@article{2624, abstract = {Metabotropic γ-aminobutyric acid receptors (GABABRs) are involved in modulation of synaptic transmission and activity of cerebellar and thalamic neurons. We used subtype-specific antibodies in pre- and postembedding immunohistochemistry combined with three-dimensional reconstruction of labelled profiles and quantification of immunoparticles to reveal the subcellular distribution of pre- and postsynaptic GABABR1a/b and GABABR2 in the rat cerebellum and ventrobasal thalamus. GABABR1a/b and R2 were extensively colocalized in most brain regions including the cerebellum and thalamus. In the cerebellum, immunoreactivity for both subtypes was prevalent in the molecular layer. The most intense immunoreactivity was found in Purkinje cell spines with a high density of immunoparticles at extrasynaptic sites peaking at around 240 nm from glutamatergic synapses between spines and parallel fibre varicosities. This is in contrast to dendrites at sites around GABAergic synapses where sparse and random distribution was found for both subtypes. In addition, more than one-tenth of the synaptic membrane specialization of spine-parallel fibre synapses were labelled at pre- or postsynaptic sites. Weak immunolabelling for both subtypes was also seen in parallel fibres but only rarely in GABAergic axons. In the ventrobasal thalamus, immunolabelling for both receptor subtypes was intense over the dendritic field of thalamocortical cells. Electron microscopy demonstrated an extrasynaptic localization of GABABR1a/b and R2 exclusively in postsynaptic elements. Quantitative analysis further revealed the density of GABABR1a/b around GABAergic synapses was higher than glutamatergic synapses on thalamocortical cell dendrites. The distinct localization of GABABRs relative to synaptic sites in the cerebellum and ventrobasal thalamus suggests that GABABRs differentially regulate activity of different neuronal populations.}, author = {Kulik, Ákos and Nakadate, Kazuhiko and Nyíri, Gábor and Notomi, Takuya and Malitschek, Barbara and Bettler, Bernhard and Shigemoto, Ryuichi}, issn = {0953-816X}, journal = {European Journal of Neuroscience}, number = {2}, pages = {291 -- 307}, publisher = {Wiley-Blackwell}, title = {{Distinct localization of GABAB receptors relative to synaptic sites in the rat cerebellum and ventrobasal thalamus}}, doi = {10.1046/j.0953-816x.2001.01855.x}, volume = {15}, year = {2002}, } @inbook{2694, abstract = {We outline the status of rigorous derivations of certain classical evolution equations as limits of Schrödinger dynamics. We explain two recent results jointly with H.T. Yau in more details. The first one is the derivation of the linear Boltzmann equation as the long time limit of the one-body Schrödinger equation with a random potential. The second one is the mean field limit of high density bosons with Coulomb interaction that leads to the nonlinear Hartree equation.}, author = {Erdös, László}, booktitle = {Dynamics of Dissipation}, isbn = {9783540441113}, pages = {487 -- 506}, publisher = {Springer}, title = {{Scaling limits of Schrödinger quantum mechanics}}, doi = {10.1007/3-540-46122-1_19}, year = {2002}, } @inproceedings{2708, author = {László Erdös}, pages = {129 -- 133}, publisher = {World Scientific Publishing}, title = {{Two dimensional Pauli operator via scalar potential}}, doi = {10.1090/conm/307}, volume = {307}, year = {2002}, } @article{2737, abstract = {We derive the time-dependent Schrödinger–Poisson equation as the weak coupling limit of the N-body linear Schrödinger equation with Coulomb potential.}, author = {Bardos, Claude and Erdös, László and Golse, François and Mauser, Norbert and Yau, Horng}, issn = {1631-073X}, journal = {Comptes Rendus Mathematique}, number = {6}, pages = {515 -- 520}, publisher = {Elsevier}, title = {{Derivation of the Schrödinger-Poisson equation from the quantum N-body problem}}, doi = {10.1016/S1631-073X(02)02253-7}, volume = {334}, year = {2002}, } @article{2738, abstract = {We consider the long time evolution of a quantum particle weakly interacting with a phonon field. We show that in the weak coupling limit the Wigner distribution of the electron density matrix converges to the solution of the linear Boltzmann equation globally in time. The collision kernel is identified as the sum of an emission and an absorption term that depend on the equilibrium distribution of the free phonon modes.