@misc{13055, abstract = {Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect' Compared to previous versions: - raw image files added - correction of URLs within README.txt file }, author = {Stroeymeyt, Nathalie and Grasse, Anna V and Crespi, Alessandro and Mersch, Danielle and Cremer, Sylvia and Keller, Laurent}, publisher = {Zenodo}, title = {{Social network plasticity decreases disease transmission in a eusocial insect}}, doi = {10.5281/ZENODO.1322669}, year = {2018}, } @misc{13059, abstract = {This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled "Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method". It also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript. The repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`. For details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).}, author = {Garriga, Edgar and di Tommaso, Paolo and Magis, Cedrik and Erb, Ionas and Mansouri, Leila and Baltzis, Athanasios and Laayouni, Hafid and Kondrashov, Fyodor and Floden, Evan and Notredame, Cedric}, publisher = {Zenodo}, title = {{Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method}}, doi = {10.5281/ZENODO.2025846}, year = {2018}, } @article{131, abstract = {XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. }, author = {Picard, Marion A and Cosseau, Celine and Ferré, Sabrina and Quack, Thomas and Grevelding, Christoph and Couté, Yohann and Vicoso, Beatriz}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Evolution of gene dosage on the Z-chromosome of schistosome parasites}}, doi = {10.7554/eLife.35684}, volume = {7}, year = {2018}, } @article{132, abstract = {Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments.}, author = {Sznurkowska, Magdalena and Hannezo, Edouard B and Azzarelli, Roberta and Rulands, Steffen and Nestorowa, Sonia and Hindley, Christopher and Nichols, Jennifer and Göttgens, Berthold and Huch, Meritxell and Philpott, Anna and Simons, Benjamin}, journal = {Developmental Cell}, number = {3}, pages = {360 -- 375}, publisher = {Cell Press}, title = {{Defining lineage potential and fate behavior of precursors during pancreas development}}, doi = {10.1016/j.devcel.2018.06.028}, volume = {46}, year = {2018}, } @article{13255, abstract = {Focused ion beams perfectly suit for patterning two-dimensional (2D) materials, but the optimization of irradiation parameters requires full microscopic understanding of defect production mechanisms. In contrast to freestanding 2D systems, the details of damage creation in supported 2D materials are not fully understood, whereas the majority of experiments have been carried out for 2D targets deposited on substrates. Here, we suggest a universal and computationally efficient scheme to model the irradiation of supported 2D materials, which combines analytical potential molecular dynamics with Monte Carlo simulations and makes it possible to independently assess the contributions to the damage from backscattered ions and atoms sputtered from the substrate. Using the scheme, we study the defect production in graphene and MoS2 sheets, which are the two most important and wide-spread 2D materials, deposited on a SiO2 substrate. For helium and neon ions with a wide range of initial ion energies including those used in a commercial helium ion microscope (HIM), we demonstrate that depending on the ion energy and mass, the defect production in 2D systems can be dominated by backscattered ions and sputtered substrate atoms rather than by the direct ion impacts and that the amount of damage in 2D materials heavily depends on whether a substrate is present or not. We also study the factors which limit the spatial resolution of the patterning process. Our results, which agree well with the available experimental data, provide not only insights into defect production but also quantitative information, which can be used for the minimization of damage during imaging in HIM or optimization of the patterning process.}, author = {Kretschmer, Silvan and Maslov, Mikhail and Ghaderzadeh, Sadegh and Ghorbani-Asl, Mahdi and Hlawacek, Gregor and Krasheninnikov, Arkady V.}, issn = {1944-8244}, journal = {ACS Applied Materials & Interfaces}, keywords = {General Materials Science}, number = {36}, pages = {30827--30836}, publisher = {American Chemical Society}, title = {{Supported two-dimensional materials under ion irradiation: The substrate governs defect production}}, doi = {10.1021/acsami.8b08471}, volume = {10}, year = {2018}, } @inproceedings{133, abstract = {Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs.