Relevant bibliographies by topics / Nuclear pore complex (NPCs)

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  2. Dissertations / Theses
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Academic literature on the topic 'Nuclear pore complex (NPCs)'

Author: Grafiati
Published: 7 December 2024

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Journal articles on the topic "Nuclear pore complex (NPCs)"

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Rout, M. P., and G. Blobel. "Isolation of the yeast nuclear pore complex." Journal of Cell Biology 123, no. 4 (November 15, 1993): 771–83. http://dx.doi.org/10.1083/jcb.123.4.771.

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Nuclear pore complexes (NPCs) have been isolated from the yeast Saccharomyces. Negative stain electron microscopy of the isolated NPCs and subsequent image reconstruction revealed the octagonal symmetry and many of the ultrastructural features characteristic of vertebrate NPCs. The overall dimensions of the yeast NPC, both in its isolated form as well as in situ, are smaller than its vertebrate counterpart. However, the diameter of the central structures are similar. The isolated yeast NPC has a sedimentation coefficient of approximately 310 S and an M(r) of approximately 66 MD. It retains all but one of the eight known NPC proteins. In addition it contains as many as 80 uncharacterized proteins that are candidate NPC proteins.
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Hampoelz, Bernhard, Amparo Andres-Pons, Panagiotis Kastritis, and Martin Beck. "Structure and Assembly of the Nuclear Pore Complex." Annual Review of Biophysics 48, no. 1 (May 6, 2019): 515–36. http://dx.doi.org/10.1146/annurev-biophys-052118-115308.

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Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange. They are exceptionally large protein complexes that fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. About 30 different protein components, termed nucleoporins, assemble in multiple copies into an intricate cylindrical architecture. Here, we review our current knowledge of the structure of nucleoporins and how those come together in situ. We delineate architectural principles on several hierarchical organization levels, including isoforms, posttranslational modifications, nucleoporins, and higher-order oligomerization of nucleoporin subcomplexes. We discuss how cells exploit this modularity to faithfully assemble NPCs.
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Reichelt, R., A. Holzenburg, E. L. Buhle, M. Jarnik, A. Engel, and U. Aebi. "Correlation between structure and mass distribution of the nuclear pore complex and of distinct pore complex components." Journal of Cell Biology 110, no. 4 (April 1, 1990): 883–94. http://dx.doi.org/10.1083/jcb.110.4.883.

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Nuclear pore complexes (NPCs) prepared from Xenopus laevis oocyte nuclear envelopes were studied in "intact" form (i.e., unexposed to detergent) and after detergent treatment by a combination of conventional transmission electron microscopy (CTEM) and quantitative scanning transmission electron microscopy (STEM). In correlation-averaged CTEM pictures of negatively stained intact NPCs and of distinct NPC components (i.e., "rings," "spoke" complexes, and "plug-spoke" complexes), several fine structural features arranged with octagonal symmetry about a central axis could reproducibly be identified. STEM micrographs of unstained/freeze-dried intact NPCs as well as of their components yielded comparable but less distinct features. Mass determination by STEM revealed the following molecular masses: intact NPC with plug, 124 +/- 11 MD; intact NPC without plug, 112 +/- 11 MD; heavy ring, 32 +/- 5 MD; light ring, 21 +/- 4 MD; plug-spoke complex, 66 +/- 8 MD; and spoke complex, 52 +/- 3 MD. Based on these combined CTEM and STEM data, a three-dimensional model of the NPC exhibiting eightfold centrosymmetry about an axis perpendicular to the plane of the nuclear envelope but asymmetric along this axis is proposed. This structural polarity of the NPC across the nuclear envelope is in accord with its well-documented functional polarity facilitating mediated nucleocytoplasmic exchange of molecules and particles.
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Lyman, Susan K., and Larry Gerace. "Nuclear pore complexes: dynamics in unexpected places." Journal of Cell Biology 154, no. 1 (July 9, 2001): 17–20. http://dx.doi.org/10.1083/jcb.200106071.

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In vivo studies on the dynamics of the nuclear pore complex (NPC) in yeast suggested that NPCs are highly mobile in the nuclear envelope. However, new evidence indicates that in mammalian cells NPCs are stably attached to a flexible lamina framework, but a peripheral component can exchange rapidly with an intranuclear pool.
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Allen, T. D., J. M. Cronshaw, S. Bagley, E. Kiseleva, and M. W. Goldberg. "The nuclear pore complex: mediator of translocation between nucleus and cytoplasm." Journal of Cell Science 113, no. 10 (May 15, 2000): 1651–59. http://dx.doi.org/10.1242/jcs.113.10.1651.

