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https://www.readbyqxmd.com/read/28088687/whole-genome-dna-methylation-profiling-identifies-epigenetic-signatures-of-uterine-carcinosarcoma
#1
Jing Li, Xiaoyun Xing, Daofeng Li, Bo Zhang, David G Mutch, Ian S Hagemann, Ting Wang
Uterine carcinosarcoma (UCS) is a form of endometrial cancer simultaneously exhibiting carcinomatous and sarcomatous elements, but the underlying molecular and epigenetic basis of this disease is poorly understood. We generated complete DNA methylomes for both the carcinomatous and the sarcomatous components of three UCS samples separated by laser capture microdissection and compared DNA methylomes of UCS with those of normal endometrium as well as methylomes derived from endometrioid carcinoma, serous endometrial carcinoma, and endometrial stromal sarcoma...
January 12, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28081238/genomic-organization-of-repetitive-dna-in-woodpeckers-aves-piciformes-implications-for-karyotype-and-zw-sex-chromosome-differentiation
#2
Thays Duarte de Oliveira, Rafael Kretschmer, Natasha Avila Bertocchi, Tiago Marafiga Degrandi, Edivaldo Herculano Corrêa de Oliveira, Marcelo de Bello Cioffi, Analía Del Valle Garnero, Ricardo José Gunski
Birds are characterized by a low proportion of repetitive DNA in their genome when compared to other vertebrates. Among birds, species belonging to Piciformes order, such as woodpeckers, show a relatively higher amount of these sequences. The aim of this study was to analyze the distribution of different classes of repetitive DNA-including microsatellites, telomere sequences and 18S rDNA-in the karyotype of three Picidae species (Aves, Piciformes)-Colaptes melanochloros (2n = 84), Colaptes campestris (2n = 84) and Melanerpes candidus (2n = 64)-by means of fluorescence in situ hybridization...
2017: PloS One
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#3
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28069135/epigenetic-control-of-gene-expression-in-maize
#4
J Huang, J S Lynn, L Schulte, S Vendramin, K McGinnis
Epigenetic gene regulation is important for proper development and gene expression in eukaryotes. Maize has a large and complex genome that includes abundant repetitive sequences which are frequently silenced by epigenetic mechanisms, making it an ideal organism to study epigenetic gene regulation. Epigenetic modifications are chromosome-bound, heritable changes to the genome that do not affect the DNA sequence, and can include DNA methylation, histone modification, and RNA processing. Our appreciation and understanding of epigenetic regulation has grown with the field since its inception ∼65 years ago...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28069063/the-ribosomal-transcription-units-of-haplorchis-pumilio-and-h-taichui-and-the-use-of-28s-rdna-sequences-for-phylogenetic-identification-of-common-heterophyids-in-vietnam
#5
Thanh Hoa Le, Khue Thi Nguyen, Nga Thi Bich Nguyen, Huong Thi Thanh Doan, Do Trung Dung, David Blair
BACKGROUND: Heterophyidiasis is now a major public health threat in many tropical countries. Species in the trematode family Heterophyidae infecting humans include Centrocestus formosanus, Haplorchis pumilio, H. taichui, H. yokogawai, Procerovum varium and Stellantchasmus falcatus. For molecular phylogenetic and systematic studies on trematodes, we need more prospective markers for taxonomic identification and classification. This study provides near-complete ribosomal transcription units (rTU) from Haplorchis pumilio and H...
January 9, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28067606/chromosomal-mapping-of-repetitive-sequences-rex3-rex6-and-rdna-genes-in-hybrids-between-colossoma-macropomum-cuvier-1818-and-piaractus-mesopotamicus-holmberg-1887
#6
Leila Braga Ribeiro, Americo Moraes Neto, Roberto Ferreira Artoni, Daniele Aparecida Matoso, Eliana Feldberg
Some species of Characiformes are known for their high economic value, such as Colossoma macropomum and Piaractus mesopotamicus, and are used in aquaculture programs to generate hybrid tambacu (interbreeding of C. macropomum females and P. mesopotamicus males). The present work aimed to investigate the location of the Rex3 and Rex6 transposable elements in the hybrid and in the species, in addition to checking the genomic organization of the 18S and 5S rDNA in tambacu. The diploid number found for the hybrid was equal to 54 chromosomes, with heterochromatic blocks distributed mainly in the centromeric portions...