}, author = {Kragl, Bernhard and Qadeer, Shaz and Henzinger, Thomas A}, issn = {18688969}, location = {Beijing, China}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Synchronizing the asynchronous}}, doi = {10.4230/LIPIcs.CONCUR.2018.21}, volume = {118}, year = {2018}, } @article{13374, abstract = {Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches—entities that can be toggled between two or more forms upon exposure to an external stimulus—often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating—and solubilizing in water—several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments.}, author = {Samanta, Dipak and Galaktionova, Daria and Gemen, Julius and Shimon, Linda J. W. and Diskin-Posner, Yael and Avram, Liat and Král, Petr and Klajn, Rafal}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Reversible chromism of spiropyran in the cavity of a flexible coordination cage}}, doi = {10.1038/s41467-017-02715-6}, volume = {9}, year = {2018}, } @article{13375, abstract = {Dissipative self-assembly leads to structures and materials that exist away from equilibrium by continuously exchanging energy and materials with the external environment. Although this mode of self-assembly is ubiquitous in nature, where it gives rise to functions such as signal processing, motility, self-healing, self-replication, and ultimately life, examples of dissipative self-assembly processes in man-made systems are few and far between. Herein, recent progress in developing diverse synthetic dissipative self-assembly systems is discussed. The systems reported thus far can be categorized into three classes, in which: i) the fuel chemically modifies the building blocks, thus triggering their self-assembly, ii) the fuel acts as a template interacting with the building blocks noncovalently, and iii) transient states are induced by the addition of two mutually exclusive stimuli. These early studies give rise to materials that would be difficult to obtain otherwise, including hydrogels with programmable lifetimes, vesicular nanoreactors, and membranes exhibiting transient conductivity.}, author = {De, Soumen and Klajn, Rafal}, issn = {1521-4095}, journal = {Advanced Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, General Materials Science}, number = {41}, publisher = {Wiley}, title = {{Dissipative self-assembly driven by the consumption of chemical fuels}}, doi = {10.1002/adma.201706750}, volume = {30}, year = {2018}, } @article{13376, abstract = {Efficient molecular switching in confined spaces is critical for the successful development of artificial molecular machines. However, molecular switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene—the key building block of light-controlled molecular machines—in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-soluble coordination cage, and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its precipitation from the solution. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light.}, author = {Samanta, Dipak and Gemen, Julius and Chu, Zonglin and Diskin-Posner, Yael and Shimon, Linda J. W. and Klajn, Rafal}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {38}, pages = {9379--9384}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Reversible photoswitching of encapsulated azobenzenes in water}}, doi = {10.1073/pnas.1712787115}, volume = {115}, year = {2018}, } @article{13377, abstract = {Confining organic molecules to the surfaces of inorganic nanoparticles can induce intermolecular interactions between them, which can affect the composition of the mixed self-assembled monolayers obtained by co-adsorption from solution of two different molecules. Two thiolated ligands (a dialkylviologen and a zwitterionic sulfobetaine) that can interact with each other electrostatically were coadsorbed onto gold nanoparticles. The nanoparticles favor a narrow range of ratios of these two molecules that is largely independent of the molar ratio in solution. Changing the solution molar ratio of the two ligands by a factor of 5 000 affects the on-nanoparticle ratio of these ligands by only threefold. This behavior is reminiscent of the formation of insoluble inorganic salts (such as AgCl), which similarly compensate positive and negative charges upon crystallizing. Our results pave the way towards developing well-defined hybrid organic–inorganic nanostructures.}, author = {Chu, Zonglin and Han, Yanxiao and Král, Petr and Klajn, Rafal}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {24}, pages = {7023--7027}, publisher = {Wiley}, title = {{“Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles}}, doi = {10.1002/anie.201800673}, volume = {57}, year = {2018}, } @article{13379, author = {Bléger, David and Klajn, Rafal}, issn = {1521-3927}, journal = {Macromolecular Rapid Communications}, keywords = {Materials Chemistry, Polymers and Plastics, Organic Chemistry}, number = {1}, publisher = {Wiley}, title = {{Integrating macromolecules with molecular switches}}, doi = {10.1002/marc.201700827}, volume = {39}, year = {2018}, } @article{134, abstract = {The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains. Previous methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface.