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https://www.readbyqxmd.com/read/29228314/demodifying-rna-for-transcriptomic-analyses-of-archival-formalin-fixed-paraffin-embedded-samples
#1
Leah C Wehmas, Charles E Wood, Remi Gagne, Andrew Williams, Carole Yauk, Mark M Gosink, Deidre Dalmas, Ruixin Hao, Raegan O'Lone, Susan Hester
Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and transcriptional responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n = 6/group) were divided and preserved for 3 months as follows: frozen (FR); 70% ethanol (OH); 10% buffered formalin for 18 hours followed by ethanol (18F); or 10% buffered formalin (3F)...
December 7, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29228254/structural-and-functional-analysis-of-an-ob-fold-in-human-ctc1-implicated-in-telomere-maintenance-and-bone-marrow-syndromes
#2
Prashanth K Shastrula, Cory T Rice, Zhuo Wang, Paul M Lieberman, Emmanuel Skordalakes
The human CST (Ctc1, Stn1 and Ten1) complex binds the telomeric overhang and regulates telomere length by promoting C-strand replication and inhibiting telomerase-dependent G-strand synthesis. Structural and biochemical studies on the human Stn1 and Ten1 complex revealed its mechanism of assembly and nucleic acid binding. However, little is known about the structural organization of the multi-domain Ctc1 protein and how each of these domains contribute to telomere length regulation. Here, we report the structure of a central domain of human Ctc1...
December 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29228234/tgfbr2-inactivation-facilitates-cellular-plasticity-and-development-of-pten-null-prostate-cancer
#3
Wei Zhao, Peng Tan, Qingyuan Zhu, Adebusola Ajibade, Teng Long, Wenyong Long, Qingtian Li, Pinghua Liu, Bo Ning, Helen Y Wang, Rong-Fu Wang
Mutations in tumors can create a state of increased cellular plasticity that promotes resistance to treatment. Thus, there is an urgent need to develop novel strategies for identifying key factors that regulate cellular plasticity in order to combat resistance to chemotherapy and radiation treatment. Here we report that prostate epithelial cell reprogramming could be exploited to identify key factors required for promoting prostate cancer tumorigenesis and cellular plasticity. Deletion of phosphatase and tensin homolog (Pten) and transforming growth factor-beta receptor type 2 (Tgfbr2) may increase prostate epithelial cell reprogramming efficiency in vitro and cause rapid tumor development and early mortality in vivo...
December 8, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/29228214/oestrogen-receptor-%C3%AE-ligand-acts-on-cd11c-cells-to-mediate-protection-in-experimental-autoimmune-encephalomyelitis
#4
Roy Y Kim, Darian Mangu, Alexandria S Hoffman, Rojan Kovash, Eunice Jung, Noriko Itoh, Rhonda Voskuhl
Oestrogen treatments are neuroprotective in a variety of neurodegenerative disease models. Selective oestrogen receptor modifiers are needed to optimize beneficial effects while minimizing adverse effects to achieve neuroprotection in chronic diseases. Oestrogen receptor beta (ERβ) ligands are potential candidates. In the multiple sclerosis model chronic experimental autoimmune encephalomyelitis, ERβ-ligand treatment is neuroprotective, but mechanisms underlying this neuroprotection remain unclear. Specifically, whether there are direct effects of ERβ-ligand on CD11c+ microglia, myeloid dendritic cells or macrophages in vivo during disease is unknown...
December 8, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29228209/cd38-knockout-suppresses-tumorigenesis-in-mice-and-clonogenic-growth-of-human-lung-cancer-cells
#5
Xiangning Bu, Jiro Kato, Julie A Hong, Maria J Merino, David S Schrump, Frances E Lund, Joel Moss
The ectodomain of the plasma membrane ecto-enzyme CD38 functions as both an NAD glycohydrolase and an ADP-ribosyl cyclase by catalyzing, respectively, the conversion of NAD to nicotinamide and ADP-ribose or cyclic ADP-ribose. CD38 is attracting particular attention in cancer therapy. An anti-CD38 monoclonal antibody (daratumumab) was approved for treatment of patients with multiple myeloma. However, the role of CD38 in non-hematological malignancies has not been explored. Previously, we reported that ADP-ribose-acceptor hydrolase (ARH)-1 deficiency in mice was associated with tumor development...
