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https://www.readbyqxmd.com/read/29775793/analysis-of-dna-methylation-at-specific-loci-in-stool-samples-detects-colorectal-cancer-and-high-grade-dysplasia-in-patients-with-inflammatory-bowel-disease
#1
John B Kisiel, Pasquale Klepp, Hatim T Allawi, William R Taylor, Maria Giakoumopoulos, Tamara Sander, Tracy C Yab, Bjorn A Moum, Graham P Lidgard, Stephan Brackmann, Douglas W Mahoney, Arne Roseth, David A Ahlquist
BACKGROUND & AIMS: Patients with inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), are at increased risk for colorectal cancer (CRC). Analyses of DNA methylation patterns in stool samples have been reported to detect CRC in patients with IBD. We sought to validate these findings in larger cohorts and assess the accuracy of analysis of DNA methylation patterns in stool for detection of CRC and high-grade dysplasia (HGD) normalized to methylation level at ZDHHC1...
May 15, 2018: Clinical Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/29774346/dft-insight-into-the-effect-of-potassium-on-the-adsorption-activation-and-dissociation-of-co-2-over-fe-based-catalysts
#2
Xiaowa Nie, Linlin Meng, Haozhi Wang, Yonggang Chen, Xinwen Guo, Chunshan Song
Catalytic conversion of CO2 including hydrogenation has attracted great attention as a method for chemical fixation of CO2 in combination with other techniques such as CO2 capture and storage. Potassium is a well-known promotor for many industrial catalytic processes such as in Fischer-Tropsch synthesis. In this work, we performed density functional theory (DFT) calculations to investigate the effect of potassium on the adsorption, activation, and dissociation of CO2 over Fe(100), Fe5C2(510) and Fe3O4(111) surfaces...
May 18, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29772233/roseburia-intestinalis-derived-flagellin-is-a-negative-regulator-of-intestinal-inflammation
#3
Yongsheng Quan, Kerui Song, Yan Zhang, Changxin Zhu, Zhaohua Shen, Shuai Wu, Weiwei Luo, Bei Tan, Zhenyu Yang, Xiaoyan Wang
Our previous study showed that the Roseburia intestinalis (R. intestinalis), one of the dominant intestinal bacterial microbiota, was significantly decreased in Crohn's disease patients and protected colon epithelial cells from inflammatory damage. However, the roles of lncRNAs in R. intestinalis flagellin-mediated anti-inflammation remain unclear. In this study, we investigate global lncRNA expression profiles using microarray analysis of ulcerative colitis samples from DSS/Flagellin-challenged mice and identified a Flagellin-induced upregulated lncRNA (HIF1A-AS2)...
May 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29762789/an-optimist-s-view-on-limiting-necrotic-enteritis-and-maintaining-broiler-gut-health-and-performance-in-today-s-marketing-food-safety-and-regulatory-climate
#4
Charles L Hofacre, John A Smith, Greg F Mathis
The future poultry nutritionist, veterinarian, and husbandryman will have many new regulatory requirements and consumer preferences to navigate in addition to their normal responsibility of raising birds in a cost-efficient and wholesome manner. New challenges include changes to antibiotic use, increased food safety regulations, and more concern over how birds are raised and how to dispose of poultry house waste. All of these new programs and new regulations will alter how we have been raising birds for the last 60 years since the inception of the integrated poultry industry...
June 1, 2018: Poultry Science
https://www.readbyqxmd.com/read/29754224/transformation-of-an-exotic-yeast-species-into-a-platform-organism-a-case-study-for-engineering-glycolipid-production-in-the-yeast-starmerella-bombicola
#5
Sofie Lodens, Marilyn De Graeve, Sophie L K W Roelants, Sofie L De Maeseneire, Wim Soetaert
In this chapter, a step-by-step approach on how to transform non-conventional yeasts or fungi into platform organisms is described. The non-conventional glycolipid producing yeast Starmerella bombicola (and in some cases also Pseudohyphozyma bogoriensis) is used as a case study. And more specifically how to engineer it toward production of new-to-nature glycolipids like bola sophorolipids. When starting genetic engineering efforts for non-lab strains, one should start at the very basis: identifying selection markers and possibly developing auxotrophic strains...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29753738/identification-and-expression-pattern-analysis-of-bomyb51-involved-in-indolic-glucosinolate-biosynthesis-from-broccoli-brassica-oleracea-var-italica
#6
Qingyue Yu, Guodong Hao, Jianxin Zhou, Jingying Wang, Ejiroghene Ruona Evivie, Jing Li
Glucosinolates are a class of amino acid-derived specialized metabolites characteristic of the Brassicales order. Trp derived indolic glucosinolates are essential for the effective plant defense responses to a wide range of pathogens and herbivores. In Arabidopsis, MYB51 is the key transcription factor positively regulates indolic glucosinolate production by activating certain biosynthetic genes. In this study, we report the isolation and identification of a MYB51 from broccoli designated as BoMYB51. Overexpression of BoMYB51 in Arabidopsis increased indolic glucosinolate production by upregulating biosynthetic genes and resulted in enhanced flagellin22 (Flg22) induced callose deposition...