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The enclosure of nuclear contents in eukaryotes means that cells require sites in the boundary that mediate exchange of material between nucleus and cytoplasm. These sites, termed nuclear pore complexes (NPCs), number 100–200 in yeast, a few thousand in mammalian cells and approximately 50 million in the giant nuclei of amphibian oocytes. NPCs are large (125 MDa) macromolecular complexes that comprise 50–100 different proteins in vertebrates. In spite of their size and complex structure, NPCs undergo complete breakdown and reformation at cell division. Transport through NPCs can be rapid (estimated at several hundred molecules/pore/second) and accommodates both passive diffusion of relatively small molecules, and active transport of complexes up to several megadaltons in molecular mass. Each pore can facilitate both import and export. The two processes apparently involve multiple pathways for different cargoes, and their transport signals, transport receptors and adapters, and the molecules (and their regulators) that underpin the transport mechanisms. Over the past few years there has been an increasing interest in the pore complex: structural studies have been followed by elucidation of the biochemical aspects of nuclear import, and subsequent investigations into nuclear export. The current challenge is to understand the interactions between the structural elements of the pore complex and the mechanisms that drive the physical processes of translocation through it.
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Makio, Tadashi, Leslie H. Stanton, Cheng-Chao Lin, David S. Goldfarb, Karsten Weis, and Richard W. Wozniak. "The nucleoporins Nup170p and Nup157p are essential for nuclear pore complex assembly." Journal of Cell Biology 185, no. 3 (May 4, 2009): 459–73. http://dx.doi.org/10.1083/jcb.200810029.

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We have established that two homologous nucleoporins, Nup170p and Nup157p, play an essential role in the formation of nuclear pore complexes (NPCs) in Saccharomyces cerevisiae. By regulating their synthesis, we showed that the loss of these nucleoporins triggers a decrease in NPCs caused by a halt in new NPC assembly. Preexisting NPCs are ultimately lost by dilution as cells grow, causing the inhibition of nuclear transport and the loss of viability. Significantly, the loss of Nup170p/Nup157p had distinct effects on the assembly of different architectural components of the NPC. Nucleoporins (nups) positioned on the cytoplasmic face of the NPC rapidly accumulated in cytoplasmic foci. These nup complexes could be recruited into new NPCs after reinitiation of Nup170p synthesis, and may represent a physiological intermediate. Loss of Nup170p/Nup157p also caused core and nucleoplasmically positioned nups to accumulate in NPC-like structures adjacent to the inner nuclear membrane, which suggests that these nucleoporins are required for formation of the pore membrane and the incorporation of cytoplasmic nups into forming NPCs.
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Akey, C. W. "Interactions and structure of the nuclear pore complex revealed by cryo-electron microscopy." Journal of Cell Biology 109, no. 3 (September 1, 1989): 955–70. http://dx.doi.org/10.1083/jcb.109.3.955.

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Nuclear pore complexes (NPCs) play a central role in mediating nucleocytoplasmic transport and exchange processes in eukaryotic cells. The arrangement and interactions of NPCs within amphibian nuclear envelopes have been studied using cryo-electron microscopy of unfixed and frozen hydrated specimens. The nuclear lamina in Necturus forms an orthogonal network with crossover distances which vary between 1,600 and 4,000 A and which may be related to the basic filament repeat of lamins. Furthermore, the NPCs are attached randomly within the confines of the lamin network, presumably by their nucleoplasmic rings. Image analysis of edge-on and en face projections of detergent-extracted NPCs has been combined with data on the coaxial thin rings to provide a quantitative evaluation of the triple ring model of NPC architecture proposed previously (Unwin, P. N. T., and R. Milligan. 1982. J. Cell Biol. 93:63-75). Additional details of the complex have been visualized including an intimate association of the inner spoke domains as an inner spoke ring, extensive domains within the spokes and coaxial thin rings, and interestingly, a central channel-like feature. Membrane-associated NPCs and detergent-extracted NPCs both possess peripherally located radial arms resulting in an effective diameter of approximately 1,450-1,500 A. In projection, the radial arms possess approximate mirror symmetry suggesting that they originate from both sides of the assembly. Moreover, membrane-associated NPCs are asymmetric at most radii and right-handed as viewed from the cytoplasm; detergent-extracted NPCs appear to be symmetric and have approximately 822 symmetry. Taken together, the data suggests that the framework of membrane-associated NPCs is perturbed from a symmetrical configuration, either during isolation of nuclei or by interactions with the lamina and the nuclear envelope in vivo. However, detergent extraction of nuclei appears to result in a more symmetrical alignment of components in apposing halves of the assembly.
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Stavru, Fabrizia, Gitte Nautrup-Pedersen, Volker C. Cordes, and Dirk Görlich. "Nuclear pore complex assembly and maintenance in POM121- and gp210-deficient cells." Journal of Cell Biology 173, no. 4 (May 15, 2006): 477–83. http://dx.doi.org/10.1083/jcb.200601002.

