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nuclear architecture

Seung Joong Kim, Javier Fernandez-Martinez, Ilona Nudelman, Yi Shi, Wenzhu Zhang, Barak Raveh, Thurston Herricks, Brian D Slaughter, Joanna A Hogan, Paula Upla, Ilan E Chemmama, Riccardo Pellarin, Ignacia Echeverria, Manjunatha Shivaraju, Azraa S Chaudhury, Junjie Wang, Rosemary Williams, Jay R Unruh, Charles H Greenberg, Erica Y Jacobs, Zhiheng Yu, M Jason de la Cruz, Roxana Mironska, David L Stokes, John D Aitchison, Martin F Jarrold, Jennifer L Gerton, Steven J Ludtke, Christopher W Akey, Brian T Chait, Andrej Sali, Michael P Rout
Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility...
March 14, 2018: Nature
Alfonso González-Briones, Pablo Chamoso, Hyun Yoe, Juan M Corchado
The gradual depletion of energy resources makes it necessary to optimize their use and to reuse them. Although great advances have already been made in optimizing energy generation processes, many of these processes generate energy that inevitably gets wasted. A clear example of this are nuclear, thermal and carbon power plants, which lose a large amount of energy that could otherwise be used for different purposes, such as heating greenhouses. The role of GreenVMAS is to maintain the required temperature level in greenhouses by using the waste energy generated by power plants...
March 14, 2018: Sensors
Katharina Wiedemeyer, Antonio Guadagno, Jonathan Davey, Thomas Brenn
Spitz nevi on acral sites are rare and poorly documented. The combination of Spitzoid cytomorphology and atypical architectural features of the junctional component may lead to an erroneous diagnosis of melanoma. To study the clinicopthologic and immunohistochemical features, 50 Spitz nevi localized on the distal extremities were retrieved from departmental files. Clinical data and follow-up were obtained and the histologic features were analyzed. P16 and P21 immunohistochemical staining of the dermal component was compared with that of 10 acral lentiginous melanomas and 10 acral nevi...
March 13, 2018: American Journal of Surgical Pathology
John F Wolters, Guillaume Charron, Alec Gaspary, Christian R Landry, Anthony C Fiumera, Heather L Fiumera
Genetic variation in mitochondrial DNA (mtDNA) provides adaptive potential although the underlying genetic architecture of fitness components within mtDNAs is not known. To dissect functional variation within mtDNAs, we first identified naturally occurring mtDNAs that conferred high or low fitness in Saccharomyces cerevisiae by comparing growth in strains containing identical nuclear genotypes but different mtDNAs. During respiratory growth under temperature and oxidative stress conditions, mitotype effects were largely independent of nuclear genotypes even in the presence of mitonuclear interactions...
March 12, 2018: Genetics
Attila Németh, Ingrid Grummt
The nucleolus is the largest nuclear sub-compartment in which the early steps of ribosome biogenesis take place. It also plays an essential role in the assembly and function of non-ribosomal ribonucleoprotein (RNP) complexes, controls cell cycle progression and senses environmental stress. The spatial organization and dynamics of nucleolar proteins and RNA is regulated at different structural levels, which finally determine nucleolar architecture. The intimate link between nucleolar structure and function is reflected by transcription-dependent changes in nucleolus-associated chromatin, overall morphological alterations in response to external cues, and the liquid droplet-like behavior of nucleolar compartments...
March 9, 2018: Current Opinion in Cell Biology
Samuel Beck, Catherine Rhee, Jawon Song, Bum-Kyu Lee, Lucy LeBlanc, Laurie Cannon, Jonghwan Kim
CpG islands (CGIs) have long been implicated in the regulation of vertebrate gene expression. However, the involvement of CGIs in chromosomal architectures and associated gene expression regulations has not yet been thoroughly explored. By combining large-scale integrative data analyses and experimental validations, we show that CGIs clearly reconcile two competing models explaining nuclear gene localizations. We first identify CGI-containing (CGI+) and CGI-less (CGI-) genes are non-randomly clustered within the genome, which reflects CGI-dependent spatial gene segregation in the nucleus and corresponding gene regulatory modes...
February 26, 2018: Nucleic Acids Research
Ezequiel Nazer, Ryan K Dale, Madoka Chinen, Behram Radmanesh, Elissa P Lei
Drosophila Argonaute2 (AGO2) has been shown to regulate expression of certain loci in an RNA interference (RNAi)-independent manner, but its genome-wide function on chromatin remains unknown. Here, we identified the nuclear scaffolding protein LaminB as a novel interactor of AGO2. When either AGO2 or LaminB are depleted in Kc cells, similar transcription changes are observed genome-wide. In particular, changes in expression occur mainly in active or potentially active chromatin, both inside and outside LaminB-associated domains (LADs)...
