@misc{7016,
abstract = {Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.},
author = {Tomanek, Isabella},
keyword = {Escherichia coli, gene amplification, galactose, DOG, experimental evolution, Illumina sequence data, FACS data, microfluidics data},
publisher = {IST Austria},
title = {{Data for the paper "Gene amplification as a form of population-level gene expression regulation"}},
doi = {10.15479/AT:ISTA:7016},
year = {2019},
}
@article{6486,
abstract = {Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow.},
author = {Kühnen, Jakob and Scarselli, Davide and Hof, Björn},
issn = {1528901X},
journal = {Journal of Fluids Engineering},
number = {11},
publisher = {ASME},
title = {{Relaminarization of pipe flow by means of 3D-printed shaped honeycombs}},
doi = {10.1115/1.4043494},
volume = {141},
year = {2019},
}
@article{7275,
abstract = {Aprotic alkali metal–oxygen batteries require reversible formation of metal superoxide or peroxide on cycling. Severe parasitic reactions cause poor rechargeability, efficiency, and cycle life and have been shown to be caused by singlet oxygen (1O2) that forms at all stages of cycling. However, its formation mechanism remains unclear. We show that disproportionation of superoxide, the product or intermediate on discharge and charge, to peroxide and oxygen is responsible for 1O2 formation. While the overall reaction is driven by the stability of peroxide and thus favored by stronger Lewis acidic cations such as Li+, the 1O2 fraction is enhanced by weak Lewis acids such as organic cations. Concurrently, the metal peroxide yield drops with increasing 1O2. The results explain a major parasitic pathway during cell cycling and the growing severity in K–, Na–, and Li–O2 cells based on the growing propensity for disproportionation. High capacities and rates with peroxides are now realized to require solution processes, which form peroxide or release O2via disproportionation. The results therefore establish the central dilemma that disproportionation is required for high capacity but also responsible for irreversible reactions. Highly reversible cell operation requires hence finding reaction routes that avoid disproportionation.},
author = {Mourad, Eléonore and Petit, Yann K. and Spezia, Riccardo and Samojlov, Aleksej and Summa, Francesco F. and Prehal, Christian and Leypold, Christian and Mahne, Nika and Slugovc, Christian and Fontaine, Olivier and Brutti, Sergio and Freunberger, Stefan Alexander},
issn = {1754-5692},
journal = {Energy & Environmental Science},
number = {8},
pages = {2559--2568},
publisher = {RSC},
title = {{Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries}},
doi = {10.1039/c9ee01453e},
volume = {12},
year = {2019},
}
@article{7282,
abstract = {Interphases that form on the anode surface of lithium-ion batteries are critical for performance and lifetime, but are poorly understood. Now, a decade-old misconception regarding a main component of the interphase has been revealed, which could potentially lead to improved devices.},
author = {Freunberger, Stefan Alexander},
issn = {1755-4330},
journal = {Nature Chemistry},
number = {9},
pages = {761--763},
publisher = {Springer Nature},
title = {{Interphase identity crisis}},
doi = {10.1038/s41557-019-0311-0},
volume = {11},
year = {2019},
}
@article{7422,
abstract = {Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions.},
author = {Sokolowski, Thomas R and Paijmans, Joris and Bossen, Laurens and Miedema, Thomas and Wehrens, Martijn and Becker, Nils B. and Kaizu, Kazunari and Takahashi, Koichi and Dogterom, Marileen and ten Wolde, Pieter Rein},
issn = {0021-9606},
journal = {The Journal of Chemical Physics},
number = {5},
publisher = {AIP Publishing},
title = {{eGFRD in all dimensions}},
doi = {10.1063/1.5064867},
volume = {150},
year = {2019},
}
@inbook{7410,
abstract = {Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed.},
author = {Bruce, Ashley E.E. and Heisenberg, Carl-Philipp J},
booktitle = {Gastrulation: From Embryonic Pattern to Form},
editor = {Solnica-Krezel, Lilianna },
isbn = {9780128127988},
issn = {0070-2153},
pages = {319--341},
publisher = {Elsevier},
title = {{Mechanisms of zebrafish epiboly: A current view}},
doi = {10.1016/bs.ctdb.2019.07.001},
volume = {136},
year = {2019},
}
@article{7395,
abstract = {The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII2. CI shows a transition between “closed” and “open” conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII2, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.},
author = {Letts, James A and Fiedorczuk, Karol and Degliesposti, Gianluca and Skehel, Mark and Sazanov, Leonid A},
issn = {1097-2765},
journal = {Molecular Cell},
number = {6},
pages = {1131--1146.e6},
publisher = {Cell Press},
title = {{Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk}},
doi = {10.1016/j.molcel.2019.07.022},
volume = {75},
year = {2019},
}
@inproceedings{6378,
abstract = {In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin.},
