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https://www.readbyqxmd.com/read/28916733/clonal-expansion-and-epigenetic-reprogramming-following-deletion-or-amplification-of-mutant-idh1
#1
Tali Mazor, Charles Chesnelong, Aleksandr Pankov, Llewellyn E Jalbert, Chibo Hong, Josie Hayes, Ivan V Smirnov, Roxanne Marshall, Camila F Souza, Yaoqing Shen, Pavithra Viswanath, Houtan Noushmehr, Sabrina M Ronen, Steven J M Jones, Marco A Marra, J Gregory Cairncross, Arie Perry, Sarah J Nelson, Susan M Chang, Andrew W Bollen, Annette M Molinaro, Henrik Bengtsson, Adam B Olshen, Samuel Weiss, Joanna J Phillips, H Artee Luchman, Joseph F Costello
IDH1 mutation is the earliest genetic alteration in low-grade gliomas (LGGs), but its role in tumor recurrence is unclear. Mutant IDH1 drives overproduction of the oncometabolite d-2-hydroxyglutarate (2HG) and a CpG island (CGI) hypermethylation phenotype (G-CIMP). To investigate the role of mutant IDH1 at recurrence, we performed a longitudinal analysis of 50 IDH1 mutant LGGs. We discovered six cases with copy number alterations (CNAs) at the IDH1 locus at recurrence. Deletion or amplification of IDH1 was followed by clonal expansion and recurrence at a higher grade...
September 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28915574/comparative-study-of-whole-genome-amplification-and-next-generation-sequencing-performance-of-single-cancer-cells
#2
Anna Babayan, Malik Alawi, Michael Gormley, Volkmar Müller, Harriet Wikman, Ryan P McMullin, Denis A Smirnov, Weimin Li, Maria Geffken, Klaus Pantel, Simon A Joosse
BACKGROUND: Whole genome amplification (WGA) is required for single cell genotyping. Effectiveness of currently available WGA technologies in combination with next generation sequencing (NGS) and material preservation is still elusive. RESULTS: In respect to the accuracy of SNP/mutation, indel, and copy number aberrations (CNA) calling, the HiSeq2000 platform outperformed IonProton in all aspects. Furthermore, more accurate SNP/mutation and indel calling was demonstrated using single tumor cells obtained from EDTA-collected blood in respect to CellSave-preserved blood, whereas CNA analysis in our study was not detectably affected by fixation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28903078/derivation-of-reliable-empirical-models-describing-lead-transfer-from-metal-polluted-soils-to-radish-raphanus-sativa-l-determining-factors-and-soil-criteria
#3
Sha Zhang, Jing Song, Yinwen Cheng, Peter Christie, Jian Long, Lingfei Liu
Reliable models describing Pb transfer from soils to food crops are useful in the improvement of soil protection guidelines. This study provides mechanistic insights from in-situ soil solution measurement on the Pb uptake in the root tissues (RF) of radish, grown in 25 representative Pb-contaminated agricultural soils. Lead speciation and regression analysis indicate that >88.6% of the variation in RF Pb is attributable to free Pb(2+) activity (aPb(2+)) in the soil solution, which is predominantly controlled by pH and DOC...
September 10, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28899736/characterization-of-genome-wide-copy-number-aberrations-in-colonic-mixed-adenoneuroendocrine-carcinoma-and-neuroendocrine-carcinoma-reveals-recurrent-amplification-of-ptger4-and-myc-genes
#4
Namita Sinha, Daniel Gaston, Daniel Manders, Marissa Goudie, Makoto Matsuoka, Tao Xie, Weei-Yuarn Huang
Colonic Mixed adenoneuroendocrine Carcinoma (MANEC) is an aggressive neoplasm with worse prognosis compared to adenocarcinoma. To gain a better understanding of the molecular features of colonic MANEC, we characterized the genome-wide copy number aberrations (CNA) of 14 MANECs and 5 neuroendocrine carcinomas using the OncoScan FFPE assay. Compared to 269 colonic adenocarcinomas, 19 of 42 chromosomal arms of MANEC exhibited a similar frequency of major aberrant events as adenocarcinomas, and 13 chromosomal arms exhibited a higher frequency of copy number gains...
