@article{2990, abstract = {Plant growth is marked by its adaptability to continuous changes in environment. A regulated, differential distribution of auxin underlies many adaptation processes including organogenesis, meristem patterning and tropisms. In executing its multiple roles, auxin displays some characteristics of both a hormone and a morphogen. Studies on auxin transport, as well as tracing the intracellular movement of its molecular components, have suggested a possible scenario to explain how growth plasticity is conferred at the cellular and molecular level. The plant perceives stimuli and changes the subcellular position of auxin-transport components accordingly. These changes modulate auxin fluxes, and the newly established auxin distribution triggers the corresponding developmental response.}, author = {Friml, Jirí}, journal = {Current Opinion in Plant Biology}, number = {1}, pages = {7 -- 12}, publisher = {Elsevier}, title = {{Auxin transport - Shaping the plant}}, doi = {10.1016/S1369526602000031}, volume = {6}, year = {2003}, } @article{2992, abstract = {Plants have many polarized cell types, but relatively little is known about the mechanisms that establish polarity. The orc mutant was identified originally by defects in root patterning, and positional cloning revealed that the affected gene encodes STEROL METHYLTRANSFERASE1, which is required for the appropriate synthesis and composition of major membrane sterols. smt1orc mutants displayed several conspicuous cell polarity defects. Columella root cap cells revealed perturbed polar positioning of different organelles, and in the smt1orc root epidermis, polar initiation of root hairs was more randomized. Polar auxin transport and expression of the auxin reporter DR5-β-glucuronidase were aberrant in smt1orc. Patterning defects in smt1orc resembled those observed in mutants of the PIN gene family of putative auxin efflux transporters. Consistently, the membrane localization of the PIN1 and PIN3 proteins was disturbed in smt1orc, whereas polar positioning of the influx carrier AUX1 appeared normal. Our results suggest that balanced sterol composition is a major requirement for cell polarity and auxin efflux in Arabidopsis.}, author = {Willemsen, Viola and Jirí Friml and Grebe, Markus and Van Den Toorn, Albert and Palme, Klaus and Scheres, Ben}, journal = {Plant Cell}, number = {3}, pages = {612 -- 625}, publisher = {American Society of Plant Biologists}, title = {{Cell polarity and PIN protein positioning in Arabidopsis require STEROL METHYLTRANSFERASE1 function}}, doi = {10.1105/tpc.008433}, volume = {15}, year = {2003}, } @article{2996, abstract = {Plants, compared to animals, exhibit an amazing adaptability and plasticity in their development. This is largely dependent on the ability of plants to form new organs, such as lateral roots, leaves, and flowers during postembryonic development. Organ primordia develop from founder cell populations into organs by coordinated cell division and differentiation. Here, we show that organ formation in Arabidopsis involves dynamic gradients of the signaling molecule auxin with maxima at the primordia tips. These gradients are mediated by cellular efflux requiring asymmetrically localized PIN proteins, which represent a functionally redundant network for auxin distribution in both aerial and underground organs. PIN1 polar localization undergoes a dynamic rearrangement, which correlates with establishment of auxin gradients and primordium development. Our results suggest that PIN-dependent, local auxin gradients represent a common module for formation of all plant organs, regardless of their mature morphology or developmental origin. }, author = {Eva Benková and Michniewicz, Marta and Sauer, Michael and Teichmann, Thomas and Seifertová, Daniela and Jürgens, Gerd and Jirí Friml}, journal = {Cell}, number = {5}, pages = {591 -- 602}, publisher = {Cell Press}, title = {{Local, efflux-dependent auxin gradients as a common module for plant organ formation}}, doi = {10.1016/S0092-8674(03)00924-3}, volume = {115}, year = {2003}, } @article{2995, abstract = {Axis formation occurs in plants, as in animals, during early embryogenesis. However, the underlying mechanism is not known. Here we show that the first manifestation of the apical-basal axis in plants, the asymmetric division of the zygote, produces a basal cell that transports and an apical cell that responds to the signalling molecule auxin. This apical-basal