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https://www.readbyqxmd.com/read/28092369/context-dependent-role-for-chromatin-remodeling-component-pbrm1-baf180-in-clear-cell-renal-cell-carcinoma
#1
A Murakami, L Wang, S Kalhorn, P Schraml, W K Rathmell, A C Tan, R Nemenoff, K Stenmark, B-H Jiang, M E Reyland, L Heasley, C-J Hu
A subset of clear cell renal cell carcinoma (ccRCC) tumors exhibit a HIF1A gene mutation, yielding two ccRCC tumor types, H1H2 type expressing both HIF1α and HIF2α, and H2 type expressing HIF2α, but not functional HIF1α protein. However, it is unclear how the H1H2 type ccRCC tumors escape HIF1's tumor-suppressive activity. The polybromo-1 (PBRM1) gene coding for the BAF180 protein, a component of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex, is inactivated in 40% ccRCCs, the function and mechanism of BAF180 mutation is unknown...
January 16, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28089519/role-of-nhp6-and-hmo1-in-swi-snf-occupancy-and-nucleosome-landscape-at-gene-regulatory-regions
#2
Matias I Hepp, Michaela Smolle, Cristian Gidi, Roberto Amigo, Nicole Valenzuela, Axel Arriagada, Alejandro Maureira, Madelaine M Gogol, Marcela Torrejón, Jerry L Workman, José L Gutiérrez
Diverse chromatin modifiers are involved in regulation of gene expression at the level of transcriptional regulation. Among these modifiers are ATP-dependent chromatin remodelers, where the SWI/SNF complex is the founding member. It has been observed that High Mobility Group (HMG) proteins can influence the activity of a number of these chromatin remodelers. In this context, we have previously demonstrated that the yeast HMG proteins Nhp6 and Hmo1 can stimulate SWI/SNF activity. Here, we studied the genome-wide binding patterns of Nhp6, Hmo1 and the SWI/SNF complex, finding that most of gene promoters presenting high occupancy of this complex also display high enrichment of these HMG proteins...
January 9, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28069309/characterizing-nutrient-distributions-and-fluxes-in-a-eutrophic-reservoir-midwestern-united-states
#3
Alexandra R Pearce, Lisa G Chambers, Elizabeth A Hasenmueller
Harmful algal blooms are increasingly common in aquatic ecosystems and have been linked to runoff from agricultural land. This study investigated the internal nutrient (i.e., phosphorus (P) and nitrogen (N)) dynamics of a eutrophic reservoir in the Midwestern United States to constrain the potential for sedimentary nutrients to stimulate harmful algal blooms. The spatial distribution of nutrients in the water column (soluble reactive P (SRP), nitrate/nitrite-N (NOx-N), and ammonium-N (NH4(+)-N)) and sediments (total P, total carbon (C), total N, and organic matter (OM)) were quantified and mapped...
January 6, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28068325/trim28-interacts-with-ezh2-and-swi-snf-to-activate-genes-that-promote-mammosphere-formation
#4
J Li, Y Xi, W Li, R L McCarthy, S A Stratton, W Zou, W Li, S Y Dent, A K Jain, M C Barton
Histone methyl transferase EZH2 (Enhancer of Zeste Homolog 2) is generally associated with H3K27 methylation and gene silencing, as a member of the polycomb repressor 2 (PRC2) complex. Immunoprecipitation and mass spectrometry of the EZH2-protein interactome in estrogen receptor positive, breast cancer-derived MCF7 cells revealed EZH2 interactions with subunits of chromatin remodeler SWI/SNF complex and TRIM28, which formed a complex with EZH2 distinct from PRC2. Unexpectedly, transcriptome profiling showed that EZH2 primarily activates, rather than represses, transcription in MCF7 cells and with TRIM28 co-regulates a set of genes associated with stem cell maintenance and poor survival of breast cancer patients...
