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https://www.readbyqxmd.com/read/28435869/a-dynamic-hydrophobic-core-orchestrates-allostery-in-protein-kinases
#1
Jonggul Kim, Lalima G Ahuja, Fa-An Chao, Youlin Xia, Christopher L McClendon, Alexandr P Kornev, Susan S Taylor, Gianluigi Veglia
Eukaryotic protein kinases (EPKs) constitute a class of allosteric switches that mediate a myriad of signaling events. It has been postulated that EPKs' active and inactive states depend on the structural architecture of their hydrophobic cores, organized around two highly conserved spines: C-spine and R-spine. How the spines orchestrate the transition of the enzyme between catalytically uncommitted and committed states remains elusive. Using relaxation dispersion nuclear magnetic resonance spectroscopy, we found that the hydrophobic core of the catalytic subunit of protein kinase A, a prototypical and ubiquitous EPK, moves synchronously to poise the C subunit for catalysis in response to binding adenosine 5'-triphosphate...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28429320/euglena-gracilis-genome-and-transcriptome-organelles-nuclear-genome-assembly-strategies-and-initial-features
#2
ThankGod Echezona Ebenezer, Mark Carrington, Michael Lebert, Steven Kelly, Mark C Field
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28428255/nucleosome-nucleosome-interactions-via-histone-tails-and-linker-dna-regulate-nuclear-rigidity
#3
Yuta Shimamoto, Sachiko Tamura, Hiroshi Masumoto, Kazuhiro Maeshima
Cells, as well as the nuclei inside them, experience significant mechanical stress in diverse biological processes including contraction, migration, and adhesion. The structural stability of nuclei must therefore be maintained in order to protect genome integrity. Despite extensive knowledge on nuclear architecture and components, however, the underlying physical and molecular mechanisms remain largely unknown. We addressed this in the present study by subjecting isolated human cell nuclei to microneedle-based quantitative micromanipulation with a series of biochemical perturbations of the chromatin...
April 20, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28426272/temperature-dependent-regulation-of-rdna-condensation-in-saccharomyces-cerevisiae
#4
Donglai Shen, Robert V Skibbens
Chromatin condensation during mitosis produces detangled and discrete DNA entities required for high fidelity sister chromatid segregation during mitosis and positions DNA away from the cleavage furrow during cytokinesis. Regional condensation during G1 also establishes a nuclear architecture through which gene transcription is regulated but remains plastic so that cells can respond to changes in nutrient levels, temperature and signaling molecules. To date, however, the potential impact of this plasticity on mitotic chromosome condensation remains unknown...
April 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28425211/importance-of-cytological-subclassification-of-thyroid-nodules-with-bethesda-category-iii-cytology-aus-flus-into-architectural-atypia-only-and-nuclear-atypia-a-prospective-study
#5
Pedro Weslley Rosario, Maria Regina Calsolari
BACKGROUND: The objective of this study was to compare two cytological subcategories of thyroid nodules with Bethesda category III initial cytology. METHODS: This was a prospective study. All patients with thyroid nodules > 1 cm were eligible and 98 patients with category III cytology were selected. Cytology was subcategorized into architectural atypia only (AA, n = 45) and nuclear atypia (NA, n = 53). All patients underwent a second fine-needle aspiration (FNA)...