auxin activity gradient triggers the specification of apical embryo structures and is actively maintained by a novel component of auxin efflux, PIN7, which is located apically in the basal cell. Later, the developmentally regulated reversal of PIN7 and onset of PIN1 polar localization reorganize the auxin gradient for specification of the basal root pole. An analysis of pin quadruple mutants identifies PIN-dependent transport as an essential part of the mechanism for embryo axis formation. Our results indicate how the establishment of cell polarity, polar auxin efflux and local auxin response result in apical-basal axis formation of the embryo, and thus determine the axiality of the adult plant. }, author = {Jirí Friml and Vieten, Anne and Sauer, Michael and Weijers, Dolf and Schwarz, Heinz and Hamann, Thorsten and Offringa, Remko and Jürgens, Gerd}, journal = {Nature}, number = {6963}, pages = {147 -- 153}, publisher = {Nature Publishing Group}, title = {{Efflux dependent auxin gradients establish the apical basal axis of Arabidopsis}}, doi = {10.1038/nature02085}, volume = {426}, year = {2003}, } @article{2994, abstract = {The regular arrangement of leaves around a plant's stem, called phyllotaxis, has for centuries attracted the attention of philosophers, mathematicians and natural scientists; however, to date, studies of phyllotaxis have been largely theoretical. Leaves and flowers are formed from the shoot apical meristem, triggered by the plant hormone auxin. Auxin is transported through plant tissues by specific cellular influx and efflux carrier proteins. Here we show that proteins involved in auxin transport regulate phyllotaxis. Our data indicate that auxin is transported upwards into the meristem through the epidermis and the outermost meristem cell layer. Existing leaf primordia act as sinks, redistributing auxin and creating its heterogeneous distribution in the meristem. Auxin accumulation occurs only at certain minimal distances from existing primordia, defining the position of future primordia. This model for phyllotaxis accounts for its reiterative nature, as well as its regularity and stability.}, author = {Reinhardt, Didier and Pesce, Eva-Rachele and Stieger, Pia and Mandel, Therese and Baltensperger, Kurt and Bennett, Malcolm and Traas, Jan and Jirí Friml and Kuhlemeier, Cris}, journal = {Nature}, number = {6964}, pages = {255 -- 260}, publisher = {Nature Publishing Group}, title = {{Regulation of phyllotaxis by polar auxin transport}}, doi = {10.1038/nature02081}, volume = {426}, year = {2003}, } @article{2993, abstract = {Plant biology is currently experiencing a growing demand for easy and reliable mRNA and protein localisation techniques. Here, we present novel whole mount in situ hybridisation and immunolocalisation protocols, suitable to localise mRNAs and proteins in Arabidopsis seedlings. We demonstrate that these methods can be used in different organs of Arabidopsis seedlings as well as in other plant species. In order to achieve better reproducibility and higher throughput, we modified these protocols for automation to be performed by a liquid handling robot. In addition, we show that other procedures such as reporter enzyme assays and tissue clearing can be similarly automated. We present examples of application of our protocols including mRNA localisation and proteins and epitope tag (co)localisations which demonstrate that these methods provide reliable and versatile tools for expression, localisation and anatomical studies in plants.}, author = {Jirí Friml and Eva Benková and Mayer, Ulrike and Palme, Klaus and Muster, Gerhard}, journal = {Plant Journal}, number = {1}, pages = {115 -- 124}, publisher = {Wiley-Blackwell}, title = {{Automated whole mount localisation techniques for plant seedlings}}, doi = {10.1046/j.1365-313X.2003.01705.x}, volume = {34}, year = {2003}, } @article{3151, abstract = {Biosynthesis of most peptide hormones and neuropeptides requires proteolytic excision of the active peptide from inactive proprotein precursors, an activity carried out by subtilisin-like proprotein convertases (SPCs) in constitutive or regulated secretory pathways. The Drosophila amontillado (amon) gene encodes a homolog of the mammalian PC2 protein, an SPC that functions in the regulated secretory pathway in neuroendocrine tissues. We have identified amon mutants by isolating ethylmethanesulfonate (EMS)-induced lethal and visible mutations that define two complementation