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https://www.readbyqxmd.com/read/27922500/facioscapulohumeral-muscular-dystrophy
#1
Jeffrey M Statland, Rabi Tawil
PURPOSE OF REVIEW: This article describes the clinical characteristics, diagnosis, molecular pathogenesis, and treatment of facioscapulohumeral muscular dystrophy (FSHD). RECENT FINDINGS: FSHD comprises two genetically distinct types that converge on a common downstream pathway of the expression of the toxic protein DUX4. Approximately 95% of patients have FSHD type 1 (FSHD1), in which loss of DNA repetitive elements (D4Z4 repeats) in the subtelomeric region of chromosome 4q causes decreased methylation and epigenetic derepression of DUX4, a gene contained within each D4Z4 repeat...
December 2016: Continuum: Lifelong Learning in Neurology
https://www.readbyqxmd.com/read/27918448/secondary-structure-adopted-by-the-gly-gly-x-repetitive-regions-of-dragline-spider-silk
#2
Geoffrey M Gray, Arjan van der Vaart, Chengchen Guo, Justin Jones, David Onofrei, Brian R Cherry, Randolph V Lewis, Jeffery L Yarger, Gregory P Holland
Solid-state NMR and molecular dynamics (MD) simulations are presented to help elucidate the molecular secondary structure of poly(Gly-Gly-X), which is one of the most common structural repetitive motifs found in orb-weaving dragline spider silk proteins. The combination of NMR and computational experiments provides insight into the molecular secondary structure of poly(Gly-Gly-X) segments and provides further support that these regions are disordered and primarily non-β-sheet. Furthermore, the combination of NMR and MD simulations illustrate the possibility for several secondary structural elements in the poly(Gly-Gly-X) regions of dragline silks, including β-turns, 310-helicies, and coil structures with a negligible population of α-helix observed...
December 2, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27915087/genetically-unrelated-multidrug-and-carbapenem-resistant-citrobacter-freundii-detected-in-outpatients-admitted-to-a-portuguese-hospital
#3
Cátia Santos, Elmano Ramalheira, Gabriela Da Silva, Sónia Mendo
OBJECTIVES: Non-clonal, carbapenem- and multidrug-resistant Citrobacter freundii isolates were collected from unrelated outpatients admitted to a Portuguese hospital emergency department. One patient lived in a nursing home and was never hospitalised, whereas the other patient was repeatedly hospitalised in this hospital. The aim of this study was to unveil the molecular mechanisms associated with the carbapenem resistance of these isolates and to assess its potential dissemination. METHODS: Isolate identification was performed by VITEK(®)2 and was confirmed by 16S rDNA sequencing...
November 15, 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/27903268/long-term-outdoor-air-pollution-and-dna-methylation-in-circulating-monocytes-results-from-the-multi-ethnic-study-of-atherosclerosis-mesa
#4
Gloria C Chi, Yongmei Liu, James W MacDonald, R Graham Barr, Kathleen M Donohue, Mark D Hensley, Lifang Hou, Charles E McCall, Lindsay M Reynolds, David S Siscovick, Joel D Kaufman
BACKGROUND: DNA methylation may mediate effects of air pollution on cardiovascular disease. The association between long-term air pollution exposure and DNA methylation in monocytes, which are central to atherosclerosis, has not been studied. We investigated the association between long-term ambient air pollution exposure and DNA methylation (candidate sites and global) in monocytes of adults (aged ≥55). METHODS: One-year average ambient fine particulate matter (PM2...
