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Tomas Duminis, Saroash Shahid, Natalia G Karpukhina, Robert G Hill
OBJECTIVE: Dental restoration aesthetics, particularly the translucency of modern dental restorative filling materials depends on the refractive index (RI) match between the different components in the material. In the case of dental composites (DC), the RI of the polymer must match the RI of the filler otherwise the material is optically opaque and has limited depth of cure. In the case of glass ionomer cements (GICs), the RI of the ion-leachable glass must match the RI of the polysalts to engineer a smart material with a tooth-like appearance...
February 2, 2018: Dental Materials: Official Publication of the Academy of Dental Materials
Roman Teimer, Jan Kosinski, Alexander von Appen, Martin Beck, Ed Hurt
Nucleocytoplasmic transport occurs through nuclear pore complexes (NPCs), which are formed from multiple copies of ~30 different nucleoporins (Nups) and inserted into the double nuclear membrane. Many of these Nups are organized into subcomplexes, of which the Y-shaped Nup84 complex is the major constituent of the nuclear and cytoplasmic rings. The Nup82-Nup159-Nsp1 complex is another module that, however, is only assembled into the cytoplasmic ring. By means of crosslinking mass spectrometry, biochemical reconstitution, and molecular modeling, we identified a short linear motif in the unstructured N-terminal region of Chaetomium thermophilum Nup145C, a subunit of the Y-complex, that is sufficient to recruit the Nup82 complex, but only in its assembled state...
October 24, 2017: Nature Communications
Sebastian Hauke, Alexander von Appen, Tooba Quidwai, Jonas Ries, Richard Wombacher
We present new fluorophore-conjugates for dual-color photoactivation and super-resolution imaging inside live mammalian cells. These custom-designed, photo-caged Q-rhodamines and fluoresceins are cell-permeable, bright and localize specifically to intracellular targets. We utilized established orthogonal protein labeling strategies to precisely attach the photoactivatable fluorophores to proteins with subsequent activation of fluorescence by irradiation with UV light. That way, diffusive cytosolic proteins, histone proteins as well as filigree mitochondrial networks and focal adhesion proteins were visualized inside living cells...
January 1, 2017: Chemical Science
Mingyu Gu, Dollie LaJoie, Opal S Chen, Alexander von Appen, Mark S Ladinsky, Michael J Redd, Linda Nikolova, Pamela J Bjorkman, Wesley I Sundquist, Katharine S Ullman, Adam Frost
Endosomal sorting complexes required for transport III (ESCRT-III) proteins have been implicated in sealing the nuclear envelope in mammals, spindle pole body dynamics in fission yeast, and surveillance of defective nuclear pore complexes in budding yeast. Here, we report that Lem2p (LEM2), a member of the LEM (Lap2-Emerin-Man1) family of inner nuclear membrane proteins, and the ESCRT-II/ESCRT-III hybrid protein Cmp7p (CHMP7), work together to recruit additional ESCRT-III proteins to holes in the nuclear membrane...
March 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
Gustav Eje Henter, W Bastiaan Kleijn
This document contains supplemental material for the IEEE Transactions on Pattern Analysis and Machine Intelligence article "Minimum Entropy Rate Simplification of Stochastic Processes." The supplement is divided into three appen- dices: the first on MERS for Gaussian processes, and the remaining two on, respectively, the theory and the experimental results of MERS for Markov chains.
February 23, 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
Jan Kosinski, Shyamal Mosalaganti, Alexander von Appen, Roman Teimer, Amanda L DiGuilio, William Wan, Khanh Huy Bui, Wim J H Hagen, John A G Briggs, Joseph S Glavy, Ed Hurt, Martin Beck
Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring...
April 15, 2016: Science
Fang Chen, Hui Wu, Yun Wu, Ren Mao, Shenghong Zhang, Ting Feng, Ruihan Tang, Baili Chen, Zhirong Zeng, Minhu Chen, Yao He
OBJECTIVE: To analyze the clinical manifestations and identify independent diagnostic predictive factors for Crohn's disease (CD) initially diagnosed as appenicitis and treated by surgery. METHODS: The medical records of patients diagnosed as acute appendicitis upon admission and treated by surgical operation in the First Affiliated Hospital of Sun Yat-sen University from January 2000 to December 2014 were retrospectively analyzed. Based on postoperative pathological examination and clinical examination results, 28 CD patients were identified (CD group), and for each CD case, 3 controls with confirmed diagnosis of appendicitis were included (appendicitis group, n=84)...