author = {Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Pourdamghani, Arash},
booktitle = {Proceedings of the 34th ACM Symposium on Applied Computing},
isbn = {9781450359337},
location = {Limassol, Cyprus},
pages = {374--381},
publisher = {ACM},
title = {{Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving}},
doi = {10.1145/3297280.3297319},
volume = {Part F147772},
year = {2019},
}
@article{6366,
abstract = {Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl.},
author = {Bellstaedt, Julia and Trenner, Jana and Lippmann, Rebecca and Poeschl, Yvonne and Zhang, Xixi and Friml, Jiří and Quint, Marcel and Delker, Carolin},
issn = {0032-0889},
journal = {Plant Physiology},
number = {2},
pages = {757--766},
publisher = {ASPB},
title = {{A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls}},
doi = {10.1104/pp.18.01377},
volume = {180},
year = {2019},
}
@article{7415,
author = {Morandell, Jasmin and Nicolas, Armel and Schwarz, Lena A and Novarino, Gaia},
issn = {0924-977X},
journal = {European Neuropsychopharmacology},
number = {Supplement 6},
pages = {S11--S12},
publisher = {Elsevier},
title = {{S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism}},
doi = {10.1016/j.euroneuro.2019.09.040},
volume = {29},
year = {2019},
}
@inbook{7453,
abstract = {We illustrate the ingredients of the state-of-the-art of model-based approach for the formal design and verification of cyber-physical systems. To capture the interaction between a discrete controller and its continuously evolving environment, we use the formal models of timed and hybrid automata. We explain the steps of modeling and verification in the tools Uppaal and SpaceEx using a case study based on a dual-chamber implantable pacemaker monitoring a human heart. We show how to design a model as a composition of components, how to construct models at varying levels of detail, how to establish that one model is an abstraction of another, how to specify correctness requirements using temporal logic, and how to verify that a model satisfies a logical requirement.},
author = {Alur, Rajeev and Giacobbe, Mirco and Henzinger, Thomas A and Larsen, Kim G. and Mikučionis, Marius},
booktitle = {Computing and Software Science},
isbn = {9783319919072},
issn = {0302-9743},
pages = {452--477},
publisher = {Springer Nature},
title = {{Continuous-time models for system design and analysis}},
doi = {10.1007/978-3-319-91908-9_22},
volume = {10000},
year = {2019},
}
@inproceedings{6676,
abstract = {It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments.
Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.},
author = {Alistarh, Dan-Adrian and Aspnes, James and Ellen, Faith and Gelashvili, Rati and Zhu, Leqi},
booktitle = {Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing},
isbn = {9781450367059},
location = {Phoenix, AZ, United States},
pages = {986--996},
publisher = {ACM Press},
title = {{Why extension-based proofs fail}},
doi = {10.1145/3313276.3316407},
year = {2019},
}
@article{6032,
abstract = {The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, co-independent, compact, local, linear, and binary, with the following caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids.},
author = {Kazda, Alexandr and Kolmogorov, Vladimir and Rolinek, Michal},
journal = {ACM Transactions on Algorithms},
number = {2},
publisher = {ACM},
title = {{Even delta-matroids and the complexity of planar boolean CSPs}},
doi = {10.1145/3230649},
volume = {15},
year = {2019},
}
@article{6575,
abstract = {Motivated by recent experimental observations of coherent many-body revivals in a constrained Rydbergatom chain, we construct a weak quasilocal deformation of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect. Our analysis suggests the existence of an underlying nonintegrableHamiltonian which supports an emergent SU(2)-spin dynamics within a small subspace of the many-bodyHilbert space. We show that such perfect dynamics necessitates the existence of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore, using these insights, we construct a toymodel that hosts exact quantum many-body scars, providing an intuitive explanation of their origin. Ourresults offer specific routes to enhancing coherent many-body revivals and provide a step towardestablishing the stability of quantum many-body scars in the thermodynamic limit.},
author = {Choi, Soonwon and Turner, Christopher J. and Pichler, Hannes and Ho, Wen Wei and Michailidis, Alexios and Papić, Zlatko and Serbyn, Maksym and Lukin, Mikhail D. and Abanin, Dmitry A.},
issn = {10797114},
journal = {Physical Review Letters},
number = {22},
publisher = {APS},
title = {{Emergent SU(2) dynamics and perfect quantum many-body scars}},
doi = {10.1103/PhysRevLett.122.220603},
volume = {122},
year = {2019},
}
@inproceedings{6556,
