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https://www.readbyqxmd.com/read/28643131/strong-comma-free-codes-in-genetic-information
#1
Elena Fimmel, Christian J Michel, Lutz Strüngmann
Comma-free codes constitute a class of circular codes, which has been widely studied, in particular by Golomb et al. (Biologiske Meddelelser, Kongelige Danske Videnskabernes Selskab 23:1-34, 1958a, Can J Math 10:202-209, 1958b), Michel et al. (Comput Math Appl 55:989-996, 2008a, Theor Comput Sci 401:17-26, 2008b, Inf Comput 212:55-63, 2012), Michel and Pirillo (Int J Comb 2011:659567, 2011), and Fimmel and Strüngmann (J Theor Biol 389:206-213, 2016). Based on a recent approach using graph theory to study circular codes Fimmel et al...
June 22, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28624222/targeting-dmpk-with-antisense-oligonucleotide-improves-muscle-strength-in-myotonic-dystrophy-type-1-mice
#2
Dominic Jauvin, Jessina Chrétien, Sanjay K Pandey, Laurie Martineau, Lucille Revillod, Guillaume Bassez, Aline Lachon, A Robert McLeod, Geneviève Gourdon, Thurman M Wheeler, Charles A Thornton, C Frank Bennett, Jack Puymirat
Myotonic dystrophy type 1 (DM1), a dominant hereditary muscular dystrophy, is caused by an abnormal expansion of a (CTG)n trinucleotide repeat in the 3' UTR of the human dystrophia myotonica protein kinase (DMPK) gene. As a consequence, mutant transcripts containing expanded CUG repeats are retained in nuclear foci and alter the function of splicing regulatory factors members of the MBNL and CELF families, resulting in alternative splicing misregulation of specific transcripts in affected DM1 tissues. In the present study, we treated DMSXL mice systemically with a 2'-4'-constrained, ethyl-modified (ISIS 486178) antisense oligonucleotide (ASO) targeted to the 3' UTR of the DMPK gene, which led to a 70% reduction in CUG(exp) RNA abundance and foci in different skeletal muscles and a 30% reduction in the heart...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28621832/break-induced-replication-links-microsatellite-expansion-to-complex-genome-rearrangements
#3
REVIEW
Michael Leffak
The instability of microsatellite DNA repeats is responsible for at least 40 neurodegenerative diseases. Recently, Mirkin and co-workers presented a novel mechanism for microsatellite expansions based on break-induced replication (BIR) at sites of microsatellite-induced replication stalling and fork collapse. The BIR model aims to explain single-step, large expansions of CAG/CTG trinucleotide repeats in dividing cells. BIR has been characterized extensively in Saccharomyces cerevisiae as a mechanism to repair broken DNA replication forks (single-ended DSBs) and degraded telomeric DNA...
June 16, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28617590/structure-and-dynamics-of-rna-repeat-expansions-that-cause-huntington-s-disease-and-myotonic-dystrophy-type-1
#4
Jonathan L Chen, Damian M VanEtten, Matthew A Fountain, Ilyas Yildirim, Matthew D Disney
RNA repeat expansions cause a host of incurable, genetically-defined diseases. The most common class of RNA repeats are trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics...
June 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28612427/simulation-based-investigation-of-deleterious-nssnp-s-in-atxn2-gene-and-its-structural-consequence-towards-spinocerebellar-ataxia
#5
Siddharth Sinha, Sharad Verma, Aditi Singh, Pallavi Somvanshi, Abhinav Grover
Spinocerebellar degeneration, termed as ataxia is a neurological disorder of central nervous system, characterized by limb in-coordination and a progressive gait. The patient also demonstrates specific symptoms of muscle weakness, slurring of speech, and decreased vibration senses. Expansion of polyglutamine trinucleotide (CAG) within ATXN2 gene with 35 or more repeats, results in spinocerebellar ataxia type-2. Protein ataxin-2 coded by ATXN2 gene has been reported to have a crucial role in translation of the genetic information through sequestering the histone acetyl transferases (HAT) resulting in a state of hypo-acetylation...