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So far, POM121 and gp210 are the only known anchoring sites of vertebrate nuclear pore complexes (NPCs) within the lipid bilayer of the nuclear envelope (NE) and, thus, are excellent candidates for initiating the NPC assembly process. Indeed, we demonstrate that POM121 can recruit several nucleoporins, such as Nup62 or Nup358, to ectopic assembly sites. It thus appears to act as a nucleation site for the assembly of NPC substructures. Nonetheless, we observed functional NPCs and intact NEs in severely POM121-depleted cells. Double knockdowns of gp210 and POM121 in HeLa cells, as well as depletion of POM121 from human fibroblasts, which do not express gp210, further suggest that NPCs can assemble or at least persist in a POM121- and gp210-free form. This points to extensive redundancies in protein–protein interactions within NPCs and suggests that vertebrate NPCs contain additional membrane-integral nucleoporins for anchorage within the lipid bilayer of the NE. In Stavru et al. (on p. 509 of this issue), we describe such an additional transmembrane nucleoporin as the metazoan orthologue of yeast Ndc1p.
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Dultz, Elisa, Matthias Wojtynek, Ohad Medalia, and Evgeny Onischenko. "The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth." Cells 11, no. 9 (April 25, 2022): 1456. http://dx.doi.org/10.3390/cells11091456.

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Nuclear pore complexes (NPCs) are the only transport channels that cross the nuclear envelope. Constructed from ~500–1000 nucleoporin proteins each, they are among the largest macromolecular assemblies in eukaryotic cells. Thanks to advances in structural analysis approaches, the construction principles and architecture of the NPC have recently been revealed at submolecular resolution. Although the overall structure and inventory of nucleoporins are conserved, NPCs exhibit significant compositional and functional plasticity even within single cells and surprising variability in their assembly pathways. Once assembled, NPCs remain seemingly unexchangeable in post-mitotic cells. There are a number of as yet unresolved questions about how the versatility of NPC assembly and composition is established, how cells monitor the functional state of NPCs or how they could be renewed. Here, we review current progress in our understanding of the key aspects of NPC architecture and lifecycle.
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Dultz, Elisa, Matthias Wojtynek, Ohad Medalia, and Evgeny Onischenko. "The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth." Cells 11, no. 9 (April 25, 2022): 1456. http://dx.doi.org/10.3390/cells11091456.

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Nuclear pore complexes (NPCs) are the only transport channels that cross the nuclear envelope. Constructed from ~500–1000 nucleoporin proteins each, they are among the largest macromolecular assemblies in eukaryotic cells. Thanks to advances in structural analysis approaches, the construction principles and architecture of the NPC have recently been revealed at submolecular resolution. Although the overall structure and inventory of nucleoporins are conserved, NPCs exhibit significant compositional and functional plasticity even within single cells and surprising variability in their assembly pathways. Once assembled, NPCs remain seemingly unexchangeable in post-mitotic cells. There are a number of as yet unresolved questions about how the versatility of NPC assembly and composition is established, how cells monitor the functional state of NPCs or how they could be renewed. Here, we review current progress in our understanding of the key aspects of NPC architecture and lifecycle.
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Dissertations / Theses on the topic "Nuclear pore complex (NPCs)"

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Lin, Junyan. "Assembly and function of cytosolic nuclear pore complexes." Electronic Thesis or Diss., Strasbourg, 2024. http://www.theses.fr/2024STRAJ037.

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Les complexes des pores nucléaires (CPN) sont d'énormes assemblages protéiques intégrés dans l'enveloppe nucléaire (EN). Ils servent de structures pour le transport bidirectionnel. Essentiels, ils permettent le maintien de l'équilibre entre le noyau et le cytoplasme. Au-delà de leur résidence dans l'EN, les CPN se trouvent également dans des feuillets du réticulum endoplasmique (RE) empilés connus sous le nom de lamelles annulaires (LA). Cependant, la fonction et les voies régissant la biogenèse des LA restent énigmatiques. Notre investigation dans les cellules de mammifères révèle un mécanisme où la formation des LA résulte de la fusion de CPN cytosoliques préassemblés. Le mouvement des CPN cytosoliques est intimement lié à la dynamique du RE, car ils migrent vers l'EN et s'y intègrent en début d'interphase en conditions de croissance normales, ce processus est médié par les microtubules. RanBP2 (Nup358), un constituant des filaments cytoplasmiques des CPN, apparaît comme nécessaire et suffisant pour la formation des LA dans le cytoplasme. Mécaniquement, les répétitions FG dans le N-terminus de RanBP2 jouent un rôle crucial en orchestrant l'état d'oligomérisation des unités de l'anneau extérieur des CPN, connues sous le nom de complexes Y. Notre étude élucide un processus d'assemblage crucial pour nourrir l'EN, assurant la fonctionnalité des pores nucléaires et soulignant l'importance des CPN cytosoliques dans l'homéostasie cellulaire des mammifères
Nuclear pore complexes (NPCs), huge protein assemblies built into the nuclear envelope (NE), serve as pivotal structures for bidirectional transport, maintaining the equilibrium between the nucleus and cytoplasm. Beyond their residence within the NE, NPCs are also found in stacked cytoplasmic membranes known as annulate lamellae (AL). However, the function and pathways governing the biogenesis of AL remain enigmatic. Our investigation in mammalian cells unveils a mechanism wherein AL formation arises through the fusion of pre-assembled cytosolic NPCs. The movement of cytosolic NPCs is intricately linked to the dynamics of the endoplasmic reticulum (ER), as they migrate towards and integrate into NE during early interphase under normal growth conditions, a process mediated by microtubules. RanBP2 (Nup358), a constituent of the NPC cytoplasmic filaments, emerges as necessary and sufficient for AL formation in the cytoplasm. Mechanistically, the FG repeats in the N-terminus of RanBP2 play a pivotal role by orchestrating the oligomerization state of the NPC outer ring units, known as Y-complexes. Our study elucidates an assembly process crucial for NE nourishment, ensuring the functionality of nuclear pores and underscoring the significance of cytosolic NPCs in mammalian cellular homeostasis
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Walther, Tobias. "The role of Peripheral Nuclear Pore Complex (NPC) structures in nuclear transport and NPC architecture." Diss., lmu, 2002. http://nbn-resolving.de/urn:nbn:de:bvb:19-4945.

