@article{2672, abstract = {Hyperpolarization-activated cyclic nucleotide-modulated (HCN) "pacemaker" channel subunits are integral membrane proteins that assemble as tetramers to form channels in cardiac conduction tissue and nerve cells. Previous studies have suggested that the HCN2 and HCN4 channel isoforms physically interact when overexpressed in mammalian cells, but whether they are able to co-assemble and form functional channels remains unclear. The extent to which co-assembly occurs over self-assembly and whether HCN2-HCN4 heteromeric channels are formed in native tissue are not known. In this study, we show co-assembly of HCN2 and HCN4 in live Chinese hamster ovary cells using bioluminescence resonance energy transfer (BRET2), a novel approach for studying tetramerization of ion channel subunits. Together with results from electrophysiological and imaging approaches, the BRET2 data show that HCN2 and HCN4 subunits self-assemble and co-assemble with equal preference. We also demonstrate colocalization of HCN2 and HCN4 and a positive correlation of their intensities in the embryonic mouse heart using immunohistochemistry, as well as physical interactions between these isoforms in the rat thalamus by coimmunoprecipitation. Together, these data support the formation of HCN2-HCN4 heteromeric channels in native tissue.}, author = {Whitaker, Gina M and Angoli, Damiano and Nazzari, Hamed and Ryuichi Shigemoto and Accili, Eric A}, journal = {Journal of Biological Chemistry}, number = {31}, pages = {22900 -- 22909}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{HCN2 and HCN4 isoforms self-assemble and co-assemble with equal preference to form functional pacemaker channels}}, doi = {10.1074/jbc.M610978200}, volume = {282}, year = {2007}, } @article{2673, abstract = {Excitatory synaptic transmission is inhibited by G protein coupled receptors, including the adenosine A1, GABAB, and metabotropic glutamate receptor 7. These receptors are present in nerve terminals where they reduce the release of glutamate through activating signaling pathways negatively coupled to Ca2+ channels and adenylyl cyclase. However, it is not clear whether these receptors operate in distinct subpopulations of nerve terminals or if they are co-expressed in the same nerve terminals, despite the functional consequences that such distributions may have on synaptic transmission. Applying Ca2+ imaging and immunocytochemistry, we show that these three G protein coupled receptors coexist in a subpopulation of cerebrocortical nerve terminals. The three receptors share an intracellular signaling pathway through which their inhibitory responses are integrated and coactivation of these receptors produced an integrated response. Indeed, this response was highly variable, from a synergistic response at subthreshold agonist concentrations to an occluded response at high agonist concentrations. The presence of multiple receptors in a nerve terminal could be responsible for the physiological effects of neurotransmitter spillover from neighboring synapses or alternatively, the co-release of transmitters by the same nerve terminal.}, author = {Ladera, Carolina and Godino, María D and Martín, Ricardo J and Luján, Rafael and Ryuichi Shigemoto and Ciruela, Francisco and Torres, Magdalena and Sánchez-Prieto, José}, journal = {Journal of Neurochemistry}, number = {6}, pages = {2314 -- 2326}, publisher = {Wiley-Blackwell}, title = {{ The coexistence of multiple receptors in a single nerve terminal provides evidence for pre-synaptic integration}}, doi = {10.1111/j.1471-4159.2007.04964.x}, volume = {103}, year = {2007}, } @inbook{2705, author = {László Erdös}, booktitle = {Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry Simon's 60th Birthday }, editor = {Gesztesy, Fritz and Deift, Percy and Galvez, Percy and Perry, Peter and Schlag, Wilhelm}, pages = {401 -- 428}, publisher = {American Mathematical Society}, title = {{Recent developments in quantum mechanics with magnetic fields}}, volume = {76}, year = {2007}, } @article{2748, abstract = {The time-dependent Gross-Pitaevskii equation describes the dynamics of initially trapped Bose-Einstein condensates. We present a rigorous proof of this fact starting from a many-body bosonic Schrödinger equation with a short-scale repulsive interaction in the dilute limit. Our proof shows the persistence of an explicit short-scale correlation structure in the condensate.