groups in the amon interval at 97D1 of the third chromosome. DNA sequencing identified the amon complementation group and the DNA sequence change for each of the nine amon alleles isolated. amon mutants display partial embryonic lethality, are defective in larval growth, and arrest during the first to second instar larval molt. Mutant larvae can be rescued by heat-shock-induced expression of the amon protein. Rescued larvae arrest at the subsequent larval molt, suggesting that amon is also required for the second to third instar larval molt. Our data indicate that the amon proprotein convertase is required during embryogenesis and larval development in Drosophila and support the hypothesis that AMON acts to proteolytically process peptide hormones that regulate hatching, larval growth, and larval ecdysis.}, author = {Rayburn, Lowell Y and Gooding, Holly C and Choksi, Semil P and Maloney, Dhea and Kidd, Ambrose R and Daria Siekhaus and Bender, Michael}, journal = {Genetics}, number = {1}, pages = {227 -- 237}, publisher = {Genetics Society of America}, title = {{Amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development}}, volume = {163}, year = {2003}, } @article{3150, abstract = {Tripartite G-protein-coupled receptors (GPCRs) represent one of the largest groups of signal transducers, transmitting signals from hormones, neuropeptides, odorants, food and light. Ligand-bound receptors catalyse GDP/GTP exchange on the G-protein α-subunit (Gα), leading to α-GTP separation from the βγ subunits and pathway activation. Activating mutations in the receptors or G proteins underlie many human diseases, including some cancers, dwarfism and premature puberty. Regulators of G-protein signalling (RGS proteins) are known to modulate the level and duration of ligand-induced signalling by accelerating the intrinsic GTPase activity of the Gα subunit, and thus reformation of the inactive GDP-bound Gα. Here we find that even in the absence of receptor, mutation of the RGS family member Sst2 (refs 6-9) permits spontaneous activation of the G-protein-coupled mating pathway in Saccharomyces cerevisiae at levels normally seen only in the presence of ligand. Our work demonstrates the occurence of spontaneous tripartite G-protein signalling in vivo and identifies a requirement for RGS proteins in preventing such receptor-independent activation.}, author = {Daria Siekhaus and Drubin, David G}, journal = {Nature Cell Biology}, number = {3}, pages = {231 -- 235}, publisher = {Nature Publishing Group}, title = {{Spontaneous receptor-independent heterotrimeric G-protein signalling in an RGS mutant}}, doi = {10.1038/ncb941}, volume = {5}, year = {2003}, } @article{3209, abstract = {We show that the fixed alphabet shortest common supersequence (SCS) and the fixed alphabet longest common subsequence (LCS) problems parameterized in the number of strings are W[1]-hard. Unless W[1]=FPT, this rules out the existence of algorithms with time complexity of O(f(k)nα) for those problems. Here n is the size of the problem instance, α is constant, k is the number of strings and f is any function of k. The fixed alphabet version of the LCS problem is of particular interest considering the importance of sequence comparison (e.g. multiple sequence alignment) in the fixed length alphabet world of DNA and protein sequences.}, author = {Krzysztof Pietrzak}, journal = {Journal of Computer and System Sciences}, number = {4}, pages = {757 -- 771}, publisher = {Elsevier}, title = {{On the parameterized complexity of the fixed alphabet shortest common supersequence and longest common subsequence problems}}, doi = {10.1016/S0022-0000(03)00078-3}, volume = {67}, year = {2003}, } @inproceedings{3210, abstract = {Luby and Rackoff showed how to construct a (super-)pseudo-random permutation {0,1}2n→ {0,1}2n from some number r of pseudo-random functions {0,1}n → {0,1}n. Their construction, motivated by DES, consists of a cascade of r Feistel permutations. A Feistel permutation 1for a pseudo-random function f is defined as (L, R) → (R,L ⊕ f (R)), where L and R are the left and right part of the input and ⊕ denotes bitwise XOR or, in this paper, any other group operation on {0,1}n. The only non-trivial step of the security proof consists of proving that the cascade of r Feistel permutations with independent uniform random functions {0,1}n → {0,1}n, denoted Ψ2nr is indistinguishable from a uniform random permutation {0,1}2n → {0,1}2n by any computationally