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Kelich, Joseph M. "Single-Molecule Studies on Nuclear Pore Complex Structure and Function." Diss., Temple University Libraries, 2018. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/511772.

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Biology
Ph.D.
Nuclear pore complexes (NPCs) are large macromolecular gateways embedded in the nuclear envelope of Eukaryotic cells that serve to regulate bi-directional trafficking of particles to and from the nucleus. NPCs have been described as creating a selectively permeable barrier mediating the nuclear export of key endogenous cargoes such as mRNA, and pre-ribosomal subunits as well as allow for the nuclear import of nuclear proteins and some viral particles. Remarkably, other particles that are not qualified for nucleocytoplasmic transport are repelled from the NPC, unable to translocate. The NPC is made up of over 30 unique proteins, each present in multiples of eight copies. The two primary protein components of the NPC can be simplified as scaffold nucleoporins which form the main structure of the NPC and the phenylalanine-glycine (FG) motif containing nucleoporins (FG-Nups) which anchor to the scaffold and together create the permeability barrier within the pore. Advances in fluorescence microscopy techniques including single-molecule and super-resolution microscopy have made it possible to label and visualize the dynamic components of the NPC as well as track the rapid nucleocytoplasmic transport process of importing and exporting cargoes. The focus of this dissertation will be on live cell fluorescence microscopy application in probing the dynamic components of the NPC as well as tracking the processes of nucleocytoplasmic transport.
Temple University--Theses
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Lolodi, Ogheneochukome. "Kinetic analysis of karyopherin-mediated transport through the nuclear pore complex." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215696.

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Authors are permitted to post the MBoC PDF of their articles (and/or supplemental material) on their personal websites or in an online institutional repository provided there appears always the proper citation of the manuscript in MBoC and a link to the original publication of the manuscript in MBoC (http://www.molbiolcell.org/site/misc/ifora.xhtml)
Kyoto University (京都大学)
0048
新制・課程博士
博士(生命科学)
甲第19869号
生博第350号
新制||生||46(附属図書館)
32905
京都大学大学院生命科学研究科統合生命科学専攻
(主査)教授 河内 孝之, 教授 藤田 尚志, 教授 永尾 雅哉
学位規則第4条第1項該当
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Liu, Hui-Lin. "Analyses of mitotic nuclear pore complex dynamics in Aspergillus nidulans." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1243862963.

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Xu, Xianfeng. "Two sides of the plant nuclear pore complex and a potential link between Ran GTPase and plant cell division." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1190050471.

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Markossian, Sarine W. "Nup2 and a Newly Discovered Nuclear Pore Complex Protein, NupA, Function at Mitotic Chromatin Controlled by the NIMA Kinase." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1306851345.

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Anderson, Daniel J. "Dynamics of nuclear envelope and nuclear pore complex formation." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3336561.

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Thesis (Ph. D.)--University of California, San Diego, 2008.
Title from first page of PDF file (viewed December 16, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 127-145).
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Onischenko, Evgeny. "Disassembly and reassembly of the nuclear pore complex /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-929-7/.

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Osmanovic, D. "Polymer theory applied to the nuclear pore complex." Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1451621/.

