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https://www.readbyqxmd.com/read/28334815/gcn5-mediated-rph1-acetylation-regulates-its-autophagic-degradation-under-dna-damage-stress
#1
Feng Li, Liang-De Zheng, Xin Chen, Xiaolu Zhao, Scott D Briggs, Hai-Ning Du
Histone modifiers regulate proper cellular activities in response to various environmental stress by modulating gene expression. In budding yeast, Rph1 transcriptionally represses many DNA damage or autophagy-related gene expression. However, little is known how Rph1 is regulated during these stress conditions. Here, we report that Rph1 is degraded upon DNA damage stress conditions. Notably, this degradation occurs via the autophagy pathway rather than through 26S proteasome proteolysis. Deletion of ATG genes or inhibition of vacuole protease activity compromises Rph1 turnover...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28322174/acanthocotyle-gurgesiella-n-sp-monogenea-acanthocotylidae-from-the-deep-sea-skate-gurgesiella-furvescens-rajidae-in-the-south-eastern-pacific
#2
L A Ñacari, F A Sepulveda, R Escribano, M E Oliva
Little is known about the diversity of parasites of the deep-sea fish of the world's oceans. Here, a new species of monogenean parasite of the deep-sea skate Gurgesiella furvescens is described. Specimens of parasites were obtained from the skin of two specimens of the dusky finless skate, G. furvescens (Rajidae), in the vicinity of Valparaiso (33°S, 72°W), central Chile, from midwater trawl fishing at depths of 350-450 m. Both morphological and molecular analyses were conducted to provide a full description of the new species, named Acanthocotyle gurgesiella...
March 21, 2017: Journal of Helminthology
https://www.readbyqxmd.com/read/28314893/integration-of-mrnp-formation-and-export
#3
REVIEW
Petra Björk, Lars Wieslander
Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA-protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs...
March 17, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28298006/nuclear-magnetic-resonance-diffusion-pore-imaging-experimental-phase-detection-by-double-diffusion-encoding
#4
Kerstin Demberg, Frederik Bernd Laun, Johannes Windschuh, Reiner Umathum, Peter Bachert, Tristan Anselm Kuder
Diffusion pore imaging is an extension of diffusion-weighted nuclear magnetic resonance imaging enabling the direct measurement of the shape of arbitrarily formed, closed pores by probing diffusion restrictions using the motion of spin-bearing particles. Examples of such pores comprise cells in biological tissue or oil containing cavities in porous rocks. All pores contained in the measurement volume contribute to one reconstructed image, which reduces the problem of vanishing signal at increasing resolution present in conventional magnetic resonance imaging...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28289229/persistence-of-the-mitochondrial-permeability-transition-in-the-absence-of-subunit-c-of-human-atp-synthase
#5
Jiuya He, Holly C Ford, Joe Carroll, Shujing Ding, Ian M Fearnley, John E Walker
The permeability transition in human mitochondria refers to the opening of a nonspecific channel, known as the permeability transition pore (PTP), in the inner membrane. Opening can be triggered by calcium ions, leading to swelling of the organelle, disruption of the inner membrane, and ATP synthesis, followed by cell death. Recent proposals suggest that the pore is associated with the ATP synthase complex and specifically with the ring of c-subunits that constitute the membrane domain of the enzyme's rotor...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28281697/measurement-and-visualization-of-tight-rock-exposed-to-co2-using-nmr-relaxometry-and-mri
#6
Haitao Wang, Zengmin Lun, Chengyuan Lv, Dongjiang Lang, Bingyu Ji, Ming Luo, Weiyi Pan, Rui Wang, Kai Gong
Understanding mechanisms of oil mobilization of tight matrix during CO2 injection is crucial for CO2 enhanced oil recovery (EOR) and sequestration engineering design. In this study exposure behavior between CO2 and tight rock of the Ordos Basin has been studied experimentally by using nuclear magnetic resonance transverse relaxation time (NMR T2) spectrum and magnetic resonance imaging (MRI) under the reservoir pressure and temperature. Quantitative analysis of recovery at the pore scale and visualization of oil mobilization are achieved...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28242692/lem2-recruits-chmp7-for-escrt-mediated-nuclear-envelope-closure-in-fission-yeast-and-human-cells
#7
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...
February 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28236735/the-nucleus-keeping-it-together-by-keeping-it-apart
#8
REVIEW
C Patrick Lusk, Megan C King
It has been postulated that the segregation of nucleus and cytoplasm supported the development of increased organismal complexity. For example, separating transcription and translation allows for mRNA splicing, while the sequestration of genomic DNA supports the innate immune system's ability to equate cytoplasmic DNA with pathogens. Consistent with the importance of nucleocytoplasmic compartmentalization in a broad array of cellular processes, defects in maintaining discrete nuclear and cytoplasmic compartments, either due to loss of nuclear pore complex integrity, disrupted nuclear transport or ruptures of the nuclear envelope, lead to cellular dysfunction, cell death and disease...
