TY - JOUR AB - Nuclear pore complexes (NPCs) are large multiprotein assemblies that allow traffic between the cytoplasm and the nucleus. During mitosis in higher eukaryotes, the Nuclear Envelope (NE) breaks down and NPCs disassemble. How NPCs reassemble and incorporate into the NE upon mitotic exit is poorly understood. We demonstrate a function for the conserved Nup107-160 complex in this process. Partial in vivo depletion of Nup133 or Nup107 via RNAi in HeLa cells resulted in reduced levels of multiple nucleoporins and decreased NPC density in the NE. Immunodepletion of the entire Nup107-160 complex from in vitro nuclear assembly reactions produced nuclei with a continuous NE but no NPCs. This phenotype was reversible only if Nup107-160 complex was readded before closed NE formation. Depletion also prevented association of FG-repeat nucleoporins with chromatin. We propose a stepwise model in which postmitotic NPC assembly initiates on chromatin via early recruitment of the Nup107-160 complex. AU - Walther, Tobias C. AU - Alves, Annabelle AU - Pickersgill, Helen AU - Loı̈odice, Isabelle AU - HETZER, Martin W AU - Galy, Vincent AU - Hülsmann, Bastian B. AU - Köcher, Thomas AU - Wilm, Matthias AU - Allen, Terry AU - Mattaj, Iain W. AU - Doye, Valérie ID - 11122 IS - 2 JF - Cell KW - General Biochemistry KW - Genetics and Molecular Biology SN - 0092-8674 TI - The conserved Nup107-160 complex is critical for nuclear pore complex assembly VL - 113 ER - TY - JOUR AB - In metazoa, the nuclear envelope breaks down and reforms during each cell cycle. Nuclear pore complexes (NPCs), which serve as channels for transport between the nucleus and cytoplasm1, assemble into the reforming nuclear envelope in a sequential process involving association of a subset of NPC proteins, nucleoporins, with chromatin followed by the formation of a closed nuclear envelope fenestrated by NPCs2,3,4,5,6,7. How chromatin recruitment of nucleoporins and NPC assembly are regulated is unknown. Here we demonstrate that RanGTP production is required to dissociate nucleoporins Nup107, Nup153 and Nup358 from Importin β, to target them to chromatin and to induce association between separate NPC subcomplexes. Additionally, either an excess of RanGTP or removal of Importin β induces formation of NPC-containing membrane structures—annulate lamellae—both in vitro in the absence of chromatin and in vivo. Annulate lamellae formation is strongly and specifically inhibited by an excess of Importin β. The data demonstrate that RanGTP triggers distinct steps of NPC assembly, and suggest a mechanism for the spatial restriction of NPC assembly to the surface of chromatin. AU - Walther, Tobias C. AU - Askjaer, Peter AU - Gentzel, Marc AU - Habermann, Anja AU - Griffiths, Gareth AU - Wilm, Matthias AU - Mattaj, Iain W. AU - HETZER, Martin W ID - 11121 IS - 6949 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - RanGTP mediates nuclear pore complex assembly VL - 424 ER - TY - JOUR AB - This paper studies the multicast routing and admission control problem on unit-capacity tree and mesh topologies in the throughput model. The problem is a generalization of the edge-disjoint paths problem and is NP-hard both on trees and meshes. We study both the offline and the online version of the problem: In the offline setting, we give the first constant-factor approximation algorithm for trees, and an -factor approximation algorithm for meshes. In the online setting, we give the first polylogarithmic competitive online algorithm for tree and mesh topologies. No polylogarithmic-competitive algorithm is possible on general network topologies (Lower bounds for on-line graph problems with application to on-line circuits and optical routing, in: Proceedings of the 28th ACM Symposium on Theory of Computing, 1996, pp. 531–540) and there exists a polylogarithmic lower bound on the competitive ratio of any online algorithm on tree topologies (Making commitments in the face of uncertainity: how to pick a winner almost every time, in: Proceedings of the 28th Annual ACM Symposium on Theory of Computing, 1996, pp. 519–530). We prove the same lower bound for meshes. AU - Henzinger, Monika H AU - Leonardi, Stefano ID - 11766 IS - 3 JF - Journal of Computer and System Sciences SN - 0022-0000 TI - Scheduling multicasts on unit-capacity trees and meshes VL - 66 ER - TY - JOUR AB - In this paper we consider the online ftp problem. The goal is to service a sequence of file transfer requests given bandwidth constraints of the underlying communication network. The main result of the paper is a technique that leads to