}, author = {Erdös, László}, issn = {0022-4715}, journal = {Journal of Statistical Physics}, number = {5-6}, pages = {1043 -- 1127}, publisher = {Springer}, title = {{Linear Boltzmann equation as the long time dynamics of an electron weakly coupled to a phonon field}}, doi = {10.1023/A:1015157624384}, volume = {107}, year = {2002}, } @article{2739, abstract = {We define the two dimensional Pauli operator and identify its core for magnetic fields that are regular Borel measures. The magnetic field is generated by a scalar potential hence we bypass the usual A L 2loc condition on the vector potential, which does not allow to consider such singular fields. We extend the Aharonov-Casher theorem for magnetic fields that are measures with finite total variation and we present a counterexample in case of infinite total variation. One of the key technical tools is a weighted L 2 estimate on a singular integral operator.}, author = {Erdös, László and Vougalter, Vitali}, issn = {0010-3616}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {399 -- 421}, publisher = {Springer}, title = {{Pauli operator and Aharonov–Casher theorem¶ for measure valued magnetic fields}}, doi = {10.1007/s002200100585}, volume = {225}, year = {2002}, } @article{2740, abstract = {We show that the lowest eigenvalue of the magnetic Schrödinger operator on a line bundle over a compact Riemann surface M is bounded by the L1-norm of the magnetic field B. This implies a similar bound on the multiplicity of the ground state. An example shows that this degeneracy can indeed be comparable with ∫M |B| even in case of the trivial bundle.}, author = {Erdös, László}, issn = {0373-0956}, journal = {Annales de l'Institut Fourier}, number = {6}, pages = {1833--1874}, publisher = {Association des Annales de l'Institut Fourier}, title = {{Spectral shift and multiplicity of the first eigenvalue of the magnetic Schrödinger operator in two dimensions}}, doi = {10.5802/aif.1936}, volume = {52}, year = {2002}, } @article{2866, abstract = {Developmental responses to the plant hormone auxin are thought to be mediated by interacting pairs from two protein families: short-lived inhibitory IAA proteins and ARF transcription factors binding to auxin-response elements. Monopteros mutants lacking activating ARF5 and the auxin-insensitive mutant bodenlos fail to initiate the root meristem during early embryogenesis. Here we show that the bodenlos phenotype results from an amino-acid exchange in the conserved degradation domain of IAA12. BODENLOS and MONOPTEROS interact in the yeast two-hybrid assay and the two genes are coexpressed in early embryogenesis, suggesting that BODENLOS inhibits MONOPTEROS action in root meristem initiation.}, author = {Hamann, Thorsten and Benková, Eva and Bäurle, Isabel and Kientz, Marika and Jürgens, Gerd}, issn = {0890-9369}, journal = {Genes and Development}, number = {13}, pages = {1610 -- 1615}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{The Arabidopsis BODENLOS gene encodes an auxin response protein inhibiting MONOPTEROS-mediated embryo patterning}}, doi = {10.1101/gad.229402}, volume = {16}, year = {2002}, } @inproceedings{2927, abstract = {In the last few years, several new algorithms based on graph cuts have been developed to solve energy minimization problems in computer vision. Each of these techniques constructs a graph such that the minimum cut on the graph also minimizes the energy. Yet because these graph constructions are complex and highly specific to a particular energy function, graph cuts have seen limited application to date. In this paper we characterize the energy functions that can be minimized by graph cuts. Our results are restricted to energy functions with binary variables. However, our work generalizes many previous constructions, and is easily applicable to vision problems that involve large numbers of labels, such as stereo, motion, image restoration and scene reconstruction. We present three main results: a necessary condition for any energy function that can be minimized by graph cuts; a sufficient condition for energy functions that can be written as a sum of functions of up to three variables at a time; and a general-purpose construction to minimize such an energy function. Researchers who are considering the use of graph cuts to optimize a particular energy function can use our results to determine if this is possible, and then follow our construction to create the appropriate graph.