December 1, 2016: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/27902367/staphylococcal-cassette-chromosome-mec-typing-and-meca-sequencing-in-methicillin-resistant-staphylococci-from-algeria-a-highly-diversified-element-with-new-mutations-in-meca
#5
Ferhat Djoudi, Celestino Bonura, Abdelaziz Touati, Aurora Aléo, Said Benallaoua, Caterina Mammina
Genetic mechanisms of methicillin resistance are still relevant in staphylococci. The aims of this study are to assess the possible exchanges of staphylococcal cassette chromosome mec (SCCmec) among isolates of methicillin-resistant staphylococci (MRS) and to check for known or new mutations in mecA DNA. A total of 35 MRS non-repetitive isolates were recovered, including 20 Staphylococcushaemolyticus, 7 Staphylococcusaureus, 4 Staphylococcussciuri, 2 Staphylococcussaprophyticus and 1 isolate each of Staphylococcusxylosus and Staphylococcuslentus...
November 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27899719/a-novel-hypothesis-for-histone-to-protamine-transition-in-bos-taurus-spermatozoa
#6
Gerly Sillaste, Lauris Kaplinski, Riho Meier, Ülle Jaakma, Elo Eriste, Andres Salumets
DNA compaction with protamines in sperm is essential for successful fertilization. However, a portion of sperm chromatin remains less tightly packed with histones, which genomic location and function remain unclear. We extracted and sequenced histone-associated DNA from sperm of nine ejaculates from three bulls. We found that the fraction of retained histones varied between samples but the variance was similar between samples from the same and different individuals. The most conserved regions showed similar abundance across all samples, while in other regions their presence correlated with the size of histone fraction...
November 29, 2016: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/27898770/the-amaranth-genome-genome-transcriptome-and-physical-map-assembly
#7
J W Clouse, D Adhikary, J T Page, T Ramaraj, M K Deyholos, J A Udall, D J Fairbanks, E N Jellen, P J Maughan
Amaranth ( L.) is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27898760/exploiting-the-repetitive-fraction-of-the-wheat-genome-for-high-throughput-single-nucleotide-polymorphism-discovery-and-genotyping
#8
Nelly Cubizolles, Elodie Rey, Frédéric Choulet, Hélène Rimbert, Christel Laugier, François Balfourier, Jacques Bordes, Charles Poncet, Peter Jack, Chris James, Jan Gielen, Odile Argillier, Jean-Pierre Jaubertie, Jérôme Auzanneau, Antje Rohde, Pieter B F Ouwerkerk, Viktor Korzun, Sonja Kollers, Laurent Guerreiro, Delphine Hourcade, Olivier Robert, Pierre Devaux, Anna-Maria Mastrangelo, Catherine Feuillet, Pierre Sourdille, Etienne Paux
Transposable elements (TEs) account for more than 80% of the wheat genome. Although they represent a major obstacle for genomic studies, TEs are also a source of polymorphism and consequently of molecular markers such as insertion site-based polymorphism (ISBP) markers. Insertion site-based polymorphisms have been found to be a great source of genome-specific single-nucleotide polymorphism (SNPs) in the hexaploid wheat ( L.) genome. Here, we report on the development of a high-throughput SNP discovery approach based on sequence capture of ISBP markers...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27898282/comparative-fingerprinting-of-the-human-microbiota-in-diabetes-and-cardiovascular-disease
#9
Emanuel Vamanu, Diana Pelinescu, Ionela Sarbu
Diabetes and cardiovascular diseases are major causes of morbidity and mortality worldwide, and are associated with changes in the human gut microbiota. To better understand the relationships between diet, disease, and the colonic microbiome, we used the in vitro GIS1 system and repetitive element palindromic polymerase chain reaction (rep-PCR) to determine the microbial fingerprints in individuals with these diseases and compared them with the fingerprints in healthy controls. Clear differences were apparent in the three groups...