June 14, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28611596/ethidium-bromide-modifies-the-agarose-electrophoretic-mobility-of-cag%C3%A2-ctg-alternative-dna-structures-generated-by-pcr
#6
Mário Gomes-Pereira, Darren G Monckton
The abnormal expansion of unstable simple sequence DNA repeats can cause human disease through a variety of mechanisms, including gene loss-of-function, toxic gain-of-function of the encoded protein and toxicity of the repeat-containing RNA transcript. Disease-associated unstable DNA repeats display unusual biophysical properties, including the ability to adopt non-B-DNA structures. CAG•CTG trinucleotide sequences, in particular, have been most extensively studied and they can fold into slipped-stranded DNA structures, which have been proposed as mutation intermediates in repeat size expansion...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28608272/ctg18-1-repeat-expansion-may-reduce-tcf4-gene-expression-in-corneal-endothelial-cells-of-german-patients-with-fuchs-dystrophy
#7
Sabine Foja, Mirjam Luther, Katrin Hoffmann, Andreas Rupprecht, Claudia Gruenauer-Kloevekorn
PURPOSE: It was the aim of this investigation to elucidate the functional effects of CTG18.1 trinucleotide repeat expansion and the polymorphism rs613872 in the transcription factor 4 (TCF4) in corneas of patients affected by Fuchs' endothelial corneal dystrophy (FECD). METHODS: Sixty-one unrelated German patients with FECD and 113 unaffected controls were investigated and genotyped for the CTG18.1 locus by triplet primed PCR (TP-PCR) and the rs613872 polymorphism via Sanger sequencing and by employing genomic DNA from peripheral blood leucocytes...
June 12, 2017: Graefe's Archive for Clinical and Experimental Ophthalmology
https://www.readbyqxmd.com/read/28606048/immunomodulatory-strategies-for-huntington-s-disease-treatment
#8
Gabriela Delevati Colpo, Natalia Pessoa Rocha, Erin Fur Stimming, Antonio Lucio Teixeira
Huntington's disease (HD) is an autosomal-dominant, progressive neurodegenerative disease characterized by selective loss of neurons in the striatum and cortex, which leads to progressive motor dysfunction, cognitive decline and behavioral symptoms. HD is caused by a trinucleotide (CAG) repeat expansion in the gene encoding for huntingtin (HTT). Despite the fact that the HD gene was identified over 20 years ago, there is no effective disease-modifying therapy for HD and only symptomatic therapies are available to date...
June 12, 2017: CNS & Neurological Disorders Drug Targets
https://www.readbyqxmd.com/read/28605995/dna-trinucleotide-gaa-repeats-in-human-genome-hint-for-disease-pathogenesis
#9
Himanshu Narayan Singh, Barbara Scheiber-Mojdehkar, Moganty R Rajeswari
Short DNA triplet repeats are generally considered to 'benign' in nature, however, it can lead to abnormal genetic features by inducing hyper expansion including mutational hotspots, unusual DNA structure etc. Thus, the expanded DNA base triplets in human genome are expected to play crucial role in disease pathogenesis. One such triplet repeat expansion of (GAA) is observed in FXN gene which is well established to cause neurological disease "Friedreich's ataxia". To explore the association of repeats in other genes if any, we performed a systematic search in the entire human genome...
June 12, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28600492/genome-wide-mapping-and-characterization-of-microsatellites-in-the-swamp-eel-genome
#10
Zhigang Li, Feng Chen, Chunhua Huang, Weixin Zheng, Chunlai Yu, Hanhua Cheng, Rongjia Zhou
We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs...
June 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28590448/striatal-vulnerability-in-huntington-s-disease-neuroprotection-versus-neurotoxicity
#11
REVIEW
Ryoma Morigaki, Satoshi Goto
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by the expansion of a CAG trinucleotide repeat encoding an abnormally long polyglutamine tract (PolyQ) in the huntingtin (Htt) protein. In HD, striking neuropathological changes occur in the striatum, including loss of medium spiny neurons and parvalbumin-expressing interneurons accompanied by neurodegeneration of the striosome and matrix compartments, leading to progressive impairment of reasoning, walking and speaking abilities...