December 8, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/29228193/deepsf-deep-convolutional-neural-network-for-mapping-protein-sequences-to-folds
#6
Jie Hou, Badri Adhikari, Jianlin Cheng
Motivation: Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a target protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228157/gut-epithelial-vitamin-d-receptor-regulates-microbiota-dependent-mucosal-inflammation-by-suppressing-intestinal-epithelial-cell-apoptosis
#7
Lei He, Tianjing Liu, Yongyan Shi, Feng Tian, Huiyuan Hu, Dilip K Deb, Yinyin Chen, Marc Bissonnette, Yan Chun Li
Recent studies show that colonic vitamin D receptor (VDR) signaling protects the mucosal epithelial barrier and suppresses colonic inflammation, but the underlying molecular mechanism remains to be fully understood. To investigate the implication of colonic VDR down-regulation seen in patients with inflammatory bowel disease, we assessed the effect of gut epithelial VDR deletion on colonic inflammatory responses in an experimental colitis model. In 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced colitis model, mice carrying VDR deletion in gut epithelial cells (VDRf/f;Villin-Cre or VDRΔIEC) or in colonic epithelial cells (VDRf/f;CDX2-Cre or VDRΔCEC) developed more severe clinical colitis than VDRf/f control mice, characterized by more robust TH1 and TH17 responses, with greater increases in mucosal IFN-γ+, IL-17+ and IFN-γ+IL-17+ T cells...
December 7, 2017: Endocrinology
https://www.readbyqxmd.com/read/29228135/reply-dguok-recessive-mutations-in-patients-with-cpeo-mitochondrial-myopathy-parkinsonism-and-mtdna-deletions
#8
Dario Ronchi, Daniela Piga, Stefano Lamberti, Monica Sciacco, Stefania Corti, Maurizio Moggio, Nereo Bresolin, Giacomo Pietro Comi
No abstract text is available yet for this article.
December 8, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29228108/dguok-recessive-mutations-in-patients-with-cpeo-mitochondrial-myopathy-parkinsonism-and-mtdna-deletions
#9
Leonardo Caporali, Luca Bello, Francesca Tagliavini, Chiara La Morgia, Alessandra Maresca, Lidia Di Vito, Rocco Liguori, Maria Lucia Valentino, Diego Cecchin, Elena Pegoraro, Valerio Carelli
No abstract text is available yet for this article.
December 8, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29228063/what-matters-in-chronic-burkholderia-cenocepacia-infection-in-cystic-fibrosis-insights-from-comparative-genomics
#10
Jaroslav Nunvar, Vaclav Capek, Karel Fiser, Libor Fila, Pavel Drevinek
Burkholderia cenocepacia causes severe pulmonary infections in cystic fibrosis (CF) patients. Since the bacterium is virtually untreatable by antibiotics, chronic infections persist for years and might develop into fatal septic pneumonia (cepacia syndrome, CS). To devise new strategies to combat chronic B. cenocepacia infections, it is essential to obtain comprehensive knowledge about their pathogenesis. We conducted a comparative genomic analysis of 32 Czech isolates of epidemic clone B. cenocepacia ST32 isolated from various stages of chronic infection in 8 CF patients...
December 11, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29228057/n-acetylcysteine-nac-ameliorates-epstein-barr-virus-latent-membrane-protein-1-induced-chronic-inflammation
#11
Xiao Gao, Eirini-Maria Lampraki, Sarwah Al-Khalidi, Muhammad Asif Qureshi, Rhea Desai, Joanna Beatrice Wilson
Chronic inflammation results when the immune system responds to trauma, injury or infection and the response is not resolved. It can lead to tissue damage and dysfunction and in some cases predispose to cancer. Some viruses (including Epstein-Barr virus (EBV)) can induce inflammation, which may persist even after the infection has been controlled or cleared. The damage caused by inflammation, can itself act to perpetuate the inflammatory response. The latent membrane protein 1 (LMP1) of EBV is a pro-inflammatory factor and in the skin of transgenic mice causes a phenotype of hyperplasia with chronic inflammation of increasing severity, which can progress to pre-malignant and malignant lesions...
