@article{1593, abstract = {Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.}, author = {Žádníková, Petra and Smet, Dajo and Zhu, Qiang and Van Der Straeten, Dominique and Benková, Eva}, journal = {Frontiers in Plant Science}, number = {4}, publisher = {Frontiers Research Foundation}, title = {{Strategies of seedlings to overcome their sessile nature: Auxin in mobility control}}, doi = {10.3389/fpls.2015.00218}, volume = {6}, year = {2015}, } @inproceedings{1594, abstract = {Quantitative extensions of temporal logics have recently attracted significant attention. In this work, we study frequency LTL (fLTL), an extension of LTL which allows to speak about frequencies of events along an execution. Such an extension is particularly useful for probabilistic systems that often cannot fulfil strict qualitative guarantees on the behaviour. It has been recently shown that controller synthesis for Markov decision processes and fLTL is decidable when all the bounds on frequencies are 1. As a step towards a complete quantitative solution, we show that the problem is decidable for the fragment fLTL\GU, where U does not occur in the scope of G (but still F can). Our solution is based on a novel translation of such quantitative formulae into equivalent deterministic automata.}, author = {Forejt, Vojtěch and Krčál, Jan and Kretinsky, Jan}, location = {Suva, Fiji}, pages = {162 -- 177}, publisher = {Springer}, title = {{Controller synthesis for MDPs and frequency LTL\GU}}, doi = {10.1007/978-3-662-48899-7_12}, volume = {9450}, year = {2015}, } @inproceedings{1595, abstract = {A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth.}, author = {Fulek, Radoslav and Pelsmajer, Michael and Schaefer, Marcus}, location = {Los Angeles, CA, USA}, pages = {99 -- 110}, publisher = {Springer}, title = {{Hanani-Tutte for radial planarity}}, doi = {10.1007/978-3-319-27261-0_9}, volume = {9411}, year = {2015}, } @inbook{1596, abstract = {Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon in the plane with the stacking order. The collection C forms a visibility clique if for everyi < j the intersection Ci and (Ci ∩ Cj)\⋃i<l<jCl =∅.elements that are stacked between them, i.e., We show that if C forms a visibility clique its size is bounded from above by O(k4) thereby improving the upper bound of 22k from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the size of a visibility clique for homothetes of a convex (not necessarily regular) k-gon.}, author = {Fulek, Radoslav and Radoičić, Radoš}, booktitle = {Graph Drawing and Network Visualization}, isbn = {978-3-319-27260-3}, location = {Los Angeles, CA, United States}, pages = {373 -- 379}, publisher = {Springer Nature}, title = {{Vertical visibility among parallel polygons in three dimensions}}, doi = {10.1007/978-3-319-27261-0_31}, volume = {9411}, year = {2015}, } @article{1598, abstract = {We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives, and examine the problem of computing the set of almost-sure winning vertices such that the objective can be ensured with probability 1 from these vertices. We study for the first time the average-case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average-case running time is linear (as compared to the worst-case linear number of iterations and quadratic time complexity). Second, for the average-case analysis over all MDPs we show that the expected number of iterations is constant and the average-case running time is linear (again as compared to the worst-case linear number of iterations and quadratic time complexity). Finally we also show that when all MDPs are equally likely, the probability that the classical algorithm requires more than a constant number of iterations is exponentially small.}, author = {Chatterjee, Krishnendu and Joglekar, Manas and Shah, Nisarg}, journal = {Theoretical Computer Science}, number = {3}, pages = {71 -- 89}, publisher = {Elsevier}, title = {{Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives}}, doi = {10.1016/j.tcs.2015.01.050}, volume = {573}, year = {2015}, } @inproceedings{1601, abstract = {We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata.}, author = {Babiak, Tomáš and Blahoudek, František and Duret Lutz, Alexandre and Klein, Joachim and Kretinsky, Jan and Mueller, Daniel and Parker, David and Strejček, Jan}, location = {San Francisco, CA, United States}, pages = {479 -- 486}, publisher = {Springer}, title = {{The Hanoi omega-automata format}}, doi = {10.1007/978-3-319-21690-4_31}, volume = {9206}, year = {2015}, } @article{1602, abstract = {Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, etc. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring, and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, etc. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in a very important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect that we consider is that the control flow graphs for most programs have constant treewidth. Our main contributions are simple and implementable algorithms that supportmultiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing, but can answer subsequent queries significantly faster as compared to the current best-known solutions for several important problems, such as interprocedural reachability and shortest path. We provide a prototype implementation for interprocedural reachability and intraprocedural shortest path that gives a significant speed-up on several benchmarks.}, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas and Goyal, Prateesh}, journal = {ACM SIGPLAN Notices}, location = {Mumbai, India}, number = {1}, pages = {97 -- 109}, publisher = {ACM}, title = {{Faster algorithms for algebraic path properties in recursive state machines with constant treewidth}}, doi = {10.1145/2676726.2676979}, volume = {50}, year = {2015}, } @inproceedings{1603, abstract = {For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation. The key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour.}, author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Chmelik, Martin and Fellner, Andreas and Kretinsky, Jan}, location = {San Francisco, CA, United States}, pages = {158 -- 177}, publisher = {Springer}, title = {{Counterexample explanation by learning small strategies in Markov decision processes}}, doi = {10.1007/978-3-319-21690-4_10}, volume = {9206}, year = {2015}, } @article{1604, abstract = {We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs.}, author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Velner, Yaron}, isbn = {978-1-4503-3300-9}, journal = {Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT }, location = {Mumbai, India}, number = {1}, pages = {539 -- 551}, publisher = {ACM}, title = {{Quantitative interprocedural analysis}}, doi = {10.1145/2676726.2676968}, volume = {50}, year = {2015}, } @inproceedings{1605, abstract = {Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model.}, author = {Bogomolov, Sergiy and Schilling, Christian and Bartocci, Ezio and Batt, Grégory and Kong, Hui and Grosu, Radu}, location = {Haifa, Israel}, pages = {19 -- 35}, publisher = {Springer}, title = {{Abstraction-based parameter synthesis for multiaffine systems}}, doi = {10.1007/978-3-319-26287-1_2}, volume = {9434}, year = {2015}, } @inproceedings{1606, abstract = {In this paper, we present the first steps toward a runtime verification framework for monitoring hybrid and cyber-physical systems (CPS) development tools based on randomized differential testing. The development tools include hybrid systems reachability analysis tools, model-based development environments like Simulink/Stateflow (SLSF), etc. First, hybrid automaton models are randomly generated. Next, these hybrid automaton models are translated to a number of different tools (currently, SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using the HyST source transformation and translation tool. Then, the hybrid automaton models are executed in the different tools and their outputs are parsed. The final step is the differential comparison: the outputs of the different tools are compared. If the results do not agree (in the sense that an analysis or verification result from one tool does not match that of another tool, ignoring timeouts, etc.), a candidate bug is flagged and the model is saved for future analysis by the user. The process then repeats and the monitoring continues until the user terminates the process. We present preliminary results that have been useful in identifying a few bugs in the analysis methods of different development tools, and in an earlier version of HyST.}, author = {Nguyen, Luan and Schilling, Christian and Bogomolov, Sergiy and Johnson, Taylor}, booktitle = {6th International Conference}, isbn = {978-3-319-23819-7}, location = {Vienna, Austria}, pages = {281 -- 286}, publisher = {Springer Nature}, title = {{Runtime verification for hybrid analysis tools}}, doi = {10.1007/978-3-319-23820-3_19}, volume = {9333}, year = {2015}, } @inproceedings{1607, abstract = {We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W)) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.}, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas}, location = {San Francisco, CA, USA}, pages = {140 -- 157}, publisher = {Springer}, title = {{Faster algorithms for quantitative verification in constant treewidth graphs}}, doi = {10.1007/978-3-319-21690-4_9}, volume = {9206}, year = {2015}, } @inproceedings{1609, abstract = {The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Vardi, Moshe}, booktitle = {42nd International Colloquium}, isbn = {978-3-662-47665-9}, location = {Kyoto, Japan}, pages = {108 -- 120}, publisher = {Springer Nature}, title = {{The complexity of synthesis from probabilistic components}}, doi = {10.1007/978-3-662-47666-6_9}, volume = {9135}, year = {2015}, } @inproceedings{1610, abstract = {The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1,L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to pushdown automata is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Ibsen-Jensen, Rasmus and Otop, Jan}, booktitle = {42nd International Colloquium}, isbn = {978-3-662-47665-9}, location = {Kyoto, Japan}, number = {Part II}, pages = {121 -- 133}, publisher = {Springer Nature}, title = {{Edit distance for pushdown automata}}, doi = {10.1007/978-3-662-47666-6_10}, volume = {9135}, year = {2015}, } @article{1611, abstract = {Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue.}, author = {Whitfield, Jason and Zhang, William and Herde, Michel and Clifton, Ben and Radziejewski, Johanna and Janovjak, Harald L and Henneberger, Christian and Jackson, Colin}, journal = {Protein Science}, number = {9}, pages = {1412 -- 1422}, publisher = {Wiley}, title = {{Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction}}, doi = {10.1002/pro.2721}, volume = {24}, year = {2015}, } @article{1614, abstract = {GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. }, author = {Strüber, Michael and Jonas, Peter M and Bartos, Marlene}, journal = {PNAS}, number = {4}, pages = {1220 -- 1225}, publisher = {National Academy of Sciences}, title = {{Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells}}, doi = {10.1073/pnas.1412996112}, volume = {112}, year = {2015}, } @article{1615, abstract = {Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches.}, author = {Hammer, Matthieu and Krueger Burg, Dilja and Tuffy, Liam and Cooper, Benjamin and Taschenberger, Holger and Goswami, Sarit and Ehrenreich, Hannelore and Jonas, Peter M and Varoqueaux, Frederique and Rhee, Jeong and Brose, Nils}, journal = {Cell Reports}, number = {3}, pages = {516 -- 523}, publisher = {Cell Press}, title = {{Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism}}, doi = {10.1016/j.celrep.2015.09.011}, volume = {13}, year = {2015}, } @article{1618, abstract = {CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed.}, author = {Veldkamp, Christopher and Kiermaier, Eva and Gabel Eissens, Skylar and Gillitzer, Miranda and Lippner, David and Disilvio, Frank and Mueller, Casey and Wantuch, Paeton and Chaffee, Gary and Famiglietti, Michael and Zgoba, Danielle and Bailey, Asha and Bah, Yaya and Engebretson, Samantha and Graupner, David and Lackner, Emily and Larosa, Vincent and Medeiros, Tysha and Olson, Michael and Phillips, Andrew and Pyles, Harley and Richard, Amanda and Schoeller, Scott and Touzeau, Boris and Williams, Larry and Sixt, Michael K and Peterson, Francis}, journal = {Biochemistry}, number = {27}, pages = {4163 -- 4166}, publisher = {American Chemical Society}, title = {{Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites}}, doi = {10.1021/acs.biochem.5b00560}, volume = {54}, year = {2015}, } @article{1619, abstract = {The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution.}, author = {Chevereau, Guillaume and Dravecka, Marta and Batur, Tugce and Guvenek, Aysegul and Ayhan, Dilay and Toprak, Erdal and Bollenbach, Mark Tobias}, journal = {PLoS Biology}, number = {11}, publisher = {Public Library of Science}, title = {{Quantifying the determinants of evolutionary dynamics leading to drug resistance}}, doi = {10.1371/journal.pbio.1002299}, volume = {13}, year = {2015}, } @article{1623, abstract = {Background Photosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible. Results We present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells. Conclusions The workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology. }, author = {Hammar, Petter and Angermayr, Andreas and Sjostrom, Staffan and Van Der Meer, Josefin and Hellingwerf, Klaas and Hudson, Elton and Joensson, Hakaan}, journal = {Biotechnology for Biofuels}, number = {1}, publisher = {BioMed Central}, title = {{Single-cell screening of photosynthetic growth and lactate production by cyanobacteria}}, doi = {10.1186/s13068-015-0380-2}, volume = {8}, year = {2015}, }