January 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28064308/-structural-studies-of-chromatin-remodeling-factors
#5
O I Volokh, N I Derkacheva, V M Studitsky, O S Sokolova
Changes of chromatin structure require participation of chromatin remodeling factors (CRFs), which are ATP-dependent multisubunit complexes that change the structure of the nucleosome without covalently modifying its components. CRFs act together with other protein factors to regulate the extent of chromatin condensation. Four CRF families are currently distinguished based on their structural and biochemical characteristics: SWI/SNF, ISWI, Mi-2/CHD, and SWR/INO80. X-ray diffraction analysis and electron microscopy are the main methods to obtain structural information about macromolecules...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28064239/recurrent-somatic-mutations-affecting-b-cell-receptor-signaling-pathway-genes-in-follicular-lymphoma
#6
Kilannin Krysiak, Felicia Gomez, Brian S White, Matthew Matlock, Christopher A Miller, Lee Trani, Catrina C Fronick, Robert S Fulton, Friederike Kreisel, Amanda F Cashen, Kenneth R Carson, Melissa M Berrien-Elliott, Nancy L Bartlett, Malachi Griffith, Obi L Griffith, Todd A Fehniger
Follicular lymphoma (FL) is the most common form of indolent non-Hodgkin lymphoma, yet it remains only partially characterized at the genomic level. In order to improve our understanding of the genetic underpinnings of this incurable and clinically heterogeneous disease, whole exome sequencing was performed on tumor/normal pairs from a discovery cohort of 24 patients with FL. Using these data, and mutations identified in other B-cell malignancies, 1716 genes were sequenced in 113 FL tumor samples, from 105 primarily treatment-naïve individuals...
November 14, 2016: Blood
https://www.readbyqxmd.com/read/28062476/arid1a-deficiency-promotes-colorectal-cancer-via-enhancer-dysregulation
#7
(no author information available yet)
ARID1A loss disrupts SWI/SNF targeting to enhancers to alter gene expression and drive colorectal cancer.
January 6, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28062474/smarcb1-mutations-disrupt-enhancer-activity-in-rhabdoid-tumors
#8
(no author information available yet)
Loss of the SWI/SNF subunit SMARCB1 disrupts enhancer activation but retains superenhancer activity.
January 6, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28060558/the-connection-between-brg1-ctcf-and-topoisomerases-at-tad-boundaries
#9
A Rasim Barutcu, Jane B Lian, Janet L Stein, Gary S Stein, Anthony N Imbalzano
The eukaryotic genome is partitioned into topologically associating domains (TADs). Despite recent advances characterizing TADs and TAD boundaries, the organization of these structures is an important dimension of genome architecture and function that is not well understood. Recently, we demonstrated that knockdown of BRG1, an ATPase driving the chromatin remodeling activity of mammalian SWI/SNF enzymes, globally alters long-range genomic interactions and results in a reduction of TAD boundary strength. We provided evidence suggesting that this effect may be due to BRG1 affecting nucleosome occupancy around CTCF sites present at TAD boundaries...
January 6, 2017: Nucleus
https://www.readbyqxmd.com/read/28056282/-diagnostic-value-of-clot-burden-score-of-susceptibility-vessel-sign-in-arterial-thrombosis-of-acute-ischemic-stroke-and-its-association-with-prognosis
#10
Y Huang, W L Mei, H Q Liu, Y L Li, Z Z Chen, D D Li, J W Zhang
Objective: To analysis the value of susceptibility vessel sign (SVS) in susceptibility weighted imaging (SWI) in detecting thrombogenesis in middle cerebral artery (MCA) and its association with clinical prognosis. Methods: From December 2014 to December 2015 in People's Hospital of Zhengzhou University, we retrospectively examined clinical, imaging and experimental datafrom 104 consecutive patients with acute ischemic strokeand compared the consistency of detecting thrombus between SWI and magnetic resonance angiography (MRA) using Kappa analysis...
January 3, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/28051884/the-risk-factors-and-pattern-of-cerebral-microbleeds-in-parkinson-s-disease
#11
Dian He, Chun-Feng Liu, Lan Chu, Ya Li, Da-Fei Xu, Ling Jiao
BACKGROUND AND PURPOSE: Cerebral microbleeds (CMBs) in Parkinson's disease (PD) have been reported recently and concerned increasingly. Our aim was to investigate the risk factors and pattern of CMBs in patients with PD, as well as the influence of risk factors on the pattern of CMBs. METHODS: We retrospectively collected medical and imaging data of 247 patients who underwent brain susceptibility-weighted imaging (SWI). Logistic regression analyses were performed to determine the risk factors of CMBs...