March 15, 2016: Zhonghua Yi Xue za Zhi [Chinese medical journal]
Gustav Eje Henter, W Bastiaan Kleijn
We propose minimum entropy rate simplification (MERS), an information-theoretic, parameterization-independent framework for simplifying generative models of stochastic processes. Applications include improving model quality for sampling tasks by concentrating the probability mass on the most characteristic and accurately described behaviors while de-emphasizing the tails, and obtaining clean models from corrupted data (nonparametric denoising). This is the opposite of the smoothing step commonly applied to classification models...
December 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
Katja Metfies, Wilken-Jon von Appen, Estelle Kilias, Anja Nicolaus, Eva-Maria Nöthig
Information on recent photosynthetic biomass distribution and biogeography of Arctic marine pico-eukaryotes (0.2-3 μm) is needed to better understand consequences of environmental change for Arctic marine ecosystems. We analysed pico-eukaryote biomass and community composition in Fram Strait and large parts of the Central Arctic Ocean (Nansen Basin, Amundsen Basin) using chlorophyll a (Chl a) measurements, automated ribosomal intergenic spacer analysis (ARISA) and 454-pyrosequencing. Samples were collected during summer 2012, the year with the most recent record sea ice minimum...
2016: PloS One
Alexander von Appen, Martin Beck
Determining the structure of the nuclear pore complex (NPC) imposes an enormous challenge due to its size, intricate composition and membrane-embedded nature. In vertebrates, about 1000 protein building blocks assemble into a 110-MDa complex that fuses the inner and outer membranes of a cell's nucleus. Here, we review the recent progress in understanding the in situ architecture of the NPC with a specific focus on approaches using three-dimensional cryo electron microscopy. We discuss technological benefits and limitations and give an outlook toward obtaining a high-resolution structure of the NPC...
May 22, 2016: Journal of Molecular Biology
Alexander von Appen, Jan Kosinski, Lenore Sparks, Alessandro Ori, Amanda L DiGuilio, Benjamin Vollmer, Marie-Therese Mackmull, Niccolo Banterle, Luca Parca, Panagiotis Kastritis, Katarzyna Buczak, Shyamal Mosalaganti, Wim Hagen, Amparo Andres-Pons, Edward A Lemke, Peer Bork, Wolfram Antonin, Joseph S Glavy, Khanh Huy Bui, Martin Beck
Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter...
October 1, 2015: Nature
S O Dodonova, P Diestelkoetter-Bachert, A von Appen, W J H Hagen, R Beck, M Beck, F Wieland, J A G Briggs
Transport of material within cells is mediated by trafficking vesicles that bud from one cellular compartment and fuse with another. Formation of a trafficking vesicle is driven by membrane coats that localize cargo and polymerize into cages to bend the membrane. Although extensive structural information is available for components of these coats, the heterogeneity of trafficking vesicles has prevented an understanding of how complete membrane coats assemble on the membrane. We combined cryo-electron tomography, subtomogram averaging, and cross-linking mass spectrometry to derive a complete model of the assembled coat protein complex I (COPI) coat involved in traffic between the Golgi and the endoplasmic reticulum...
July 10, 2015: Science
Gary Male, Alexander von Appen, Sebastian Glatt, Nicholas M I Taylor, Michele Cristovao, Helga Groetsch, Martin Beck, Christoph W Müller
In eukaryotes, RNA Polymerase III (Pol III) is specifically responsible for transcribing genes encoding tRNAs and other short non-coding RNAs. The recruitment of Pol III to tRNA-encoding genes requires the transcription factors (TF) IIIB and IIIC. TFIIIC has been described as a conserved, multi-subunit protein complex composed of two subcomplexes, called τA and τB. How these two subcomplexes are linked and how their interaction affects the formation of the Pol III pre-initiation complex (PIC) is poorly understood...