June 7, 2017: Brain Sciences
https://www.readbyqxmd.com/read/28576825/identification-of-an-optimized-2-o-methylated-tri-nucleotide-rna-motif-inhibiting-toll-like-receptor-7-and-8
#12
Felix C F Schmitt, Isabel Freund, Markus A Weigand, Mark Helm, Alexander H Dalpke, Tatjana Eigenbrod
Bacterial RNA serves an important function as activator of the innate immune system. In humans bacterial RNA is sensed by the endosomal receptors TLR7 and TLR8. Differences in the posttranscriptional modification profile of prokaryotic as compared to eukaryotic RNA allow innate immune cells to discriminate between 'host' and 'foreign' RNA. Ribose 2'-O-methylation is of particular importance and has been reported to antagonize TLR7/8 activation. Yet, the exact sequence context in which 2'-O-methylation has to occur to mediate its inhibitory activity remains largely undefined...
June 2, 2017: RNA
https://www.readbyqxmd.com/read/28561926/quantitative-sonographic-assessment-of-myotonia
#13
Alon Abraham, Ari Breiner, Carolina Barnett, Vera Bril, Hans D Katzberg
INTRODUCTION: The goal of this study was to explore ultrasound imaging for qualitative and quantitative assessment of myotonia. METHODS: 16 patients with myotonia and 16 controls underwent sonographic evaluation of the thenar eminence muscles to assess the relaxation time after muscle percussion. RESULTS: The mean time for complete muscle relaxation in patients with myotonia was longer than that of controls. A cut-off of >0.9 seconds for myotonia detection had a sensitivity of 88% and a specificity of 100%...
May 31, 2017: Muscle & Nerve
https://www.readbyqxmd.com/read/28544401/induced-fit-recognition-of-ccg-trinucleotide-repeats-by-a-nickel-chromomycin-complex-results-in-large-scale-dna-deformation
#14
Wen-Hsuan Tseng, Chung-Ke Chang, Pei-Ching Wu, Nien-Jen Hu, Gene-Hsiang Lee, Ching-Cherng Tzeng, Stephen Neidle, Ming-Hon Hou
Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII(Chro)2 (Chro = chromomycin A3) was found to bind specifically to the minor groove of (CCG)n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies have revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the Ni(II) chelate itself...
May 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28542371/whole-genome-sequencing-of-spermatocytic-tumors-provides-insights-into-the-mutational-processes-operating-in-the-male-germline
#15
Eleni Giannoulatou, Geoffrey J Maher, Zhihao Ding, Ad J M Gillis, Lambert C J Dorssers, Alexander Hoischen, Ewa Rajpert-De Meyts, Gilean McVean, Andrew O M Wilkie, Leendert H J Looijenga, Anne Goriely
Adult male germline stem cells (spermatogonia) proliferate by mitosis and, after puberty, generate spermatocytes that undertake meiosis to produce haploid spermatozoa. Germ cells are under evolutionary constraint to curtail mutations and maintain genome integrity. Despite constant turnover, spermatogonia very rarely form tumors, so-called spermatocytic tumors (SpT). In line with the previous identification of FGFR3 and HRAS selfish mutations in a subset of cases, candidate gene screening of 29 SpTs identified an oncogenic NRAS mutation in two cases...
2017: PloS One
https://www.readbyqxmd.com/read/28535287/a-flow-cytometry-based-screen-identifies-mbnl1-modulators-that-rescue-splicing-defects-in-myotonic-dystrophy-type-i
#16
Fan Zhang, Nicole E Bodycombe, Keith M Haskell, Yumei L Sun, Eric T Wang, Carl A Morris, Lyn H Jones, Lauren D Wood, Mathew T Pletcher
Myotonic Dystrophy Type 1 (DM1) is a rare genetic disease caused by expansion of CTG trinucleotide repeats ((CTG)exp) in the 3' untranslated region of the DMPK gene. The repeat transcripts sequester the RNA binding protein Muscleblind-like protein 1 (MBNL1) and hamper its normal function in pre-mRNA splicing. Overexpressing exogenous MBNL1 in the DM1 mouse model has been shown to rescue the splicing defects and reverse myotonia. Although a viable therapeutic strategy, pharmacological modulators of MBNL1 expression have not been identified...