January 9, 2017: Zebrafish
https://www.readbyqxmd.com/read/28060850/a-framework-to-evaluate-the-impact-of-armourstones-on-the-chemical-quality-of-surface-water
#7
Lars Duester, Dierk-Steffen Wahrendorf, Corinna Brinkmann, Anne-Lena Fabricius, Björn Meermann, Juergen Pelzer, Dennis Ecker, Monika Renner, Harald Schmid, Thomas A Ternes, Peter Heininger
Today, basic requirements for construction works include the protection of human health and of the environment. In the tension area between economic demands, circular flow economy and environmental safety, a link between the results from standardized leaching tests and the respective environmental quality standards must be created. To derive maximum release limits of metals and metalloids for armourstones in hydraulic engineering, this link is accomplished via a simple model approach. By treating natural materials and industrial by-products the same way, the article delivers an overview on the recent regulative situation in Europe as well as describes and discusses an innovative approach to derive maximum release limits for monolithic construction products in hydraulic engineering on a conceptual level...
2017: PloS One
https://www.readbyqxmd.com/read/28057732/satellite-dna-and-transposable-elements-in-seabuckthorn-hippophae-rhamnoides-a-dioecious-plant-with-small-y-and-large-x-chromosomes
#8
Janka Puterova, Olga Razumova, Tomas Martinek, Oleg Alexandrov, Mikhail Divashuk, Zdenek Kubat, Roman Hobza, Gennady Karlov, Eduard Kejnovsky
Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28054361/the-metabolic-sensor-akin10-modulates-the-arabidopsis-circadian-clock-in-a-light-dependent-manner
#9
Jieun Shin, Alfredo Sánchez-Villarreal, Amanda M Davis, Shen-Xiu Du, Kenneth W Berendzen, Csaba Koncz, Zhaojun Ding, Cuiling Li, Seth J Davis
Plants generate rhythmic metabolism during the repetitive day/night cycle. The circadian clock produces internal biological rhythms to synchronize numerous metabolic processes such that they occur at the required time of day. Metabolism conversely influences clock function by controlling circadian period and phase, and the expression of core-clock genes. Here we show that AKIN10, a catalytic subunit of the evolutionarily conserved key energy sensor Snf1 (sucrose non-fermenting 1)-related kinase 1 (SnRK1) complex, plays an important role in the circadian clock...
January 5, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28051130/the-histone-3-lysine-9-methyltransferase-inhibitor-chaetocin-improves-prognosis-in-a-rat-model-of-high-salt-diet-induced-heart-failure
#10
Tomohiko Ono, Naomi Kamimura, Tomohiro Matsuhashi, Toshihiro Nagai, Takahiko Nishiyama, Jin Endo, Takako Hishiki, Tsuyoshi Nakanishi, Noriaki Shimizu, Hirotoshi Tanaka, Shigeo Ohta, Makoto Suematsu, Masaki Ieda, Motoaki Sano, Keiichi Fukuda, Ruri Kaneda
Histone acetylation has been linked to cardiac hypertrophy and heart failure. However, the pathological implications of changes in histone methylation and the effects of interventions with histone methyltransferase inhibitors for heart failure have not been fully clarified. Here, we focused on H3K9me3 status in the heart and investigated the effects of the histone H3K9 methyltransferase inhibitor chaetocin on prognoses in Dahl salt-sensitive rats, an animal model of chronic heart failure. Chaetocin prolonged survival and restored mitochondrial dysfunction...
