@article{6013, abstract = {The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”}, author = {Camus, Nicolas and Yakaboylu, Enderalp and Fechner, Lutz and Klaiber, Michael and Laux, Martin and Mi, Yonghao and Hatsagortsyan, Karen Z. and Pfeifer, Thomas and Keitel, Christoph H. and Moshammer, Robert}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {2}, publisher = {American Physical Society}, title = {{Experimental evidence for quantum tunneling time}}, doi = {10.1103/PhysRevLett.119.023201}, volume = {119}, year = {2017}, } @article{603, abstract = {During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.}, author = {Bernecky, Carrie A and Plitzko, Jürgen and Cramer, Patrick}, issn = {15459993}, journal = {Nature Structural and Molecular Biology}, number = {10}, pages = {809 -- 815}, publisher = {Nature Publishing Group}, title = {{Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp}}, doi = {10.1038/nsmb.3465}, volume = {24}, year = {2017}, } @inbook{604, abstract = {In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies.}, author = {Lemeshko, Mikhail and Schmidt, Richard}, booktitle = {Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero }, editor = {Dulieu, Oliver and Osterwalder, Andreas}, issn = {20413181}, pages = {444 -- 495}, publisher = {The Royal Society of Chemistry}, title = {{Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets}}, doi = {10.1039/9781782626800-00444}, volume = {11}, year = {2017}, } @inproceedings{605, abstract = {Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes.}, author = {Brody, Joshua and Dziembowski, Stefan and Faust, Sebastian and Pietrzak, Krzysztof Z}, editor = {Kalai, Yael and Reyzin, Leonid}, isbn = {978-331970499-9}, location = {Baltimore, MD, United States}, pages = {56 -- 81}, publisher = {Springer}, title = {{Position based cryptography and multiparty communication complexity}}, doi = {10.1007/978-3-319-70500-2_3}, volume = {10677}, year = {2017}, } @article{6059, abstract = {Neutrophils or polymorphonuclear cells (PMN) eliminate bacteria via phagocytosis and/or NETosis. Apartfrom these conventional roles, PMN also have immune-regulatory functions. They can transdifferentiateand upregulate MHCII as well as ligands for costimulatory receptors which enables them to behave asantigen presenting cells (APC). The initial step for activating T-cells is the formation of an immunesynapse between T-cells and antigen-presenting cells. However, the immune synapse that develops atthe PMN/T-cell contact zone is as yet hardly investigated due to the non-availability of methods foranalysis of large number of PMN interactions. In order to overcome these obstacles, we introduce herea workflow to analyse the immune synapse of primary human PMN and T-cells using multispectral imag-ing flow cytometry (InFlow microscopy) and super-resolution microscopy. For that purpose, we used CD3and CD66b as the lineage markers for T-cells and PMN, respectively. Thereafter, we applied and criticallydiscussed various ‘‘masks” for identification of T-cell PMN interactions. Using this approach, we foundthat a small fraction of transdifferentiated PMN (CD66b+CD86high) formed stable PMN/T-cell conjugates.Interestingly, while both CD3 and CD66b accumulation in the immune synapse was dependent on thematuration state of the PMN, only CD3 accumulation was greatly enhanced by the presence of superanti-gen. The actin cytoskeleton was weakly rearranged at the PMN side on the immune synapse upon contactwith a T-cell in the presence of superantigen. A more detailed analysis using super-resolution microscopy(structured-illumination microscopy, SIM) confirmed this finding. Together, we present an InFlow micro-scopy based approach for the large scale analysis of PMN/T-cell interactions and – combined with SIM – apossibility for an in-depth analysis of protein translocation at the site of interactions.}, author = {Balta, Emre and Stopp, Julian A and Castelletti, Laura and Kirchgessner, Henning and Samstag, Yvonne and Wabnitz, Guido H.}, issn = {1046-2023}, journal = {Methods}, number = {1}, pages = {25--38}, publisher = {Elsevier}, title = {{Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy}}, doi = {10.1016/j.ymeth.2016.09.013}, volume = {112}, year = {2017}, } @inproceedings{609, abstract = {Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover.}, author = {Alwen, Joel F and Tackmann, Björn}, editor = {Kalai, Yael and Reyzin, Leonid}, isbn = {978-331970499-9}, location = {Baltimore, MD, United States}, pages = {493 -- 526}, publisher = {Springer}, title = {{Moderately hard functions: Definition, instantiations, and applications}}, doi = {10.1007/978-3-319-70500-2_17}, volume = {10677}, year = {2017}, } @article{610, abstract = {The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.}, author = {Goaoc, Xavier and Mabillard, Isaac and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, journal = {Israel Journal of Mathematics}, number = {2}, pages = {841 -- 866}, publisher = {Springer}, title = {{On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result}}, doi = {10.1007/s11856-017-1607-7}, volume = {222}, year = {2017}, } @article{611, abstract = {Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.