}, author = {Kolmogorov, Vladimir and Zabih, Ramin}, booktitle = {Proceedings of the 7th European Conference on Computer Vision}, isbn = {9783540437468}, location = {Copenhagen, Denmark}, pages = {65 -- 81}, publisher = {Springer}, title = {{Multi-camera scene reconstruction via graph cuts}}, doi = {10.1007/3-540-47977-5_5}, year = {2002}, } @article{2986, abstract = {Long-standing models propose that plant growth responses to light or gravity are mediated by asymmetric distribution of the phytohormone auxin. Physiological studies implicated a specific transport system that relocates auxin laterally, thereby effecting differential growth; however, neither the molecular components of this system nor the cellular mechanism of auxin redistribution on light or gravity perception have been identified. Here, we show that auxin accumulates asymmetrically during differential growth in an efflux-dependent manner. Mutations in the Arabidopsis gene PIN3, a regulator of auxin efflux, alter differential growth. PIN3 is expressed in gravity-sensing tissues, with PIN3 protein accumulating predominantly at the lateral cell surface. PIN3 localizes to the plasma membrane and to vesicles that cycle in an actin-dependent manner. In the root columella, PIN3 is positioned symmetrically at the plasma membrane but rapidly relocalizes laterally on gravity stimulation. Our data indicate that PIN3 is a component of the lateral auxin transport system regulating tropic growth. In addition, actin-dependent relocalization of PIN3 in response to gravity provides a mechanism for redirecting auxin flux to trigger asymmetric growth.}, author = {Friml, Jirí and Wiśniewska, Justyna and Benková, Eva and Mendgen, Kurt and Palme, Klaus}, issn = {0028-0836}, journal = {Nature}, number = {6873}, pages = {806 -- 809}, publisher = {Nature Publishing Group}, title = {{Lateral relocation of auxin efflux regulator PIN3 mediates tropism in Arabidopsis}}, doi = {10.1038/415806a}, volume = {415}, year = {2002}, } @article{2987, abstract = {The hydra mutants of Arabidopsis are characterized by a pleiotropic phenotype that shows defective embryonic and seedling cell patterning, morphogenesis, and root growth. We demonstrate that the HYDRA1 gene encodes a Δ8-Δ7 sterol isomerase, whereas HYDRA2 encodes a sterol C14 reductase, previously identified as the FACKEL gene product. Seedlings mutant for each gene are similarly defective in the concentrations of the three major Arabidopsis sterols. Promoter::reporter gene analysis showed misexpression of the auxin-regulated DR5 and ACS1 promoters and of the epidermal cell file-specific GL2 promoter in the mutants. The mutants exhibit enhanced responses to auxin. The phenotypes can be rescued partially by inhibition of auxin and ethylene signaling but not by exogenous sterols or brassinosteroids. We propose a model in which correct sterol profiles are required for regulated auxin and ethylene signaling through effects on membrane function.}, author = {Souter, Martin and Topping, Jennifer and Pullen, Margaret and Friml, Jirí and Palme, Klaus and Hackett, Rachel and Grierson, Don and Lindsey, Keith}, issn = {1040-4651}, journal = {Plant Cell}, number = {5}, pages = {1017 -- 1031}, publisher = {American Society of Plant Biologists}, title = {{Hydra mutants of Arabidopsis are defective in sterol profiles and auxin and ethylene signaling}}, doi = {10.1105/tpc.001248}, volume = {14}, year = {2002}, } @article{2988, abstract = {Coordination of cell and tissue polarity commonly involves directional signaling [1]. In the Arabidopsis root epidermis, cell polarity is revealed by basal, root tip-oriented, hair outgrowth from hair-forming cells (trichoblasts) [2]. The plant hormone auxin displays polar movements [1, 3] and accumulates at maximum concentration in the root tip [4, 5]. The application of polar auxin transport inhibitors [3] evokes changes in trichoblast polarity only at high concentrations and after long-term application [2, 4]. Thus, it remains open whether components of the auxin transport machinery mediate establishment of trichoblast polarity. Here we report that the presumptive auxin influx carrier AUX1 [6, 7] contributes to apical-basal hair cell polarity. AUX1 function is required for polarity changes induced by exogenous application of the auxin 2,4-D, a preferential influx carrier substrate. Similar to aux1 mutants, the vesicle trafficking inhibitor brefeldin A (BFA) interferes with polar hair initiation, and AUX1 function is required for BFA-mediated polarity changes. Consistently, BFA inhibits membrane trafficking of AUX1, trichoblast hyperpolarization induced by 2,4-D, and alters the distal auxin maximum. Our results identify AUX1 as one component of a novel BFA-sensitive auxin transport pathway polarizing cells toward a hormone maximum.}, author = {Grebe, Markus and Friml, Jirí and Swarup, Ranjan and Ljung, Karin and Sandberg, Göran and Terlou, Maarten and Palme, Klaus and Bennett, Malcolm and Scheres, Ben}, issn = {0960-9822}, journal = {Current Biology}, number = {4}, pages = {329 -- 334}, publisher = {Cell Press}, title = {{Cell polarity signaling in Arabidopsis involves a BFA sensitive auxin influx pathway}}, doi = {10.1016/S0960-9822(02)00654-1}, volume = {12}, year = {2002}, } @article{2989, abstract = {In contrast to animals, little is known about pattern formation in plants. Physiological and genetic data suggest the involvement of the phytohormone auxin in this process. Here, we characterize a novel member of the PIN family of putative auxin efflux carriers, Arabidopsis PIN4, that is localized in developing and mature root meristems. Atpin4 mutants are defective in establishment and maintenance of endogenous auxin gradients, fail to canalize externally applied auxin, and display various patterning defects in both embryonic and seedling roots. We propose a role for AtPIN4 in generating a sink for auxin below the quiescent center of the root meristem that is essential for auxin distribution and patterning.}, author = {Friml, Jirí and Benková, Eva and Blilou, Ikram and Wiśniewska, Justyna and Hamann, Thorsten and Ljung, Karin and Woody, Scott and Sandberg, Göran and Scheres, Ben and Jürgens, Gerd and Palme, Klaus}, issn = {0092-8674}, journal = {Cell}, number = {5}, pages = {661 -- 673}, publisher = {Cell Press}, title = {{AtPIN4 mediates sink-driven auxin gradients and root patterning in Arabidopsis}}, doi = {10.1016/S0092-8674(02)00656-6}, volume = {108}, year = {2002}, } @article{2991, abstract = {Polar auxin transport controls multiple aspects of plant development including differential growth, embryo and root patterning and vascular tissue differentiation. Identification of proteins involved in this process and availability of new tools enabling `visualization' of auxin and auxin routes in planta largely contributed to the significant progress that has recently been made. New data support classical concepts, but several recent findings are likely to challenge our view on the mechanism of auxin transport. The aim of this review is to provide a comprehensive overview of the polar auxin transport field. It starts with classical models resulting from physiological studies, describes the genetic contributions and discusses the molecular basis of auxin influx and efflux. Finally, selected questions are presented in the context of developmental biology, integrating available data from different fields.}, author = {Friml, Jirí and Palme, Klaus}, journal = {Plant Molecular Biology}, number = {3-4}, pages = {273 -- 284}, publisher = {Springer}, title = {{Polar auxin transport - Old questions and new concepts?