February 21, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28229152/an-anionic-metal-organic-framework-with-ternary-building-units-for-rapid-and-selective-adsorption-of-dyes
#9
Shuo Yao, Tong Xu, Nian Zhao, Lirong Zhang, Qisheng Huo, Yunling Liu
A novel metal-organic framework, [(CH3)2NH2]2[Cu3O(SO4)3Cu2L2(DMF)(H2O)]·9DMF (JLU-Liu39) H2L = pyridine-3,5-bis(phenyl-4-carboxylic acid), has been successfully synthesized under solvothermal conditions. Structure analysis indicates that the framework of JLU-Liu39 is constructed by ternary building units which include a rare hexa-nuclear [Cu6O2(SO4)6] cluster, a classical [Cu2(CO2)4] paddlewheel, and a 3-connected hetero-N, O donor ligand. The whole 3D framework possesses a (3,4,4)-connected fjh topology and a large window size of 25...
February 23, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28226231/cell-biology-of-the-plant-nucleus
#10
Iris Meier, Eric J Richards, David E Evans
The eukaryotic nucleus is enclosed by the nuclear envelope, which is perforated by the nuclear pores, the gateways of macromolecular exchange between the nucleoplasm and cytoplasm. The nucleoplasm is organized in a complex three-dimensional fashion that changes over time and in response to stimuli. Within the cell, the nucleus must be viewed as an organelle (albeit a gigantic one) that is a recipient of cytoplasmic forces and capable of morphological and positional dynamics. The most dramatic reorganization of this organelle occurs during mitosis and meiosis...
February 22, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28221134/human-nup98-regulates-the-localization-and-activity-of-dexh-d-box-helicase-dhx9
#11
Juliana S Capitanio, Ben Montpetit, Richard W Wozniak
Beyond their role at nuclear pore complexes, some nucleoporins function in the nucleoplasm. One such nucleoporin, Nup98, binds chromatin and regulates gene expression. To gain insight into how Nup98 contributes to this process, we focused on identifying novel binding partners and understanding the significance of these interactions. Here we report on the identification of the DExH/D-box helicase DHX9 as an intranuclear Nup98 binding partner. Various results, including in vitro assays, show that the FG/GLFG region of Nup98 binds to N- and C-terminal regions of DHX9 in an RNA facilitated manner...
February 21, 2017: ELife
https://www.readbyqxmd.com/read/28213497/mitochondrial-damage-elicits-a-tcdd-inducible-poly-adp-ribose-polymerase-mediated-antiviral-response
#12
Tatsuya Kozaki, Jun Komano, Daiki Kanbayashi, Michihiro Takahama, Takuma Misawa, Takashi Satoh, Osamu Takeuchi, Taro Kawai, Shigeomi Shimizu, Yoshiharu Matsuura, Shizuo Akira, Tatsuya Saitoh
The innate immune system senses RNA viruses by pattern recognition receptors (PRRs) and protects the host from virus infection. PRRs mediate the production of immune modulatory factors and direct the elimination of RNA viruses. Here, we show a unique PRR that mediates antiviral response. Tetrachlorodibenzo-p-dioxin (TCDD)-inducible poly(ADP ribose) polymerase (TIPARP), a Cysteine3 Histidine (CCCH)-type zinc finger-containing protein, binds to Sindbis virus (SINV) RNA via its zinc finger domain and recruits an exosome to induce viral RNA degradation...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28202688/super-resolution-mapping-of-scaffold-nucleoporins-in-the-nuclear-pore-complex
#13
Jiong Ma, Joseph M Kelich, Samuel L Junod, Weidong Yang
The nuclear pore complex (NPC), composed of ∼30 different nucleoporins (Nups), is one of the largest supramolecular structures in eukaryotic cells. Its octagonal ring-scaffold perforates the nuclear envelope and features a unique molecular machinery that regulates nucleocytoplasmic transport. However, the precise copy number and the spatial location of each Nup in the native NPC remain obscure due to the inherent difficulty of counting and localizing proteins inside the sub-micrometer supramolecular complex...