June 10, 2015: Nature Communications
Jan Kosinski, Alexander von Appen, Alessandro Ori, Kai Karius, Christoph W Müller, Martin Beck
Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques. Cross-linking mass spectrometry (XL-MS) identifies proximal protein residues and thus is increasingly used to map protein interactions and determine the relative orientation of subunits within the structure of protein complexes. To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures...
March 2015: Journal of Structural Biology
Monika Gaik, Dirk Flemming, Alexander von Appen, Panagiotis Kastritis, Norbert Mücke, Jessica Fischer, Philipp Stelter, Alessandro Ori, Khanh Huy Bui, Jochen Baßler, Elisar Barbar, Martin Beck, Ed Hurt
Nuclear pore complexes (NPCs) are huge assemblies formed from ∼30 different nucleoporins, typically organized in subcomplexes. One module, the conserved Nup82 complex at the cytoplasmic face of NPCs, is crucial to terminate mRNA export. To gain insight into the structure, assembly, and function of the cytoplasmic pore filaments, we reconstituted in yeast the Nup82-Nup159-Nsp1-Dyn2 complex, which was suitable for biochemical, biophysical, and electron microscopy analyses. Our integrative approach revealed that the yeast Nup82 complex forms an unusual asymmetric structure with a dimeric array of subunits...
February 2, 2015: Journal of Cell Biology
Konstanze Behrmann, Hartmut Rehbein, Annika von Appen, Markus Fischer
The number of fishery products with a quite detailed description of the origin is increasing. This trend is driven by the interest of consumers and the fight against illegal unregulated and unreported fisheries. Unfortunately, there is a lack of methods to prove this information experimentally besides the document-based traceability assessments. For marine fish population genetics is a promising strategy, but research is concentrated only on a few species. Saithe is a commercially important fish species, despite the fact that genetic knowledge is scarce regarding the specification of populations...
January 28, 2015: Journal of Agricultural and Food Chemistry
Jörg von Appen, Richard Dronskowski, Aurab Chakrabarty, Tilmann Hickel, Robert Spatschek, Jörg Neugebauer
Hydrogen interstitials in austenitic Fe-Mn alloys were studied using density-functional theory to gain insights into the mechanisms of hydrogen embrittlement in high-strength Mn steels. The investigations reveal that H atoms at octahedral interstitial sites prefer a local environment containing Mn atoms rather than Fe atoms. This phenomenon is closely examined combining total energy calculations and crystal orbital Hamilton population analysis. Contributions from various electronic phenomena such as elastic, chemical, and magnetic effects are characterized...
December 5, 2014: Journal of Computational Chemistry
Frederik Bachhuber, Jörg von Appen, Richard Dronskowski, Peer Schmidt, Tom Nilges, Arno Pfitzner, Richard Weihrich
Phosphorus displays fascinating structural diversity and the discovery of new modifications continues to attract attention. In this work, a complete stability range of known and novel crystalline allotropes of phosphorus is described for the first time. This includes recently discovered tubular modifications and the prediction of not-yet-known crystal structures of [P12] nanorods and not-yet-isolated [P14] nanorods. Despite significant structural differences, all P allotropes consist of covalent substructures, which are held together by van der Waals interactions...
October 20, 2014: Angewandte Chemie
Khanh Huy Bui, Alexander von Appen, Amanda L DiGuilio, Alessandro Ori, Lenore Sparks, Marie-Therese Mackmull, Thomas Bock, Wim Hagen, Amparo Andrés-Pons, Joseph S Glavy, Martin Beck
The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC...
December 5, 2013: Cell
Karsten Thierbach, Alexander von Appen, Matthias Thoms, Martin Beck, Dirk Flemming, Ed Hurt
A key building block of the nuclear pore complex (NPC) is the Nup84 subcomplex that has been structurally analyzed predominantly in the yeast system. To expand this analysis and gain insight into the evolutionary conservation of its structure, we reconstituted an octameric Nup84 complex using the subunits from a thermophile, Chaetomium thermophilum (ct). This assembly carries Nup37 and Elys, which are characteristic subunits of the orthologous human Nup107-Nup160 complex but absent from the yeast Saccharomyces cerevisiae...
September 3, 2013: Structure
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