}}, doi = {10.1023/A:1015248926412}, volume = {49}, year = {2002}, } @article{3140, abstract = {The maturation of synaptic structures depends on inductive interactions between axons and their prospective targets. One example of such an interaction is the influence of proprioceptive sensory axons on the differentiation of muscle spindles. We have monitored the expression of three transcription factors, Egr3, Pea3, and Erm, that delineate early muscle spindle development in an assay of muscle spindle-inducing signals. We provide genetic evidence that Neuregulin1 (Nrg1) is required for proprioceptive afferent-evoked induction of muscle spindle differentiation in the mouse. Ig-Nrg1 isoforms are preferentially expressed by proprioceptive sensory neurons and are sufficient to induce muscle spindle differentiation in vivo, whereas CRD-Nrg1 isoforms are broadly expressed in sensory and motor neurons but are not required for muscle spindle induction.}, author = {Hippenmeyer, Simon and Shneider, Neil and Birchmeier, Carmen and Burden, Steven and Jessell, Thomas and Arber, Silvia}, issn = {0896-6273}, journal = {Neuron}, number = {6}, pages = {1035 -- 1049}, publisher = {Elsevier}, title = {{A role for Neuregulin1 signaling in muscle spindle differentiation}}, doi = {10.1016/S0896-6273(02)01101-7}, volume = {36}, year = {2002}, } @article{11123, abstract = {The small GTPase Ran is a key regulator of nucleocytoplasmic transport during interphase. The asymmetric distribution of the GTP-bound form of Ran across the nuclear envelope — that is, large quantities in the nucleus compared with small quantities in the cytoplasm — determines the directionality of many nuclear transport processes. Recent findings that Ran also functions in spindle formation and nuclear envelope assembly during mitosis suggest that Ran has a general role in chromatin-centred processes. Ran functions in these events as a signal for chromosome position.}, author = {HETZER, Martin W and Gruss, Oliver J. and Mattaj, Iain W.}, issn = {1476-4679}, journal = {Nature Cell Biology}, keywords = {Cell Biology}, number = {7}, pages = {E177--E184}, publisher = {Springer Nature}, title = {{The Ran GTPase as a marker of chromosome position in spindle formation and nuclear envelope assembly}}, doi = {10.1038/ncb0702-e177}, volume = {4}, year = {2002}, } @article{11124, abstract = {Ran GTPase plays important roles in nucleocytoplasmic transport in interphase [1, 2] and in both spindle formation and nuclear envelope (NE) assembly during mitosis [3, 4, 5]. The latter functions rely on the presence of high local concentrations of GTP-bound Ran near mitotic chromatin [3, 4, 5]. RanGTP localization has been proposed to result from the association of Ran's GDP/GTP exchange factor, RCC1, with chromatin [6, 7, 8, 9], but Ran is shown here to bind directly to chromatin in two modes, either dependent or independent of RCC1, and, where bound, to increase the affinity of chromatin for NE membranes. We propose that the Ran binding capacity of chromatin contributes to localized spindle and NE assembly.}, author = {Bilbao-Cortés, Daniel and HETZER, Martin W and Längst, Gernot and Becker, Peter B. and Mattaj, Iain W.}, issn = {0960-9822}, journal = {Current Biology}, keywords = {General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology}, number = {13}, pages = {1151--1156}, publisher = {Elsevier BV}, title = {{Ran binds to chromatin by two distinct mechanisms}}, doi = {10.1016/s0960-9822(02)00927-2}, volume = {12}, year = {2002}, } @article{859, abstract = {The polymeric ubiquitin (poly-u) genes are composed of tandem 228-bp repeats with no spacer sequences between individual monomer units. Ubiquitin is one of the most conserved proteins known to date, and the individual units within a number of poly-u genes are significantly more similar to each other than would be expected if each unit evolved independently. It has been proposed that the rather striking similarity among poly-u monomers in some lineages is caused by a series of homogenization events. Here we report the sequences of the polyubiquitin-C (Ubc) genes in two mouse strains. Analysis of these sequences, as well as those of the previously reported Chinese hamster and rat poly-u genes, supports the assertion that the homogenization of the ubiquitin-C gene in rodents is due to unequal crossing-over events. The sequence divergence of noncoding DNA was used to estimate the frequency of unequal crossing-over events (6.3 x 10-5 events per generation) in the Ubc gene, as well as to provide evidence of apparent selection in the poly-u gene.