algorithms that optimize several natural metrics, such as max-stretch, total flow time, max flow time, and total completion time. In particular, we show how to achieve optimum total flow time and optimum max-stretch if we increase the capacity of the underlying network by a logarithmic factor. We show that the resource augmentation is necessary by proving polynomial lower bounds on the max-stretch and total flow time for the case where online and offline algorithms are using same-capacity edges. Moreover, we also give polylogarithmic lower bounds on the resource augmentation factor necessary in order to keep the total flow time and max-stretch within a constant factor of optimum. AU - Goel, Ashish AU - Henzinger, Monika H AU - Plotkin, Serge AU - Tardos, Eva ID - 11764 IS - 2 JF - Journal of Algorithms SN - 0196-6774 TI - Scheduling data transfers in a network and the set scheduling problem VL - 48 ER - TY - CONF AB - This paper addresses the problem of topic distillation on the World Wide Web, namely, given a typical user query to find quality documents related to the query topic. Connectivity analysis has been shown to be useful in identifying high quality pages within a topic specific graph of hyperlinked documents. The essence of our approach is to augment a previous connectivity analysis based algorithm with content analysis. We identify three problems with the existing approach and devise algorithms to tackle them. The results of a user evaluation are reported that show an improvement of precision at 10 documents by at least 45% over pure connectivity analysis. AU - Bharat, Krishna AU - Henzinger, Monika H ID - 11897 SN - 01635840 T2 - 21st annual international ACM SIGIR conference on Research and development in information retrieval TI - Improved algorithms for topic distillation in a hyperlinked environment ER - TY - CONF AB - Many daily activities present information in the form of a stream of text, and often people can benefit from additional information on the topic discussed. TV broadcast news can be treated as one such stream of text; in this paper we discuss finding news articles on the web that are relevant to news currently being broadcast.We evaluated a variety of algorithms for this problem, looking at the impact of inverse document frequency, stemming, compounds, history, and query length on the relevance and coverage of news articles returned in real time during a broadcast. We also evaluated several postprocessing techniques for improving the precision, including reranking using additional terms, reranking by document similarity, and filtering on document similarity. For the best algorithm, 84%-91% of the articles found were relevant, with at least 64% of the articles being on the exact topic of the broadcast. In addition, a relevant article was found for at least 70% of the topics. AU - Henzinger, Monika H AU - Chang, Bay-Wei AU - Milch, Brian AU - Brin, Sergey ID - 11860 SN - 978-158113680-7 T2 - Proceedings of the 12th international conference on World Wide Web TI - Query-free news search ER - TY - CONF AB - This article presents a high-level discussion of some problems that are unique to web search engines. The goal is to raise awareness and stimulate research in these areas. AU - Henzinger, Monika H AU - Motwani, Rajeev AU - Silverstein, Craig ID - 11909 SN - 1045-0823 T2 - 18th International Joint Conference on Artificial Intelligence TI - Challenges in web search engines ER - TY - JOUR AB - Among the major mathematical approaches to mirror symmetry are those of Batyrev-Borisov and Stromdnger-Yau-Zaslow (SYZ). The first is explicit and amenable to computation but is not clearly related to the physical motivation; the second is the opposite. Furthermore, it is far from obvious that mirror partners in one sense will also be mirror partners in the other. This paper concerns a class of examples that can be shown to satisfy the requirements of SYZ, but whose Hodge numbers are also equal. This provides significant evidence in support of SYZ. Moreover, the examples are of great interest in their own right: they are spaces of flat SLr-connections on a smooth curve. The mirror is the corresponding space for the Langlands dual group PGLr. These examples therefore throw a bridge from mirror symmetry to the duality theory of Lie groups and, more broadly, to the geometric Langlands program. AU - Tamas Hausel AU - Thaddeus, Michael ID - 1457 IS - 1 JF - Inventiones Mathematicae TI - Mirror symmetry, langlands duality, and the Hitchin system VL - 153 ER - TY - JOUR AB - The moduli space of stable bundles of rank $2$ and degree $1$ on a Riemann surface has rational cohomology generated by the so-called universal classes. The work of Baranovsky, King-Newstead, Siebert-Tian and Zagier provided a complete set of relations between these classes, expressed in terms of a recursion in the genus. This paper accomplishes the same thing for the noncompact moduli spaces of Higgs bundles, in the sense of Hitchin and Simpson. There are many more independent relations than for stable bundles, but in a sense the answer is simpler, since the formulas are completely explicit, not recursive. The results of Kirwan on equivariant cohomology for holomorphic circle actions are of key importance. AU - Tamas Hausel AU - Thaddeus, Michael ID - 1458 IS - 2 JF - Journal of the American Mathematical Society TI - Relations in the cohomology ring of the moduli space of rank 2 Higgs bundles VL - 16 ER - TY - JOUR AB - In this paper we explicitly calculate the analogue of the 't Hooft SU (2) Yang-Mills instantons on Gibbons-Hawking multi-centered gravitational instantons, which come in two parallel families: the multi-Eguchi-Hanson, or Ak ALE gravitational instantons and the multi-Taub-NUT spaces, or Ak ALF gravitational instantons. We calculate their energy and find the reducible ones. Following Kronheimer we also exploit the U(1) invariance of our solutions and study the corresponding explicit singular SU (2) magnetic monopole solutions of the Bogomolny equations on flat ℝ3. AU - Etesi, Gábor AU - Tamas Hausel ID - 1459 IS - 2 JF - Communications in Mathematical Physics TI - On Yang-Mills instantons over multi-centered gravitational instantons VL - 235 ER - TY - JOUR AB - For any number field k, upper bounds are established for the number of k-rational points of bounded height on non-singular del Pezzo surfaces defined over k, which are equipped with suitable conic bundle structures over k. AU - Browning, Timothy D AU - Swarbick Jones, M ID - 166 JF - Proceedings of the Bonn session in analytic number theory and diophantine equations TI - Counting rational points on del Pezzo surfaces of degree 5 VL - 360 ER - TY - JOUR AB - The molecular organization of bacterial NADH: ubiquinone oxidoreductase (complex I or NDH-1) is not established, apart from a rough separation into dehydrogenase, connecting and membrane domains. In this work, complex I was purified from Escherichia coli and fragmented by replacing dodecylmaltoside with other detergents. Exchange into decyl maltoside led to the removal of the hydrophobic subunit NuoL from the otherwise intact complex. Diheptanoyl phosphocholine led to the loss of NuoL and NuoM subunits, whereas other subunits remained in the complex. The presence of N,N-dimethyldodecylamine N-oxide or Triton X-100 led to further disruption of the membrane domain into fragments containing NuoL/M/N, NuoA/K/N, and NuoH/J subunits. Among the hydrophilic subunits, NuoCD was most readily dissociated from the complex, whereas NuoB was partially dissociated from the peripheral arm assembly in N,N-dimethyldodecylamine N-oxide. A model of subunit arrangement in bacterial complex I based on these data is proposed. Subunits NuoL and NuoM, which are homologous to antiporters and are implicated in proton pumping, are located at the distal end of the membrane arm, spatially separated from the redox centers of the peripheral arm. This is consistent with proposals that the mechanism of proton pumping by complex I is likely to involve long range conformational changes. AU - Holt, Peter J AU - Morgan, David J AU - Leonid Sazanov ID - 1959 IS - 44 JF - Journal of Biological Chemistry TI - The location of NuoL and NuoM subunits in the membrane domain of the Escherichia coli Complex I: implications for the mechanism of proton pumping VL - 278 ER - TY - JOUR AB - NADH-ubiquinone oxidoreductase (complex I or NDH-1) was purified from the BL21 strain of Escherichia coli using an improved procedure. The complex was effectively stabilized by addition of divalent cations and lipids, making the preparation suitable for structural studies. The ubiquinone reductase activity of the enzyme was fully restored by addition of native E. coli lipids. Two different two-dimensional crystal forms, with p2 and p3 symmetry, were obtained using lipids containing native E. coli extracts. Analysis of the crystals showed that they are formed by fully intact complex I in an L-shaped conformation. Activity assays and single particle analysis indicated that complex I maintains this structure in detergent solution and does not adopt a different conformation in the active state. Thus, we provide the first experimental evidence