unbounded adaptive distinguisher making at most O(2cn) combined chosen plaintext/ciphertext queries for any c < α, where a is a security parameter. Luby and Rackoff proved α = 1/2 for r = 4. A natural problem, proposed by Pieprzyk is to improve on α for larger r. The best known result, α = 3/4 for r = 6, is due to Patarin. In this paper we prove a = 1 -O(1/r), i.e., the trivial upper bound α = 1 can be approached. The proof uses some new techniques that can be of independent interest. }, author = {Maurer, Ueli M and Krzysztof Pietrzak}, pages = {544 -- 561}, publisher = {Springer}, title = {{The security of many round Luby Rackoff pseudo random permutations}}, doi = {10.1007/3-540-39200-9_34}, volume = {2656}, year = {2003}, } @inproceedings{3425, author = {Bollenbach, Mark Tobias and Strother, T. and Bauer, Wolfgang}, pages = {277 -- 288}, publisher = {Springer}, title = {{3D supernova collapse calculations}}, doi = {10.1007/978-1-4020-2705-5_21}, volume = {166}, year = {2003}, } @inbook{3458, author = {Peter Jonas and Unsicker, Klaus}, booktitle = {Lehrbuch Vorklinik}, editor = {Schmidt, R. F.}, pages = {3 -- 26}, publisher = {Deutscher Ärzte Verlag}, title = {{Molekulare und zelluläre Grundlagen des Nervensystems.}}, volume = {B}, year = {2003}, } @article{3536, abstract = {Genetic engineering of the mouse brain allows investigators to address novel hypotheses in vivo. Because of the paucity of information on the network patterns of the mouse hippocampus, we investigated the electrical patterns in the behaving animal using multisite silicon probes and wire tetrodes. Theta (6-9 Hz) and gamma (40-100 Hz) oscillations were present during exploration and rapid eye movement sleep. Gamma power and theta power were comodulated and gamma power varied as a function of the theta cycle. Pyramidal cells and putative interneurons were phase-locked to theta oscillations. During immobility, consummatory behaviors and slow-wave sleep, sharp waves were present in cornu ammonis region CA1 of the hippocampus stratum radiatum associated with 140-200-Hz “ripples” in the pyramidal cell layer and population burst of CA1 neurons. In the hilus, large-amplitude “dentate spikes” occurred in association with increased discharge of hilar neurons. The amplitude of field patterns was larger in the mouse than in the rat, likely reflecting the higher neuron density in a smaller brain. We suggest that the main hippocampal network patterns are mediated by similar pathways and mechanisms in mouse and rat. }, author = {Buzsáki, György and Buhl, Derek L and Harris, Kenneth D and Jozsef Csicsvari and Czéh, Boldizsár and Morozov, Alexei}, journal = {Neuroscience}, number = {1}, pages = {201 -- 211}, publisher = {Elsevier}, title = {{Hippocampal network patterns of activity in the mouse}}, doi = {10.1016/S0306-4522(02)00669-3}, volume = {116}, year = {2003}, } @inproceedings{3556, abstract = {We define the Morse-Smale complex of a Morse function over a 3-manifold as the overlay of the descending and as- cending manifolds of all critical points. In the generic case, its 3-dimensional cells are shaped like crystals and are sepa- rated by quadrangular faces. In this paper, we give a combi- natorial algorithm for constructing such complexes for piece- wise linear data.}, author = {Herbert Edelsbrunner and Harer, John and Natarajan, Vijay and Pascucci, Valerio}, pages = {361 -- 370}, publisher = {ACM}, title = {{Morse-Smale complexes for piecewise linear 3-manifolds}}, doi = {10.1145/777792.777846}, year = {2003}, } @inbook{3573, abstract = {Given a finite point set in R, the surface reconstruction problem asks for a surface that passes through many but not necessarily all points. We describe an unambigu- ous definition of such a surface in geometric and topological terms, and sketch a fast algorithm for constructing it. Our solution overcomes past limitations to special point distributions and heuristic design decisions.}, author = {Herbert Edelsbrunner}, booktitle = {Discrete & Computational Geometry}, pages = {379 -- 404}, publisher = {Springer}, title = {{Surface reconstruction by wrapping finite sets in space}}, doi = {10.1007/978-3-642-55566-4_17}, year = {2003}, } @article{3584, abstract = {We develop fast algorithms for computing the linking number of a simplicial complex within a filtration.We give experimental results in applying our work toward the detection of non-trivial tangling in biomolecules, modeled as alpha complexes.