April 19, 2017: Diagnostic Cytopathology
https://www.readbyqxmd.com/read/28424555/hmgb1-is-negatively-correlated-with-the-development-of-endometrial-carcinoma-and-prevents-cancer-cell-invasion-and-metastasis-by-inhibiting-the-process-of-epithelial-to-mesenchymal-transition
#6
Xiaorong Luan, Chunjing Ma, Ping Wang, Fenglan Lou
High-mobility group box protein 1 (HMGB1), a nuclear protein that plays a significant role in DNA architecture and transcription, was correlated with the progression of some types of cancer. However, the role of HMGB1 in endometrial cancer cell invasion and metastasis remains unexplored. HMGB1 expression was initially assessed by immunohistochemistry and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in normal endometrial tissue and endometrial carcinoma tissue. High expressions of HMGB1 protein were detected in normal endometrial tissues; however, in endometrial cancer tissues, the expressions of HMGB1 were found to be very weak...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28422222/electron-transfer-in-silicon-bridged-adjacent-chromophores-the-source-for-blue-green-emission
#7
Malgorzata Bayda, Gonzalo Angulo, Gordon L Hug, Monika Ludwiczak, Jerzy Karolczak, Jacek Koput, Jacek Dobkowski, Bronislaw Marciniak
Si-Bridged chromophores have been proposed as sources for blue-green emission in several technological applications. The origin of this dual emission is to be found in an internal charge transfer reaction. The current work is an attempt to describe the details of these processes in these kinds of substances, and to design a molecular architecture to improve their performance. Nuclear motions essential for intramolecular charge transfer (ICT) can involve processes from twisted internal moieties to dielectric relaxation of the solvent...
April 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28422154/integration-of-liver-gene-co-expression-networks-and-egwas-analyses-highlighted-candidate-regulators-implicated-in-lipid-metabolism-in-pigs
#8
Maria Ballester, Yuliaxis Ramayo-Caldas, Manuel Revilla, Jordi Corominas, Anna Castelló, Jordi Estellé, Ana I Fernández, Josep M Folch
In the present study, liver co-expression networks and expression Genome Wide Association Study (eGWAS) were performed to identify DNA variants and molecular pathways implicated in the functional regulatory mechanisms of meat quality traits in pigs. With this purpose, the liver mRNA expression of 44 candidates genes related with lipid metabolism was analysed in 111 Iberian x Landrace backcross animals. The eGWAS identified 92 eSNPs located in seven chromosomal regions and associated with eight genes: CROT, CYP2U1, DGAT1, EGF, FABP1, FABP5, PLA2G12A, and PPARA...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28420615/the-mechanism-and-clinical-significance-of-long-noncoding-rna-mediated-gene-expression-via-nuclear-architecture
#9
Shi Jian, Li Yanming, Fang Xiangdong
Long noncoding RNAs (lncRNAs) are a class of non-protein coding transcripts exceeding 200 nucleotides in length. Accumulating evidence achieved by several sophisticated techniques such as chromatin conformation capture and RNA-seq has led to new questions concerning correlations between lncRNAs and chromatin structures. Many studies have revealed that lncRNAs exert great influences on gene expression through regulating chromatin 3D structures. In addition, lncRNAs play a crucial role in tumorigenesis and therefore hold great promises in disease diagnosis and prognosis...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28420320/pediatric-non-vestibular-schwannoma
#10
Cory Broehm, Alyaa Al-Ibraheemi, Karen J Fritchie
While the clinicopathologic features of pediatric vestibular schwannomas, often in the context of neurofibromatosis type 2 (NF2), have been well studied, there is less data regarding the characteristics of pediatric non-vestibular schwannomas (NVS). Additionally, the rate of loss of SMARCB1/INI1 expression in this population has not been systematically evaluated. Our institutional archives were searched for cases of NVS arising in patients 18 years or younger. Clinicopathologic features including SMARCB1/INI1 status were assessed for each case...
January 1, 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28419762/hobnail-variant-of-papillary-thyroid-carcinoma-a-case-with-an-unusual-presentation
#11
Mohammed T Lilo, Justin A Bishop, Syed Z Ali
Variants of papillary thyroid carcinoma (PTC) account for up to 25% of the cases, some of which are proven to be associated with aggressive clinical behavior such as tall cell and columnar cell variants. Hobnail variant of PTC (HVPTC) is recently described as a rare and aggressive variant of PTC. Herein, we are reporting a case of HVPTC in a patient who presented with hemoptysis and an intratracheal blood clot that was aspirated and submitted for cytopathological examination. Cytomorphology displayed neoplastic cells with profound micropapillary architecture, elongated nuclei, and prominent hobnail configuration...