that complex I from E. coli has an L-shape in a lipid bilayer and confirm that this is also the case for the active enzyme in solution. This suggests strongly that bacterial complex I exists in an L-shaped conformation in vivo. Our results also indicate that native lipids play an important role in the activation, stabilization and, as a consequence, crystallization of purified complex I from E. coli. AU - Leonid Sazanov AU - Carroll, Joe D AU - Holt, Peter J AU - Toime, Laurence J AU - Fearnley, Ian M ID - 1960 IS - 21 JF - Journal of Biological Chemistry TI - A role for native lipids in the stabilization and two dimensional crystallization of the Escherichia coli NADH ubiquinone oxidoreductase (complex I) VL - 278 ER - TY - JOUR AU - Timothy Browning ID - 205 IS - 3 JF - Acta Arithmetica TI - Counting rational points on cubic and quartic surfaces VL - 108 ER - TY - JOUR AB - Let T ⊂ ℙ 4 be a non-singular threefold of degree at least four. Then we show that the number of points in T(ℚ), with height at most B, is o(B 3) or B → ∞. AU - Timothy Browning ID - 206 IS - 1 JF - Quarterly Journal of Mathematics TI - A note on the distribution of rational points on threefolds VL - 54 ER - TY - JOUR AU - Browning, Timothy D ID - 207 IS - 3 JF - Mathematical Proceedings of the Cambridge Philosophical Society TI - Sums of four biquadrates VL - 134 ER - TY - JOUR AB - For any ε > 0 and any diagonal quadratic form Q ∈ ℤ[x 1, x 2, x 3, x 4] with a square-free discriminant of modulus Δ Q ≠ 0, we establish the uniform estimate ≪ε B 3/2+ε + B 2+ε/Δ Q 1/6 for the number of rational points of height at most B lying in the projective surface Q = 0. AU - Timothy Browning ID - 208 IS - 1 JF - Quarterly Journal of Mathematics TI - Counting rational points on diagonal quadratic surfaces VL - 54 ER - TY - CONF AU - Lieb, Élliott H AU - Robert Seiringer ED - Karpeshina, Yulia ED - Weikard, Rudi ED - Zeng, Yanni ID - 2337 TI - Bose-Einstein condensation of dilute gases in traps VL - 327 ER - TY - JOUR AB - The classic Poincaré inequality bounds the L q-norm of a function f in a bounded domain Ω ⊂ ℝ n in terms of some L p-norm of its gradient in Ω. We generalize this in two ways: In the first generalization we remove a set Τ from Ω and concentrate our attention on Λ = Ω \ Τ. This new domain might not even be connected and hence no Poincaré inequality can generally hold for it, or if it does hold it might have a very bad constant. This is so even if the volume of Τ is arbitrarily small. A Poincaré inequality does hold, however, if one makes the additional assumption that f has a finite L p gradient norm on the whole of Ω, not just on Λ. The important point is that the Poincaré inequality thus obtained bounds the L q-norm of f in terms of the L p gradient norm on Λ (not Ω) plus an additional term that goes to zero as the volume of Τ goes to zero. This error term depends on Τ only through its volume. Apart from this additive error term, the constant in the inequality remains that of the 'nice' domain Ω. In the second generalization we are given a vector field A and replace ∇ by ∇ + iA(x) (geometrically, a connection on a U(1) bundle). Unlike the A = 0 case, the infimum of ∥(∇ + iA)f∥ p over all f with a given ∥f∥ q is in general not zero. This permits an improvement of the inequality by the addition of a term whose sharp value we derive. We describe some open problems that arise from these generalizations. AU - Lieb, Élliott H AU - Robert Seiringer AU - Yngvason, Jakob ID - 2357 IS - 3 JF - Annals of Mathematics TI - Poincaré inequalities in punctured domains VL - 158 ER - TY - JOUR AB - We investigate the ground state properties of a gas of interacting particles confined in an external potential in three dimensions and subject to rotation around an axis of symmetry. We consider the Gross-Pitaevskii (GP) limit of a dilute gas. Analysing both the absolute and the bosonic ground states of the system, we show, in particular, their different behaviour for a certain range of parameters. This parameter range is determined by the question whether the rotational symmetry in the minimizer of the GP functional is broken or not. For the absolute ground state, we prove that in the GP limit a modified GP functional depending on density matrices correctly describes the energy and reduced density matrices, independent of symmetry breaking. For the bosonic ground state this holds true if and only if the symmetry is unbroken. AU - Robert Seiringer ID - 2354 IS - 37 JF - Journal of Physics A: Mathematical and Theoretical TI - Ground state asymptotics of a dilute, rotating gas VL - 36 ER -