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043536/assessing-genetic-diversity-of-mycobacterium-tuberculosis-by-spoligotyping-and-is6110-based-restriction-fragment-length-polymorphism-in-north-india
#11
Jitendra Prasad Mathuria, Pragya Sharma, Pradyot Prakash, Jai Kumar Samaria, Vishwa Mohan Katoch, Shampa Anupurba
OBJECTIVE/BACKGROUND: Molecular epidemiology methods are very useful for differentiating between strains, assessing their diversity, and measuring the prevalence of the most circulating strain in an area. Various molecular typing methods using different molecular markers have been utilized worldwide, such as restriction fragment length polymorphism (RFLP), spoligotyping, Mycobacterial Interspersed Repetitive Unit - Variable Number of Tandem Repeat (MIRU-VNTR), and Double repetitive element-PCR (DRE-PCR) typing, for simultaneous detection and epidemiologic typing of Mycobacterium tuberculosis...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28040729/polycomb-repressive-complex-1-provides-a-molecular-explanation-for-repeat-copy-number-dependency-in-fshd-muscular-dystrophy
#12
Valentina Casa, Valeria Runfola, Stefano Micheloni, Arif Aziz, F Jeffrey Dilworth, Davide Gabellini
Repression of repetitive elements is crucial to preserve genome integrity and has been traditionally ascribed to constitutive heterochromatin pathways. FacioScapuloHumeral Muscular Dystrophy (FSHD), one of the most common myopathies, is characterized by a complex interplay of genetic and epigenetic events. The main FSHD form is linked to reduced copy number of the D4Z4 macrosatellite repeat on 4q35, causing loss of silencing and aberrant expression of the D4Z4-embedded DUX4 gene leading to disease. By an unknown mechanism, D4Z4 copy-number correlates with FSHD phenotype...
December 30, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/28040171/comparison-of-pcr-assays-targeting-the-multi-copy-targets-b1-gene-and-529%C3%A2-bp-repetitive-element-for-detection-of-toxoplasma-gondii-in-swine-muscle
#13
Fabrizia Veronesi, Azzurra Santoro, Giovanni Luigi Milardi, Manuela Diaferia, Raffaella Branciari, Dino Miraglia, Attilia Cioffi, Simona Gabrielli, David Ranucci
The comparison of the sensitivities of two molecular assays designed to target the multi-copy sequences of the Toxoplasma gondii genomic B1 region and 529 bp-RE respectively, in detecting T. gondii in swine muscle was assessed. Diaphragm pillars were obtained from 498 slaughtered pigs managed in intensive farms in Central Italy. Genomic DNA was extracted from the tissues and T. gondii-B1 and 529 bp-RE sequences were amplified by specific PCR protocols. Toxoplasma gondii DNA was detected in 165 samples (33...
May 2017: Food Microbiology
https://www.readbyqxmd.com/read/28036308/early-detection-and-control-of-an-acinetobacter-baumannii-multi-resistant-outbreak-in-a-hospital-in-quito-ecuador
#14
Monica Cartelle Gestal, Jeannete Zurita, Gabriela Gualpa, Cecibel Gonzalez, Ariane Paz Y Mino
INTRODUCTION: Acinetobacter baumannii (ABA) is an important opportunistic pathogen associated with high mortality rates in intensive care units (ICUs). An outbreak in the ICU of a secondary-level hospital in Quito, Ecuador, occurred during April and May 2015 and was successfully controlled. METHODOLOGY: Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) and repetitive element palindromic (REP)-PCR was conducted on all isolates recovered from patients, as well as environmental samples, to confirm the presence of an outbreak...
December 30, 2016: Journal of Infection in Developing Countries
https://www.readbyqxmd.com/read/28027305/evaluation-of-polymerase-chain-reaction-pcr-with-slit-skin-smear-examination-sss-to-confirm-clinical-diagnosis-of-leprosy-in-eastern-nepal
#15
Shraddha Siwakoti, Keshav Rai, Narayan Raj Bhattarai, Sudha Agarwal, Basudha Khanal
BACKGROUND: Detection of Mycobacterium leprae in slit skin smear (SSS) is a gold standard technique for the leprosy diagnosis. Over recent years, molecular diagnosis by using PCR has been increasingly used as an alternative for its diagnosis due to its higher sensitivity. This study was carried out for comparative evaluation of PCR and SSS microscopy in a cohort of new leprosy cases diagnosed in B. P. Koirala Institute of health Sciences, Dharan, Nepal. METHODOLOGY/PRINCIPAL FINDINGS: In this prospective crossectional study, 50 new clinically diagnosed cases of leprosy were included...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28025364/-managing-the-placebo-effect-the-single-blind-placebo-lead-in-response-in-two-pain-models
#16
R Norman Harden, Meryem Saracoglu, Sara Connolly, Amy Kirsling, Kelly Comstock, Katherine Khazey, Trevor Gerson, John Burns
OBJECTIVE: "Placebo effects" in analgesic medication trials for chronic pain are pervasive; however, little is known regarding mechanisms or factors that may influence the presence or magnitude of these effects. Our objective is to consider elements of the placebo response in the context of two pain models using a "single-blind placebo lead-in" design (SBPLI). METHODS: As part of two pilot drug trials using knee osteoarthritis (KOA) and non-radicular low back pain (LBP) subjects, SBPLI protocols were conducted...
