@unpublished{13312,
abstract = {Superconductor/semiconductor hybrid devices have attracted increasing
interest in the past years. Superconducting electronics aims to complement
semiconductor technology, while hybrid architectures are at the forefront of
new ideas such as topological superconductivity and protected qubits. In this
work, we engineer the induced superconductivity in two-dimensional germanium
hole gas by varying the distance between the quantum well and the aluminum. We
demonstrate a hard superconducting gap and realize an electrically and flux
tunable superconducting diode using a superconducting quantum interference
device (SQUID). This allows to tune the current phase relation (CPR), to a
regime where single Cooper pair tunneling is suppressed, creating a $ \sin
\left( 2 \varphi \right)$ CPR. Shapiro experiments complement this
interpretation and the microwave drive allows to create a diode with $ \approx
100 \%$ efficiency. The reported results open up the path towards monolithic
integration of spin qubit devices, microwave resonators and (protected)
superconducting qubits on a silicon technology compatible platform.},
author = {Valentini, Marco and Sagi, Oliver and Baghumyan, Levon and Gijsel, Thijs de and Jung, Jason and Calcaterra, Stefano and Ballabio, Andrea and Servin, Juan Aguilera and Aggarwal, Kushagra and Janik, Marian and Adletzberger, Thomas and Souto, Rubén Seoane and Leijnse, Martin and Danon, Jeroen and Schrade, Constantin and Bakkers, Erik and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios},
booktitle = {arXiv},
keywords = {Mesoscale and Nanoscale Physics},
title = {{Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas}},
doi = {10.48550/arXiv.2306.07109},
year = {2023},
}
@article{13314,
abstract = {The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division.},
author = {Dunajova, Zuzana and Prats Mateu, Batirtze and Radler, Philipp and Lim, Keesiang and Brandis, Dörte and Velicky, Philipp and Danzl, Johann G and Wong, Richard W. and Elgeti, Jens and Hannezo, Edouard B and Loose, Martin},
issn = {1745-2481},
journal = {Nature Physics},
pages = {1916--1926},
publisher = {Springer Nature},
title = {{Chiral and nematic phases of flexible active filaments}},
doi = {10.1038/s41567-023-02218-w},
volume = {19},
year = {2023},
}
@article{13315,
abstract = {How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties.},
author = {Barbier, Jean and Camilli, Francesco and Mondelli, Marco and Sáenz, Manuel},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {30},
publisher = {National Academy of Sciences},
title = {{Fundamental limits in structured principal component analysis and how to reach them}},
doi = {10.1073/pnas.2302028120},
volume = {120},
year = {2023},
}
@article{13316,
abstract = {Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN.},
author = {Toshima, Junko Y. and Tsukahara, Ayana and Nagano, Makoto and Tojima, Takuro and Siekhaus, Daria E and Nakano, Akihiko and Toshima, Jiro},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network}},
doi = {10.7554/eLife.84850},
volume = {12},
year = {2023},
}
@article{13317,
abstract = {We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction.},
author = {Sugimoto, Shoki and Henheik, Sven Joscha and Riabov, Volodymyr and Erdös, László},
issn = {1572-9613},
journal = {Journal of Statistical Physics},
number = {7},
publisher = {Springer Nature},
title = {{Eigenstate thermalisation hypothesis for translation invariant spin systems}},
doi = {10.1007/s10955-023-03132-4},
volume = {190},
year = {2023},
}
@article{13318,
abstract = {Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes.},
author = {Volberg, Alexander and Zhang, Haonan},
issn = {1432-1807},
journal = {Mathematische Annalen},
publisher = {Springer Nature},
title = {{Noncommutative Bohnenblust–Hille inequalities}},
doi = {10.1007/s00208-023-02680-0},
year = {2023},
}
@article{13319,