}, author = {László Erdös and Schlein, Benjamin and Yau, Horng-Tzer}, journal = {Physical Review Letters}, number = {4}, publisher = {American Physical Society}, title = {{Rigorous derivation of the Gross-Pitaevskii equation}}, doi = {10.1103/PhysRevLett.98.040404}, volume = {98}, year = {2007}, } @misc{2749, abstract = {We prove rigorously that the one-particle density matrix of three dimensional interacting Bose systems with a short-scale repulsive pair interaction converges to the solution of the cubic non-linear Schrödinger equation in a suitable scaling limit. The result is extended to k-particle density matrices for all positive integer k. }, author = {László Erdös and Schlein, Benjamin and Yau, Horng-Tzer}, booktitle = {Inventiones Mathematicae}, number = {3}, pages = {515 -- 614}, publisher = {Springer}, title = {{Derivation of the cubic non linear Schrödinger equation from quantum dynamics of many body systems}}, doi = {10.1007/s00222-006-0022-1}, volume = {167}, year = {2007}, } @article{2750, abstract = {We consider random Schrödinger equations on ℝd for d ≥ 3 with a homogeneous Anderson-Poisson type random potential. Denote by λ the coupling constant and ψt the solution with initial data ψ0. The space and time variables scale as χ ≃λ-2-κ/2, t ≃λ-2-κ with 0 < kappa; < kappa;0(d). We prove that, in the limit λ → 0, the expectation of the Wigner distribution of ψt converges weakly to the solution of a heat equation in the space variable x for arbitrary L2 initial data. The proof is based on a rigorous analysis of Feynman diagrams. In the companion paper [10] the analysis of the non-repetition diagrams was presented. In this paper we complete the proof by estimating the recollision diagrams and showing that the main terms, i.e. the ladder diagrams with renormalized propagator, converge to the heat equation.}, author = {László Erdös and Salmhofer, Manfred and Yau, Horng-Tzer}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {1 -- 53}, publisher = {Springer}, title = {{Quantum diffusion of the random Schrödinger evolution in the scaling limit II. The recollision diagrams}}, doi = {10.1007/s00220-006-0158-2}, volume = {271}, year = {2007}, } @article{2751, abstract = {We consider random Schrödinger equations on ℤd for d ≥ 3 with identically distributed random potential. Denote by λ the coupling constant and ψ t the solution with initial data ψ 0. The space and time variables scale as x ∼ λ -2-κ/2,t ∼ λ-2-κ with 0 < κ < κ0(d). We prove that, in the limit λ → 0, the expectation of the Wigner distribution of ψ t converges weakly to a solution of a heat equation in the space variable x for arbitrary L 2 initial data. The diffusion coefficient is uniquely determined by the kinetic energy associated to the momentum υ. This work is an extension to the lattice case of our previous result in the continuum [8,9]. Due to the non-convexity of the level surfaces of the dispersion relation, the estimates of several Feynman graphs are more involved.}, author = {László Erdös and Salmhofer, Manfred and Yau, Horng-Tzer}, journal = {Annales Henri Poincare}, number = {4}, pages = {621 -- 685}, publisher = {Birkhäuser}, title = {{Quantum diffusion for the Anderson model in the scaling limit}}, doi = {10.1007/s00023-006-0318-0}, volume = {8}, year = {2007}, } @article{2752, abstract = {We prove L p -bounds on the Fourier transform of measures μ supported on two dimensional surfaces. Our method allows to consider surfaces whose Gauss curvature vanishes on a one-dimensional submanifold. Under a certain non-degeneracy condition, we prove that μ ∧ ε L 4+β, β > 0, and we give a logarithmically divergent bound on the L 4-norm. We use this latter bound to estimate almost singular integrals involving the dispersion relation, e(p)= ∑13 [1-\cos p_j]} , of the discrete Laplace operator on the cubic lattice. We briefly explain our motivation for this bound originating in the theory of random Schrödinger operators.