May 10, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29753718/early-tgf-%C3%AE-inhibition-in-mice-reduces-the-incidence-of-breast-cancer-induced-bone-disease-in-a-myeloid-dependent-manner
#7
Denise Buenrostro, Kristin A Kwakwa, Nicole E Putnam, Alyssa R Merkel, Joshua R Johnson, James E Cassat, Julie A Sterling
The tumor-cell microenvironment is recognized as a dynamic place where critical cell interactions occur and play an important role in altering tumorigenesis. While many studies have investigated the effects of cellular cross-talk within distinct tumor microenvironments, these interactions have yet to be fully examined in bone. It is well-established that many common cancers metastasize to bone, resulting in the development of tumor-induced bone disease (TIBD), a multi-facetted illness that is driven by complex cell interactions within the bone marrow...
May 10, 2018: Bone
https://www.readbyqxmd.com/read/29752851/idh-mutated-astrocytomas-with-19q-loss-constitute-a-subgroup-that-confers-better-prognosis
#8
Ryohei Otani, Takeo Uzuka, Fumi Higuchi, Hadzki Matsuda, Masashi Nomura, Shota Tanaka, Akitake Mukasa, Koichi Ichimura, Phyo Kim, Keisuke Ueki
IDH-mutant gliomas are classified into astrocytic or oligodendroglial tumors by 1p/19q status in WHO 2016 classification, with the latter presenting with characteristic morphology and better prognosis in general. However, the morphological and genetic features within each category are varied, and there may be distinguishable subtypes. We analyzed 170 WHO grade II to IV gliomas resected in our institution. 1p/19q status was analyzed by microsatellite analysis, and genetic mutations were analyzed by next-generation sequencing and Sanger sequencing...
May 12, 2018: Cancer Science
https://www.readbyqxmd.com/read/29748206/deep-learning-convolutional-neural-networks-accurately-classify-genetic-mutations-in-gliomas
#9
P Chang, J Grinband, B D Weinberg, M Bardis, M Khy, G Cadena, M-Y Su, S Cha, C G Filippi, D Bota, P Baldi, L M Poisson, R Jain, D Chow
BACKGROUND AND PURPOSE: The World Health Organization has recently placed new emphasis on the integration of genetic information for gliomas. While tissue sampling remains the criterion standard, noninvasive imaging techniques may provide complimentary insight into clinically relevant genetic mutations. Our aim was to train a convolutional neural network to independently predict underlying molecular genetic mutation status in gliomas with high accuracy and identify the most predictive imaging features for each mutation...
May 10, 2018: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/29745673/nucleophilic-substitutions-of-alcohols-in-high-levels-of-catalytic-efficiency
#10
Tanja Stach, Julia Dräger, Peter H Huy
A practical method for the nucleophilic substitution (S N ) of alcohols furnishing alkyl chlorides, bromides, and iodides under stereochemical inversion in high catalytic efficacy is introduced. The fusion of diethylcyclopropenone as a simple Lewis base organocatalyst and benzoyl chloride as a reagent allows notable turnover numbers up to 100. Moreover, the use of plain acetyl chloride as a stoichiometric promotor in an invertive S N -type transformation is demonstrated for the first time. The operationally straightforward protocol exhibits high levels of stereoselectivity and scalability and tolerates a variety of functional groups...
May 10, 2018: Organic Letters
https://www.readbyqxmd.com/read/29739842/development-and-testing-of-a-smartphone-application-prototype-for-oral-health-promotion
#11
Sara L Nolen, Lori J Giblin-Scanlon, Linda D Boyd, Lori Rainchuso
Purpose: The purpose of this study was to develop and test a smartphone application (app) prototype, ToothSense, as an oral health promotion tool for the prevention of Early Childhood Caries (ECC) based on the Theory of Planned Behavior (TPB). Methods: A quantitative and qualitative design process based on the TPB was used for the app development in the first phase of the study. A behavioral intervention technologic model was used to document the app features design, accounting for Doshi's intervention strategies for the TPB...