January 4, 2017: International Journal of Neuroscience
https://www.readbyqxmd.com/read/28050058/sustainable-crop-intensification-through-surface-water-irrigation-in-bangladesh-a-geospatial-assessment-of-landscape-scale-production-potential
#12
Timothy J Krupnik, Urs Schulthess, Zia Uddin Ahmed, Andrew J McDonald
Changing dietary preferences and population growth in South Asia have resulted in increasing demand for wheat and maize, along side high and sustained demand for rice. In the highly productive northwestern Indo-Gangetic Plains of South Asia, farmers utilize groundwater irrigation to assure that at least two of these crops are sequenced on the same field within the same year. Such double cropping has had a significant and positive influence on regional agricultural productivity. But in the risk-prone and food insecure lower Eastern Indo-Gangetic Plains (EIGP), cropping is less intensive...
January 2017: Land Use Policy
https://www.readbyqxmd.com/read/28045858/diagnosis-of-electrical-status-epilepticus-during-slow-wave-sleep-with-100-seconds-of-sleep
#13
Amanda B Weber, Dara V Albert, Han Yin, Timothy P Held, Anup D Patel
PURPOSE: Strategies for diagnosing electrical status epilepticus during slow-wave sleep (ESES) vary among interpreting neurologists. Our aim was to evaluate if the spike-wave index (SWI) for the first 100 seconds of sleep is reflective of the SWI when compared with a conventional method. METHODS: We reviewed EEGs from 2005 to 2011 that were considered diagnostic of ESES based on unspecified methods. The SWI for the first nonrapid eye movement sleep cycle (long method) was calculated by two neurophysiologists...
January 2017: Journal of Clinical Neurophysiology: Official Publication of the American Electroencephalographic Society
https://www.readbyqxmd.com/read/28041841/actl6a-is-co-amplified-with-p63-in-squamous-cell-carcinoma-to-drive-yap-activation-regenerative-proliferation-and-poor-prognosis
#14
Srinivas Vinod Saladi, Kenneth Ross, Mihriban Karaayvaz, Purushothama R Tata, Hongmei Mou, Jayaraj Rajagopal, Sridhar Ramaswamy, Leif W Ellisen
Loss-of-function mutations in SWI/SNF chromatin-remodeling subunit genes are observed in many cancers, but an oncogenic role for SWI/SNF is not well established. Here, we reveal that ACTL6A, encoding an SWI/SNF subunit linked to stem cell and progenitor cell function, is frequently co-amplified and highly expressed together with the p53 family member p63 in head and neck squamous cell carcinoma (HNSCC). ACTL6A and p63 physically interact, cooperatively controlling a transcriptional program that promotes proliferation and suppresses differentiation, in part through activation of the Hippo-YAP pathway via regulators including WWC1...
January 9, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28038711/smarca4-and-smarca2-deficiency-in-non-small-cell-lung-cancer-immunohistochemical-survey-of-316-consecutive-specimens
#15
Esther Herpel, Ralf J Rieker, Hendrik Dienemann, Thomas Muley, Michael Meister, Arndt Hartmann, Arne Warth, Abbas Agaimy
The chromatin remodeling switch sucrose nonfermentable (SWI/SNF) complex has been increasingly implicated in the pathogenesis and dedifferentiation of neoplasms from several organs with prognostic and potential therapeutic implications. We herein investigated the expression of the SWI/SNF complex catalytic subunits SMARCA4 (BRG1) and SMARCA2 (BRM) in 316 consecutive non-small cell lung cancer (NSCLC) specimens on tissue microarrays (171 adenocarcinomas [ADCAs], 130 squamous cell carcinomas [SCCs], 9 adenosquamous carcinomas, and 6 large cell carcinomas) excluding undifferentiated/giant cell or rhabdoid carcinomas...
February 2017: Annals of Diagnostic Pathology
https://www.readbyqxmd.com/read/28035761/analysis-of-swi-formation-and-propagation-events
#16
Zhiqiang Du, Dustin Kenneth Goncharoff, Xudong Cheng, Liming Li
The budding yeast, Saccharomyces cerevisiae, harbors several prions that are transmitted as altered, heritable protein conformations. [SWI(+) ] is one such prion whose determinant is Swi1, a subunit of the evolutionarily conserved chromatin-remodeling complex SWI/SNF. Despite the importance of Swi1, the molecular events that lead to [SWI(+) ] prionogenesis remain poorly understood. In this study, we have constructed floccullin-promoter-based URA3 reporters for [SWI(+) ] identification. Using these reporters, we show that the spontaneous formation frequency of [SWI(+) ] is significantly higher than that of [PSI(+) ] (prion form of Sup35)...