April 16, 2017: Diagnostic Cytopathology
https://www.readbyqxmd.com/read/28418582/cop1-conveys-warm-temperature-information-to-hypocotyl-thermomorphogenesis
#12
Young-Joon Park, Hyo-Jun Lee, Jun-Ho Ha, Jae Young Kim, Chung-Mo Park
Plants adjust their architecture to optimize growth and reproductive success under changing climates. Hypocotyl elongation is a pivotal morphogenic trait that is profoundly influenced by light and temperature conditions. While hypocotyl photomorphogenesis has been well characterized at the molecular level, molecular mechanisms underlying hypocotyl thermomorphogenesis remains elusive. Here, we demonstrate that the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) conveys warm temperature signals to hypocotyl thermomorphogenesis...
April 18, 2017: New Phytologist
https://www.readbyqxmd.com/read/28416576/pathways-involved-in-formation-of-mammary-organoid-architecture-have-keys-to-understanding-drug-resistance-and-to-discovery-of-druggable-targets
#13
Saori Furuta, Mina J Bissell
Signals from the extracellular matrix (ECM) are received at the cell surface receptor, transmitted to the cytoskeletons, and transferred to the nucleus and chromatin for tissue- and context-specific gene expression. Cells, in return, modulate the cell shape and ECM, allowing for the maintenance of tissue homeostasis as well as for coevolution and adaptation to the environmental signals. We postulated the existence of dynamic and reciprocal interactions between the ECM and the nucleus more than three decades ago, but now these pathways have been proven experimentally thanks to the advances in imaging and cell/molecular biology techniques...
April 17, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28416106/categorizing-renal-oncocytic-neoplasms-on-core-needle-biopsy-a-morphologic-and-immunophenotypic-study-of-144-cases-with-clinical-follow-up-alderman-ma-daignault-s-wolf-js-jr-palapattu-gs-weizer-az-hafez-ks-kunju-lp-wu-aj-hum-pathol-september-2016-55-1-10
#14
Oleksandr N Kryvenko
There is limited literature on renal oncocytic neoplasms diagnosed on core biopsy. All renal oncocytic neoplasm core biopsies from 2006 to 2013 were, retrospectively, reviewed. Morphologic features and an immunohistochemical panel of CK7, c-KIT, and S100A1 were assessed. Concordance with resection diagnosis, statistical analysis including a random forest classification, and follow-up were recorded. The postimmunohistochemical diagnoses of 144 renal oncocytic core biopsies were favor oncocytoma (67%), favor renal cell carcinoma (RCC) (12%), and cannot exclude RCC (21%)...
April 13, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28414157/commiphora-molmol-resin-attenuates-diethylnitrosamine-phenobarbital-induced-hepatocarcinogenesis-by-modulating-oxidative-stress-inflammation-angiogenesis-and-nrf2-are-ho-1-signaling
#15
Ayman M Mahmoud, Amr R Zaki, Manal E Hassan, Gomaa Mostafa-Hedeab
The objective of the current study was to investigate the possible chemopreventive activity of Commiphora molmol resin (myrrh) extract using a rat model of diethylnitrosamine (DEN)/phenobarbital (PB)-induced early stage hepatocarcinogenesis. Here, we pointed to the modulatory effect of myrrh on oxidative stress, angiogenesis, inflammation and nuclear factor (erythroid-derived 2)-like 2 (Nrf2). Hepatocarcinogenesis was induced in Wistar rats using DEN for initiation and PB as a promoting agent. The rats received 125 or 250 mg/kg C...
