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repetitive elements

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https://www.readbyqxmd.com/read/28324041/line1-cpg-dna-hypomethylation-in-granulosa-cells-and-blood-leukocytes-is-associated-with-pcos-and-related-traits
#1
Pooja Sagvekar, Vijay Mangoli, Sadhana Desai, Anushree Patil, Srabani Mukherjee
CONTEXT: Altered global DNA methylation is indicative of epigenomic instability concerning chronic disease-states. Investigating its incidence and association with polycystic ovary syndrome (PCOS) is essential towards understanding the etiopathogenesis of this disorder. OBJECTIVES: To assess, global DNA methylation differences in peripheral blood leukocytes (PBLs) and cumulus granulosa cells (CGCs) of PCOS and controls and their association with PCOS and its traits...
January 9, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28315381/alfa-helix-to-beta-sheet-transition-in-long-chain-poly-l-lysine-formation-of-alfa-helical-fibrils-by-poly-l-lysine
#2
Katarzyna Cieślik-Boczula
The temperature-induced α-helix to β-sheet transition in long-chain poly-l-lysine (PLL), accompanied by the gauche-to-trans isomerization of CH2 groups in the hydrocarbon side chains of Lys amino acid residues, and formation of β-sheet as well as α-helix fibrillar aggregates of PLL have been studied using Fourier-transform infrared (FT-IR) and vibrational circular dichroism (VCD) spectroscopy, and transmission electron microscopy (TEM). In a low-temperature alkaline water solution or in a methanol-rich water mixture, the secondary structure of PLL is represented by α-helical conformations with unordered and gauche-rich hydrocarbon side chains...
March 14, 2017: Biochimie
https://www.readbyqxmd.com/read/28294943/a-team-of-heterochromatin-factors-collaborates-with-small-rna-pathways-to-combat-repetitive-elements-and-germline-stress
#3
Alicia N McMurchy, Przemyslaw Stempor, Tessa Gaarenstroom, Brian Wysolmerski, Yan Dong, Darya Aussianikava, Alex Appert, Ni Huang, Paulina Kolasinska-Zwierz, Alexandra Sapetschnig, Eric A Miska, Julie Ahringer
Repetitive sequences derived from transposons make up a large fraction of eukaryotic genomes and must be silenced to protect genome integrity. Repetitive elements are often found in heterochromatin; however, the roles and interactions of heterochromatin proteins in repeat regulation are poorly understood. Here we show that a diverse set of C. elegans heterochromatin proteins act together with the piRNA and nuclear RNAi pathways to silence repetitive elements and prevent genotoxic stress in the germ line. Mutants in genes encoding HPL-2/HP1, LIN-13, LIN-61, LET-418/Mi-2, and H3K9me2 histone methyltransferase MET-2/SETDB1 also show functionally redundant sterility, increased germline apoptosis, DNA repair defects, and interactions with small RNA pathways...
March 15, 2017: ELife
https://www.readbyqxmd.com/read/28293300/silencing-markers-are-retained-on-pericentric-heterochromatin-during-murine-primordial-germ-cell-development
#4
Aristea Magaraki, Godfried van der Heijden, Esther Sleddens-Linkels, Leonidas Magarakis, Wiggert A van Cappellen, Antoine H F M Peters, Joost Gribnau, Willy M Baarends, Maureen Eijpe
BACKGROUND: In the nuclei of most mammalian cells, pericentric heterochromatin is characterized by DNA methylation, histone modifications such as H3K9me3 and H4K20me3, and specific binding proteins like heterochromatin-binding protein 1 isoforms (HP1 isoforms). Maintenance of this specialized chromatin structure is of great importance for genome integrity and for the controlled repression of the repetitive elements within the pericentric DNA sequence. Here we have studied histone modifications at pericentric heterochromatin during primordial germ cell (PGC) development using different fixation conditions and fluorescent immunohistochemical and immunocytochemical protocols...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28284701/visualizing-stressful-aspects-of-repetitive-motion-tasks-and-opportunities-for-ergonomic-improvements-using-computer-vision
#5
Runyu L Greene, David P Azari, Yu Hen Hu, Robert G Radwin
Patterns of physical stress exposure are often difficult to measure, and the metrics of variation and techniques for identifying them is underdeveloped in the practice of occupational ergonomics. Computer vision has previously been used for evaluating repetitive motion tasks for hand activity level (HAL) utilizing conventional 2D videos. The approach was made practical by relaxing the need for high precision, and by adopting a semi-automatic approach for measuring spatiotemporal characteristics of the repetitive task...