March 12, 2018: PLoS Genetics
Miria Ricchetti
Mitochondrial DNA (mtDNA), which is essential for mitochondrial and cell function, is replicated and transcribed in the organelle by proteins that are entirely coded in the nucleus. Replication of mtDNA is challenged not only by threats related to the replication machinery and orchestration of DNA synthesis, but also by factors linked to the peculiarity of this genome. Indeed the architecture, organization, copy number, and location of mtDNA, which are markedly distinct from the nuclear genome, require ad hoc and complex regulation to ensure coordinated replication...
February 1, 2018: Mutation Research
Neil M Carleton, Guangjing Zhu, Mikhail Gorbounov, M Craig Miller, Kenneth J Pienta, Linda M S Resar, Robert W Veltri
BACKGROUND: There are few tissue-based biomarkers that can accurately predict prostate cancer (PCa) progression and aggressiveness. We sought to evaluate the clinical utility of prostate and breast overexpressed 1 (PBOV1) as a potential PCa biomarker. METHODS: Patient tumor samples were designated by Grade Groups using the 2014 Gleason grading system. Primary radical prostatectomy tumors were obtained from 48 patients and evaluated for PBOV1 levels using Western blot analysis in matched cancer and benign cancer-adjacent regions...
March 9, 2018: Prostate
Ernesto Amato, Antonio Italiano, Lucrezia Auditore, Sergio Baldari
The availability of a resource collecting dose factors for the evaluation of the absorbed doses from external exposure during the manipulation of radioactive substances is fundamental for radiological protection purposes. Monte Carlo simulations are useful for the accurate calculation of dose distributions in complex geometries, particularly in presence of extended spectra of multi-radiation sources. We considered, as possible irradiation scenarios, a point source, a uniform planar source resembling a contaminated surface, several source volumes contained in plastic or glass receptacles, and the direct skin contamination case, implementing the corresponding Monte Carlo simulations in GAMOS (GEANT4-based Architecture for Medicine-Oriented Simulations)...
February 2018: Physica Medica: PM
Boyce S Chang, Stephanie Oyola-Reynoso, Joel Cutinho, Martin M Thuo
A facile method is reported for rapid, room-temperature synthesis of block copolymers (BCP) of complex morphology and hence nontraditional spherical assembly. The use of solvated electrons generates radical anions on olefinic monomers, and with a felicitous choice of monomer pairs, this species will propagate bimechanistically (via radical and the anion) to form BCPs. Molecular weight of the obtained BCP range from Mw = 97 000-404 000 g mol-1 (polydispersity index, PDI = 1.4-3.0) depending on monomer pairs...
March 8, 2018: Macromolecular Rapid Communications
Margarita Sobol, Alžběta Krausová, Sukriye Yildirim, Ilona Kalasová, Veronika Fáberová, Vladimír Vrkoslav, Vlada Philimonenko, Pavel Marášek, Lukáš Pastorek, Martin Čapek, Zuzana Lubovská, Lívia Uličná, Takuma Tsuji, Miroslav Lísa, Josef Cvačka, Toyoshi Fujimoto, Pavel Hozak
This paper describes a novel type of nuclear structures - nuclear lipid islets (NLIs). They are of 40-100 nm with a lipidic interior, and PtdIns(4,5)P2 molecules comprise a significant part of their surface. Most of NLIs have RNA at the periphery. Consistently with that, RNA is required for their integrity. NLI periphery is associated with Pol II transcription machinery, including the Pol II largest subunit, transcription factors, and NM1. The PtdIns(4,5)P2 -NM1 interaction is significant for Pol II transcription, since NM1 knock-down reduces the Pol II transcription level, and the overexpression of wild-type NM1 (but not NM1 mutated in the PtdIns(4,5)P2 -binding site) rescues the transcription...
March 5, 2018: Journal of Cell Science
Tayfun Toptaş, Elif Peştereli, Selen Bozkurt, Gülgün Erdoğan, Tayup Şimşek
OBJECTIVE: To examine correlations among nuclear, architectural, and International Federation of Gynecology and Obstetrics (FIGO) grading systems, and their relationships with lymph node (LN) involvement in endometrioid endometrial cancer. MATERIAL AND METHODS: Histopathology slides of 135 consecutive patients were reviewed with respect to tumor grade and LN metastasis. Notable nuclear atypia was defined as grade 3 nuclei. FIGO grade was established by raising the architectural grade (AG) by one grade when the tumor was composed of cells with nuclear grade (NG) 3...
