@article{2863, abstract = {Neural populations encode information about their stimulus in a collective fashion, by joint activity patterns of spiking and silence. A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input. For large populations, direct sampling of these distributions is impossible, and so we must rely on constructing appropriate models. We show here that in a population of 100 retinal ganglion cells in the salamander retina responding to temporal white-noise stimuli, dependencies between cells play an important encoding role. We introduce the stimulus-dependent maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-coupled neural population. We find that the SDME model gives a more accurate account of single cell responses and in particular significantly outperforms uncoupled models in reproducing the distributions of population codewords emitted in response to a stimulus. We show how the SDME model, in conjunction with static maximum entropy models of population vocabulary, can be used to estimate information-theoretic quantities like average surprise and information transmission in a neural population.}, author = {Granot Atedgi, Einat and Tkacik, Gasper and Segev, Ronen and Schneidman, Elad}, journal = {PLoS Computational Biology}, number = {3}, publisher = {Public Library of Science}, title = {{Stimulus-dependent maximum entropy models of neural population codes}}, doi = {10.1371/journal.pcbi.1002922}, volume = {9}, year = {2013}, } @article{2877, abstract = {Premise of the study: To reach favorable conditions for photosynthesis, seedlings grow upward when deprived of light upon underground germination. To direct their growth, they use their negative gravitropic capacity. Negative gravitropism is under tight control of multiple hormones. • Methods: By counting the number of standing plants in a population or by real time monitoring of the reorientation of gravistimulated seedlings of Arabidopsis thaliana, we evaluated the negative gravitropism of ethylene or brassinosteroid (BR) treated plants. Meta-analysis of transcriptomic data on AUX / IAA genes was gathered, and subsequent mutant analysis was performed. • Key results: Ethylene and BR have opposite effects in regulating shoot gravitropism. Lack of BR enhances gravitropic reorientation in 2-d-old seedlings, whereas ethylene does not. Lack of ethylene signaling results in enhanced BR sensitivity. Ethylene and BRs regulate overlapping sets of AUX / IAA genes. BRs regulate a wider range of auxin signaling components than ethylene. • Conclusions: Upward growth in seedlings depends strongly on the internal hormonal balance. Endogenous ethylene stimulates, whereas BRs reduce negative gravitropism in a manner that depends on the function of different, yet overlapping sets of auxin signaling components.}, author = {Vandenbussche, Filip and Callebert, Pieter and Žádníková, Petra and Eva Benková and Van Der Straeten, Dominique}, journal = {American Journal of Botany}, number = {1}, pages = {215 -- 225}, publisher = {Botanical Society of America}, title = {{Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components}}, doi = {10.3732/ajb.1200264}, volume = {100}, year = {2013}, } @article{2880, abstract = {Lateral root (LR) formation is initiated when pericycle cells accumulate auxin, thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions, giving rise to a new primordium. How this auxin maximum in pericycle cells builds up and remains focused is not understood. We report that the endodermis plays an active role in the regulation of auxin accumulation and is instructive for FCs to progress during the LR initiation (LRI) phase. We describe the functional importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux pathway causes dramatic defects in the progress of FCs towards the next initiation phase. Our data identify an unexpected regulatory function for the endodermis in LRI as part of the fine-tuning mechanism that appears to act as a check point in LR organogenesis after FCs are specified.