May 23, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28523552/epigenetics-of-huntington-s-disease
#17
Silvia Bassi, Takshashila Tripathi, Alan Monziani, Francesca Di Leva, Marta Biagioli
Huntington's disease (HD) is a genetic, fatal autosomal dominant neurodegenerative disorder typically occurring in midlife with symptoms ranging from chorea, to dementia, to personality disturbances (Philos Trans R Soc Lond Ser B Biol Sci 354:957-961, 1999). HD is inherited in a dominant fashion, and the underlying mutation in all cases is a CAG trinucleotide repeat expansion within exon 1 of the HD gene (Cell 72:971-983, 1993). The expanded CAG repeat, translated into a lengthened glutamine tract at the amino terminus of the huntingtin protein, affects its structural properties and functional activities...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523296/a-systematic-review-of-the-possible-carcinogenic-role-of-the-aristolochic-acid
#18
Tivadar Bara, Simona Gurzu, Haruhiko Sugimura, Tivadar Bara, Marius Alexandru Beleaua, Ioan Jung
Aristolochic acid (AA) is a bioactive component of Chinese herbs, dietary supplements, slimming pills and contaminated flour, which is known to induce chronic tubulointerstitial disease. AA is also shown to be involved in the genesis of the upper urinary tract urothelial carcinoma (UTUC) and some other cancers, but its tumorigenic role is far to be understood. We performed a systematic literature review regarding the involvement of AA in malignant processes and molecular pathways of carcinogenesis. Twenty representative papers were selected for this review...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
https://www.readbyqxmd.com/read/28504725/metformin-ameliorates-core-deficits-in-a-mouse-model-of-fragile-x-syndrome
#19
Ilse Gantois, Arkady Khoutorsky, Jelena Popic, Argel Aguilar-Valles, Erika Freemantle, Ruifeng Cao, Vijendra Sharma, Tine Pooters, Anmol Nagpal, Agnieszka Skalecka, Vinh T Truong, Shane Wiebe, Isabelle A Groves, Seyed Mehdi Jafarnejad, Clément Chapat, Elizabeth A McCullagh, Karine Gamache, Karim Nader, Jean-Claude Lacaille, Christos G Gkogkas, Nahum Sonenberg
Fragile X syndrome (FXS) is the leading monogenic cause of autism spectrum disorders (ASD). Trinucleotide repeat expansions in FMR1 abolish FMRP expression, leading to hyperactivation of ERK and mTOR signaling upstream of mRNA translation. Here we show that metformin, the most widely used drug for type 2 diabetes, rescues core phenotypes in Fmr1(-/y) mice and selectively normalizes ERK signaling, eIF4E phosphorylation and the expression of MMP-9. Thus, metformin is a potential FXS therapeutic.
June 2017: Nature Medicine
https://www.readbyqxmd.com/read/28489852/recurrent-promoter-mutations-in-melanoma-are-defined-by-an-extended-context-specific-mutational-signature
#20
Nils Johan Fredriksson, Kerryn Elliott, Stefan Filges, Jimmy Van den Eynden, Anders Ståhlberg, Erik Larsson
Sequencing of whole tumor genomes holds the promise of revealing functional somatic regulatory mutations, such as those described in the TERT promoter. Recurrent promoter mutations have been identified in many additional genes and appear to be particularly common in melanoma, but convincing functional data such as influence on gene expression has been more elusive. Here, we show that frequently recurring promoter mutations in melanoma occur almost exclusively at cytosines flanked by a distinct sequence signature, TTCCG, with TERT as a notable exception...
May 2017: PLoS Genetics
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