@article{11116,
  abstract     = {The metazoan nuclear envelope (NE) breaks down and re-forms during each cell cycle. Nuclear pore complexes (NPCs), which allow nucleocytoplasmic transport during interphase, assemble into the re-forming NE at the end of mitosis. Using in vitro NE assembly, we show that the vertebrate homologue of MEL-28 (maternal effect lethal), a recently discovered NE component in Caenorhabditis elegans, functions in postmitotic NPC assembly. MEL-28 interacts with the Nup107–160 complex (Nup for nucleoporin), an important building block of the NPC, and is essential for the recruitment of the Nup107–160 complex to chromatin. We suggest that MEL-28 acts as a seeding point for NPC assembly.},
  author       = {Franz, Cerstin and Walczak, Rudolf and Yavuz, Sevil and Santarella, Rachel and Gentzel, Marc and Askjaer, Peter and Galy, Vincent and HETZER, Martin W and Mattaj, Iain W and Antonin, Wolfram},
  issn         = {1469-3178},
  journal      = {EMBO reports},
  keywords     = {Genetics, Molecular Biology, Biochemistry},
  number       = {2},
  pages        = {165--172},
  publisher    = {EMBO},
  title        = {{MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly}},
  doi          = {10.1038/sj.embor.7400889},
  volume       = {8},
  year         = {2007},
}

@article{11117,
  abstract     = {Over the last years it has become evident that the nuclear envelope (NE) is more than a passive membrane barrier that separates the nucleus from the cytoplasm. The NE not only controls the trafficking of macromolecules between the nucleoplasm and the cytosol, but also provides anchoring sites for chromosomes and cytoskeleton to the nuclear periphery. Targeting of chromatin to the NE might actually be part of gene expression regulation in eukaryotes. Mutations in certain NE proteins are associated with a diversity of human diseases, including muscular dystrophy, neuropathy, lipodistrophy, torsion dystonia and the premature aging condition progeria. Despite the importance of the NE for cell division and differentiation, relatively little is known about its biogenesis and its role in human diseases. It is our goal to provide a comprehensive view of the NE and to discuss possible implications of NE-associated changes for gene expression, chromatin organization and signal transduction.},
  author       = {D’Angelo, M. A. and HETZER, Martin W},
  issn         = {1420-9071},
  journal      = {Cellular and Molecular Life Sciences},
  keywords     = {Cell Biology, Cellular and Molecular Neuroscience, Pharmacology, Molecular Biology, Molecular Medicine},
  number       = {3},
  pages        = {316--332},
  publisher    = {Springer Nature},
  title        = {{The role of the nuclear envelope in cellular organization}},
  doi          = {10.1007/s00018-005-5361-3},
  volume       = {63},
  year         = {2006},
}

@article{11120,
  abstract     = {The nuclear envelope (NE) is a highly specialized membrane that delineates the eukaryotic cell nucleus. It is composed of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) and, in metazoa, the lamina. The NE not only regulates the trafficking of macromolecules between nucleoplasm and cytosol but also provides anchoring sites for chromatin and the cytoskeleton. Through these interactions, the NE helps position the nucleus within the cell and chromosomes within the nucleus, thereby regulating the expression of certain genes. The NE is not static, rather it is continuously remodeled during cell division. The most dramatic example of NE reorganization occurs during mitosis in metazoa when the NE undergoes a complete cycle of disassembly and reformation. Despite the importance of the NE for eukaryotic cell life, relatively little is known about its biogenesis or many of its functions. We thus are far from understanding the molecular etiology of a diverse group of NE-associated diseases.},
  author       = {HETZER, Martin W and Walther, Tobias C. and Mattaj, Iain W.},
  issn         = {1530-8995},
  journal      = {Annual Review of Cell and Developmental Biology},
  keywords     = {Cell Biology, Developmental Biology},
  pages        = {347--380},
  publisher    = {Annual Reviews},
  title        = {{Pushing the envelope: Structure, function, and dynamics of the nuclear periphery}},
  doi          = {10.1146/annurev.cellbio.21.090704.151152},
  volume       = {21},
  year         = {2005},
}

@article{12203,
  abstract     = {Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs.},
  author       = {Liao, Zhihua and Chen, Min and Gong, Yifu and Guo, Liang and Tan, Qiumin and Feng, Xiaoqi and Sun, Xiaofen and Tan, Feng and Tang, Kexuan},
  issn         = {1042-5179},
  journal      = {DNA Sequence},
  keywords     = {Endocrinology, Genetics, Molecular Biology, Biochemistry},
  number       = {2},
  pages        = {153--158},
  publisher    = {Informa UK Limited},
  title        = {{A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides}},
  doi          = {10.1080/10425170410001667348},
  volume       = {15},
  year         = {2004},
}