}, author = {Marhavy, Peter and Vanstraelen, Marleen and De Rybel, Bert and Zhaojun, Ding and Bennett, Malcolm and Beeckman, Tom and Benková, Eva}, journal = {EMBO Journal}, number = {1}, pages = {149 -- 158}, publisher = {Wiley-Blackwell}, title = {{Auxin reflux between the endodermis and pericycle promotes lateral root initiation}}, doi = {10.1038/emboj.2012.303}, volume = {32}, year = {2013}, } @article{2881, abstract = {The puzzle piece-shaped Arabidopsis leaf pavement cells (PCs) with interdigitated lobes and indents is a good model system to investigate the mechanisms that coordinate cell polarity and shape formation within a tissue. Auxin has been shown to coordinate the interdigitation by activating ROP GTPase-dependent signaling pathways. To identify additional components or mechanisms, we screened for mutants with abnormal PC morphogenesis and found that cytokinin signaling regulates the PC interdigitation pattern. Reduction in cytokinin accumulation and defects in cytokinin signaling (such as in ARR7-over-expressing lines, the ahk3cre1 cytokinin receptor mutant, and the ahp12345 cytokinin signaling mutant) enhanced PC interdigitation, whereas over-production of cytokinin and over-activation of cytokinin signaling in an ARR20 over-expression line delayed or abolished PC interdigitation throughout the cotyledon. Genetic and biochemical analyses suggest that cytokinin signaling acts upstream of ROPs to suppress the formation of interdigitated pattern. Our results provide novel mechanistic understanding of the pathways controlling PC shape and uncover a new role for cytokinin signaling in cell morphogenesis.}, author = {Hongjiang Li and Xu, Tongda and Lin, Deshu and Wen, Mingzhang and Xie, Mingtang and Duclercq, Jérôme and Bielach, Agnieszka and Kim, Jungmook and Reddy, G Venugopala and Zuo, Jianru and Eva Benková and Jirí Friml and Guo, Hongwei and Yang, Zhenbiao}, journal = {Cell Research}, number = {2}, pages = {290 -- 299}, publisher = {Nature Publishing Group}, title = {{Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis}}, doi = {10.1038/cr.2012.146}, volume = {23}, year = {2013}, } @article{2882, abstract = {Gravitropic bending of plant organs is mediated by an asymmetric signaling of the plant hormone auxin between the upper and lower side of the respective organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows asymmetric action during gravitropic responses. Immunodetection using an antibody against GA and monitoring GA signaling output by downstream degradation of DELLA proteins revealed an asymmetric GA distribution and response with the maximum at the lower side of gravistimulated roots. Genetic or pharmacological manipulation of GA levels or response affects gravity-mediated auxin redistribution and root bending response. The higher GA levels at the lower side of the root correlate with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane. The observed increase in PIN2 stability is caused by a specific GA effect on trafficking of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin A-sensitive endosomes. Our results suggest that asymmetric auxin distribution instructive for gravity-induced differential growth is consolidated by the asymmetric action of GA that stabilizes the PIN-dependent auxin stream along the lower side of gravistimulated roots.}, author = {Löfke, Christian and Zwiewka, Marta and Heilmann, Ingo and Van Montagu, Marc and Teichmann, Thomas and Friml, Jirí}, journal = {PNAS}, number = {9}, pages = {3627 -- 3632}, publisher = {National Academy of Sciences}, title = {{Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism}}, doi = {10.1073/pnas.1300107110}, volume = {110}, year = {2013}, } @article{2883, abstract = {Plant architecture is influenced by the polar, cell-to-cell transport of auxin that is primarily provided and regulated by plasma membrane efflux catalysts of the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1 (TWD1), although underlying mechanisms are unclear. By genetic manipulation of TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and, thus, downstream developmental traits, such as epidermal twisting and gravitropism of the root. Using immunological assays, we demonstrate a predominant lateral, mainly outward-facing, plasma membrane location for TWD1 in the root epidermis characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3. At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1. In planta bioluminescence resonance energy transfer analysis was used to verify specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein interaction at the plasma membrane, minimizing reflux from the root apoplast into the cytoplasm.