}, author = {László Erdös and Salmhofer, Manfred}, journal = {Mathematische Zeitschrift}, number = {2}, pages = {261 -- 294}, publisher = {Springer}, title = {{Decay of the Fourier transform of surfaces with vanishing curvature}}, doi = {10.1007/s00209-007-0125-4}, volume = {257}, year = {2007}, } @misc{2793, abstract = {Pipe flow is a prominent example among the shear flows that undergo transition to turbulence without mediation by a linear instability of the laminar profile. Experiments on pipe flow, as well as plane Couette and plane Poiseuille flow, show that triggering turbulence depends sensitively on initial conditions, that between the laminar and the turbulent states there exists no intermediate state with simple spatial or temporal characteristics, and that turbulence is not persistent, i.e., it can decay again, if the observation time is long enough. All these features can consistently be explained on the assumption that the turbulent state corresponds to a chaotic saddle in state space. The goal of this review is to explain this concept, summarize the numerical and experimental evidence for pipe flow, and outline the consequences for related flows.}, author = {Eckhardt, Bruno and Schneider, Tobias M and Björn Hof and Westerweel, Jerry}, booktitle = {Annual Review of Fluid Mechanics}, pages = {447 -- 468}, publisher = {Annual Reviews}, title = {{Turbulence transition in pipe flow}}, doi = {10.1146/annurev.fluid.39.050905.110308}, volume = {39}, year = {2007}, } @inproceedings{2794, author = {Björn Hof and Tax, Wilco and Westerweel, Jerry}, pages = {556 -- 558}, publisher = {Springer}, title = {{Lifetime of turbulence in pipe flow}}, doi = {10.1007/978-3-540-72604-3_177}, volume = {117}, year = {2007}, } @article{2893, abstract = {Summary: Regulatory CD4+ T cells, enriched in the CD25 pool of healthy individuals, mediate natural tolerance and prevent autoimmune diseases. Despite their fundamental and potential clinical significance, regulatory T (TR) cells have not yet been incorporated in a coherent theory of the immune system. This article reviews experimental evidence and theoretical arguments supporting a model of TR cell dynamics, uncovering some of its most relevant biological implications. According to this model, the persistence and expansion of TR cell populations depend strictly on specific interactions they make with antigen-presenting cells (APCs) and conventional effector T (TE) cells. This three-partner crossregulation imposes that TR cells feed on the specific autoimmune activities they suppress, with implications ranging from their interactions with other cells to their repertoire selection in the periphery and in the thymus, and to the relationship between these cells and the innate immune system. These implications stem from the basic prediction that the peripheral dynamics sort the CD4+ T-cell repertoire into two subsets: a less diverse set of small clones of autoreactive effector and regulatory cells that regulate each other’s growth, and a more diverse set of barely autoreactive TE cell clones, whose expansion is limited only by APC availability. It is argued that such partitioning of the repertoire sets the ground for self–non-self discrimination. }, author = {Carneiro, Jorge and Leon, Kalet and Caramalho, Íris and Van Den Dool, Carline and Gardner, Rui and Oliveira, Vanessa and Bergman, Marie L and Sepúlveda, Nuno and Tiago Paixao and Faro, Jose and Demengeot, Jocelyne}, journal = {Immunological Reviews}, number = {1}, pages = {48 -- 68}, publisher = {Wiley-Blackwell}, title = {{When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells}}, doi = {10.1111/j.1600-065X.2007.00487.x}, volume = {216}, year = {2007}, } @article{2896, abstract = {Gene expression from both parental alleles is beneficial by masking the effects of deleterious recessive mutations and by reducing the noise in gene expression in diploid organisms. However, a class of genes are expressed preferentially or strictly from a single allele. The selective advantage of avoiding biallelic expression is clear for allelic-excluded antigen receptor and odorant receptor