}, author = {Edelsbrunner, Herbert and Zomorodian, Afra}, journal = {Homology, Homotopy and Applications}, number = {2}, pages = {19 -- 37}, publisher = {International Press}, title = {{Computing linking numbers of a filtration}}, volume = {5}, year = {2003}, } @article{3620, abstract = {Stable hybrid zones in which ecologically divergent taxa give rise to a range of recombinants are natural laboratories in which the genetic basis of adaptation and reproductive isolation can be unraveled. One such hybrid zone is formed by the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae). Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped numerous phenotypic differences between the taxa. All of these are, in principle, candidates for a genetic dissection via QTL mapping. We present here a linkage map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross, markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20 linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance of compound and frequently interleaved CA-TA repeats as well as a striking polarity at the 5′ end of the repeats.}, author = {Nürnberger, Beate and Hofman, Sebastian and Förg-Brey, Bqruni and Praetzel, Gabriele and Maclean, Alan W and Szymura, Jacek M and Abbott, Catherine M and Nicholas Barton}, journal = {Heredity}, number = {2}, pages = {136 -- 142}, publisher = {Nature Publishing Group}, title = {{A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae)}}, doi = {10.1038/sj.hdy.6800291}, volume = {91}, year = {2003}, } @article{3619, abstract = {What is the chance that some part of a stretch of genome will survive? In a population of constant size, and with no selection, the probability of survival of some part of a stretch of map length y<1 approaches View the MathML source for View the MathML source. Thus, the whole genome is certain to be lost, but the rate of loss is extremely slow. This solution extends to give the whole distribution of surviving block sizes as a function of time. We show that the expected number of blocks at time t is 1+yt and give expressions for the moments of the number of blocks and the total amount of genome that survives for a given time. The solution is based on a branching process and assumes complete interference between crossovers, so that each descendant carries only a single block of ancestral material. We consider cases where most individuals carry multiple blocks, either because there are multiple crossovers in a long genetic map, or because enough time has passed that most individuals in the population are related to each other. For species such as ours, which have a long genetic map, the genome of any individual which leaves descendants (∼80% of the population for a Poisson offspring number with mean two) is likely to persist for an extremely long time, in the form of a few short blocks of genome.}, author = {Baird, Stuart J and Nicholas Barton and Etheridge, Alison M}, journal = {Theoretical Population Biology}, number = {4}, pages = {451 -- 471}, publisher = {Academic Press}, title = {{The distribution of surviving blocks of an ancestral genome}}, doi = {10.1016/S0040-5809(03)00098-4}, volume = {64}, year = {2003}, } @article{3618, abstract = {There are several analyses in evolutionary ecology which assume that a family of offspring has come from only two parents. Here, we present a simple test for detecting when a batch involves two or more subfamilies. It is based on the fact that the mixing of families generates associations amongst unlinked marker loci. We also present simulations illustrating the power of our method for varying numbers of loci, alleles per locus and genotyped individuals.}, author = {Vines, Timothy H and Nicholas Barton}, journal = {Molecular Ecology}, number = {7}, pages = {1999 -- 2002}, publisher = {Wiley-Blackwell}, title = {{A new approach to detecting mixed families}}, doi = {10.1046/j.1365-294X.2003.01867.x}, volume = {12}, year = {2003}, } @article{3752, abstract = {We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description (molecular, cellular, and that of cell population) into a single model, which seems to capture many experimental aspects of the system.}, author = {Vilar,Jose M and Calin Guet and Leibler, Stanislas}, journal = {Journal of Cell Biology}, number = {3}, pages = {471 -- 476}, publisher = {Rockefeller University Press}, title = {{Modeling network dynamics: the lac operon, a case study}}, doi = {10.1083/jcb.200301125}, volume = {161}, year = {2003}, }