}, author = {Wang, Bangjun and Bailly, Aurélien and Zwiewk, Marta and Henrichs, Sina and Azzarello, Elisa and Mancuso, Stefano and Maeshima, Masayoshi and Friml, Jirí and Schulz, Alexander and Geisler, Markus}, journal = {Plant Cell}, number = {1}, pages = {202 -- 214}, publisher = {American Society of Plant Biologists}, title = {{Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane}}, doi = {10.1105/tpc.112.105999}, volume = {25}, year = {2013}, } @article{2884, author = {Maître, Jean-Léon and Berthoumieux, Hélène and Krens, Gabriel and Salbreux, Guillaume and Julicher, Frank and Paluch, Ewa and Heisenberg, Carl-Philipp J}, journal = {Medecine Sciences}, number = {2}, pages = {147 -- 150}, publisher = {Éditions Médicales et Scientifiques}, title = {{Cell adhesion mechanics of zebrafish gastrulation}}, doi = {10.1051/medsci/2013292011}, volume = {29}, year = {2013}, } @proceedings{2885, abstract = {This volume contains the post-proceedings of the 8th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, MEMICS 2012, held in Znojmo, Czech Republic, in October, 2012. The 13 thoroughly revised papers were carefully selected out of 31 submissions and are presented together with 6 invited papers. The topics covered by the papers include: computer-aided analysis and verification, applications of game theory in computer science, networks and security, modern trends of graph theory in computer science, electronic systems design and testing, and quantum information processing.}, editor = {Kucera, Antonin and Henzinger, Thomas A and Nesetril, Jaroslav and Vojnar, Tomas and Antos, David}, location = {Znojmo, Czech Republic}, pages = {1 -- 228}, publisher = {Springer}, title = {{Mathematical and Engineering Methods in Computer Science}}, doi = {10.1007/978-3-642-36046-6}, volume = {7721}, year = {2013}, } @inproceedings{2886, abstract = {We focus on the realizability problem of Message Sequence Graphs (MSG), i.e. the problem whether a given MSG specification is correctly distributable among parallel components communicating via messages. This fundamental problem of MSG is known to be undecidable. We introduce a well motivated restricted class of MSG, so called controllable-choice MSG, and show that all its models are realizable and moreover it is decidable whether a given MSG model is a member of this class. In more detail, this class of MSG specifications admits a deadlock-free realization by overloading existing messages with additional bounded control data. We also show that the presented class is the largest known subclass of MSG that allows for deadlock-free realization.}, author = {Chmelik, Martin and Řehák, Vojtěch}, location = {Znojmo, Czech Republic}, pages = {118 -- 130}, publisher = {Springer}, title = {{Controllable-choice message sequence graphs}}, doi = {10.1007/978-3-642-36046-6_12}, volume = {7721}, year = {2013}, } @article{2887, abstract = {Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent towhich the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes.}, author = {Fang, Suqin and Clark, Randy and Zheng, Ying and Iyer Pascuzzi, Anjali and Weitz, Joshua and Kochian, Leon and Edelsbrunner, Herbert and Liao, Hong and Benfey, Philip}, journal = {PNAS}, number = {7}, pages = {2670 -- 2675}, publisher = {National Academy of Sciences}, title = {{Genotypic recognition and spatial responses by rice roots}}, doi = {10.1073/pnas.1222821110}, volume = {110}, year = {2013}, } @article{2900, author = {Azevedo, Ricardo B and Lohaus, Rolf and Tiago Paixao}, journal = {Evolution & Development}, number = {5}, pages = {514 -- 515}, publisher = {Wiley-Blackwell}, title = {{Networking networks}}, volume = {10}, year = {2013}, } @inproceedings{2901, abstract = { We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. }, author = {Chen, Chao and Kolmogorov, Vladimir and Yan, Zhu and Metaxas, Dimitris and Lampert, Christoph}, location = {Scottsdale, AZ, United States}, pages = {161 -- 169}, publisher = {JMLR}, title = {{Computing the M most probable modes of a graphical model}}, volume = {31}, year = {2013}, } @inproceedings{2906, abstract = {Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented using CGAL, following the exact geometric computation paradigm. We report on several techniques to accelerate the computation that turn our implementation applicable to the underlying biological problem.