genes, genes undergoing X-chromosome inactivation in females and parental genomic imprinted genes. In contrast, there is no clear biological rationale for the predominant and stochastic monoallelic expression of cytokine genes in the immune system, and the underlying mechanism is elusive and controversial. A clarification of the mechanism of predominant monoallelic expression would be instrumental in better understanding its eventual biological functional. This prompted the development of a quantitative framework that could describe the dynamics of the pattern of allele expression of the IL-10 gene, from which general quantitative insights could be gained. We report that the experimental observations on these patterns of allelic expression cannot be easily reconciled with a simple model of stochastic transcriptional activation, in which the two alleles are, at any time, equally competent for transcription. Instead, these observations call into action a general model of eukaryotic transcriptional regulation according to which the locus competence for transcription is dynamic, involving multiple, cooperative and stochastic modification steps. In this model, the probability that an allele becomes transcriptionally active is a function of the number of chromatin modifications that it accumulated. On the basis of the properties of this model, we argue that predominant monoallelic expression might have had no adaptive role, and may have evolved under indirect selection for low frequency of expressing cells.}, author = {Tiago Paixao and Carvalho, Tiago P and Calado, Dinis P and Carneiro, Jorge}, journal = {Immunology and Cell Biology}, number = {4}, pages = {315 -- 322}, publisher = {Nature Publishing Group}, title = {{Quantitative insights into stochastic monoallelic expression of cytokine genes}}, doi = {10.1038/sj.icb.7100057}, volume = {85}, year = {2007}, } @inproceedings{2933, author = {Kumar, M Pawan and Vladimir Kolmogorov and Torr, Philip H}, publisher = {Neural Information Processing Systems}, title = {{An Analysis of Convex Relaxations for MAP Estimation}}, year = {2007}, } @article{3019, abstract = { Directional transport of the phytohormone auxin is established primarily at the point of cellular afflux and is required for the establishment and maintenance of plant polarity. Studies in whole plants and heterologous systems indicate that PIN-FORMED (PIN) and P-glycoprotein (PGP) transport proteins mediate the cellular efflux of natural and synthetic auxins. However, aromatic anion transport resulting from PGP and PIN expression in nonplant systems was also found to lack tha high level of substrate specificity seen in planta. Furthermore, previous reports that PGP19 stabilizes PIN1 on the plasma membrane suggested that PIN-PGP interactions might regulate polar auxin efflux. Hare, we show that PGP1 and PGP19 colocalized with PIN1 in the shoot apax in Arabidopsis thaliana and with PIN1 and PIN2 in root tissues. Specific PGP-PIN interactions were seen in yeast two-hybrid and colmmunoprecipitation assays. PIN-PGP interactions appeared to enhance transport activity and, to a greater extent, substrate/inhibitor specificities when coexpressed in heterologous systems. By contrast, no interactions between PGPs and the AUXIN1 influx carrier were observed. Phenotypes of pin and pgp mutants suggest discrete functional roles in auxin transport, but pin pgp mutants exhibited phenotypes that are both additive and synergistic. These results suggest that PINs and PGPs characterize coordinated, Independent auxin transport mechanisms but also function interactively in a tissue-specific manner.