abstract = {We prove that the generator of the L2 implementation of a KMS-symmetric quantum Markov semigroup can be expressed as the square of a derivation with values in a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially symmetric semigroups and the second-named author for GNS-symmetric semigroups. This result hinges on the introduction of a new completely positive map on the algebra of bounded operators on the GNS Hilbert space. This transformation maps symmetric Markov operators to symmetric Markov operators and is essential to obtain the required inner product on the Hilbert bimodule.},
author = {Vernooij, Matthijs and Wirth, Melchior},
issn = {1432-0916},
journal = {Communications in Mathematical Physics},
pages = {381--416},
publisher = {Springer Nature},
title = {{Derivations and KMS-symmetric quantum Markov semigroups}},
doi = {10.1007/s00220-023-04795-6},
volume = {403},
year = {2023},
}
@inproceedings{13321,
abstract = {We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm.},
author = {Xu, Yizhou and Hou, Tian Qi and Liang, Shan Suo and Mondelli, Marco},
booktitle = {2023 IEEE Information Theory Workshop},
isbn = {9798350301496},
issn = {2475-4218},
location = {Saint-Malo, France},
pages = {294--298},
publisher = {Institute of Electrical and Electronics Engineers},
title = {{Approximate message passing for multi-layer estimation in rotationally invariant models}},
doi = {10.1109/ITW55543.2023.10160238},
year = {2023},
}
@phdthesis{13331,
abstract = {The extension of extremal combinatorics to the setting of exterior algebra is a work
in progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.
},
author = {Köse, Seyda},
issn = {2791-4585},
pages = {26},
publisher = {Institute of Science and Technology Austria},
title = {{Exterior algebra and combinatorics}},
doi = {10.15479/at:ista:13331},
year = {2023},
}
@misc{13336,
author = {Kleshnina, Maria},
publisher = {Zenodo},
title = {{kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games}},
doi = {10.5281/ZENODO.8059564},
year = {2023},
}
@article{13340,
abstract = {Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation.},
author = {Gemen, Julius and Church, Jonathan R. and Ruoko, Tero-Petri and Durandin, Nikita and Białek, Michał J. and Weissenfels, Maren and Feller, Moran and Kazes, Miri and Borin, Veniamin A. and Odaybat, Magdalena and Kalepu, Rishir and Diskin-Posner, Yael and Oron, Dan and Fuchter, Matthew J. and Priimagi, Arri and Schapiro, Igor and Klajn, Rafal},
issn = {1095-9203},
journal = {Science},
number = {6664},
pages = {1357--1363},
publisher = {American Association for the Advancement of Science},
title = {{Disequilibrating azoarenes by visible-light sensitization under confinement}},
doi = {10.1126/science.adh9059},
volume = {381},
year = {2023},
}
@article{13342,
abstract = {Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease.},
author = {Kroll, Janina and Hauschild, Robert and Kuznetcov, Arthur and Stefanowski, Kasia and Hermann, Monika D. and Merrin, Jack and Shafeek, Lubuna B and Müller-Taubenberger, Annette and Renkawitz, Jörg},
issn = {1460-2075},
journal = {EMBO Journal},
publisher = {Embo Press},
title = {{Adaptive pathfinding by nucleokinesis during amoeboid migration}},
doi = {10.15252/embj.2023114557},
year = {2023},
}
@article{8682,
abstract = {It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces.},
author = {Browning, Timothy D and Boudec, Pierre Le and Sawin, Will},
issn = {0003-486X},
journal = {Annals of Mathematics},
number = {3},
pages = {1115--1203},
publisher = {Princeton University},
title = {{The Hasse principle for random Fano hypersurfaces}},
doi = {10.4007/annals.2023.197.3.3},
volume = {197},
year = {2023},
}
@article{9034,
abstract = {We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors.},
author = {Wilsch, Florian Alexander},
issn = {1687-0247},
journal = {International Mathematics Research Notices},
number = {8},
pages = {6780--6808},
publisher = {Oxford Academic},
title = {{Integral points of bounded height on a log Fano threefold}},
doi = {10.1093/imrn/rnac048},
volume = {2023},