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Physically interesting behaviour can arise when soft matter is confined to nanoscale dimensions. A highly relevant biological example of such a phenomenon is the Nuclear Pore Complex (NPC), found perforating the Nuclear Envelope of all eukaryotic cells. In the central conduit of the NPC, of 30-60 nm diameter, a disordered arrangement of proteins regulates all macromolecular transport between the nucleus and the cytoplasm. Its selectivity for larger macromolecules relies on changes in a permeability barrier that is formed by these unstructured proteins, induced by interactions of these proteins with molecules called Nuclear Transport Receptors (NTRs), which can chaperone larger macromolecules through the NPC. The exact mechanism for the transport selectivity is unknown. To model these unstructured proteins in the nanoscale channel of the NPC, a density functional theory approach is developed that treats the proteins as interacting polymers. This new method is tested against Monte Carlo to show its validity. A detailed comparison between this model system and those previously proposed in the literature is provided. In a parameter range relevant for the NPC, the system shows bimodal behaviour The polymers can alternate between two condensed states: An open state, in which this condensation takes place at the channel wall, and a closed state in which it occurs at the channel centre. We then extend this model by including explicitly the effect of Nuclear Transport Receptors on the conformations of the polymers. The model takes into account the finite size of the transport receptors relative to the NPC diameter. Mapping the polymer and transport receptor behaviour over a set of physiologically relevant parameters gives different structural scenarios for the various hypothesized transport mechanisms. Further to this, the transport rates for each parameter set can be obtained, showing whether such parameters are consistent with experimental evidence. In addition to this, we study the effect of relaxing some of the assumptions of our model, specifically by looking at azimuthal symmetry breaking effects in two dimensions. We also compare our model to experimental results measuring the thickness of planar polymer brushes comprised of NPC proteins to further justify parameter choices.
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Books on the topic "Nuclear pore complex (NPCs)"

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Goldberg, Martin W., ed. The Nuclear Pore Complex. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2337-4.

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Rollenhagen, Christiane. Investigation of the functional dynamics of the Nuclear Pore Complex (NPC). 2001.

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Nuclear Pore Complex: Methods and Protocols. Springer, 2022.

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Goldberg, Martin W. Nuclear Pore Complex: Methods and Protocols. Springer, 2022.

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Brown, Christopher Richard. Transcriptional regulation at the nuclear pore complex. 2008.

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Oakford, Lawrence Xavier. The isolation and initial characterization of nuclear envelope "ghosts" and nuclear pore complex morphology from Physarum polycephalum. 1986.

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Book chapters on the topic "Nuclear pore complex (NPCs)"

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Hazawa, Masaharu, Akiko Kobayashi, and Richard W. Wong. "NPCs in Mitosis and Chromosome Segregation." In Nuclear Pore Complexes in Genome Organization, Function and Maintenance, 219–40. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-71614-5_10.

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Heese-Peck, Antje, and Natasha V. Raikhel. "The nuclear pore complex." In Protein Trafficking in Plant Cells, 145–62. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-011-5298-3_8.

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Yu, Jingjie, Joseph Kelich, and Weidong Yang. "Assembly of Nuclear Pore Complex." In Nucleic Acids and Molecular Biology, 1–14. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-77309-4_1.

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Simon, Dan N., and Michael P. Rout. "Cancer and the Nuclear Pore Complex." In Cancer Biology and the Nuclear Envelope, 285–307. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4899-8032-8_13.

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Fahrenkrog, B., D. Stoffler, and U. Aebi. "Nuclear Pore Complex Architecture and Functional Dynamics." In Nuclear Export of Viral RNAs, 95–117. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56597-7_5.

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Bodoor, Khaldon, and Brian Burke. "Mitotic Control of Nuclear Pore Complex Assembly." In Nuclear Envelope Dynamics in Embryos and Somatic Cells, 73–86. Boston, MA: Springer US, 2002. http://dx.doi.org/10.1007/978-1-4615-0129-9_6.

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Kahms, Martin, Jana Hüve, and Reiner Peters. "4Pi Microscopy of the Nuclear Pore Complex." In Methods in Molecular Biology, 193–211. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-2080-8_11.

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Liu, Winny, and Jason H. Brickner. "Nuclear Pore Complex-Regulated Transcription and Memory." In Epigenetics in Biological Communication, 255–75. Cham: Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-59286-7_11.

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Oborská-Oplová, Michaela, Ute Fischer, Martin Altvater, and Vikram Govind Panse. "Eukaryotic Ribosome assembly and Nucleocytoplasmic Transport." In Ribosome Biogenesis, 99–126. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_7.

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AbstractThe process of eukaryotic ribosome assembly stretches across the nucleolus, the nucleoplasm and the cytoplasm, and therefore relies on efficient nucleocytoplasmic transport. In yeast, the import machinery delivers ~140,000 ribosomal proteins every minute to the nucleus for ribosome assembly. At the same time, the export machinery facilitates translocation of ~2000 pre-ribosomal particles every minute through ~200 nuclear pore complexes (NPC) into the cytoplasm. Eukaryotic ribosome assembly also requires >200 conserved assembly factors, which transiently associate with pre-ribosomal particles. Their site(s) of action on maturing pre-ribosomes are beginning to be elucidated. In this chapter, we outline protocols that enable rapid biochemical isolation of pre-ribosomal particles for single particle cryo-electron microscopy (cryo-EM) and in vitro reconstitution of nuclear transport processes. We discuss cell-biological and genetic approaches to investigate how the ribosome assembly and the nucleocytoplasmic transport machineries collaborate to produce functional ribosomes.
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Milligan, R. A. "A Structural Model for the Nuclear Pore Complex." In Nucleocytoplasmic Transport, 113–22. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-71565-5_10.