September 9, 2017: Human Pathology
https://www.readbyqxmd.com/read/28892140/biofilm-formation-and-its-relationship-with-the-molecular-characteristics-of-food-related-methicillin-resistant-staphylococcus-aureus-mrsa
#5
Alberto Vergara, Giovanni Normanno, Pierluigi Di Ciccio, Francesca Pedonese, Roberta Nuvoloni, Antonio Parisi, Gianfranco Santagada, Angelo Colagiorgi, Emanuela Zanardi, Sergio Ghidini, Adriana Ianieri
The capability to produce biofilm is an important persistence and dissemination mechanism of some foodborne bacteria. This paper investigates the relationship between some molecular characteristics (SCCmec, ST, spa-type, agr-type, cna, sarA, icaA, icaD, clfA, fnbA, fnbB, hla, hlb) of 22 food-related methicillin-resistant Staphylococcus aureus (MRSA) strains and their ability to form biofilm on stainless steel and polystyrene. Five (22.7%, 5/22) strains were able to synthesize biofilm on polystyrene, and one of these (4...
September 11, 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28882579/accelerator-mass-spectrometry-ams-in-radioecology
#6
M García-León
Accelerator Mass Spectrometry (AMS) provides with an excellent sensitivity for the determination of radionuclides in the environment. In fact, conventional radiometric techniques can hardly compete with AMS in the solution of many problems involving the measurement of very low levels of radioactivity in Nature. For that reason, during the last years AMS has become a powerful tool for Radioecology studies. In this paper a review is done on the evolution of AMS applications to the measurement of environmental radioactivity and, therefore, its contribution to the understanding of radionuclide behavior in Nature...
September 4, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28875323/evodiamine-inhibits-angiotensin-ii-induced-rat-cardiomyocyte-hypertrophy
#7
Na He, Qi-Hai Gong, Feng Zhang, Jing-Yi Zhang, Shu-Xian Lin, Hua-Hua Hou, Qin Wu, An-Sheng Sun
OBJECTIVE: To investigate the effects of evodiamine (Evo), a component of Evodiaminedia rutaecarpa Juss.) Benth, on cardiomyocyte hypertrophy induced by angiotensin II (Ang II) and further explore the potential mechanisms. METHODS: Cardiomyocytes from neonatal Sprague Dawley rats were isolated and characterized, and then the cadiomyocyte cultures were randomly divided into control, model (Ang II 0.1 μmol/L), and Evo (0.03, 0.3, 3 μmol/L) groups. The cardiomyocyte surface area, protein level, intracellular free calcium ([Ca(2+)]i) concentration, activity of nitric oxide synthase (NOS) and content of nitric oxide (NO) were measured, respectively...
September 5, 2017: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/28842480/the-unique-c-terminus-of-calcineurin-isoform-cna%C3%AE-1-confers-non-canonical-regulation-of-enzyme-activity-by-ca-2-and-calmodulin
#8
Rachel Bond, Nina Ly, Martha S Cyert
Calcineurin, the conserved Ca(2+)/calmodulin-regulated phosphatase and target of immunosuppressants, plays important roles in the circulatory, nervous, and immune systems. Calcineurin activity strictly depends on Ca(2+) and Ca(2+)-bound calmodulin (Ca(2+)/CaM) to relieve autoinhibition of the catalytic subunit (CNA) by its C-terminus. The C-terminus contains two regulatory domains, the autoinhibitory domain (AID) and calmodulin-binding domain (CBD), which block the catalytic center and a conserved substrate-binding groove, respectively...