@article{11122,
  abstract     = {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.},
  author       = {Walther, Tobias C. and Alves, Annabelle and Pickersgill, Helen and Loı̈odice, Isabelle and HETZER, Martin W and Galy, Vincent and Hülsmann, Bastian B. and Köcher, Thomas and Wilm, Matthias and Allen, Terry and Mattaj, Iain W. and Doye, Valérie},
  issn         = {0092-8674},
  journal      = {Cell},
  keywords     = {General Biochemistry, Genetics and Molecular Biology},
  number       = {2},
  pages        = {195--206},
  publisher    = {Elsevier},
  title        = {{The conserved Nup107-160 complex is critical for nuclear pore complex assembly}},
  doi          = {10.1016/s0092-8674(03)00235-6},
  volume       = {113},
  year         = {2003},
}

@article{13438,
  abstract     = {ICln is an ion channel identified by expression cloning using a cDNA library from Madin-Darby canine kidney cells. In all organisms tested so far, only one transcript for the ICln protein could be identified. Here we show that two splice variants of the ICln ion channel can be found in Caenorhabditis elegans. Moreover, we show that these two splice variants of the ICln channel protein, which we termed IClnN1 and IClnN2, can be functionally reconstituted and tested in an artificial lipid bilayer. In these experiments, the IClnN1-induced currents showed no voltage-dependent inactivation, whereas the IClnN2-induced currents fully inactivated at positive potentials. The molecular entity responsible for the voltage-dependent inactivation of IClnN2 is a cluster of positively charged amino acids encoded by exon 2a, which is absent in IClnN1. Our experiments suggest a mechanism of channel inactivation that is similar to the “ball and chain” model proposed for the Shaker potassium channel,i.e. a cluster of positively charged amino acids hinders ion permeation through the channel by a molecular and voltage-dependent interaction at the inner vestibulum of the pore. This hypothesis is supported by the finding that synthetic peptides with the same amino acid sequence as the positive cluster can transform the IClnN1-induced current to the current observed after reconstitution of IClnN2. Furthermore, we show that the nematode ICln gene is embedded in an operon harboring two additional genes, which we termed Nx and Ny. Co-reconstitution of Nx and IClnN2 and functional analysis of the related currents revealed a functional interaction between the two proteins, as evidenced by the fact that the IClnN2-induced current in the presence of Nx was no longer voltage-sensitive. The experiments described indicate that the genome organization in nematodes allows an effective approach for the identification of functional partner proteins of ion channels.},
  author       = {Fürst, Johannes and Ritter, Markus and Rudzki, Jakob and Danzl, Johann G and Gschwentner, Martin and Scandella, Elke and Jakab, Martin and König, Matthias and Oehl, Bernhard and Lang, Florian and Deetjen, Peter and Paulmichl, Markus},
  issn         = {0021-9258},
  journal      = {Journal of Biological Chemistry},
  keywords     = {Cell Biology, Molecular Biology, Biochemistry},
  number       = {6},
  pages        = {4435--4445},
  publisher    = {Elsevier},
  title        = {{ICln Ion channel splice variants in Caenorhabditis elegans}},
  doi          = {10.1074/jbc.m107372200},
  volume       = {277},
  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{11125,
  abstract     = {Although nuclear envelope (NE) assembly is known to require the GTPase Ran, the membrane fusion machinery involved is uncharacterized. NE assembly involves formation of a reticular network on chromatin, fusion of this network into a closed NE and subsequent expansion. Here we show that p97, an AAA-ATPase previously implicated in fusion of Golgi and transitional endoplasmic reticulum (ER) membranes together with the adaptor p47, has two discrete functions in NE assembly. Formation of a closed NE requires the p97–Ufd1–Npl4 complex, not previously implicated in membrane fusion. Subsequent NE growth involves a p97–p47 complex. This study provides the first insights into the molecular mechanisms and specificity of fusion events involved in NE formation.},
  author       = {HETZER, Martin W and Meyer, Hemmo H. and Walther, Tobias C. and Bilbao-Cortes, Daniel and Warren, Graham and Mattaj, Iain W.},
  issn         = {1476-4679},
  journal      = {Nature Cell Biology},
  keywords     = {Cell Biology},
  number       = {12},
  pages        = {1086--1091},
  publisher    = {Springer Nature},
  title        = {{Distinct AAA-ATPase p97 complexes function in discrete steps of nuclear assembly}},
  doi          = {10.1038/ncb1201-1086},
  volume       = {3},
  year         = {2001},
}