December 2016: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
https://www.readbyqxmd.com/read/28024146/genome-wide-mapping-of-autonomous-promoter-activity-in-human-cells
#17
Joris van Arensbergen, Vincent D FitzPatrick, Marcel de Haas, Ludo Pagie, Jasper Sluimer, Harmen J Bussemaker, Bas van Steensel
Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of the sequences that could be tested. Here we present 'survey of regulatory elements' (SuRE), a method that assays more than 10(8) DNA fragments, each 0.2-2 kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library of random genomic fragments upstream of a 20-bp barcode is constructed, and decoded by paired-end sequencing...
December 26, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/28018282/perceived-duration-increases-with-contrast-but-only-a-little
#18
Christopher P Benton, Annabelle S Redfern
Recent adaptation studies provide evidence for early visual areas playing a role in duration perception. One explanation for the pronounced duration compression commonly found with adaptation is that it reflects adaptation-driven stimulus-specific reduction in neural activity in early visual areas. If this level of stimulus-associated neural activity does drive duration, then we would expect a strong effect of contrast on perceived duration as electrophysiological studies shows neural activity in early visual areas to be strongly related to contrast...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/28010926/increased-methylation-of-repetitive-elements-and-dna-repair-genes-is-associated-with-higher-dna-oxidation-in-children-in-an-urbanized-industrial-environment
#19
Isabel Alvarado-Cruz, Marco Sánchez-Guerra, Leticia Hernández-Cadena, Andrea De Vizcaya-Ruiz, Violeta Mugica, Nadia Azenet Pelallo-Martínez, María de Jesús Solís-Heredia, Hyang-Min Byun, Andrea Baccarelli, Betzabet Quintanilla-Vega
DNA methylation in DNA repair genes participates in the DNA damage regulation. Particulate matter (PM), which has metals and polycyclic aromatic hydrocarbons (PAHs) adsorbed, among others has been linked to adverse health outcomes and may modify DNA methylation. To evaluate PM exposure impact on repetitive elements and gene-specific DNA methylation and DNA damage, we conducted a cross-sectional study in 150 schoolchildren (7-10 years old) from an urbanized, industrial area of the metropolitan area of Mexico City (MAMC), which frequently exhibits PM concentrations above safety standards...
January 2017: Mutation Research
https://www.readbyqxmd.com/read/28009107/detection-of-salmonella-enterica-serovar-montevideo-and-newport-in-free-ranging-sea-turtles-and-beach-sand-in-the-caribbean-and-persistence-in-sand-and-seawater-microcosms
#20
A-K Ives, E Antaki, K Stewart, S Francis, M T Jay-Russell, F Sithole, M T Kearney, M J Griffin, E Soto
Salmonellae are Gram-negative zoonotic bacteria that are frequently part of the normal reptilian gastrointestinal flora. The main objective of this project was to estimate the prevalence of non-typhoidal Salmonella enterica in the nesting and foraging populations of sea turtles on St. Kitts and in sand from known nesting beaches. Results suggest a higher prevalence of Salmonella in nesting leatherback sea turtles compared with foraging green and hawksbill sea turtles. Salmonella was cultured from 2/9 and identified by molecular diagnostic methods in 3/9 leatherback sea turtle samples...
December 23, 2016: Zoonoses and Public Health
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