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Conference papers on the topic "Nuclear pore complex (NPCs)"

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Pidaparti, R. M., P. A. Sarma, A. S. C. Sinha, G. Vemuri, and A. M. Gacy. "Nuclear Membrane Dynamics of a Nuclear Pore Complex Structure." In ASME 2001 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2001. http://dx.doi.org/10.1115/imece2001/bed-23162.

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Abstract The nuclear pore complex (NPC) is an excellent example of a bio-molecular motor, since it operates primarily via energy dependent processes, and performs some of the most vital functions required for the survival of a cell. In the presence of appropriate chemical stimuli, the NPC apparently opens or closes, like a gating mechanism, and permits the flow of material in to and out of the nucleus. An NPC, with typical dimensions of 100–200 nm, is a megadalton (MDa) heteromultimeric protein complex, which spans the nuclear envelope and is postulated to possess a transporter-containing central cylindrical body embedded between cytoplasmic and nucleoplasmic rings as shown in Fig.1. A cell has many, presumably identical, NPCs, each of which participates in the import and export of nuclear material from within the nucleus [1–2]. Exactly how this transport occurs through the NPC is an open question, and a very important one, with profound implications for nanoscale devices for fluidic transport, genetic engineering and targeted drug delivery.
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Gorav, Gorav, Vrushali Khedekar, Geetha K. Varier, and P. Nandakumar. "Enhanced Uptake and Retention of Graphene Quantum Dots in HeLa Cell Nuclei." In Bio-Optics: Design and Application. Washington, D.C.: Optica Publishing Group, 2023. http://dx.doi.org/10.1364/boda.2023.jtu4a.6.

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The nuclear pore complex (NPC) is an intricate protein structure located on the nuclear envelope that functions as the sole gateway for nuclear cytoplasm transport. Our experimental studies show the dual uptake rates of GQDs in HeLa nuclei indicate two phenomena occurring simultaneously. Export studies confirm bidirectionality and retention.
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Otsuka, Shotaro, Hirohide Takahashi, and Shige Yoshimura. "Single-molecule Structural and Functional Analyses of Nuclear Pore Complex." In 2006 IEEE International Symposium on MicroNanoMechanical and Human Science. IEEE, 2006. http://dx.doi.org/10.1109/mhs.2006.320314.

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Itoh, Goichi, Jinya Nakamura, Koji Kono, Tadashi Watanabe, Hirotada Ohashi, Yu Chen, and Shinya Nagasaki. "Pore-Scale Simulation for Predicting Material Transport Through Porous Media." In 10th International Conference on Nuclear Engineering. ASMEDC, 2002. http://dx.doi.org/10.1115/icone10-22563.

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Microscopic models of real-coded lattice gas automata (RLG) method with a special boundary condition and lattice Boltzmann method (LBM) are developed for simulating three-dimensional fluid dynamics in complex geometry. Those models enable us to simulate pore-scale fluid dynamics that is an essential part for predicting material transport in porous media precisely. For large-scale simulation of porous media with high resolution, the RLG and LBM programs are designed for parallel computation. Simulation results of porous media flow by the LBM with different pressure gradient conditions show quantitative agreements with macroscopic relations of Darcy’s law and Kozeny-Carman equation. As for the efficiency of parallel computing, a standard parallel computation by using MPI (Message Passing Interface) is compared with the hybrid parallel computation of MPI-node parallel technique. The benchmark tests conclude that in case of using large number of computing node, the parallel performance declines due to increase of data communication between nodes and the hybrid parallel computation totally shows better performance in comparison with the standard parallel computation.
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Gao, Jun, Hyung T. Kwak, and Marwah AlSinan. "Accurate Carbonate Pore System Characterization by Nuclear Magnetic Resonance and Micro-CT Techniques." In SPE Middle East Oil & Gas Show and Conference. SPE, 2021. http://dx.doi.org/10.2118/204659-ms.

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Abstract Carbonate reservoir rocks usually have complex pore systems of broad size distributions, which determine many aspects of oil exploitation, from petrophysical properties to oil/water displacements. An accurate and complete description of these pore systems remains a challenge. A single technique often gives one measurement of complicated microscopic pore space. The new techniques (i.e., micro-CT and NMR) are utilized together with conventional methods (e.g., MICP, BET) to capture a more accurate and complete picture of pore structures. MICP measures the pore throat while the NMR T2 mainly measures the pore body. Micro-CT provides a 3D image of a limited sample size. Recently, NMR DDIF (decay due to diffusion in the internal field) for direct pore body size is extended from high to low magnetic field, which overcomes many limitations in pore system characterization. This study obtains pore throat size distributions from in-situ centrifuge capillary pressure and pore body size distributions from low field DDIF measurement and verifies them with micro-CT and BET/T2 in different types of carbonate rocks. The pore throat size distribution of the conventional sample is obtained from in-situ centrifuge capillary pressure. The major features of both macro and micro pore throat size distributions are captured. Pore size distributions are directly obtained from glass beads and carbonate rocks without calibration. Combined analysis of the pore size distribution from two methods reveals the underlying causes of their different petrophysical properties. The pore throat size distribution from in-situ centrifuge capillary pressure and pore size distribution from NMR DDIF can be employed to obtain a better understanding of conventional carbonate pore systems.
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Toumelin, E., C. Torres-Verdin, and S. Chen. "Quantification of Multi-Phase Fluid Saturations in Complex Pore Geometries From Simulations of Nuclear Magnetic Resonance Measurements." In SPE Annual Technical Conference and Exhibition. Society of Petroleum Engineers, 2002. http://dx.doi.org/10.2118/77399-ms.