November 29, 2016: Journal of Medicinal Food
https://www.readbyqxmd.com/read/27895805/blood-based-dna-methylation-as-biomarker-for-breast-cancer-a-systematic-review
#10
REVIEW
Qiuqiong Tang, Jie Cheng, Xue Cao, Harald Surowy, Barbara Burwinkel
Multiple studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop powerful screening markers for cancer. This systematic review summarizes the current evidence on methylation studies that investigated methylation level of blood-derived DNA of breast cancer (BC) patients in comparison to healthy controls by conducting a systematic literature review in PubMed and Web of Science. Essential results, such as methylation levels of BC cases and healthy controls, p values, and odds ratios, were extracted from these studies by two investigators independently...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27889452/an-rb-ezh2-complex-mediates-silencing-of-repetitive-dna-sequences
#11
Charles A Ishak, Aren E Marshall, Daniel T Passos, Carlee R White, Seung J Kim, Matthew J Cecchini, Sara Ferwati, William A MacDonald, Christopher J Howlett, Ian D Welch, Seth M Rubin, Mellissa R W Mann, Frederick A Dick
Repetitive genomic regions include tandem sequence repeats and interspersed repeats, such as endogenous retroviruses and LINE-1 elements. Repressive heterochromatin domains silence expression of these sequences through mechanisms that remain poorly understood. Here, we present evidence that the retinoblastoma protein (pRB) utilizes a cell-cycle-independent interaction with E2F1 to recruit enhancer of zeste homolog 2 (EZH2) to diverse repeat sequences. These include simple repeats, satellites, LINEs, and endogenous retroviruses as well as transposon fragments...
November 12, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27887908/the-yin-and-yang-of-nucleic-acid-based-therapy-in-the-brain
#12
REVIEW
Stefano Gustincich, Silvia Zucchelli, Antonello Mallamaci
The post-genomic era has unveiled the existence of a large repertory of non-coding RNAs and repetitive elements that play a fundamental role in cellular homeostasis and dysfunction. These may represent unprecedented opportunities to modify gene expression at the right time in the correct space in vivo, providing an almost unlimited reservoir of new potential pharmacological agents. Hijacking their mode of actions, the druggable genome can be extended to regulatory RNAs and DNA elements in a scalable fashion...
November 22, 2016: Progress in Neurobiology
https://www.readbyqxmd.com/read/27887721/comparative-multimodal-meta-analysis-of-structural-and-functional-brain-abnormalities-in-autism-spectrum-disorder-and-obsessive-compulsive-disorder
#13
Christina O Carlisi, Luke J Norman, Steve S Lukito, Joaquim Radua, David Mataix-Cols, Katya Rubia
BACKGROUND: Autism spectrum disorder (ASD) and obsessive-compulsive disorder (OCD) share inhibitory control deficits possibly underlying poor control over stereotyped and repetitive g., v/r/ dACC /MPFC); and (iv) to indicate a pathway (e.g., if this is a pathway: bilateral putamen/caudate/nucleus accumbens / pallidum /amygdala/insula). BPS style does not allow virgules to be used to represent expressions of duality or alternatives. Please express these as and/or, and, or or . BPS style does not allow virgules to be used to represent a compound modifier such as "rostral/ dorsomedial ," which should be changed to hyphen(s), such as rostral- dorsomedial ...
October 13, 2016: Biological Psychiatry
https://www.readbyqxmd.com/read/27871228/genome-wide-analysis-of-g-quadruplexes-in-herpesvirus-genomes
#14
Banhi Biswas, Manish Kandpal, Utkarsh Kumar Jauhari, Perumal Vivekanandan
BACKGROUND: G-quadruplexes are increasingly recognized as regulatory elements in human, animal, bacterial and plant genomes. The presence and function of G-quadruplexes are not well studied among herpesviruses; in particular, there are no systematic genome-wide analysis of these important secondary structures in herpesvirus genomes. RESULTS: We performed genome-wide analysis of putative quadruplex sequences (PQS) in human herpesviruses. We found unusually high PQS densities among human herpesviruses...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27859179/revisiting-the-destiny-compulsion
#15
Anna Potamianou
This paper is an attempt to deal with some questions raised by the so-called 'compulsion of destiny' constellation. In presenting the standpoints of Freud and of psychoanalysts who after him were concerned with this problematic, the author takes the view that several aspects of the configuration merit further discussion. Accordingly, the dynamics of repetition compulsion, the complexity of the projective strategy, the coexistence of passive and omnipotent trends are considered. Concerning compulsive repetitions the dimension of drive intrication is underlined, thus moderating the understanding of this clinical entity as mainly related to death drive trends...