March 9, 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/28278269/small-rodents-as-paratenic-or-intermediate-hosts-of-carnivore-parasites-in-berlin-germany
#6
Jürgen Krücken, Julia Blümke, Denny Maaz, Janina Demeler, Sabrina Ramünke, Daniela Antolová, Roland Schaper, Georg von Samson-Himmelstjerna
Rodents are important intermediate and paratenic hosts for carnivore parasites, including the important zoonotic agents Toxoplasma, Echinococcus and Toxocara. Monitoring of such parasites in rodents can be used to detect increasing risks for human and veterinary public health. Rodents were trapped at four sites in Berlin, two near the city center, two at the periphery. PCRs were conducted to detect Coccidia (target ITS-1) and specifically Toxoplasma gondii (repetitive element) in brain and ascarids (ITS-2) in muscle or brain tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28262624/a-novel-four-dimensional-angiographic-approach-to-assess-dynamic-superficial-wall-stress-of-coronary-arteries-in-vivo-initial-experience-in-evaluating-vessel-sites-with-subsequent-plaque-rupture
#7
Xinlei Wu, Clemens von Birgelen, Takashi Muramatsu, Yingguang Li, Niels Ramsing Holm, Johan H C Reiber, Shengxian Tu
AIMS: Repetitive and fluctuating stress is one important biomechanical mechanism that underlies the rupture of atherosclerotic plaques. We developed a novel coronary angiography-based method for in vivo 4-dimensional analysis of dynamic superficial wall stress (SWS) in coronary plaques and applied it for the first time in two clinical cases to investigate the potential relationship between dynamic stress concentration at baseline and plaque rupture during acute coronary syndrome (ACS) several months later...
March 7, 2017: EuroIntervention
https://www.readbyqxmd.com/read/28261276/dietary-intake-is-associated-with-respiratory-health-outcomes-and-dna-methylation-in-children-with-asthma
#8
L Montrose, T J Ward, E O Semmens, Y H Cho, B Brown, C W Noonan
BACKGROUND: Asthma is an increasingly common chronic disease among children, and data point toward a complex mechanism involving genetic, environmental and epigenetic factors. Epigenetic modifications such as DNA hypo- or hyper-methylation have been shown to occur in response to environmental exposures including dietary nutrients. METHODS: Within the context of the asthma randomized trial of indoor wood smoke (ARTIS) study, we investigated relationships between diet, asthma health measures, and DNA methylation...
2017: Allergy, Asthma, and Clinical Immunology
https://www.readbyqxmd.com/read/28257158/dna-methylation-of-retrotransposons-dna-transposons-and-genes-in-sugar-beet-beta-vulgaris-l
#9
Falk Zakrzewski, Martin Schmidt, Mieke Van Lijsebettens, Thomas Schmidt
The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses activity of transposable elements (TEs), affects gene expression, and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of the worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%) in particular, satellite DNA, retrotransposons, and DNA transposons...
