TY - JOUR
AB - 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.
AU - Habig, Michael
AU - Grasse, Anna V
AU - Müller, Judith
AU - Stukenbrock, Eva H.
AU - Leitner, Hanna
AU - Cremer, Sylvia
ID - 14478
IS - 11
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
TI - Frequent horizontal chromosome transfer between asexual fungal insect pathogens
VL - 121
ER -
TY - JOUR
AB - 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.
AU - Dvorak, Martin
AU - Kolmogorov, Vladimir
ID - 10045
JF - Mathematical Programming
KW - minimum 0-extension problem
KW - metric labeling problem
KW - discrete metric spaces
KW - metric extensions
KW - computational complexity
KW - valued constraint satisfaction problems
KW - discrete convex analysis
KW - L-convex functions
SN - 0025-5610
TI - Generalized minimum 0-extension problem and discrete convexity
ER -
TY - JOUR
AB - 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.
AU - Zheng, Da Wei
AU - Henzinger, Monika H
ID - 15121
JF - Mathematical Programming
SN - 0025-5610
TI - Multiplicative auction algorithm for approximate maximum weight bipartite matching
ER -
TY - JOUR
AB - 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.
AU - Yao, Zihao
AU - Liu, Xu
AU - Bunting, Rhys
AU - Wang, Jianguo
ID - 15114
JF - Chemical Engineering Science
SN - 0009-2509
TI - Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling
VL - 291
ER -
TY - JOUR
AB - 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.
AU - Giubertoni, Giulia
AU - Feng, Liru
AU - Klein, Kevin
AU - Giannetti, Guido
AU - Rutten, Luco
AU - Choi, Yeji
AU - Van Der Net, Anouk
AU - Castro-Linares, Gerard
AU - Caporaletti, Federico
AU - Micha, Dimitra
AU - Hunger, Johannes
AU - Deblais, Antoine
AU - Bonn, Daniel
AU - Sommerdijk, Nico
AU - Šarić, Anđela
AU - Ilie, Ioana M.
AU - Koenderink, Gijsje H.
AU - Woutersen, Sander
ID - 15116
IS - 11
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
TI - Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration
VL - 121
ER -
TY - JOUR
AB - 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.
AU - Vandael, David H
AU - Jonas, Peter M
ID - 15117
IS - 6687
JF - Science
TI - Structure, biophysics, and circuit function of a "giant" cortical presynaptic terminal
VL - 383
ER -
TY - THES
AB - 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.
AU - Cultrera di Montesano, Sebastiano
ID - 15094
SN - 2663 - 337X
TI - Persistence and Morse theory for discrete geometric structures
ER -
TY - CONF
AB - 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.
AU - Cultrera di Montesano, Sebastiano
AU - Edelsbrunner, Herbert
AU - Henzinger, Monika H
AU - Ost, Lara
ED - Woodruff, David P.
ID - 15093
T2 - Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)
TI - Dynamically maintaining the persistent homology of time series
ER -
TY - GEN
AB - 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.
AU - Cultrera di Montesano, Sebastiano
AU - Draganov, Ondrej
AU - Edelsbrunner, Herbert
AU - Saghafian, Morteza
ID - 15091
T2 - arXiv
TI - Chromatic alpha complexes
ER -
TY - JOUR
AB - 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.
AU - Agnes, Everton J.
AU - Vogels, Tim P
ID - 15171
JF - Nature Neuroscience
SN - 1097-6256
TI - Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks
ER -