November 17, 2016: International Journal of Psycho-analysis
https://www.readbyqxmd.com/read/27853990/multi-parametric-study-of-temperature-and-thermal-damage-of-tumor-exposed-to-high-frequency-nanosecond-pulsed-electric-fields-based-on-finite-element-simulation
#16
Yan Mi, Shaoqin Rui, Chengxiang Li, Chenguo Yao, Jin Xu, Changhao Bian, Xuefeng Tang
High-frequency nanosecond-pulsed electric fields were recently introduced for tumor or abnormal tissue ablation to solve some problems of conventional electroporation. However, it is necessary to study the thermal effects of high-field-intensity nanosecond pulses inside tissues. The multi-parametric analysis performed here is based on a finite element model of liver tissue with a tumor that has been punctured by a pair of needle electrodes. The pulse voltage used in this study ranges from 1 to 4 kV, the pulse width ranges from 50 to 500 ns, and the repetition frequency is between 100 kHz and 1 MHz...
November 16, 2016: Medical & Biological Engineering & Computing
https://www.readbyqxmd.com/read/27852842/high-throughput-deep-sequencing-for-mapping-mammalian-dna-methylation
#17
Paul M Lizardi, Qin Yan, Narendra Wajapeyee
This protocol describes methylation mapping analysis by paired-end sequencing (Methyl-MAPS). In addition to the sequence information, paired-end sequencing provides information about the physical distance between the two reads in the genome. Methyl-MAPS typically samples ∼80% of the CpG dinucleotides in the genome and is also able to report the methylation status of individual genomic loci harboring repetitive elements. This is achieved by enzymatic fractionation of the genome into methylated and unmethylated compartments...
November 16, 2016: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/27847870/computational-multiheterodyne-spectroscopy
#18
David Burghoff, Yang Yang, Qing Hu
Dual-comb spectroscopy allows for high-resolution spectra to be measured over broad bandwidths, but an essential requirement for coherent integration is the availability of a phase reference. Usually, this means that the combs' phase and timing errors must be measured and either minimized by stabilization or removed by correction, limiting the technique's applicability. We demonstrate that it is possible to extract the phase and timing signals of a multiheterodyne spectrum completely computationally, without any extra measurements or optical elements...
November 2016: Science Advances
https://www.readbyqxmd.com/read/27836984/recurrent-innovation-at-genes-required-for-telomere-integrity-in-drosophila
#19
Yuh Chwen G Lee, Courtney Leek, Mia T Levine
Telomeres are nucleoprotein complexes at the ends of linear chromosomes. These specialized structures ensure genome integrity and faithful chromosome inheritance. Recurrent addition of repetitive, telomere-specific DNA elements to chromosome ends combats end-attrition, while specialized telomere-associated proteins protect naked, double-stranded chromosome ends from promiscuous repair into end-to-end fusions. Although telomere length homeostasis and end-protection are ubiquitous across eukaryotes, there is sporadic but building evidence that the molecular machinery supporting these essential processes evolves rapidly...
November 11, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27830653/control-of-transcriptional-pausing-by-biased-thermal-fluctuations-on-repetitive-genomic-sequences
#20
Masahiko Imashimizu, Ariel Afek, Hiroki Takahashi, Lucyna Lubkowska, David B Lukatsky
In the process of transcription elongation, RNA polymerase (RNAP) pauses at highly nonrandom positions across genomic DNA, broadly regulating transcription; however, molecular mechanisms responsible for the recognition of such pausing positions remain poorly understood. Here, using a combination of statistical mechanical modeling and high-throughput sequencing and biochemical data, we evaluate the effect of thermal fluctuations on the regulation of RNAP pausing. We demonstrate that diffusive backtracking of RNAP, which is biased by repetitive DNA sequence elements, causes transcriptional pausing...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
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