year = {2023},
}
@article{14783,
abstract = {Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy.},
author = {Cheung, Giselle T and Chever, Oana and Rollenhagen, Astrid and Quenech’du, Nicole and Ezan, Pascal and Lübke, Joachim H. R. and Rouach, Nathalie},
issn = {2073-4409},
journal = {Cells},
keywords = {General Medicine},
number = {8},
publisher = {MDPI},
title = {{Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses}},
doi = {10.3390/cells12081133},
volume = {12},
year = {2023},
}
@article{14784,
abstract = {The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.},
author = {Gallardo-Dodd, Carlos J. and Oertlin, Christian and Record, Julien and Galvani, Rômulo G. and Sommerauer, Christian and Kuznetsov, Nikolai V. and Doukoumopoulos, Evangelos and Ali, Liaqat and Oliveira, Mariana M. S. and Seitz, Christina and Percipalle, Mathias and Nikić, Tijana and Sadova, Anastasia A. and Shulgina, Sofia M. and Shmarov, Vjacheslav A. and Kutko, Olga V. and Vlasova, Daria D. and Orlova, Kseniya D. and Rykova, Marina P. and Andersson, John and Percipalle, Piergiorgio and Kutter, Claudia and Ponomarev, Sergey A. and Westerberg, Lisa S.},
issn = {2375-2548},
journal = {Science Advances},
keywords = {Multidisciplinary},
number = {34},
publisher = {American Association for the Advancement of Science},
title = {{Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells}},
doi = {10.1126/sciadv.adg1610},
volume = {9},
year = {2023},
}
@article{14785,
abstract = {Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid‐encoded genes is similar to that of chromosome‐encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.},
author = {Nies, Fabian and Wein, Tanita and Hanke, Dustin M. and Springstein, Benjamin L and Alcorta, Jaime and Taubenheim, Claudia and Dagan, Tal},
issn = {1758-2229},
journal = {Environmental Microbiology Reports},
keywords = {Agricultural and Biological Sciences (miscellaneous), Ecology, Evolution, Behavior and Systematics},
number = {6},
pages = {656--668},
publisher = {Wiley},
title = {{Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803}},
doi = {10.1111/1758-2229.13203},
volume = {15},
year = {2023},
}
@article{14786,
abstract = {Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species.},
author = {Filipović Marijić, Vlatka and Subirana, Maria Angels and Schaumlöffel, Dirk and Barišić, Josip and Gontier, Etienne and Krasnici, Nesrete and Mijošek, Tatjana and Hernández-Orts, Jesús S. and Scholz, Tomáš and Erk, Marijana},
issn = {0048-9697},
journal = {Science of The Total Environment},
keywords = {Pollution, Waste Management and Disposal, Environmental Chemistry, Environmental Engineering},
publisher = {Elsevier},
title = {{First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS}},
doi = {10.1016/j.scitotenv.2023.164010},
volume = {887},
year = {2023},
}
@article{14787,
abstract = {Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes ofMimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system.},
author = {Stankowski, Sean and Chase, Madeline A. and McIntosh, Hanna and Streisfeld, Matthew A.},
issn = {1365-294X},
journal = {Molecular Ecology},
keywords = {Genetics, Ecology, Evolution, Behavior and Systematics},
number = {8},
pages = {2041--2054},
publisher = {Wiley},
title = {{Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone}},
doi = {10.1111/mec.16849},
volume = {32},
year = {2023},
}
@article{14788,
abstract = {Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.
Here, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane.},
author = {Mund, Markus and Tschanz, Aline and Wu, Yu-Le and Frey, Felix F and Mehl, Johanna L. and Kaksonen, Marko and Avinoam, Ori and Schwarz, Ulrich S. and Ries, Jonas},
issn = {1540-8140},
journal = {Journal of Cell Biology},
keywords = {Cell Biology},
number = {3},
publisher = {Rockefeller University Press},
title = {{Clathrin coats partially preassemble and subsequently bend during endocytosis}},
doi = {10.1083/jcb.202206038},
volume = {222},
year = {2023},
}