@article{14478, abstract = {Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens.}, author = {Habig, Michael and Grasse, Anna V and Müller, Judith and Stukenbrock, Eva H. and Leitner, Hanna and Cremer, Sylvia}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {11}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Frequent horizontal chromosome transfer between asexual fungal insect pathogens}}, doi = {10.1073/pnas.2316284121}, volume = {121}, year = {2024}, } @article{10045, abstract = {Given a fixed finite metric space (V,μ), the {\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs. }, author = {Dvorak, Martin and Kolmogorov, Vladimir}, issn = {1436-4646}, journal = {Mathematical Programming}, keywords = {minimum 0-extension problem, metric labeling problem, discrete metric spaces, metric extensions, computational complexity, valued constraint satisfaction problems, discrete convex analysis, L-convex functions}, publisher = {Springer Nature}, title = {{Generalized minimum 0-extension problem and discrete convexity}}, doi = {10.1007/s10107-024-02064-5}, year = {2024}, } @article{15121, abstract = {We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges.}, author = {Zheng, Da Wei and Henzinger, Monika H}, issn = {1436-4646}, journal = {Mathematical Programming}, publisher = {Springer Nature}, title = {{Multiplicative auction algorithm for approximate maximum weight bipartite matching}}, doi = {10.1007/s10107-024-02066-3}, year = {2024}, } @article{15114, abstract = {As a key liquid organic hydrogen carrier, investigating the decomposition of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms and key intermediates involved in the dehydrogenation process of formic acid remain a great topic of debate due to ambiguous adsorbate interactions. In this research, we develop an advanced microkinetic model based on first-principles calculations, accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage effects in formic acid dehydrogenation. Our findings unequivocally demonstrate that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental results, the selectivity of H2 in the decomposition of formic acid on the Pd (1 1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic analysis aligns perfectly with experimental values at a temperature of 373 K.}, author = {Yao, Zihao and Liu, Xu and Bunting, Rhys and Wang, Jianguo}, issn = {0009-2509}, journal = {Chemical Engineering Science}, publisher = {Elsevier}, title = {{Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling}}, doi = {10.1016/j.ces.2024.119959}, volume = {291}, year = {2024}, } @article{15116, abstract = {Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.}, author = {Giubertoni, Giulia and Feng, Liru and Klein, Kevin and Giannetti, Guido and Rutten, Luco and Choi, Yeji and Van Der Net, Anouk and Castro-Linares, Gerard and Caporaletti, Federico and Micha, Dimitra and Hunger, Johannes and Deblais, Antoine and Bonn, Daniel and Sommerdijk, Nico and Šarić, Anđela and Ilie, Ioana M. and Koenderink, Gijsje H. and Woutersen, Sander}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {11}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration}}, doi = {10.1073/pnas.2313162121}, volume = {121}, year = {2024}, } @article{15117, abstract = {The hippocampal mossy fiber synapse, formed between axons of dentate gyrus granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the trisynaptic circuitry of the hippocampus. Because of its comparatively large size, this synapse is accessible to direct presynaptic recording, allowing a rigorous investigation of the biophysical mechanisms of synaptic transmission and plasticity. Furthermore, because of its placement in the very center of the hippocampal memory circuit, this synapse seems to be critically involved in several higher network functions, such as learning, memory, pattern separation, and pattern completion. Recent work based on new technologies in both nanoanatomy and nanophysiology, including presynaptic patch-clamp recording, paired recording, super-resolution light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy, has provided new insights into the structure, biophysics, and network function of this intriguing synapse. This brings us one step closer to answering a fundamental question in neuroscience: how basic synaptic properties shape higher network computations.}, author = {Vandael, David H and Jonas, Peter M}, issn = {1095-9203}, journal = {Science}, number = {6687}, pages = {eadg6757}, publisher = {AAAS}, title = {{Structure, biophysics, and circuit function of a "giant" cortical presynaptic terminal}}, doi = {10.1126/science.adg6757}, volume = {383}, year = {2024}, } @phdthesis{15094, abstract = {Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in discrete geometry that have captivated mathematicians for centuries, if not millennia. This thesis seeks to cast new light on these structures by illustrating specific instances where a topological perspective, specifically through discrete Morse theory and persistent homology, provides valuable insights. At first glance, the topology of these geometric objects might seem uneventful: point sets essentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which is a contractible space, and the topology of a network primarily involves the enumeration of connected components and cycles within the network. However, beneath this apparent simplicity, there lies an array of intriguing structures, a small subset of which will be uncovered in this thesis. Focused on three case studies, each addressing one of the mentioned objects, this work will showcase connections that intertwine topology with diverse fields such as combinatorial geometry, algorithms and data structures, and emerging applications like spatial biology. }, author = {Cultrera di Montesano, Sebastiano}, issn = {2663 - 337X}, pages = {108}, publisher = {Institute of Science and Technology Austria}, title = {{Persistence and Morse theory for discrete geometric structures}}, doi = {10.15479/at:ista:15094}, year = {2024}, } @inproceedings{15093, abstract = {We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right.}, author = {Cultrera di Montesano, Sebastiano and Edelsbrunner, Herbert and Henzinger, Monika H and Ost, Lara}, booktitle = {Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)}, editor = {Woodruff, David P.}, location = {Alexandria, VA, USA}, pages = {243 -- 295}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Dynamically maintaining the persistent homology of time series}}, doi = {10.1137/1.9781611977912.11}, year = {2024}, } @unpublished{15091, abstract = {Motivated by applications in the medical sciences, we study finite chromatic sets in Euclidean space from a topological perspective. Based on the persistent homology for images, kernels and cokernels, we design provably stable homological quantifiers that describe the geometric micro- and macro-structure of how the color classes mingle. These can be efficiently computed using chromatic variants of Delaunay and alpha complexes, and code that does these computations is provided.}, author = {Cultrera di Montesano, Sebastiano and Draganov, Ondrej and Edelsbrunner, Herbert and Saghafian, Morteza}, booktitle = {arXiv}, title = {{Chromatic alpha complexes}}, year = {2024}, } @article{15171, abstract = {The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity, they also affect each other. The nature of such ‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalizes synaptic co-dependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity while neighboring excitatory–excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, co-dependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighborly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena.}, author = {Agnes, Everton J. and Vogels, Tim P}, issn = {1546-1726}, journal = {Nature Neuroscience}, publisher = {Springer Nature}, title = {{Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks}}, doi = {10.1038/s41593-024-01597-4}, year = {2024}, }