}, author = {Blakeslee, Joshua and Bandyopadhyay, Anindita and Ok, Ran Lee and Mravec, Jozef and Titapiwatanakun, Boosaree and Sauer, Michael and Makam, Srinivas N and Cheng, Yan and Bouchard, Rodolphe and Adamec, Jiří and Geisler, Markus and Nagashima, Akitomo and Sakai, Tatsuya and Martinoia, Enrico and Jirí Friml and Peer, Wendy A and Murphy, Angus S}, journal = {Plant Cell}, number = {1}, pages = {131 -- 147}, publisher = {American Society of Plant Biologists}, title = {{Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis}}, doi = {10.1105/tpc.106.040782}, volume = {19}, year = {2007}, } @inproceedings{3021, abstract = {Polarized transport of the plant hormone auxin influences multiple growth processes in plants and is regulated by plasma-membrane-localized efflux and uptake carriers. The PGP (P-glycoprotein) ABC transporters (ATP-binding-cassette transporters), PIN (pin-formed) subfamily of major facilitator proteins and members of AUX/LAX families have been shown to independently transport auxin both in planta and in heterologous systems. However, PIN- and PGP-mediated transport in heterologous systems exhibits decreased substrate specificity and inhibitor-sensitivity compared with what is seen in plants and plant cells. To determine whether PIN-PGP interactions enhance transport specificity, we analysed interactions of the representative auxin-transporting PGPs with PIN1 and AUX1 in planta and in heterologous systems. Here, we provide evidence that PINs and PGPs interact and function both independently and co-ordinately to control polar auxin transport and impart transport specificity and directionality. These interactions take place in protein complexes stabilized by PGPs in detergent-resistant microdomains.}, author = {Bandyopadhyay, Anindita and Blakeslee, Joshua and Lee, Ok Ran and Mravec, Jozef and Sauer, Michael and Titapiwatanakun, Boosaree and Makam, Srinivas N and Bouchard, Rodolphe and Geisler, Markus and Martinoia, Enrico and Jirí Friml and Peer, Wendy A and Murphy, Angus S}, number = {1}, pages = {137 -- 141}, publisher = {Portland Press}, title = {{Interactions of PIN and PGP auxin transport mechanisms}}, doi = {10.1042/BST0350137}, volume = {35}, year = {2007}, } @article{3022, abstract = {Endocytosis is an essential process by which eukaryotic cells internalize exogenous material or regulate signaling at the cell surface [1]. Different endocytic pathways are well established in yeast and animals; prominent among them is clathrin-dependent endocytosis [2, 3]. In plants, endocytosis is poorly defined, and no molecular mechanism for cargo internalization has been demonstrated so far [4, 5], although the internalization of receptor-ligand complexes at the plant plasma membrane has recently been shown [6]. Here we demonstrate by means of a green-to-red photoconvertible fluorescent reporter, EosFP [7], the constitutive endocytosis of PIN auxin efflux carriers [8] and their recycling to the plasma membrane. Using a plant clathrin-specific antibody, we show the presence of clathrin at different stages of coated-vesicle formation at the plasma membrane in Arabidopsis. Genetic interference with clathrin function inhibits PIN internalization and endocytosis in general. Furthermore, pharmacological interference with cargo recruitment into the clathrin pathway blocks internalization of PINs and other plasma-membrane proteins. Our data demonstrate that clathrin-dependent endocytosis is operational in plants and constitutes the predominant pathway for the internalization of numerous plasma-membrane-resident proteins including PIN auxin efflux carriers.}, author = {Dhonukshe, Pankaj and Aniento, Fernando and Hwang, Inhwan and Robinson, David G and Mravec, Jozef and Stierhof, York-Dieter and Jirí Friml}, journal = {Current Biology}, number = {6}, pages = {520 -- 527}, publisher = {Cell Press}, title = {{Clathrin-mediated constitutive endocytosis of PIN auxin efflux carriers in Arabidopsis}}, doi = {10.1016/j.cub.2007.01.052}, volume = {17}, year = {2007}, } @article{3023, abstract = {Cytokinesis ensures proper partitioning of the nucleocytoplasmic contents into two daughter cells. It has generally been thought that cytokinesis is accomplished differently in animals and plants because of the differences in the preparatory phases, into the centrosomal or acentrosomal nature of the process, the presence or absence of rigid cell walls, and on the basis of ‘outside‐in’ or ‘inside‐out’ mechanism. However, this long‐standing paradigm needs further reevaluation based on new findings. Recent advances reveal that plant cells, similarly to animal cells, possess astral microtubules that regulate the cell division plane. Furthermore, endocytosis has been found to be important for cytokinesis in animal and plant cells: vesicles containing endocytosed cargo provide material for the cell plate formation in plants and for closure of the midbody channel in animals. Thus, although the preparatory phases of the cell division process differ between plant and animal cells, the later phases show similarities. We unify these findings in a model that suggests a conserved mode of cytokinesis.