}, author = {Jeschke, Stefan and Skrivan, Tomas and Mueller Fischer, Matthias and Chentanez, Nuttapong and Macklin, Miles and Wojtan, Christopher J}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Water surface wavelets}}, doi = {10.1145/3197517.3201336}, volume = {37}, year = {2018}, } @article{13473, abstract = {Stripped-envelope stars form in binary systems after losing mass through Roche-lobe overflow. They bear astrophysical significance as sources of UV and ionizing radiation in older stellar populations and, if sufficiently massive, as stripped supernova progenitors. Binary evolutionary models predict that they are common, but only a handful of subdwarfs with B-type companions are known. The question is whether a large population of such systems has evaded detection as a result of biases, or whether the model predictions are wrong. We reanalyze the well-studied post-interaction binary φ Persei. Recently, new data have improved the orbital solution of the system, which contains an ~1.2M⊙ stripped-envelope star and a rapidly rotating ~9.6M⊙ Be star. We compare with an extensive grid of evolutionary models using a Bayesian approach and constrain the initial masses of the progenitor to 7.2 ± 0.4M⊙ for the stripped star and 3.8 ± 0.4M⊙ for the Be star. The system must have evolved through near-conservative mass transfer. These findings are consistent with earlier studies. The age we obtain, 57 ± 9 Myr, is in excellent agreement with the age of the α Persei cluster. We note that neither star was initially massive enough to produce a core-collapse supernova, but mass exchange pushed the Be star above the mass threshold. We find that the subdwarf is overluminous for its mass by almost an order of magnitude, compared to the expectations for a helium core burning star. We can only reconcile this if the subdwarf resides in a late phase of helium shell burning, which lasts only 2–3% of the total lifetime as a subdwarf. Assuming continuous star formation implies that up to ~50 less evolved, dimmer subdwarfs exist for each system similar to φ Persei, but have evaded detection so far. Our findings can be interpreted as a strong indication that a substantial population of stripped-envelope stars indeed exists, but has so far evaded detection because of observational biases and lack of large-scale systematic searches.}, author = {Schootemeijer, A. and Götberg, Ylva Louise Linsdotter and de Mink, S. E. and Gies, D. and Zapartas, E.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei}}, doi = {10.1051/0004-6361/201731194}, volume = {615}, year = {2018}, } @article{13474, abstract = {Recent surveys of the Magellanic Clouds have revealed a subtype of Wolf–Rayet (WR) star with peculiar properties. WN3/O3 spectra exhibit both WR-like emission and O3 V-like absorption – but at lower luminosity than O3 V or WN stars. We examine the projected spatial distribution of WN3/O3 stars in the Large Magellanic Cloud as compared to O-type stars. Surprisingly, WN3/O3 stars are among the most isolated of all classes of massive stars; they have a distribution similar to red supergiants dominated by initial masses of 10–15 M⊙, and are far more dispersed than classical WR stars or luminous blue variables. Their lack of association with clusters of O-type stars suggests strongly that WN3/O3 stars are not the descendants of single massive stars (30 M⊙ or above). Instead, they are likely products of interacting binaries at lower initial mass (10–18 M⊙). Comparison with binary models suggests a probable origin with primaries in this mass range that were stripped of their H envelopes through non-conservative mass transfer by a low-mass secondary. We show that model spectra and positions on the Hertzsprung–Russell diagram for binary-stripped stars are consistent with WN3/O3 stars. Monitoring radial velocities with high-resolution spectra can test for low-mass companions or runaway velocities. With lower initial mass and environments that avoid very massive stars, the WN3/O3 stars fit expectations for progenitors of Type Ib and possibly Type Ibn supernovae.