August 25, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28841143/extract-of-sheng-mai-san-ameliorates-myocardial-ischemia-induced-heart-failure-by-modulating-ca-2-calcineurin-mediated-drp1-signaling-pathways
#9
Ye Yang, Yushan Tian, Siyao Hu, Suxia Bi, Suxia Li, Yuanjia Hu, Junping Kou, Jin Qi, Boyang Yu
Sheng-Mai-San (SMS) is a well-known traditional Chinese medicine (TCM) complex prescription used to treat heart failure (HF) and angina in clinic. However, its potential therapeutic mechanisms remain unclear. The present study evaluated the cardioprotection of extract of SMS (ESMS) on myocardial ischemia (MI)-induced HF, and explored the underlying molecular mechanisms. The results demonstrated that ESMS (728.0 mg/kg) significantly attenuated MI injury-induced HF by improving cardiac function and pathological changes, decreasing lactate dehydrogenase (LDH), creatine kinase (CK) activities, and brain natriuretic peptide (BNP) levels; increasing ATPase activity; and reducing intracellular Ca(2+) levels in MI-induced HF mice model...
August 25, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28805151/recognizing-and-responding-to-the-toxic-work-environment-worker-safety-patient-safety-and-abuse-neglect-in-nursing-homes
#10
Carolyn E Z Pickering, Katie Nurenberg, Lawrence Schiamberg
This grounded theory study examined how the certified nursing assistant (CNA) understands and responds to bullying in the workplace. Constant comparative analysis was used to analyze data from in-depth telephone interviews with CNAs ( N = 22) who experienced bullying while employed in a nursing home. The result of the analysis is a multistep model describing CNA perceptions of how, over time, they recognized and responded to the "toxic" work environment. The strategies used in responding to the "toxic" environment affected their care provision and were attributed to the development of several resident and worker safety outcomes...
August 1, 2017: Qualitative Health Research
https://www.readbyqxmd.com/read/28804123/integrating-genomic-alterations-in-diffuse-large-b-cell-lymphoma-identifies-new-relevant-pathways-and-potential-therapeutic-targets
#11
K Karube, A Enjuanes, I Dlouhy, P Jares, D Martin-Garcia, F Nadeu, G R Ordóñez, J Rovira, G Clot, C Royo, A Navarro, B Gonzalez-Farre, A Vaghefi, G Castellano, C Rubio-Perez, D Tamborero, J Briones, A Salar, J M Sancho, S Mercadal, E Gonzalez-Barca, L Escoda, H Miyoshi, K Ohshima, K Miyawaki, K Kato, K Akashi, A Mozos, L Colomo, M Alcoceba, A Valera, A Carrió, D Costa, N Lopez-Bigas, R Schmitz, L M Staudt, I Salaverria, A López-Guillermo, E Campo
Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations. However, the clinical significance of these alterations is still not well defined. In this study, we have integrated the analysis of targeted next-generation sequencing of 106 genes and genomic copy number alterations (CNA) in 150 DLBCL. The clinically significant findings were validated in an independent cohort of 111 patients. Germinal center B-cell and activated B-cell DLBCL had a differential profile of mutations, altered pathogenic pathways and CNA...
August 14, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28802642/prognostic-value-of-tert-alterations-mutational-and-copy-number-alterations-burden-in-urothelial-carcinoma
#12
Sumit Isharwal, François Audenet, Esther Drill, Eugene J Pietzak, Gopa Iyer, Irina Ostrovnaya, Eugene Cha, Timothy Donahue, Maria Arcila, Gowtham Jayakumaran, Michael F Berger, Jonathan E Rosenberg, Dean F Bajorin, Jonathan Coleman, Guido Dalbagni, Victor E Reuter, Bernard H Bochner, David B Solit, Hikmat A Al-Ahmadie
Missense mutations in the TERT gene promoter occur at high frequency in multiple cancers, including urothelial carcinoma (UC). However, the relationship between TERT promoter mutations and UC patient outcomes is unclear due to conflicting reports in the literature. In this study, we examined the association of TERT alterations, tumor mutational burden per megabase (Mb), and copy number alteration (CNA) burden with clinical parameters and their prognostic value in a cohort of 398 urothelial tumors. The majority of TERT mutations were located at two promoter region hotspots (chromosome 5, 1 295 228 C>T and 1 295 250 C>T)...