April 2018: Journal of Dental Hygiene: JDH
https://www.readbyqxmd.com/read/29733378/assessing-the-predictability-of-idh-mutation-and-mgmt-methylation-status-in-glioma-patients-using-relaxation-compensated-multi-pool-cest-mri-at-7-0-tesla
#12
Daniel Paech, Johannes Windschuh, Johanna Oberhollenzer, Constantin Dreher, Felix Sahm, Jan-Eric Meissner, Steffen Goerke, Patrick Schuenke, Moritz Zaiss, Sebastian Regnery, Sebastian Bickelhaupt, Philipp Bäumer, Martin Bendszus, Wolfgang Wick, Andreas Unterberg, Peter Bachert, Mark Edward Ladd, Heinz-Peter Schlemmer, Alexander Radbruch
Background: Early identification of prognostic superior characteristics in glioma patients such as Isocitrate dehydrogenase(IDH)-mutation and O6-methylguanine-DNA-methyltransferase (MGMT) promotor methylation status is of great clinical importance. The study purpose was to investigate the non-invasive predictability of IDH-mutation status, MGMT promotor methylation, and differentiation of lower versus higher grade glioma (LGG vs. HGG) in newly-diagnosed patients employing relaxation-compensated multi-pool Chemical Exchange Saturation Transfer (CEST) magnetic resonance imaging (MRI) at 7...
May 4, 2018: Neuro-oncology
https://www.readbyqxmd.com/read/29728108/decitabine-demonstrates-antileukemic-activity-in-b-cell-precursor-acute-lymphoblastic-leukemia-with-mll-rearrangements
#13
C Roolf, A Richter, C Konkolefski, G Knuebel, A Sekora, S Krohn, J Stenzel, B J Krause, B Vollmar, H Murua Escobar, C Junghanss
BACKGROUND: Promotor hypermethylation of CpG islands is common in B cell precursor acute lymphoblastic leukemia (BCP-ALL) with mixed lineage leukemia (MLL) gene rearrangements. Hypomethylating agents (HMA) such as azacitidine (AZA) and decitabine (DEC) reduce DNA hypermethylation by incorporation into DNA and were successfully introduced into the clinic for the treatment of myeloid neoplasias. METHODS: Here, we investigated whether HMA induce comparable biological effects in MLL-positive BCP-ALL...
May 4, 2018: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/29716618/focs-a-novel-method-for-analyzing-enhancer-and-gene-activity-patterns-infers-an-extensive-enhancer-promoter-map
#14
Tom Aharon Hait, David Amar, Ron Shamir, Ran Elkon
Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer-promoter links. We show that current enhancer-promoter inference methods produce a high rate of false positive links. We introduce FOCS, a new inference method, and by benchmarking against ChIA-PET, HiChIP, and eQTL data show that it results in lower false discovery rates and at the same time higher inference power. By applying FOCS to 2630 samples taken from ENCODE, Roadmap Epigenomics, FANTOM5, and a new compendium of GRO-seq samples, we provide extensive enhancer-promotor maps ( http://acgt...
May 1, 2018: Genome Biology
https://www.readbyqxmd.com/read/29704322/macrophage-phenotype-in-the-epigallocatechin-3-gallate-egcg-modified-collagen-determines-foreign-body-reaction
#15
Chenyu Chu, Li Liu, Yufei Wang, Shimin Wei, Yuanjing Wang, Yi Man, Yili Qu
Collagen has been widely used in guided bone regeneration, and the implantation of collagen membranes will elicit the foreign body reaction (FBR). The imbalance of FBR often leads to failure of dental implants. Therefore, modulation of the FBR after implantation of collagen membranes becomes increasingly important. Macrophages, pivotal in FBR, have been distinguished into pro-inflammatory (M1) and anti-inflammatory (M2) phenotypes. Epigallocatechin-3-gallate (EGCG)-modified collagen membranes have been previously shown to regulate secretion of inflammatory factors...