}, author = {Smith, Nathan and Götberg, Ylva Louise Linsdotter and de Mink, Selma E}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {1}, pages = {772--782}, publisher = {Oxford University Press}, title = {{Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries}}, doi = {10.1093/mnras/stx3181}, volume = {475}, year = {2018}, } @article{13475, abstract = {Stars stripped of their hydrogen-rich envelope through interaction with a binary companion are generally not considered when accounting for ionizing radiation from stellar populations, despite the expectation that stripped stars emit hard ionizing radiation, form frequently, and live 10–100 times longer than single massive stars. We compute the first grid of evolutionary and spectral models specially made for stars stripped in binaries for a range of progenitor masses (2–20 M⊙) and metallicities ranging from solar to values representative for pop II stars. For stripped stars with masses in the range 0.3–7 M⊙, we find consistently high effective temperatures (20 000–100 000 K, increasing with mass), small radii (0.2–1 R⊙), and high bolometric luminosities, comparable to that of their progenitor before stripping. The spectra show a continuous sequence that naturally bridges subdwarf-type stars at the low-mass end and Wolf-Rayet-like spectra at the high-mass end. For intermediate masses we find hybrid spectral classes showing a mixture of absorption and emission lines. These appear for stars with mass-loss rates of 10−8−10−6 M⊙ yr−1, which have semi-transparent atmospheres. At low metallicity, substantial hydrogen-rich layers are left at the surface and we predict spectra that resemble O-type stars instead. We obtain spectra undistinguishable from subdwarfs for stripped stars with masses up to 1.7 M⊙, which questions whether the widely adopted canonical value of 0.47 M⊙ is uniformly valid. Only a handful of stripped stars of intermediate mass have currently been identified observationally. Increasing this sample will provide necessary tests for the physics of interaction, internal mixing, and stellar winds. We use our model spectra to investigate the feasibility to detect stripped stars next to an optically bright companion and recommend systematic searches for their UV excess and possible emission lines, most notably HeII λ4686 in the optical and HeII λ1640 in the UV. Our models are publicly available for further investigations or inclusion in spectral synthesis simulations.}, author = {Götberg, Ylva Louise Linsdotter and de Mink, S. E. and Groh, J. H. and Kupfer, T. and Crowther, P. A. and Zapartas, E. and Renzo, M.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars}}, doi = {10.1051/0004-6361/201732274}, volume = {615}, year = {2018}, } @article{135, abstract = {The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion.}, author = {Sato, Takahiro and Wojtan, Christopher J and Thuerey, Nils and Igarashi, Takeo and Ando, Ryoichi}, issn = {0167-7055}, journal = {Computer Graphics Forum}, number = {2}, pages = {169 -- 177}, publisher = {Wiley}, title = {{Extended narrow band FLIP for liquid simulations}}, doi = {10.1111/cgf.13351}, volume = {37}, year = {2018}, } @article{136, abstract = {Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space.}, author = {Suri, Balachandra and Tithof, Jeffrey and Grigoriev, Roman and Schatz, Michael}, journal = {Physical Review E}, number = {2}, publisher = {American Physical Society}, title = {{Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow}}, doi = {10.1103/PhysRevE.98.023105}, volume = {98}, year = {2018}, } @article{137, abstract = {Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli.}, author = {Zhang, William and Herde, Michel and Mitchell, Joshua and Whitfield, Jason and Wulff, Andreas and Vongsouthi, Vanessa and Sanchez Romero, Inmaculada and Gulakova, Polina and Minge, Daniel and Breithausen, Björn and Schoch, Susanne and Janovjak, Harald L and Jackson, Colin and Henneberger, Christian}, journal = {Nature Chemical Biology}, number = {9}, pages = {861 -- 869}, publisher = {Nature Publishing Group}, title = {{Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS}}, doi = {10.1038/s41589-018-0108-2}, volume = {14}, year = {2018}, } @article{139, abstract = {Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.}, author = {Fraisse, Christelle and Roux, Camille and Gagnaire, Pierre and Romiguier, Jonathan and Faivre, Nicolas and Welch, John and Bierne, Nicolas}, journal = {PeerJ}, number = {7}, publisher = {PeerJ}, title = {{The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies}}, doi = {10.7717/peerj.5198}, volume = {2018}, year = {2018}, } @article{14, abstract = {The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta.}, author = {Hille, Sander and Akhmanova, Maria and Glanc, Matous and Johnson, Alexander J and Friml, Jirí}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, number = {11}, publisher = {MDPI}, title = {{Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation}}, doi = {10.3390/ijms19113566}, volume = {19}, year = {2018}, }