}, author = {Perelygin, Andrey and Kondrashov, Fyodor and Rogozin, Igor and Brinton, Margo}, issn = {0022-2844}, journal = {Journal of Molecular Evolution}, number = {2}, pages = {202 -- 210}, publisher = {Springer}, title = {{Evolution of the mouse polyubiquitin C gene}}, doi = {10.1007/s00239-002-2318-0}, volume = {55}, year = {2002}, } @article{871, abstract = {BACKGROUND: Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolution of a new function. RESULTS: In search of systematic evidence of accelerated evolution after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic genomes to compare the mode and strength of selection acting on recently duplicated genes (paralogs) and on similarly diverged, unduplicated orthologous genes in different species. We find that the ratio of nonsynonymous to synonymous substitutions (Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve at similar rates, without significant asymmetry, indicating that both paralogs produced by a duplication are subject to purifying selection. This selection is, however, substantially weaker than the purifying selection affecting unduplicated orthologs that have diverged to the same extent as the analyzed paralogs. Most of the recently duplicated genes appear to be involved in various forms of environmental response; in particular, many of them encode membrane and secreted proteins. CONCLUSIONS: The results of this analysis indicate that recently duplicated paralogs evolve faster than orthologs with the same level of divergence and similar functions, but apparently do not experience a phase of neutral evolution. We hypothesize that gene duplications that persist in an evolving lineage are beneficial from the time of their origin, due primarily to a protein dosage effect in response to variable environmental conditions; duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached.}, author = {Kondrashov, Fyodor and Rogozin, Igor and Wolf, Yuri and Koonin, Eugene}, issn = {1465-6906}, journal = {Genome Biology}, number = {2}, publisher = {BioMed Central}, title = {{Selection in the evolution of gene duplications }}, doi = {10.1186/gb-2002-3-2-research0008}, volume = {3}, year = {2002}, } @article{885, abstract = {We study fitness landscape in the space of protein sequences by relating sets of human pathogenic missense mutations in 32 proteins to amino acid substitutions that occurred in the course of evolution of these proteins. On average, ≈10% of deviations of a nonhuman protein from its human ortholog are compensated pathogenic deviations (CPDs), i.e., are caused by an amino acid substitution that, at this site, would be pathogenic to humans. Normal functioning of a CPD-containing protein must be caused by other, compensatory deviations of the nonhuman species from humans. Together, a CPD and the corresponding compensatory deviation form a Dobzhansky-Muller incompatibility that can be visualized as the corner on a fitness ridge. Thus, proteins evolve along fitness ridges which contain only ≈10 steps between sucessive corners. The fraction of CPDs among all deviations of a protein from its human ortholog does not increase with the evolutionary distance between the proteins, indicating that subtitutions that carry evolving proteins around these corners occur in rapid succession, driven by positive selection. Data on fitness of interspecies hybrids suggest that the compensatory change that makes a CPD fit usually occurs within the same protein. Data on protein structures and on cooccurrence of amino acids at different sites of multiple orthologous proteins often make it possible to provisionally identify the substitution that compensates a partiCUlar CPD.}, author = {Kondrashov, Alexey and Sunyaev, Shamil and Kondrashov, Fyodor}, issn = {0027-8424}, journal = {PNAS}, number = {23}, pages = {14878 -- 14883}, publisher = {National Academy of Sciences}, title = {{Dobzhansky-Muller incompatibilities in protein evolution}}, doi = {10.1073/pnas.232565499}, volume = {99}, year = {2002}, }