April 28, 2018: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/29679610/mutated-mitf-e87r-in-melanoma-enhances-tumor-progression-via-s100a4
#16
Alice Nordlinger, Shani Dror, Abdel Elkahloun, Justine Del Rio, Elisa Stubbs, Tami Golan, Hagar Malcov, Todd D Pricket, Julia C Cronin, Shivang Parikh, Sapir Labes, Laetitia Thomas, Gal Yankovitz, Yuval Tabach, Carmit Levy, Yardena Samuels, Mehdi Khaled
Melanoma, a melanocyte origin neoplasm, is the most lethal type of skin cancer and incidence is increasing. Several familial and somatic mutations have been identified in the gene encoding the melanocyte lineage master regulator, microphthalmia-associated transcription factor (MITF); however, the neoplastic mechanisms of these mutant MITF variants are mostly unknown. Here, by performing unbiased analysis of the transcriptomes in cells expressing mutant MITF, we identified calcium-binding protein S100A4, as a downstream target of MITF-E87R...
April 18, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29661881/genetic-diversity-among-s-aureus-isolates-showing-oxacillin-and-or-cefoxitin-resistance-not-linked-to-the-presence-of-mec-genes
#17
M Angeles Argudín, S Roisin, L Nienhaus, M Dodémont, R de Mendonça, C Nonhoff, A Deplano, O Denis
Methicillin-resistant Staphylococcus aureus isolates lacking mec -genes (n=32) collected from Belgian hospitals were characterized for their β-lactamase production and the presence of mutations in pbp -genes, the pbp4 -promotor and genes ( gdpP, yjbH ) involved in PBP4-overproduction. Twelve isolates were β-lactamase hyperproducers (BHP), while 12 non-BHPs isolates may produce an incomplete GdpP protein. Most isolates showed nucleotide missense mutations at pbp genes. Few isolates showed also mutations at the pbp4 -promoter...
April 16, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29660341/evaluation-of-synthetic-promoters-in-physcomitrella-patens
#18
Anantha Peramuna, Hansol Bae, Erling Koch Rasmussen, Bjørn Dueholm, Thomas Waibel, Joanna H Critchley, Kerstin Brzezek, Michael Roberts, Henrik Toft Simonsen
Securing a molecular toolbox including diverse promoters is essential for genome engineering. However, native promoters have limitations such as the available number or the length of the promoter. In this work, three short synthetic promoters were characterized by using the yellow fluorescent protein Venus. All of the tested promoters were active and showed mRNA activity higher than housekeeping gene PpAct7, and similar protein expression level to AtUBQ10 promoter. This study shows that few cis-elements are enough to establish a strong promoter for continuous expression of genes in plants...
April 13, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29660214/precore-g1896a-mutation-is-associated-with-reduced-rates-of-hbsag-seroclearance-in-treated-hiv-hepatitis-b-virus-co-infected-patients-from-western-africa
#19
Anders Boyd, Raoul Moh, Sarah Maylin, Mariama Abdou Chekaraou, Nadia Mahjoub, Delphine Gabillard, Xavier Anglaret, Serge Paul Eholié, Constance Delaugerre, Christine Danel, Fabien Zoulim, Karine Lacombe
The nucleotide substitution G1896A on the precore (pc) region has been implicated in virological and serological responses during treatment in hepatitis B virus (HBV)-infected patients. Whether this mutation affects the therapeutic course of HIV-HBV co-infected patients, especially from Western Africa, is unknown. In this prospective cohort study, 86 antiretroviral (ARV)-naïve HIV-HBV co-infected patients from Côte d'Ivoire, initiating ARV-treatment containing lamivudine (n=53) or tenofovir (n=33), had available baseline pc sequences...
April 16, 2018: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/29655816/sex-specific-transcription-and-dna-methylation-profiles-of-reproductive-and-epigenetic-associated-genes-in-the-gonads-and-livers-of-breeding-zebrafish
#20
L V Laing, J Viana, E Dempster, T M Uren Webster, R van Aerle, J Mill, E M Santos
Reproduction is an essential process for life and is regulated by complex hormone networks and environmental factors. To date, little is known about the contribution of epigenetic mechanisms to the regulation of reproduction, particularly in lower vertebrates. We used the zebrafish (Danio rerio) model to investigate the sex-specific transcription and DNA methylation profiles for genes involved in the regulation of reproduction and in epigenetic signalling in the livers and gonads. We found evidence for associations between DNA promotor methylation and transcription for esr1 (gonads and female livers), amh (gonads) and dnmt1 (livers)...
April 12, 2018: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
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