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Hanzawa, Daiki, Kyosuke Katsumata, and Tomio Okawa. "A Study on High Heat Flux Heat Removal With Boiling Using Porous Microchannel." In 2014 22nd International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/icone22-30104.

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This paper reports the critical heat flux (CHF) enhancement that was observed experimentally when a porous metal was placed in a small flow channel (hereafter, this channel is called a “porous microchannel”). In the porous microchannel, the CHF value increased almost linearly with increased values of the mass flux and the inlet subcooling. In consequence, higher cooling performance was achieved under high mass flux and high inlet subcooling conditions. It was also found that considerable fluctuation of the pressure loss frequently encountered in a small heated channel disappears in the porous microchannel. It was considered that the stabilization of the pressure loss can mainly be attributed to inhibition of the formation of large bubbles. The effects of the material and the pore size of the porous metal were also investigated. Silver and nickel were selected as the porous metal material and the pore size tested was 0.2 and 0.6 mm. In the present experiments, the CHF value was not influenced significantly by the material in spite of the distinct difference of the thermal conductivity between silver and nickel, whilst it was dependent noticeably on the pore size. It was hence suggested that the CHF enhancement observed in this work was mainly caused by the complex thermal-hydraulic field formed in the porous microchannel. Preliminary results of the flow visualization performed to reveal the mechanisms of the CHF enhancement in the porous microchannel was also reported.
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Cinar, Yildiray, Ahmed Zayer, Naseem Dawood, and Dimitris Krinis. "A New Approach for Building Composite Cores for Corefloods in Complex Carbonate Rocks." In SPE Middle East Oil & Gas Show and Conference. SPE, 2021. http://dx.doi.org/10.2118/204655-ms.

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Abstract Carbonate reservoir rocks are composed of complex pore structures and networks, forming a wide range of sedimentary facies. Considering this complexity, we present a novel approach for a better selection of coreflood composites. In this approach, reservoir plugs undergo a thorough filtration process by completing several lab tests before they get classified into reservoir rock types. Those tests include conventional core analysis (CCA), liquid permeability, plug computed tomography (CT), nuclear magnetic resonance (NMR), end-trim mercury injection capillary pressure (MICP), X-ray diffraction (XRD), thin-section analysis (TS), scanning electron microscopy (SEM), and drainage capillary pressure (Pc). We recommend starting with a large pool of plugs and narrowing down the selection as they complete different stages of the screening process. The CT scans help to exclude plugs exhibiting composite-like behavior or containing vugs and fractures that potentially influence coreflood results. After that, the plugs are categorized into separate groups representing the available reservoir rock types. Then, we look into each rock type and determine whether the selected plugs share similar pore-structures, rock texture, and mineral content. The end-trim MICP is usually helpful in clustering plugs having similar pore-throat size distributions. Nevertheless, it also poses a challenge because it may not represent the whole plug, especially for heterogeneous carbonates. In such a case, we recommend harnessing the NMR capabilities to verify the pore-size distribution. After pore-size distribution verification, plugs are further screened for textural and mineral similarity using the petrographic data (XRD, TS, and SEM). Finally, we evaluate the similarity of brine permeability (Kb), irreducible water saturation (Swir) from Pc, and effective oil permeability data at Swir (Koe, after wettability restoration for unpreserved plugs) before finalizing the composite selection. The paper demonstrates significant aspects of applying the proposed approach to carbonate reservoir rock samples. It integrates geology, petrophysics, and reservoir engineering elements when deciding the best possible composite for coreflood experiments. By practicing this workflow, we also observe considerable differences in rock types depending on the data source, suggesting that careful use of end-trim data for carbonates is advisable compared to more representative full-plug MICP and NMR test results. In addition, we generally observe that Kb and Koe are usually lower than the Klinkenberg permeability with a varying degree that is plug-specific, highlighting the benefit of incorporating these measurements as additional criteria in coreflood composite selection for carbonate reservoirs.
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Chen, Wen An, Dai Guo Yu, Guo Liang Liu, Qing Bo Li, Di Zhang, Meng Zhao, Fang fang Wu, et al. "Evaluating Complex Lacustrine Carbonate Reservoir by Integrating Advanced Logging Techniques and Core Measurements-A Case Study in Qiadam Basin." In SPE Reservoir Characterisation and Simulation Conference and Exhibition. SPE, 2023. http://dx.doi.org/10.2118/212607-ms.

