study sumsets 𝒜 + ℬ in the set of squares 𝒮 (and, more generally, in the set of kth powers 𝒮k, where k ≥2 is an integer). It is known by a result of Gyarmati that 𝒜 + ℬ ⊂ 𝒮k ∩[1,N] implies that min(|𝒜|,|ℬ|) =Ok(logN). Here, we study how the upper bound on |ℬ| decreases, when the size of |𝒜| increases (or vice versa). In particular, if |𝒜| ≥ Ck1m m(logN)1m , then |ℬ| = Ok(m2logN), for sufficiently large N, a positive integer m and an explicit constant C > 0. For example, with m ∼ loglogN this gives: If |𝒜| ≥ CkloglogN,then |ℬ| = Ok(logN(loglogN)2).},
author = {Elsholtz, Christian and Wurzinger, Lena},
issn = {1464-3847},
journal = {The Quarterly Journal of Mathematics},
number = {4},
pages = {1243--1254},
publisher = {Oxford University Press},
title = {{Sumsets in the set of squares}},
doi = {10.1093/qmath/haae044},
volume = {75},
year = {2024},
}
@article{18934,
abstract = {The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt .},
author = {Sárkány, Zsuzsa and Figueiredo, Francisco and Macedo-Ribeiro, Sandra and Martins, Pedro M.},
issn = {1939-4586},
journal = {Molecular Biology of the Cell},
number = {3},
publisher = {American Society for Cell Biology},
title = {{NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation}},
doi = {10.1091/mbc.e23-07-0289},
volume = {35},
year = {2024},
}
@article{18937,
abstract = {A detailed structural, magnetic as well as dielectric dynamics study is carried out to investigate the influence of Bi3+ on YCrO3. All the samples crystalize in orthorhombic structure with Pnma symmetry and the grains are mostly stretched with Bi. A coexisting tunable fraction of both antiferromagnetic (AFM) and weak ferromagnetic (WFM) phases is acquired by the system down to Low-T. An abnormal negative magnetization in zero field is correlated to the competition among AFM and WFM phases. Maximum magnetization decreases while the coercivity first increases and then decreases with Bi is correlated to the competing effect between the local deformation and Cr–O–Cr exchange interaction. The magnetodielectric coupling with improved permittivity might be associated with the 6s2 lone pair electron of Bi3+. Furthermore, ac-conductivity increases with a decrease in activation energy (0.27–0.11 eV), is explained in the framework of structural model and charge carrier hopping between Cr3+ and Cr4+ ions.},
author = {Ray, Sujata Kumari and Pati, Anupama and Sahoo, Payala and Sahoo, A.K. and Singh, Saurabh and Takeuchi, Tsunehiro and Dash, S.},
issn = {0921-4526},
journal = {Physica B: Condensed Matter},
publisher = {Elsevier},
title = {{Tunable magnetoelectronic properties in Bi3+ substituted YCrO3}},
doi = {10.1016/j.physb.2024.416018},
volume = {685},
year = {2024},
}
@article{18938,
abstract = {The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the –1 frame, occur at specific evolutionarily optimized “slippery” sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry–based method called “translational tiling proteomics” for interrogating the full set of possible –1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical “slippery” sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed.},
author = {Springstein, Benjamin L and Paulo, Joao A. and Park, Hankum and Henry, Kemardo and Fleming, Eleanor and Feder, Zoë and Harper, J. Wade and Hochschild, Ann},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {6},
publisher = {National Academy of Sciences},
title = {{Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics}},
doi = {10.1073/pnas.2317453121},
volume = {121},
year = {2024},
}
@article{18940,
abstract = {BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression.},
author = {Knabl, Paul and Schauer, Alexandra and Pomreinke, Autumn P and Zimmermann, Bob and Rogers, Katherine W and Čapek, Daniel and Müller, Patrick and Genikhovich, Grigory},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator}},
doi = {10.7554/elife.80803},
volume = {13},
year = {2024},
}
@article{18944,
abstract = {Understanding connectivity patterns exhibited by endangered species living in fragmented habitats is fundamental to improving management and conservation actions. Such improvements can be particularly pressing at the trailing edges of these habitats, where populations are facing the greatest challenges from climate change, and appear even more crucial if the species is commercially harvested. Seascape genetics have been increasingly used to meet these needs. In this study, we examined connectivity patterns among 32 populations of the oarweed kelp Laminaria digitata located at the species’ southern range limit. The distance (or sampling gap) between neighboring populations ranged from a few km to a few 100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses of population structure; (2) test whether on-shelf islands are genetically more differentiated than mainland populations; (3) evaluate the relative importance of various abiotic conditions in shaping the genetic structure; and (4) evaluate if the relative importance of each environmental factor varied according to sampling schemes. Our analyses revealed a positive relationship between connectivity links and genetic diversity: populations with high levels of connectivity were genetically enriched while isolated populations showed signs of genetic erosion. The genetically impoverished populations corresponded to the southernmost populations as well as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay) and the northernmost population in Pas-de-Calais. By performing distance-based redundancy analysis on various sampling schemes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor when analyzing at a final spatial resolution.},
author = {Fouqueau, Louise and Reynes, L and Tempera, F and Bajjouk, T and Blanfuné, A and Chevalier, C and Laurans, M and Mauger, S and Sourisseau, M and Assis, J and Lévêque, L and Valero, M},
issn = {1616-1599},
journal = {Marine Ecology Progress Series},
pages = {23--42},
publisher = {Inter-Research Science Center},
title = {{Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes}},
doi = {10.3354/meps14640},
volume = {740},
year = {2024},
}