2017: PloS One
https://www.readbyqxmd.com/read/29227991/predicting-the-pathogenicity-of-novel-variants-in-mitochondrial-trna-with-mitotip
#12
Sanjay Sonney, Jeremy Leipzig, Marie T Lott, Shiping Zhang, Vincent Procaccio, Douglas C Wallace, Neal Sondheimer
Novel or rare variants in mitochondrial tRNA sequences may be observed after mitochondrial DNA analysis. Determining whether these variants are pathogenic is critical, but confirmation of the effect of a variant on mitochondrial function can be challenging. We have used available databases of benign and pathogenic variants, alignment between diverse tRNAs, structural information and comparative genomics to predict the impact of all possible single-base variants and deletions. The Mitochondrial tRNA Informatics Predictor (MitoTIP) is available through MITOMAP at www...
December 11, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29227829/a-long-noncoding-rna-from-the-hbs1l-myb-intergenic-region-on-chr6q23-regulates-human-fetal-hemoglobin-expression
#13
Tasha A Morrison, Ibifiri Wilcox, Hong-Yuan Luo, John J Farrell, Ryo Kurita, Yukio Nakamura, George J Murphy, Shuaiying Cui, Martin H Steinberg, David H K Chui
The HBS1L-MYB intergenic region (chr6q23) regulates erythroid cell proliferation, maturation, and fetal hemoglobin (HbF) expression. An enhancer element within this locus, highlighted by a 3-bp deletion polymorphism (rs66650371), is known to interact with the promoter of the neighboring gene, MYB, to increase its expression, thereby regulating HbF production. RNA polymerase II binding and a 50-bp transcript from this enhancer region reported in ENCODE datasets suggested the presence of a long noncoding RNA (lncRNA)...
November 29, 2017: Blood Cells, Molecules & Diseases
https://www.readbyqxmd.com/read/29227713/a-case-report-of-in-utero-williams-syndrome-arterial-malformation
#14
Andrew John Kobalka, Robert E Mrak, William T Gunning
INTRODUCTION: Williams syndrome (WS), an autosomal dominant condition linked to gene deletions on chromosome 7, can cause supravalvular aortic narrowing and death. WS-associated mutations are believed to disrupt arterial elastin fibers, causing smooth muscle malformation, endomysial fibrosis and severe hypertension. Previous studies demonstrated arterial ultrastructural anomalies in adult WS patients. It is not presently known if the arterial phenotype of WS is also present in utero. CASE REPORT: A 34-week stillborn was delivered to a 28-year-old with genetically confirmed WS...
December 11, 2017: Fetal and Pediatric Pathology
https://www.readbyqxmd.com/read/29227538/abberent-expression-of-nor1-protein-in-tumor-associated-macrophages-contributes-to-the-development-of-den-induced-hepatocellular-carcinoma
#15
Shengnan Chen, Pan Zheng, Wei Wang, Mei Yi, Pan Chen, Jing Cai, Junjun Li, Qian Peng, Yuanyuan Ban, Ying Zhou, Zhaoyang Zeng, Xiaoling Li, Wei Xiong, Guiyuan Li, Bo Xiang
Hepatocellular carcinoma (HCC) is the most common primary tumor of the liver and the sixth most common lethal cancer worldwide. Recent evidences demonstrated that oxidored nitro domain containing protein 1(NOR1), a putative tumor suppressor gene, is overexpressed in human HCC tissues. However, the role of NOR1 in HCC development remains unclear. Here, we described that NOR1 protein level is elevated in HCC and is associated with poorer clinical outcome. However, ecotopic overexpression of NOR1 protein in human HCC cell line HepG2 cells had no effect on cells proliferation, migration and clonality...
December 11, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29227476/the-molecular-landscape-of-pediatric-acute-myeloid-leukemia-reveals-recurrent-structural-alterations-and-age-specific-mutational-interactions
#16
Hamid Bolouri, Jason E Farrar, Timothy Triche, Rhonda E Ries, Emilia L Lim, Todd A Alonzo, Yussanne Ma, Richard Moore, Andrew J Mungall, Marco A Marra, Jinghui Zhang, Xiaotu Ma, Yu Liu, Yanling Liu, Jaime M Guidry Auvil, Tanja M Davidsen, Patee Gesuwan, Leandro C Hermida, Bodour Salhia, Stephen Capone, Giridharan Ramsingh, Christian Michel Zwaan, Sanne Noort, Stephen R Piccolo, E Anders Kolb, Alan S Gamis, Malcolm A Smith, Daniela S Gerhard, Soheil Meshinchi
We present the molecular landscape of pediatric acute myeloid leukemia (AML) and characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The COG-National Cancer Institute (NCI) TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA and microRNA sequencing and CpG methylation profiling. Validated DNA variants corresponded to diverse, infrequent mutations, with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including new gene fusions and focal deletions of MBNL1, ZEB2 and ELF1, were disproportionately prevalent in young individuals as compared to adults...