abstract = {Motivated by fixed-parameter tractable (FPT) problems in computational topology, we consider the treewidth tw(M) of a compact, connected 3-manifold M, defined to be the minimum treewidth of the face pairing graph of any triangulation T of M. In this setting the relationship between the topology of a 3-manifold and its treewidth is of particular interest. First, as a corollary of work of Jaco and Rubinstein, we prove that for any closed, orientable 3-manifold M the treewidth tw(M) is at most 4g(M)-2, where g(M) denotes Heegaard genus of M. In combination with our earlier work with Wagner, this yields that for non-Haken manifolds the Heegaard genus and the treewidth are within a constant factor. Second, we characterize all 3-manifolds of treewidth one: These are precisely the lens spaces and a single other Seifert fibered space. Furthermore, we show that all remaining orientable Seifert fibered spaces over the 2-sphere or a non-orientable surface have treewidth two. In particular, for every spherical 3-manifold we exhibit a triangulation of treewidth at most two. Our results further validate the parameter of treewidth (and other related parameters such as cutwidth or congestion) to be useful for topological computing, and also shed more light on the scope of existing FPT-algorithms in the field.},
author = {Huszár, Kristóf and Spreer, Jonathan},
booktitle = {35th International Symposium on Computational Geometry (SoCG 2019)},
isbn = {978-3-95977-104-7},
issn = {1868-8969},
keyword = {computational 3-manifold topology, fixed-parameter tractability, layered triangulations, structural graph theory, treewidth, cutwidth, Heegaard genus},
location = {Portland, Oregon, United States},
pages = {44:1--44:20},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{3-manifold triangulations with small treewidth}},
doi = {10.4230/LIPIcs.SoCG.2019.44},
volume = {129},
year = {2019},
}
@inproceedings{6931,
abstract = {Consider a distributed system with n processors out of which f can be Byzantine faulty. In the
approximate agreement task, each processor i receives an input value xi and has to decide on an
output value yi such that
1. the output values are in the convex hull of the non-faulty processors’ input values,
2. the output values are within distance d of each other.
Classically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.
In this work, we study the task in a discrete setting, where input values with some structure
expressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to
output vertices that are within distance d of each other in G, but still remain in the graph-induced
convex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with
a deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,
we show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,
where ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a
variant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact
variants of these and related tasks over a large class of combinatorial structures.},
author = {Nowak, Thomas and Rybicki, Joel},
booktitle = {33rd International Symposium on Distributed Computing},
keyword = {consensus, approximate agreement, Byzantine faults, chordal graphs, lattice agreement},
location = {Budapest, Hungary},
pages = {29:1----29:17},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Byzantine approximate agreement on graphs}},
doi = {10.4230/LIPICS.DISC.2019.29},
volume = {146},
year = {2019},
}
@article{6467,
abstract = {Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.},
author = {Fraisse, Christelle and Welch, John J.},
issn = {1744957X},
journal = {Biology Letters},
number = {4},
publisher = {Royal Society of London},
title = {{The distribution of epistasis on simple fitness landscapes}},
doi = {10.1098/rsbl.2018.0881},
volume = {15},
year = {2019},
}
@article{6900,
abstract = {Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks.},
author = {Cepeda Humerez, Sarah A and Ruess, Jakob and Tkačik, Gašper},
issn = {15537358},
journal = {PLoS computational biology},
number = {9},
pages = {e1007290},
publisher = {Public Library of Science},
title = {{Estimating information in time-varying signals}},
doi = {10.1371/journal.pcbi.1007290},
volume = {15},
year = {2019},
}
@article{301,
abstract = {A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense.},
author = {Gerencser, Mate and Gyöngy, István},
journal = {Stochastic Processes and their Applications},
number = {3},
pages = {995--1012},
publisher = {Elsevier},
title = {{A Feynman–Kac formula for stochastic Dirichlet problems}},
doi = {10.1016/j.spa.2018.04.003},
volume = {129},
year = {2019},
}
@article{5908,
abstract = {The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants.},
author = {Lee, Eunkyoung and Vanneste, Steffen and Pérez-Sancho, Jessica and Benitez-Fuente, Francisco and Strelau, Matthew and Macho, Alberto P. and Botella, Miguel A. and Friml, Jiří and Rosado, Abel},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {4},
pages = {1420--1429},
publisher = {National Academy of Sciences},
title = {{Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis}},
doi = {10.1073/pnas.1818099116},
volume = {116},
year = {2019},
}