August 10, 2017: European Urology Focus
https://www.readbyqxmd.com/read/28791573/development-of-a%C3%A2-clinical-version-of-the-carers-needs-assessment-for-schizophrenia
#13
Johannes Wancata, Fabian Friedrich, Annemarie Unger, Rebecca Jahn
OBJECTIVE: Based on the research version of the Carers' Needs Assessment for Schizophrenia (CNA-S) a shortened clinical version was developed for routine assessment of interventions needed by the caregivers of schizophrenia patients in everyday clinical work. METHODS: The development of this questionnaire (including a manual explaining its use) was based on results from earlier studies and suggestions from Austrian researchers involved in previous studies using the research version...
August 8, 2017: Neuropsychiatrie: Klinik, Diagnostik, Therapie und Rehabilitation
https://www.readbyqxmd.com/read/28763841/-copy-number-aberrations-of-genes-related-to-extrohepatic-metastasis-free-survival-after-operation-for-hepatocellular-carcinoma
#14
L L Bao, Z Z Zhu, B J Wen, X X Wan, Y Q Ye, L Chen, S Q He, W M Cong
Objective: To investigate the molecular markers of copy number aberrations (CNAs) of genes related to extrohepatic metastasis-free survival after the operation for hepatocellular carcinoma (HCC). Methods: The CNA status of 20 candidate genes in 66 HCC samples was detected by microarray comparative genomic hybridization. The associations between gene CNAs and extrohepatic metastasis-free survival were evaluated using the Cox regression model, Log-rank test, and Kaplan-Meier survival analysis. Results: Multivariate Cox analysis revealed that the independent risk factors for metastasis-free survival were MDM4 gain (hazard ratio [HR] = 2...
May 20, 2017: Zhonghua Gan Zang Bing za Zhi, Zhonghua Ganzangbing Zazhi, Chinese Journal of Hepatology
https://www.readbyqxmd.com/read/28758283/copy-number-profiling-of-adult-relapsed-b-cell-precursor-acute-lymphoblastic-leukemia-reveals-potential-leukemia-progression-mechanisms
#15
Jordi Ribera, Lurdes Zamora, Mireia Morgades, Mar Mallo, Neus Solanes, Montserrat Batlle, Susana Vives, Isabel Granada, Jordi Juncà, Roberto Malinverni, Eulàlia Genescà, Ramon Guàrdia, Santiago Mercadal, Lourdes Escoda, Joaquín Martinez-Lopez, Mar Tormo, Jordi Esteve, Marta Pratcorona, Carmen Martinez-Losada, Francesc Solé, Evarist Feliu, Josep-Maria Ribera
The outcome of relapsed adult acute lymphoblastic leukemia (ALL) remains dismal despite new therapeutic approaches. Previous studies analyzing relapse samples have shown a high degree of heterogeneity regarding gene alterations without an evident relapse signature. Bone marrow or peripheral blood samples from 31 adult B-cell precursor ALL patients at first relapse, and 21 paired diagnostic samples were analyzed by multiplex ligation probe-dependent amplification (MLPA). Nineteen paired diagnostic and relapse samples of these 21 patients were also analyzed by SNP arrays...