December 11, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29227474/a-proteolytic-fragment-of-histone-deacetylase-4-protects-the-heart-from-failure-by-regulating-the-hexosamine-biosynthetic-pathway
#17
Lorenz H Lehmann, Zegeye H Jebessa, Michael M Kreusser, Axel Horsch, Tao He, Mariya Kronlage, Matthias Dewenter, Viviana Sramek, Ulrike Oehl, Jutta Krebs-Haupenthal, Albert H von der Lieth, Andrea Schmidt, Qiang Sun, Julia Ritterhoff, Daniel Finke, Mirko Völkers, Andreas Jungmann, Sven W Sauer, Christian Thiel, Alexander Nickel, Michael Kohlhaas, Michaela Schäfer, Carsten Sticht, Christoph Maack, Norbert Gretz, Michael Wagner, Ali El-Armouche, Lars S Maier, Juan E Camacho Londoño, Benjamin Meder, Marc Freichel, Hermann-Josef Gröne, Patrick Most, Oliver J Müller, Stephan Herzig, Eileen E M Furlong, Hugo A Katus, Johannes Backs
The stress-responsive epigenetic repressor histone deacetylase 4 (HDAC4) regulates cardiac gene expression. Here we show that the levels of an N-terminal proteolytically derived fragment of HDAC4, termed HDAC4-NT, are lower in failing mouse hearts than in healthy control hearts. Virus-mediated transfer of the portion of the Hdac4 gene encoding HDAC4-NT into the mouse myocardium protected the heart from remodeling and failure; this was associated with decreased expression of Nr4a1, which encodes a nuclear orphan receptor, and decreased NR4A1-dependent activation of the hexosamine biosynthetic pathway (HBP)...
December 11, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29227332/recent-advances-in-the-diagnosis-of-malignant-mesothelioma-focus-on-approach-in-challenging-cases-and-in-limited-tissue-and-cytologic-samples
#18
Sara Monaco, Mitra Mehrad, Sanja Dacic
Mesothelial proliferations can be diagnostically challenging in small specimens, such as body fluid cytology and small tissue biopsies. A great morphologic challenge for pathologists is the separation of benign reactive mesothelial proliferations from malignant mesotheliomas. Reactive mesothelial proliferations may have histologic features that resemble malignancy including increased cellularity, cytologic atypia, and mitoses. Recent advances in mesothelioma genetics resulted in identification of BAP1 mutations and p16 deletions as features of malignant mesotheliomas...
January 2018: Advances in Anatomic Pathology
https://www.readbyqxmd.com/read/29227307/a-patient-with-chromosome-18p-deletion-and-congenital-hypoglossia
#19
Sanne Klaphake, Marieke F van Dooren, Richelle E M Senden, A Jeannette M Hoogeboom, Eppo B Wolvius, Maarten J Koudstaal
No abstract text is available yet for this article.
December 8, 2017: Clinical Dysmorphology
https://www.readbyqxmd.com/read/29227285/shifts-in-podocyte-histone-h3k27me3-regulate-mouse-and-human-glomerular-disease
#20
Syamantak Majumder, Karina Thieme, Sri N Batchu, Tamadher A Alghamdi, Bridgit B Bowskill, M Golam Kabir, Youan Liu, Suzanne L Advani, Kathryn E White, Laurette Geldenhuys, Karthik K Tennankore, Penelope Poyah, Ferhan S Siddiqi, Andrew Advani
Histone protein modifications control fate determination during normal development and dedifferentiation during disease. Here, we set out to determine the extent to which dynamic changes to histones affect the differentiated phenotype of ordinarily quiescent adult glomerular podocytes. To do this, we examined the consequences of shifting the balance of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark in podocytes. Adriamycin nephrotoxicity and subtotal nephrectomy (SNx) studies indicated that deletion of the histone methylating enzyme EZH2 from podocytes decreased H3K27me3 levels and sensitized mice to glomerular disease...
December 11, 2017: Journal of Clinical Investigation
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