March 3, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28250819/smyd5-regulates-h4k20me3-marked-heterochromatin-to-safeguard-es-cell-self-renewal-and-prevent-spurious-differentiation
#10
Benjamin L Kidder, Gangqing Hu, Kairong Cui, Keji Zhao
BACKGROUND: Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated histone 4 lysine 20 (H4K20me3) in pluripotency and development are largely unknown. RESULTS: Here, we show that the histone lysine methyltransferase SMYD5 mediates H4K20me3 at heterochromatin regions. Depletion of SMYD5 leads to compromised self-renewal, including dysregulated expression of OCT4 targets, and perturbed differentiation...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28245223/phylogeny-and-chromosomal-diversification-in-the-dichroplus-elongatus-species-group-orthoptera-melanoplinae
#11
Elio R D Castillo, Alberto Taffarel, Maximiliano M Maronna, María Marta Cigliano, Octavio M Palacios-Gimenez, Diogo C Cabral-de-Mello, Dardo A Martí
In an attempt to track the chromosomal differentiation in the Dichroplus elongatus species group, we analyzed the karyotypes of four species with classical cytogenetic and mapping several multigene families through fluorescent in situ hybridization (FISH). We improved the taxon sampling of the D. elongatus species group adding new molecular data to infer the phylogeny of the genus and reconstruct the karyotype evolution. Our molecular analyses recovered a fully resolved tree with no evidence for the monophyly of Dichroplus...
2017: PloS One
https://www.readbyqxmd.com/read/28244250/resolving-fine-grained-dynamics-of-retrotransposons-comparative-analysis-of-inferential-methods-and-genomic-resources
#12
Rimjhim Roy Choudhury, Jean-Marc Neuhaus, Christian Parisod
Transposable elements support genome diversification, but comparison of their proliferation and genomic distribution within and among species is necessary to characterize their role in evolution. Such inferences are challenging because of potential bias with incomplete sampling of repetitive genome regions. Here, using the assembled genome as well as genome skimming datasets in Arabis alpina, we assessed the limits of current approaches inferring the biology of transposable elements. Long terminal repeat-retrotransposons (LTR-RTs) identified in the assembled genome were classified into monophyletic lineages (here called tribes), including families of similar copies in Arabis along with elements from related Brassicaceae...
February 28, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28230735/new-evidence-for-the-theory-of-chromosome-organization-by-repetitive-elements-core
#13
Shao-Jun Tang
Repetitive DNA elements were proposed to coordinate chromatin folding and interaction in chromosomes by their intrinsic homology-based clustering ability. A recent analysis of the data sets from chromosome-conformation-capture experiments confirms the spatial clustering of DNA repeats of the same family in the nuclear space, and thus provides strong new support for the CORE theory.
February 20, 2017: Genes
https://www.readbyqxmd.com/read/28228849/considerations-and-complications-of-mapping-small-rna-high-throughput-data-to-transposable-elements
#14
Alexandros Bousios, Brandon S Gaut, Nikos Darzentas
BACKGROUND: High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28225007/full-3d-modelling-of-pulse-propagation-enables-efficient-nonlinear-frequency-conversion-with-low-energy-laser-pulses-in-a-single-element-tripler
#15
Tomasz M Kardaś, Michał Nejbauer, Paweł Wnuk, Bojan Resan, Czesław Radzewicz, Piotr Wasylczyk
Although new optical materials continue to open up access to more and more wavelength bands where femtosecond laser pulses can be generated, light frequency conversion techniques are still indispensable in filling the gaps on the ultrafast spectral scale. With high repetition rate, low pulse energy laser sources (oscillators) tight focusing is necessary for a robust wave mixing and the efficiency of broadband nonlinear conversion is limited by diffraction as well as spatial and temporal walk-off. Here we demonstrate a miniature third harmonic generator (tripler) with conversion efficiency exceeding 30%, producing 246 fs UV pulses via cascaded second order processes within a single laser beam focus...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28221953/comparative-evaluation-of-genomic-and-laboratory-approaches-for-determination-of-shiga-toxin-subtypes-in-escherichia-coli
#16
Catherine D Carrillo, Adam G Koziol, Amit Mathews, Noriko Goji, Dominic Lambert, George Huszczynski, Martine Gauthier, Kingsley Amoako, Burton W Blais
The determination of Shiga toxin (ST) subtypes can be an important element in the risk characterization of foodborne ST-producing Escherichia coli (STEC) isolates for making risk management decisions. ST subtyping methods include PCR techniques based on electrophoretic or pyrosequencing analysis of amplicons and in silico techniques based on whole genome sequence analysis using algorithms that can be readily incorporated into bioinformatics analysis pipelines for characterization of isolates by their genetic composition...