July 30, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28751446/gene-copy-number-estimation-from-targeted-next-generation-sequencing-of-prostate-cancer-biopsies-analytic-validation-and-clinical-qualification
#16
George Seed, Wei Yuan, Joaquin Mateo, Suzanne Carreira, Claudia Bertan, Maryou Lambros, Gunther Boysen, Roberta Ferraldeschi, Susana Miranda, Ines Figueiredo, Ruth Riisnaes, Mateus Crespo, Daniel Nava Rodrigues, Eric Talevich, Dan R Robinson, Lakshmi P Kunju, Yi-Mi Wu, Robert Lonigro, Shahneen Sandhu, Arul Chinnayan, Johann S de Bono
Abstract <p>Purpose</p> <p>Precise detection of copy number aberrations (CNAs) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next generation sequencing (NGS) is inexpensive, high throughput and easily feasible, allowing single nucleotide variant calls, but CNA estimation from this remains challenging..</p> <p>Experimental Design</p> <p>We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration resistant prostate cancer biopsies, and used capture based whole exome sequencing (WES), array comparative genomic hybridization (aCGH), and fluorescent in situ hybridization (FISH) to explore the viability of this approach...
July 27, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28735055/analysis-of-virulence-genes-and-accessory-gene-regulator-agr-types-among-methicillin-resistant-staphylococcus-aureus-strains-in-iran
#17
Sara Cheraghi, Leyla Pourgholi, Maryam Shafaati, Shirinsadat Hashemi Fesharaki, Arash Jalali, Rahim Nosrati, Mohammad Ali Boroumand
OBJECTIVES: Methicillin-resistant Staphylococcus aureus (MRSA) strains are a major cause of hospital-acquired infections and are considered a serious public health concern. MRSA isolates have abundant virulence factors that are the basis for their pathogenicity. The accessory gene regulator (agr) locus co-ordinates the expression of these genes. The aim of this study was to determine the presence and frequency of various virulence genes encoding enterotoxins and adhesins as well as to identify agr specificity groups in MRSA isolates...
September 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28712776/clonal-evolution-in-paired-endometrial-intraepithelial-neoplasia-atypical-hyperplasia-and-endometrioid-adenocarcinoma
#18
Mariano Russo, James Broach, Kathryn Sheldon, Kenneth R Houser, Dajiang J Liu, Joshua Kesterson, Rebecca Phaeton, Carrie Hossler, Nadine Hempel, Maria Baker, Jordan M Newell, Richard Zaino, Joshua I Warrick
Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically-defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma...
July 13, 2017: Human Pathology
https://www.readbyqxmd.com/read/28710315/shallow-whole-genome-sequencing-on-circulating-cell-free-dna-allows-reliable-non-invasive-copy-number-profiling-in-neuroblastoma-patients
#19
Nadine Van Roy, Malaika Van der Linden, Björn Menten, Annelies Dheedene, Charlotte Vandeputte, Jo Van Dorpe, Geneviève Laureys, Marleen Renard, Tom Sante, Tim Lammens, Bram De Wilde, Frank Speleman, Katleen De Preter
<p>Neuroblastoma (NB) is a heterogeneous disease characterized by distinct clinical features and by the presence of typical copy number alterations (CNAs). Given the strong association of these CNA profiles with prognosis, analysis of the CNA profile at diagnosis is mandatory. Therefore, we tested whether the analysis of circulating cell-free DNA (cfDNA) present in plasma samples of NB patients could offer a valuable alternative to primary tumor DNA for CNA profiling.</p> <br /><br />Experimental Design: <p>In 37 NB patients cfDNA analysis using shallow whole genome sequencing (sWGS) was compared to arrayCGH analysis of primary tumor tissue...
July 14, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28701032/bcl2-regulation-according-to-molecular-subtype-of-breast-cancer-by-analysis-of-the-cancer-genome-atlas-database
#20
Ki-Tae Hwang, Kwangsoo Kim, Ji Hyun Chang, Sohee Oh, Young A Kim, Jong Yoon Lee, Se Hee Jung, In Sil Choi
Purpose: We investigated BCL2 regulation across DNA, RNA, protein, and methylation status according to molecular subtype of breast cancer using The Cancer Genome Atlas (TCGA) database. Materials and Methods: We analyzed clinical and biological data on 1,096 breast cancers from the TCGA database. Biological data included reverse phase protein array (RPPA), mRNA sequencing (mRNA seq), mRNA microarray, methylation, copy number alteration linear, copy number alteration nonlinear, and mutation data...
July 4, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
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