March 1, 2018: Journal of the Turkish German Gynecological Association
Stefano Motta, Claudia Minici, Dario Corrada, Laura Bonati, Alessandro Pandini
Hypoxia inducible factors (HIFs) are transcription factors belonging to the basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) protein family with a role in sensing oxygen levels in the cell. Under hypoxia, the HIF-α degradation pathway is blocked and dimerization with the aryl hydrocarbon receptor nuclear translocator (ARNT) makes HIF-α transcriptionally active. Due to the common hypoxic environment of tumors, inhibition of this mechanism by destabilization of HIF-α:ARNT dimerization has been proposed as a promising therapeutic strategy...
February 28, 2018: PLoS Computational Biology
Jillian Belgrad, R Douglas Fields
The temporal coding of action potential activity is fundamental to nervous system function. Here we consider how gene expression in neurons is regulated by specific patterns of action potential firing, with an emphasis on new information on epigenetic regulation of gene expression. Patterned action potential activity activates intracellular signaling networks selectively in accordance with the kinetics of activation and inactivation of second messengers, phosphorylation and dephosphorylation of protein kinases, and cytoplasmic and nuclear calcium dynamics, which differentially activate specific transcription factors...
February 1, 2018: Neuroscientist: a Review Journal Bringing Neurobiology, Neurology and Psychiatry
Brenda J Green, Magdalini Panagiotakopoulou, Francesca Michela Pramotton, Georgios Stefopoulos, Shana O Kelley, Dimos Poulikakos, Aldo Ferrari
Invasion of dense tissues by cancer cells involves the interplay between the penetration resistance offered by interstitial pores and the deformability of cells. Metastatic cancer cells find optimal paths of minimal resistance through an adaptive path-finding process, which leads to successful dissemination. The physical limit of nuclear deformation is related to the minimal cross section of pores that can be successfully penetrated. However, this single biophysical parameter does not fully describe the architectural complexity of tissues featuring pores of variable area and shape...
February 26, 2018: Nano Letters
Jasmine Li, Stephen J Turner
Understanding how cell fate decisions are made during cellular differentiation and the mechanisms that drive them is a holy grail of cell biology. In this issue of Immunity, Hu et al. (2018) and Johnson et al. (2018) demonstrate that key transcriptional regulators and global changes in nuclear architecture underlie differentiation decisions during T cell development.
February 20, 2018: Immunity
Mina Khoshdeli, Bahram Parvin
Detection of nuclei is an important step in phenotypic profiling of 1) histology sections imaged in bright field; and 2) colony formation of the 3-D cell culture models that are imaged using confocal microscopy. It is shown that feature-based representation of the original image improves color decomposition (CD) and subsequent nuclear detection using convolutional neural networks independent of the imaging modality. The feature-based representation utilizes the Laplacian of Gaussian (LoG) filter, which accentuates blob-shape objects...
March 2018: IEEE Transactions on Bio-medical Engineering
Matthieu Cavaillès, Aurélien Bornet, Xavier Jaurand, Basile Vuichoud, David Baudouin, Mathieu Baudin, Laurent Veyre, Geoffrey Baudenhausen, Jean-Nicolas Dumez, Sami Jannin, Christophe Copéret, Chloé Thieuleux
Tailoring the physical features and the porous network architecture of silica-based hyperpolarizing solids containing TEMPO radicals, known as HYPSO (HYbrid Polarizing SOlids), enable unprecedented performance of dissolution Dynamic Nuclear Polarization (d-DNP). High polarization values up to P(1H) = 99 % were reached for samples impregnated with a mixture of H2O:D2O and loaded in a 6.7 T polarizer at temperatures around 1.2 K. These HYPSO materials combine the best performance of homogeneous DNP formulations with the advantages of solid polarizing matrices which provide hyperpolarized solutions free of any - potentially toxic - additives (radicals and glass-forming agents)...
February 19, 2018: Angewandte Chemie
Pedro Serrano, John A Hammond, Michael Geralt, Kurt Wüthrich
Splicing factor RBM10 and its close homologues RBM5 and RBM6 govern the splicing of oncogenes such as Fas, NUMB, and Bcl-X. The molecular architecture of these proteins includes zinc fingers (ZnFs) and RNA recognition motifs (RRMs). Three of these domains in RBM10 that constitute the RNA binding part of this splicing factor were found to individually bind RNAs with micromolar affinities. It was thus of interest to further investigate the structural basis of the well-documented high-affinity RNA recognition by RMB10...
February 16, 2018: Biochemistry
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