}, author = {Bradley, Desmond and Xu, Ping and Mohorianu, Irina and Whibley, Annabel and Field, David and Tavares, Hugo and Couchman, Matthew and Copsey, Lucy and Carpenter, Rosemary and Li, Miaomiao and Li, Qun and Xue, Yongbiao and Dalmay, Tamas and Coen, Enrico}, issn = {00368075}, journal = {Science}, number = {6365}, pages = {925 -- 928}, publisher = {American Association for the Advancement of Science}, title = {{Evolution of flower color pattern through selection on regulatory small RNAs}}, doi = {10.1126/science.aao3526}, volume = {358}, year = {2017}, } @article{6113, author = {Oda, Shigekazu and Toyoshima, Yu and de Bono, Mario}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {23}, pages = {E4658--E4665}, publisher = {National Academy of Sciences}, title = {{Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans}}, doi = {10.1073/pnas.1614596114}, volume = {114}, year = {2017}, } @article{6115, abstract = {Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that Caenorhabditis elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2-sensing neurons reprograms the properties of their postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.}, author = {Fenk, Lorenz A. and de Bono, Mario}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {16}, pages = {4195--4200}, publisher = {National Academy of Sciences}, title = {{Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans}}, doi = {10.1073/pnas.1618934114}, volume = {114}, year = {2017}, } @article{6117, abstract = {Interleukin-17 (IL-17) is a major pro-inflammatory cytokine: it mediates responses to pathogens or tissue damage, and drives autoimmune diseases. Little is known about its role in the nervous system. Here we show that IL-17 has neuromodulator-like properties in Caenorhabditis elegans. IL-17 can act directly on neurons to alter their response properties and contribution to behaviour. Using unbiased genetic screens, we delineate an IL-17 signalling pathway and show that it acts in the RMG hub interneurons. Disrupting IL-17 signalling reduces RMG responsiveness to input from oxygen sensors, and renders sustained escape from 21% oxygen transient and contingent on additional stimuli. Over-activating IL-17 receptors abnormally heightens responses to 21% oxygen in RMG neurons and whole animals. IL-17 deficiency can be bypassed by optogenetic stimulation of RMG. Inducing IL-17 expression in adults can rescue mutant defects within 6 h. These findings reveal a non-immunological role of IL-17 modulating circuit function and behaviour.}, author = {Chen, Changchun and Itakura, Eisuke and Nelson, Geoffrey M. and Sheng, Ming and Laurent, Patrick and Fenk, Lorenz A. and Butcher, Rebecca A. and Hegde, Ramanujan S. and de Bono, Mario}, issn = {0028-0836}, journal = {Nature}, number = {7639}, pages = {43--48}, publisher = {Springer Nature}, title = {{IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses}}, doi = {10.1038/nature20818}, volume = {542}, year = {2017}, } @article{613, abstract = {Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.}, author = {Chait, Remy P and Ruess, Jakob and Bergmiller, Tobias and Tkacik, Gasper and Guet, Calin C}, issn = {20411723}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group}, title = {{Shaping bacterial population behavior through computer interfaced control of individual cells}}, doi = {10.1038/s41467-017-01683-1}, volume = {8}, year = {2017}, } @article{614, abstract = {Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.}, author = {Fraisse, Christelle and Picard, Marion A and Vicoso, Beatriz}, issn = {20411723}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group}, title = {{The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W}}, doi = {10.1038/s41467-017-01663-5}, volume = {8}, year = {2017}, } @article{615, abstract = {We show that the Dyson Brownian Motion exhibits local universality after a very short time assuming that local rigidity and level repulsion of the eigenvalues hold. These conditions are verified, hence bulk spectral universality is proven, for a large class of Wigner-like matrices, including deformed Wigner ensembles and ensembles with non-stochastic variance matrices whose limiting densities differ from Wigner's semicircle law.}, author = {Erdös, László and Schnelli, Kevin}, issn = {02460203}, journal = {Annales de l'institut Henri Poincare (B) Probability and Statistics}, number = {4}, pages = {1606 -- 1656}, publisher = {Institute of Mathematical Statistics}, title = {{Universality for random matrix flows with time dependent density}}, doi = {10.1214/16-AIHP765}, volume = {53}, year = {2017}, } @article{618, abstract = {Background: Increasing temperatures are predicted to strongly impact host-parasite interactions, but empirical tests are rare. Host species that are naturally exposed to a broad temperature spectrum offer the possibility to investigate the effects of elevated temperatures on hosts and parasites. Using three-spined sticklebacks, Gasterosteus aculeatus L., and tapeworms, Schistocephalus solidus (Müller, 1776), originating from a cold and a warm water site of a volcanic lake, we