}, author = {Kerber, Michael and Edelsbrunner, Herbert}, booktitle = {2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments}, location = {New Orleans, LA, United States}, pages = {70 -- 77}, publisher = {Society of Industrial and Applied Mathematics}, title = {{3D kinetic alpha complexes and their implementation}}, doi = {10.1137/1.9781611972931.6}, year = {2013}, } @inbook{2907, abstract = {Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on.}, author = {Barton, Nicholas H}, booktitle = {The Princeton Guide to Evolution}, isbn = {9780691149776}, pages = {328 -- 333}, publisher = {Princeton University Press}, title = {{Recombination and sex}}, year = {2013}, } @article{2908, abstract = {Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence.}, author = {Barton, Nicholas H}, journal = {Journal of Evolutionary Biology}, number = {2}, pages = {267 -- 269}, publisher = {Wiley-Blackwell}, title = {{Does hybridisation influence speciation? }}, doi = {10.1111/jeb.12015}, volume = {26}, year = {2013}, } @article{2909, abstract = {We survey a class of models for spatially structured populations which we have called spatial Λ-Fleming–Viot processes. They arise from a flexible framework for modelling in which the key innovation is that random genetic drift is driven by a Poisson point process of spatial ‘events’. We demonstrate how this overcomes some of the obstructions to modelling populations which evolve in two- (and higher-) dimensional spatial continua, how its predictions match phenomena observed in data and how it fits with classical models. Finally we outline some directions for future research.}, author = {Barton, Nicholas H and Etheridge, Alison and Véber, Amandine}, journal = {Journal of Statistical Mechanics Theory and Experiment}, number = {1}, publisher = {IOP Publishing Ltd.}, title = {{Modelling evolution in a spatial continuum}}, doi = {10.1088/1742-5468/2013/01/P01002}, volume = {2013}, year = {2013}, } @article{2910, abstract = {Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation by distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module.}, author = {Kelleher, Jerome and Barton, Nicholas H and Etheridge, Alison}, journal = {Bioinformatics}, number = {7}, pages = {955 -- 956}, publisher = {Oxford University Press}, title = {{Coalescent simulation in continuous space}}, doi = {10.1093/bioinformatics/btt067}, volume = {29}, year = {2013}, } @article{2913, abstract = {The ability of an organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this "neural metric" tells us how distinguishable a pair of stimulus clips is to the retina, based on the similarity between the induced distributions of population responses. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the support-vector-machine- like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding.}, author = {Tkacik, Gasper and Granot Atedgi, Einat and Segev, Ronen and Schneidman, Elad}, journal = {Physical Review Letters}, number = {5}, publisher = {American Physical Society}, title = {{Retinal metric: a stimulus distance measure derived from population neural responses}}, doi = {10.1103/PhysRevLett.110.058104}, volume = {110}, year = {2013}, } @article{2914, abstract = {The scale invariance of natural images suggests an analogy to the statistical mechanics of physical systems at a critical point. Here we examine the distribution of pixels in small image patches and show how to construct the corresponding thermodynamics. We find evidence for criticality in a diverging specific heat, which corresponds to large fluctuations in how "surprising" we find individual images, and in the quantitative form of the entropy vs energy. We identify special image configurations as local energy minima and show that average patches within each basin are interpretable as lines and edges in all orientations.}, author = {Stephens, Greg and Mora, Thierry and Tkacik, Gasper and Bialek, William}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Statistical thermodynamics of natural images}}, doi = {10.1103/PhysRevLett.110.018701}, volume = {110}, year = {2013}, } @article{2918, abstract = {Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis. }, author = {Castanon, Irinka and Abrami, Laurence and Holtzer, Laurent and Heisenberg, Carl-Philipp J and Van Der Goot, Françoise and González Gaitán, Marcos}, journal = {Nature Cell Biology}, number = {1}, pages = {28 -- 39}, publisher = {Nature Publishing Group}, title = {{Anthrax toxin receptor 2a controls mitotic spindle positioning}}, doi = {10.1038/ncb2632}, volume = {15}, year = {2013}, }