April 14, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28413956/structure-roles-and-inhibitors-of-a-mitotic-protein-kinase-haspin
#16
Katrin Kestav, Asko Uri, Darja Lavogina
Background Haspin (haploid germ cell-specific nuclear protein kinase) is an atypical serine/threonine-protein kinase that was for a long time considered an inactive pseudokinase due to low degree of structural homology of Haspin with the 'classical' protein kinases. However, the discovery of Haspin-catalyzed phosphorylation of histone H3 at Thr3 residue unveiled importance of Haspin in mitosis and provided yet another link between mitotic phosphorylation pathways and chromatin modifications. Results In this review of 111 publications, we have (1) briefly summarized catalytic properties and physiological roles of Haspin, (2) focussed on the architecture of Haspin and mechanisms behind its substrate recognition, (3) provided detailed insight into the advances in the development and characterization of Haspin-selective inhibitors, and (4) given overview of inhibitor scaffolds that despite targeting other protein kinases feature Haspin as a common off-target...
April 14, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28413047/a-homolog-of-teleostean-signal-transducer-and-activator-of-transcription-3-stat3-from-rock-bream-oplegnathus-fasciatus-structural-insights-transcriptional-modulation-and-subcellular-localization
#17
S D N K Bathige, William Shanthakumar Thulasitha, Navaneethaiyer Umasuthan, J D H E Jayasinghe, Qiang Wan, Bo-Hye Nam, Jehee Lee
Signal transducer and activator of transcription 3 (STAT3) is one of the crucial transcription factors in the Janus kinase (JAK)/STAT signaling pathway, and it was previously considered as acute phase response factor. A number of interleukins (ILs) such as IL-5, IL-6, IL-9, IL-10, IL-12, and IL-22 are known to be involved in activation of STAT3. In addition, various growth factors and pathogenic or oxidative stresses mediate the activation of a wide range of functions via STAT3. In this study, a STAT3 homolog was identified and functionally characterized from rock bream (RbSTAT3), Oplegnathus fasciatus...
April 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/28411415/chromosome-conformation-capture-based-studies-reveal-novel-features-of-plant-nuclear-architecture
#18
REVIEW
Stefan Grob, Ueli Grossniklaus
Nuclear genome organization has recently received increasing attention due to its manifold functions in basic nuclear processes, such as replication, transcription, and the maintenance of genome integrity. Using technologies based on chromosome conformation capture, such as Hi-C, we now have the possibility to study the three-dimensional organization of the genome at unprecedented resolution, shedding light onto a previously unexplored level of nuclear architecture. In plants, research in this field is still in its infancy but a number of publications provided first insights into basic principles of nuclear genome organization and the factors that influence it...
April 12, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28411275/odorant-sensory-input-modulates-dna-secondary-structure-formation-and-heterogeneous-ribonucleoprotein-recruitment-on-the-tyrosine-hydroxylase-and-glutamic-acid-decarboxylase-1-promoters-in-the-olfactory-bulb
#19
Meng Wang, Elizabeth Cai, Nana Fujiwara, Lilah Fones, Elizabeth Brown, Yuchio Yanagawa, John W Cave
Adaptation of neural circuits to changes in sensory input can modify several cellular processes within neurons, including neurotransmitter biosynthesis levels. For a subset of olfactory bulb interneurons, activity-dependent changes in GABA are reflected by corresponding changes in Glutamate decarboxylase 1 (Gad1) expression levels. Mechanisms regulating Gad1 promoter activity are poorly understood, but here we show that a conserved G:C-rich region in the mouse Gad1 proximal promoter region both recruits heterogeneous nuclear ribonucleoproteins (hnRNPs) that facilitate transcription and forms single-stranded DNA secondary structures associated with transcriptional repression...
April 14, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28408976/when-tads-go-bad-chromatin-structure-and-nuclear-organisation-in-human-disease
#20
REVIEW
Vera B Kaiser, Colin A Semple
Chromatin in the interphase nucleus is organised as a hierarchical series of structural domains, including self-interacting domains called topologically associating domains (TADs). This arrangement is thought to bring enhancers into closer physical proximity with their target genes, which often are located hundreds of kilobases away in linear genomic distance. TADs are demarcated by boundary regions bound by architectural proteins, such as CTCF and cohesin, although much remains to be discovered about the structure and function of these domains...
2017: F1000Research
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