subjected sympatric and allopatric host-parasite combinations to cold and warm conditions in a fully crossed design. We predicted that warm temperatures would promote the development of the parasites, while the hosts might benefit from cooler temperatures. We further expected adaptations to the local temperature and mutual adaptations of local host-parasite pairs. Results: Overall, S. solidus parasites grew faster at warm temperatures and stickleback hosts at cold temperatures. On a finer scale, we observed that parasites were able to exploit their hosts more efficiently at the parasite’s temperature of origin. In contrast, host tolerance towards parasite infection was higher when sticklebacks were infected with parasites at the parasite’s ‘foreign’ temperature. Cold-origin sticklebacks tended to grow faster and parasite infection induced a stronger immune response. Conclusions: Our results suggest that increasing environmental temperatures promote the parasite rather than the host and that host tolerance is dependent on the interaction between parasite infection and temperature. Sticklebacks might use tolerance mechanisms towards parasite infection in combination with their high plasticity towards temperature changes to cope with increasing parasite infection pressures and rising temperatures.}, author = {Franke, Frederik and Armitage, Sophie and Kutzer, Megan and Kurtz, Joachim and Scharsack, Jörn}, issn = {17563305}, journal = {Parasites & Vectors}, number = {252}, publisher = {BioMed Central}, title = {{Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association }}, doi = {10.1186/s13071-017-2192-7}, volume = {10}, year = {2017}, } @article{6196, abstract = {PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem.}, author = {Gazi, Peter and Pietrzak, Krzysztof Z and Rybar, Michal}, issn = {2519-173X}, journal = {IACR Transactions on Symmetric Cryptology}, number = {2}, pages = {145--161}, publisher = {Ruhr University Bochum}, title = {{The exact security of PMAC}}, doi = {10.13154/TOSC.V2016.I2.145-161}, volume = {2016}, year = {2017}, } @article{621, abstract = {The mammalian cerebral cortex is responsible for higher cognitive functions such as perception, consciousness, and acquiring and processing information. The neocortex is organized into six distinct laminae, each composed of a rich diversity of cell types which assemble into highly complex cortical circuits. Radial glia progenitors (RGPs) are responsible for producing all neocortical neurons and certain glia lineages. Here, we discuss recent discoveries emerging from clonal lineage analysis at the single RGP cell level that provide us with an inaugural quantitative framework of RGP lineage progression. We further discuss the importance of the relative contribution of intrinsic gene functions and non-cell-autonomous or community effects in regulating RGP proliferation behavior and lineage progression.}, author = {Beattie, Robert J and Hippenmeyer, Simon}, issn = {00145793}, journal = {FEBS letters}, number = {24}, pages = {3993 -- 4008}, publisher = {Wiley-Blackwell}, title = {{Mechanisms of radial glia progenitor cell lineage progression}}, doi = {10.1002/1873-3468.12906}, volume = {591}, year = {2017}, } @inbook{623, abstract = {Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology.}, author = {Hill Yardin, Elisa and Mckeown, Sonja and Novarino, Gaia and Grabrucker, Andreas}, booktitle = {Translational Anatomy and Cell Biology of Autism Spectrum Disorder}, editor = {Schmeisser, Michael and Boekers, Tobias}, isbn = {978-3-319-52496-2}, issn = {03015556}, pages = {159 -- 187}, publisher = {Springer}, title = {{Extracerebral dysfunction in animal models of autism spectrum disorder}}, doi = {10.1007/978-3-319-52498-6_9}, volume = {224}, year = {2017}, } @article{624, abstract = {Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.}, author = {Nikolic, Nela and Didara, Zrinka and Moll, Isabella}, issn = {21678359}, journal = {PeerJ}, number = {9}, publisher = {PeerJ}, title = {{MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations}}, doi = {10.7717/peerj.3830}, volume = {2017}, year = {2017}, } @inbook{625, abstract = {In the analysis of reactive systems a quantitative objective assigns a real value to every trace of the system. The value decision problem for a quantitative objective requires a trace whose value is at least a given threshold, and the exact value decision problem requires a trace whose value is exactly the threshold. We compare the computational complexity of the value and exact value decision problems for classical quantitative objectives, such as sum, discounted sum, energy, and mean-payoff for two standard models of reactive systems, namely, graphs and graph games.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, booktitle = {Models, Algorithms, Logics and Tools}, editor = {Aceto, Luca and Bacci, Giorgio and Ingólfsdóttir, Anna and Legay, Axel and Mardare, Radu}, isbn = {978-3-319-63120-2}, issn = {0302-9743}, pages = {367 -- 381}, publisher = {Springer}, title = {{The cost of exactness in quantitative reachability}}, doi = {10.1007/978-3-319-63121-9_18}, volume = {10460}, year = {2017}, }