December 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28214512/dynamics-and-context-dependent-roles-of-dna-methylation
#17
REVIEW
Christina Ambrosi, Massimiliano Manzo, Tuncay Baubec
DNA methylation is one of the most extensively studied epigenetic marks. It is involved in transcriptional gene silencing, it plays important roles during mammalian development and its perturbation is often associated with human diseases. In mammalian genomes, DNA methylation is a prevalent modification that decorates the majority of cytosines. It is found at the promoters and enhancers of inactive genes, at repetitive elements and within transcribed gene bodies. Its presence at promoters is dynamically linked to gene activity, suggesting that it could directly influence gene expression patterns and cellular identity...
February 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28198363/gut-memories-do-not-fade-epigenetic-regulation-of-lasting-gut-homing-receptor-expression-in-cd4-memory-t-cells
#18
B A Szilagyi, J Triebus, C Kressler, M de Almeida, S Tierling, P Durek, M Mardahl, A Szilagyi, S Floess, J Huehn, U Syrbe, J Walter, J K Polansky, A Hamann
The concept of a "topographical memory" in lymphocytes implies a stable expression of homing receptors mediating trafficking of lymphocytes back to the tissue of initial activation. However, a significant plasticity of the gut-homing receptor α4β7 was found in CD8(+) T cells, questioning the concept. We now demonstrate that α4β7 expression in murine CD4(+) memory T cells is, in contrast, imprinted and remains stable in the absence of the inducing factor retinoic acid (RA) or other stimuli from mucosal environments...
February 15, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/28195345/in-vivo-measurements-of-human-neck-skin-elasticity-using-mri-and-finite-element-modeling
#19
Yunqiang An, Changjin Ji, Yong Li, Jianxia Wang, Xinyue Zhang, Yaqi Huang
PURPOSE: The assessment of mechanical properties of the human skin is very important in investigating the mechanism of obstructive sleep apnea, a common disorder characterized by repetitive collapse and obstruction of the upper airway during sleep. In this study, a unique method, combining magnetic resonance imaging (MRI) and finite element modeling (FEM), was developed to obtain the value of the in vivo elastic modulus of the neck skin. MEHTHOD: A total of 22 subjects, 16 males and 6 females, were recruited to participate in the MRI studies...
February 13, 2017: Medical Physics
https://www.readbyqxmd.com/read/28194445/diverse-repetitive-element-rna-expression-defines-epigenetic-and-immunologic-features-of-colon-cancer
#20
Niyati Desai, Dipti Sajed, Kshitij S Arora, Alexander Solovyov, Mihir Rajurkar, Jacob R Bledsoe, Srinjoy Sil, Ramzi Amri, Eric Tai, Olivia C MacKenzie, Mari Mino-Kenudson, Martin J Aryee, Cristina R Ferrone, David L Berger, Miguel N Rivera, Benjamin D Greenbaum, Vikram Deshpande, David T Ting
There is tremendous excitement for the potential of epigenetic therapies in cancer, but the ability to predict and monitor response to these drugs remains elusive. This is in part due to the inability to differentiate the direct cytotoxic and the immunomodulatory effects of these drugs. The DNA-hypomethylating agent 5-azacitidine (AZA) has shown these distinct effects in colon cancer and appears to be linked to the derepression of repeat RNAs. LINE and HERV are two of the largest classes of repeats in the genome, and despite many commonalities, we found that there is heterogeneity in behavior among repeat subtypes...
February 9, 2017: JCI Insight
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