December 30, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/28035426/diagnostic-imaging-of-dementia-with-lewy-bodies-by-susceptibility-weighted-imaging-of-nigrosomes-versus-striatal-dopamine-transporter-single-photon-emission-computed-tomography-a-retrospective-observational-study
#17
Koji Kamagata, Tomoya Nakatsuka, Ryuji Sakakibara, Yohei Tsuyusaki, Tomohiro Takamura, Kanako Sato, Michimasa Suzuki, Masaaki Hori, Kanako K Kumamaru, Tsutomu Inaoka, Shigeki Aoki, Hitoshi Terada
INTRODUCTION: The characteristics of dementia with Lewy bodies (DLB), Alzheimer's disease (AD) and amnestic mild cognitive impairment (a-MCI) overlap but require different treatments; therefore, it is important to differentiate these pathologies. Assessment of dopamine uptake in the striatum using dopamine transporter (DaT) single-photon emission computed tomography (SPECT) is the gold standard for diagnosing DLB; however, this modality is expensive, time consuming and involves radiation exposure...
January 2017: Neuroradiology
https://www.readbyqxmd.com/read/28029185/case-control-study-demonstrates-that-surfactant-without-intubation-delayed-mechanical-ventilation-in-preterm-infants
#18
Sigrid Dannheim Vik, Torstein Vik, Stian Lydersen, Ragnhild Støen
AIM: This Norwegian study explored whether administering surfactant without intubation (SWI) delayed the need for early mechanical ventilation and reduced respiratory and non-respiratory complications in infants born before 32 weeks of gestational age. METHODS: We compared 262 infants admitted to a level three neonatal intensive care unit: 134 born before the introduction of SWI on 1 December 2011 were in the control group and 128 infants born after this date were in the study group...
December 28, 2016: Acta Paediatrica
https://www.readbyqxmd.com/read/28027291/interaction-of-prions-causes-heritable-traits-in-saccharomyces-cerevisiae
#19
Anton A Nizhnikov, Tatyana A Ryzhova, Kirill V Volkov, Sergey P Zadorsky, Julia V Sopova, Sergey G Inge-Vechtomov, Alexey P Galkin
The concept of "protein-based inheritance" defines prions as epigenetic determinants that cause several heritable traits in eukaryotic microorganisms, such as Saccharomyces cerevisiae and Podospora anserina. Previously, we discovered a non-chromosomal factor, [NSI+], which possesses the main features of yeast prions, including cytoplasmic infectivity, reversible curability, dominance, and non-Mendelian inheritance in meiosis. This factor causes omnipotent suppression of nonsense mutations in strains of S. cerevisiae bearing a deleted or modified Sup35 N-terminal domain...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/28003623/internal-structures-of-the-globus-pallidus-in-patients-with-parkinson-s-disease-evaluation-with-phase-difference-enhanced-imaging
#20
Satoru Ide, Shingo Kakeda, Tetsuya Yoneda, Junji Moriya, Keita Watanabe, Atsushi Ogasawara, Koichiro Futatsuya, Norihiro Ohnari, Toru Sato, Yasuhiro Hiai, Atsuji Matsuyama, Hitoshi Fujiwara, Masanori Hisaoka, Yukunori Korogi
PURPOSE: The medial medullary lamina (MML) separates the medial globus pallidus (GPm) from the lateral. The aim of this study was to assess the changes in appearance of MML related to age using the phase difference-enhanced imaging (PADRE) and to determine whether PADRE can depict the MML in the patients with Parkinson's disease (PD). MATERIALS AND METHODS: We enrolled 20 patients with PD and 50 normal control subjects (NC). First, for the visualization of the MML in the NC, we compared the PADRE, susceptibility-weighted imaging (SWI)-like images and T2 weighted imaging (WI) by using multiple comparison...
December 22, 2016: Magnetic Resonance in Medical Sciences: MRMS
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