}, author = {Dhonukshe, Pankaj and Šamaj, Jozef and Baluška, František and Friml, Jirí}, journal = {Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology}, number = {4}, pages = {371 -- 381}, publisher = {Wiley-Blackwell}, title = {{A unifying new model of cytokinesis for the dividing plant and animal cells}}, doi = {10.1002/bies.20559}, volume = {29}, year = {2007}, } @article{3024, abstract = {The plant hormone auxin is frequently observed to be asymmetrically distributed across adjacent cells during crucial stages of growth and development. These auxin gradients depend on polar transport and regulate a wide variety of processes, including embryogenesis, organogenesis, vascular tissue differentiation, root meristem maintenance and tropic growth. Auxin can mediate such a perplexing array of developmental processes by acting as a general trigger for the change in developmental program in cells where it accumulates and by providing vectorial information to the tissues by its polar intercellular flow. In recent years, a wealth of molecular data on the mechanism of auxin transport and its regulation has been generated, providing significant insights into the action of this versatile coordinative signal.}, author = {Vieten, Anne and Sauer, Michael and Brewer, Philip and Friml, Jirí}, journal = {Trends in Plant Science}, number = {4}, pages = {160 -- 168}, publisher = {Cell Press}, title = {{Molecular and cellular aspects of auxin-transport-mediated development}}, doi = {10.1016/j.tplants.2007.03.006}, volume = {12}, year = {2007}, } @article{3026, abstract = {In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery.}, author = {Růžička, Kamil and Ljung, Karin and Vanneste, Steffen and Podhorská, Radka and Beeckman, Tom and Jirí Friml and Eva Benková}, journal = {Plant Cell}, number = {7}, pages = {2197 -- 2212}, publisher = {American Society of Plant Biologists}, title = {{Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution}}, doi = {10.1105/tpc.107.052126}, volume = {19}, year = {2007}, } @article{3027, abstract = {Polar transport of the phytohormone auxin controls numerous growth responses in plants. Molecular characterization of auxin transport in Arabidopsis thaliana has provided important insights into the mechanisms underlying the regulation of auxin distribution. In particular, the control of subcellular localization and expression of PIN-type auxin efflux components appears to be fundamental for orchestrated distribution of the growth regulator throughout the entire plant body. Here we describe the identification of two Arabidopsis loci, MOP2 and MOP3 (for MODULATOR OF PIN), that are involved in control of the steady-state levels of PIN protein. Mutations in both loci result in defects in auxin distribution and polar auxin transport, and cause phenotypes consistent with a reduction of PIN protein levels. Genetic interaction between PIN2 and both MOP loci is suggestive of functional cross-talk, which is further substantiated by findings demonstrating that ectopic PIN up-regulation is compensated in the mop background. Thus, in addition to pathways that control PIN localization and transcription, MOP2 and MOP3 appear to be involved in fine-tuning of auxin distribution via post-transcriptional regulation of PIN expression.}, author = {Malenica, Nenad and Abas, Lindy and Benjamins, René and Kitakura, Saeko and Sigmund, Harald F and Jun, Kim S and Hauser, Marie-Theres and Jirí Friml and Luschnig, Christian}, journal = {Plant Journal}, number = {4}, pages = {537 -- 550}, publisher = {Wiley-Blackwell}, title = {{MODULATOR of PIN genes control steady state levels of Arabidopsis PIN proteins}}, doi = {10.1111/j.1365-313X.2007.03158.x}, volume = {51}, year = {2007}, }