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Abstract A complex and tight lacustrine carbonate reservoir is the main target reservoir in Qaidam Basin. The diagenesis of shallow-shore lake deposition has created a highly heterogeneous reservoir in both vertical and horizontal directions in terms of lithologies, pore structures, and permeability. The core analysis shows a wide variety of lithologies that include terrigenous clastics (quartz, orthoclase, and plagioclase), carbonate (calcite, dolomite, and ankerite), and evaporite minerals such as anhydrite, etc. Electron microscope analysis shows mainly intercrystallite pores with dolomite, dissolved pores, and microfractures. Associated with the complex lithology and pore structure, reservoir permeability is varied and is mostly less than 0.02mD. Evaluating and characterizing this complex reservoir to find a better pay zone was the objective of this study. To evaluate the lithologies, pore structures, porosities, and permeability in quantities accurately, the advanced gamma-ray spectroscopy logs, nuclear magnetic resonance (NMR) logs, and high-resolution micro-resistivity borehole image logs were acquired in some key wells. Integrated with core data such as X-ray diffraction (XRD), mercury injection capillary (MICP), the lithofacies, texture facies, and pore facies were classified based on the minerals from gamma-ray spectroscopy, the textures from borehole image, and the pore sizes from NMR. The combination of these three facies represents the reservoir quality. In the study area, the lithofacies were classified into four types, which are high carbonate content facies, middle carbonate content facies, high clay content facies, and high clastic content facies. The texture facies were classified into four types, which are massive texture, layered texture, dissolved texture, and algal texture. The pore structure facies were classified into four types, which are macro facies, meso facies, meso-micro facies, and microfacies. The better pay zone is the combination of high carbonate content facies, algal texture, and macro facies. The pay zone of the reservoir was well defined and mapped with the combination facies vertically and horizontally in the whole study area. The integrated solution described in this study leverages the advantages of advanced gamma-ray spectroscopy, NMR, borehole images, and core measurements. It develops a comprehensive understanding of the complex carbonate reservoir and provides the solution to pinpoint the sweet spots and place the horizontal well.
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Gonzalez, Andres, and Zoya Heidari. "Multi-Scale and Multi-Physics Quantitative Workflow for Integrated and Image-Assisted Rock Classification in Complex Carbonate Formations." In 2022 SPWLA 63rd Annual Symposium. Society of Petrophysicists and Well Log Analysts, 2022. http://dx.doi.org/10.30632/spwla-2022-0104.

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Diagenetic processes in carbonate formations result in rapid spatial variation in rock fabric (i.e., spatial distribution of rock components) and complex pore structure. Therefore, assessment of petrophysical properties, necessary for efficient exploitation of hydrocarbon-bearing carbonate reservoirs, can be challenging. Estimation of the aforementioned properties requires integration of multi-scale and multi-physics data that captures rock fabric at multiple scales. Image logs offer high-resolution information of the rock fabric and its variation. However, this information is typically employed qualitatively, especially in carbonate formations. The objectives of this paper include (a) quantifying the visual content of high-resolution image logs through computation of image-based rock-fabricrelated features, (b) integrating conventional well logs with image-based features and core measurements for rock classification. First, we conducted joint inversion of well logs to estimate volumetric concentration of minerals and total porosity. Then, we characterized the pore structure of the evaluated intervals fitting a multimodal Gaussian model to the available nuclear magnetic resonance (NMR) transverse relaxation (T2) distribution logs and core measurements. Next, we employed image analysis techniques to capture variations of rock fabric in the form of greyscale and textural features. We integrated compositional, pore structure, and image-based rock fabric related features for rock classification. Finally, we evaluated various strategies to select the adequate number of rock classes using the available data on the evaluated depth interval. We applied the proposed workflow to one well intersecting a complex carbonate formation. We demonstrated that the extracted image-based rock fabric features and the pore structure features from NMR T2 distribution captured the complex pore structure and rapid spatial variation of rock fabric observed in the evaluated depth interval. We honored spatial variation in rock fabric at pore- and log-scale by selecting the adequate number of rock classes using log and core NMR T2 distribution data, image-based features, and petrophysical properties of the evaluated depth interval. The number and location of obtained integrated rock classes honored rock fabric variation at both the coreand log-scale. A unique contribution of the proposed workflow is the quantification of the visual content of image logs and their integration with core-/log-scale measurements, improving rock classification and potentially formation evaluation efforts by accounting for rock fabric variation at different scales and honoring various physical measurements, which is not attainable through conventional rock typing techniques. This becomes specifically important in carbonate formations, with complex pore structure and rapid variation in rock fabric.
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