February 15, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28197909/sumo-and-nucleocytoplasmic-transport
#14
Christopher Ptak, Richard W Wozniak
The transport of proteins between the nucleus and cytoplasm occurs through nuclear pore complexes and is facilitated by numerous transport factors. These transport processes are often regulated by post-translational modification or, reciprocally, transport can function to control post-translational modifications through regulated transport of key modifying enzymes. This interplay extends to relationships between nucleocytoplasmic transport and SUMO-dependent pathways. Examples of protein sumoylation inhibiting or stimulating nucleocytoplasmic transport have been documented, both through its effects on the physical properties of cargo molecules and by directly regulating the functions of components of the nuclear transport machinery...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28195488/surface-sensitive-nmr-detection-of-the-solid-electrolyte-interphase-layer-on-reduced-graphene-oxide
#15
Michal Leskes, Gunwoo Kim, Tao Liu, Alison L Michan, Fabien Aussenac, Patrick Dorffer, Subhradip Paul, Clare P Grey
Forming a stable solid electrolyte interphase (SEI) is critical for rechargeable batteries' performance and lifetime. Understanding its formation requires analytical techniques that provide molecular-level insight. Here, dynamic nuclear polarization (DNP) is utilized for the first time to enhance the sensitivity of solid-state NMR (ssNMR) spectroscopy to the SEI. The approach is demonstrated on reduced graphene oxide (rGO) cycled in Li-ion cells in natural abundance and (13)C-enriched electrolyte solvents. Our results indicate that DNP enhances the signal of outer SEI layers, enabling detection of natural abundance (13)C spectra from this component of the SEI on reasonable time frames...
February 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28193881/strong-signal-increase-in-sted-fluorescence-microscopy-by-imaging-regions-of-subdiffraction-extent
#16
Fabian Göttfert, Tino Pleiner, Jörn Heine, Volker Westphal, Dirk Görlich, Steffen J Sahl, Stefan W Hell
Photobleaching remains a limiting factor in superresolution fluorescence microscopy. This is particularly true for stimulated emission depletion (STED) and reversible saturable/switchable optical fluorescence transitions (RESOLFT) microscopy, where adjacent fluorescent molecules are distinguished by sequentially turning them off (or on) using a pattern of light formed as a doughnut or a standing wave. In sample regions where the pattern intensity reaches or exceeds a certain threshold, the molecules are essentially off (or on), whereas in areas where the intensity is lower, that is, around the intensity minima, the molecules remain in the initial state...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28189102/coordinated-events-of-nuclear-assembly
#17
REVIEW
Dollie LaJoie, Katharine S Ullman
Each time a metazoan cell undergoes open mitosis, the nucleus is dismantled in order to partition DNA content to the daughter cells. After chromosomes separate, changes at the chromatin surface usher in reestablishment of nuclear architecture. Proteins destined for the nuclear envelope are attracted to chromatin and concomitantly recruit membrane. As nuclear envelope and protein constituents spread to coat chromatin, distinct regions emerge-some rich in rapid pore formation, others occupied by microtubules that remain attached to kinetochores...
February 8, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28188228/time-resolved-phosphoproteome-analysis-of-paradoxical-raf-activation-reveals-novel-targets-of-erk
#18
Peter Kubiniok, Hugo Lavoie, Marc Therrien, Pierre Thibault
Small molecules targeting aberrant RAF activity, like Vemurafenib (PLX4032), are highly effective against cancers harboring the V600E BRAF mutation, and are now approved for clinical use against metastatic melanoma. However, in tissues showing elevated RAS activity and in RAS-mutant tumors, these inhibitors stimulate RAF dimerization, resulting in inhibitor resistance and downstream paradoxical ERK activation. To understand the global signaling response of cancer cells to RAF inhibitors, we profiled the temporal changes of the phosphoproteome of two colon cancer cell lines (Colo205 and HCT116) that respond differently to Vemurafenib...
February 10, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28187419/dynamics-of-mirna-biogenesis-and-nuclear-transport
#19
Aneesh Kotipalli, Ravikumar Gutti, Chanchal K Mitra
MicroRNAs (miRNAs) are short noncoding RNA sequences ~22 nucleotides in length that play an important role in gene regulation-transcription and translation. The processing of these miRNAs takes place in both the nucleus and the cytoplasm while the final maturation occurs in the cytoplasm. Some mature miRNAs with nuclear localisation signals (NLS) are transported back to the nucleus and some remain in the cytoplasm. The functional roles of these miRNAs are seen in both the nucleus and the cytoplasm. In the nucleus, miRNAs regulate gene expression by binding to the targeted promoter sequences and affect either the transcriptional gene silencing (TGS) or transcriptional gene activation (TGA)...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28179529/differential-disruption-of-nucleocytoplasmic-trafficking-pathways-by-rhinovirus-2a-proteases
#20
Kelly Watters, Bahar Inankur, Jaye C Gardiner, Jay Warrick, Nathan M Sherer, John Yin, Ann C Palmenberg
The RNA rhinoviruses (RV) encode 2A proteases (2A(pro)) that contribute essential polyprotein processing and host-cell shutoff functions during infection, including the cleavage of Phe/Gly-containing nucleoporin proteins (Nups) within nuclear pore complexes (NPC). Within the 3 RV species, multiple divergent genotypes encode diverse 2A(pro) sequences which act differentially on specific Nups. Since only subsets of Phe/Gly motifs, particularly those within Nup62, Nup98 and Nup153, are recognized by transport receptors (karyopherins) when trafficking large molecular cargos through the NPC, the processing preferences of individual 2A(pro) predict RV genotype-specific targeting of NPC pathways and cargos...
February 8, 2017: Journal of Virology
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