@article{11126,
  abstract     = {Nuclear import of the two uracil-rich small nuclear ribonucleoprotein (U snRNP) components U1A and U2B′′ is mediated by unusually long and complex nuclear localization signals (NLSs). Here we investigate nuclear import of U1A and U2B′′ in vitro and demonstrate that it occurs by an active, saturable process. Several lines of evidence suggest that import of the two proteins occurs by an import mechanism different to those characterized previously. No cross competition is seen with a variety of previously studied NLSs. In contrast to import mediated by members of the importin-β family of nucleocytoplasmic transport receptors, U1A/U2B′′ import is not inhibited by either nonhydrolyzable guanosine triphosphate (GTP) analogues or by a mutant of the GTPase Ran that is incapable of GTP hydrolysis. Adenosine triphosphate is capable of supporting U1A and U2B′′ import, whereas neither nonhydrolyzable adenosine triphosphate analogues nor GTP can do so. U1A and U2B′′ import in vitro does not require the addition of soluble cytosolic proteins, but a factor or factors required for U1A and U2B′′ import remains tightly associated with the nuclear fraction of conventionally permeabilized cells. This activity can be solubilized in the presence of elevated MgCl2. These data suggest that U1A and U2B′′ import into the nucleus occurs by a hitherto uncharacterized mechanism.},
  author       = {HETZER, Martin W and Mattaj, Iain W.},
  issn         = {1540-8140},
  journal      = {Journal of Cell Biology},
  keywords     = {Cell Biology},
  number       = {2},
  pages        = {293--304},
  publisher    = {Rockefeller University Press},
  title        = {{An Atp-dependent, Ran-independent mechanism for nuclear import of the U1a and U2b′′ spliceosome proteins}},
  doi          = {10.1083/jcb.148.2.293},
  volume       = {148},
  year         = {2000},
}

@article{11127,
  abstract     = {Nuclear formation in Xenopus egg extracts requires cytosol and is inhibited by GTPγS, indicating a requirement for GTPase activity. Nuclear envelope (NE) vesicle fusion is extensively inhibited by GTPγS and two mutant forms of the Ran GTPase, Q69L and T24N. Depletion of either Ran or RCC1, the exchange factor for Ran, from the assembly reaction also inhibits this step of NE formation. Ran depletion can be complemented by the addition of Ran loaded with either GTP or GDP but not with GTPγS. RCC1 depletion is only complemented by RCC1 itself or by RanGTP. Thus, generation of RanGTP by RCC1 and GTP hydrolysis by Ran are both required for the extensive membrane fusion events that lead to NE formation.},
  author       = {HETZER, Martin W and Bilbao-Cortés, Daniel and Walther, Tobias C and Gruss, Oliver J and Mattaj, Iain W},
  issn         = {1097-2765},
  journal      = {Molecular Cell},
  keywords     = {Cell Biology, Molecular Biology},
  number       = {6},
  pages        = {1013--1024},
  publisher    = {Elsevier},
  title        = {{GTP hydrolysis by Ran is required for nuclear envelope assembly}},
  doi          = {10.1016/s1097-2765(00)80266-x},
  volume       = {5},
  year         = {2000},
}

@article{11679,
  abstract     = {We are given a set T = {T 1 ,T 2 , . . .,T k } of rooted binary trees, each T i leaf-labeled by a subset L(Ti)⊂{1,2,...,n} . If T is a tree on {1,2, . . .,n }, we let T|L denote the minimal subtree of T induced by the nodes of L and all their ancestors. The consensus tree problem asks whether there exists a tree T * such that, for every i , T∗|L(Ti) is homeomorphic to T i .

We present algorithms which test if a given set of trees has a consensus tree and if so, construct one. The deterministic algorithm takes time min{O(N n 1/2 ), O(N+ n 2 log n )}, where N=∑i|Ti| , and uses linear space. The randomized algorithm takes time O(N log3 n) and uses linear space. The previous best for this problem was a 1981 O(Nn) algorithm by Aho et al. Our faster deterministic algorithm uses a new efficient algorithm for the following interesting dynamic graph problem: Given a graph G with n nodes and m edges and a sequence of b batches of one or more edge deletions, then, after each batch, either find a new component that has just been created or determine that there is no such component. For this problem, we have a simple algorithm with running time O(n 2 log n + b 0 min{n 2 , m log n }), where b 0 is the number of batches which do not result in a new component. For our particular application, b0≤1 . If all edges are deleted, then the best previously known deterministic algorithm requires time O(mn−−√) to solve this problem. We also present two applications of these consensus tree algorithms which solve other problems in computational evolutionary biology.},
  author       = {Henzinger, Monika H and King, V. and Warnow, T.},
  issn         = {1432-0541},
  journal      = {Algorithmica},
  keywords     = {Algorithms, Data structures, Evolutionary biology, Theory of databases},
  pages        = {1--13},
  publisher    = {Springer Nature},
  title        = {{Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology}},
  doi          = {10.1007/pl00009268},
  volume       = {24},
  year         = {1999},
}

@inbook{4317,
  author       = {Barton, Nicholas H},
  booktitle    = {Analytical biogeography: An integrated approach to the study of animal and plant distributions},
  editor       = {Myers, Alan and Giller, Paul},
  isbn         = {978-0-412-40050-6},
  issn         = {978-94-009-0435-4},
  keywords     = {biogeography, biology, complexity, distribution, evolution, geology},
  pages        = {185 -- 218},
  publisher    = {Springer},
  title        = {{Speciation}},
  doi          = {10.1007/978-94-009-0435-4},
  year         = {1988},
}