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Si Chen, Lih-Yuan Deng, Dale Bowman, Jyh-Jen Horng Shiau, Tit-Yee Wong, Behrouz Madahian, Henry Horng-Shing Lu
BACKGROUND: It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature frequency profile (FFP-k), finds the frequency distribution for all words of certain length k over the whole genome sequence using (overlapping) windows of the same length. For a satisfactory result, the recommended word length (k) ranges from 6 to 15 and it may not be a multiple of 3 (codon length)...
October 6, 2016: BMC Bioinformatics
Amy Krans, Michael G Kearse, Peter K Todd
OBJECTIVE: Repeat associated non-AUG (RAN) translation drives production of toxic proteins from pathogenic repeat sequences in multiple untreatable neurodegenerative disorders. Fragile X-associated tremor/ataxia syndrome (FXTAS) is one such condition, resulting from a CGG trinucleotide repeat expansion in the 5' leader sequence of the FMR1 gene. RAN proteins from the CGG repeat accumulate in ubiquitinated inclusions in FXTAS patient brains and elicit toxicity. In addition to the CGG repeat, an antisense mRNA containing a CCG repeat is also transcribed from the FMR1 locus...
October 19, 2016: Annals of Neurology
Allen O Eghrari, Shivakumar Vasanth, Jiangxia Wang, Farnoosh Vahedi, S Amer Riazuddin, John D Gottsch
PURPOSE: Fuchs dystrophy is the leading indication of corneal transplantation in the United States. A CTG18.1 trinucleotide repeat in TCF4 correlates with increased severity in Fuchs dystrophy; however, quantitative estimates of increased transplantation risk, including effects of age and sex, are unclear. METHODS: In a tertiary institution clinical practice, 574 participants were enrolled in a longitudinal study of Fuchs dystrophy after slit-lamp biomicroscopy confirmed significant central guttae and/or corneal transplantation in both eyes...
October 14, 2016: Cornea
Lakkhana Kanhayuwa, Robert H A Coutts
Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4-14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences...
2016: PloS One
Yoojin Park, Ki Tae Kim, Byeang Hyean Kim
We have developed a simple and sensitive system for detecting AGG trinucleotide repeats through the formation of intermolecular G-quadruplexes using a fluorescent oligonucleotide. The fluorescence signal increased rapidly and dramatically by 44.7-fold with respect to the low background signal in the presence of RNA agg repeats and by 35.0-fold in the presence of DNA AGG repeats.
October 20, 2016: Chemical Communications: Chem Comm
Petr Ráb, Cassia F Yano, Sébastien Lavoué, Oladele I Jegede, Luiz A C Bertollo, Tariq Ezaz, Zuzana Majtánová, Ezequiel A de Oliveira, Marcelo B Cioffi
The monophyletic order Osteoglossiformes represents one of the most ancestral groups of teleosts and has at least 1 representative in all continents of the southern hemisphere, with the exception of Antarctica. However, despite its phylogenetic and biogeographical importance, cytogenetic data in Osteoglossiformes are scarce. Here, karyotype and chromosomal characteristics of the lower Niger River population of the African butterfly fish Pantodon buchholzi, the sole species of the family Pantodontidae (Osteoglossiformes), were examined using conventional and molecular cytogenetic approaches...
October 7, 2016: Cytogenetic and Genome Research
Jennifer Ashley Ciarochi, Vince D Calhoun, Spencer Lourens, Jeffrey D Long, Hans J Johnson, H Jeremy Bockholt, Jingyu Liu, Sergey M Plis, Jane S Paulsen, Jessica A Turner
Huntington disease (HD) is caused by an abnormally expanded cytosine-adenine-guanine (CAG) trinucleotide repeat in the HTT gene. Age and CAG-expansion number are related to age at diagnosis and can be used to index disease progression. However, observed onset-age variability suggests that other factors also modulate progression. Indexing prodromal (pre-diagnosis) progression may highlight therapeutic targets by isolating the earliest-affected factors. We present the largest prodromal HD application of the univariate method voxel-based morphometry (VBM) and the first application of the multivariate method source-based morphometry (SBM) to, respectively, compare gray matter concentration (GMC) and capture co-occurring GMC patterns in control and prodromal participants...
2016: Frontiers in Neurology
Yasser Vega, Sergio Arias, Irene Paradisi
Martin-Bell syndrome is mainly caused by the expansion of CGG trinucleotide repeats (>200 CGG) in the first exon of the FMR1 gene, leading to hypermethylation of the promoter region and silencing of the FMR1 protein expression. These changes are responsible for a phenotype with varying degrees of mental retardation, a long face with large and protruding ears, macroorchidism and autistic behavior. There may also be, however, patients who exhibit typical features of the syndrome without any expansion in the FMR1 gene; thus, other mechanisms affecting the expression of the FMR1 gene were assessed in 25 out of 29 ascertained patients with the typical phenotype without full mutation...
October 6, 2016: Journal of Human Genetics
H Zhou, B H Cai, Z Q Lü, Z H Gao, Y S Qiao
Simple sequence repeats (SSRs), one of the most powerful molecular markers, can be used for DNA fingerprinting, variety identification, genetic mapping, and marker-assisted selection. Using the pear's (Pyrus pyrifolia Nakai) 75,764 unigenes (55,676,271 bp) obtained by deep transcriptome sequencing, a total of 10,622 novel SSRs were identified in 9154 unigenes, accounting for 14.02% of all unigenes. The average length and distribution of these SSRs was about 16 bp and 5.24 kb, respectively. Dinucleotide repeat motifs were the main type, with a frequency of 55...
September 23, 2016: Genetics and Molecular Research: GMR
Chang Heng Hsieh, Li-Ching Lee, Wai-Yin Leong, Tsai-Chen Yang, Ching-Fa Yao, Kang Fang
Trinucleotide CAG repeat expansion in the coding region of genes has a propensity to form polyglutamine (polyQ) aggregates that contribute to neuronal disorders. Strategies in elevating autophagy to disintegrate the insoluble aggregates without injuring cells have become a major goal for therapy. In this work, a triazole derivative, OC-13, was found accelerating autophagic clearance of polyQ aggregation in human neuroblastoma cells following induction of the enhanced green fluorescence-conjugated chimeric protein that enclosed 79 polyQ repeats (Q79-EGFP)...
2016: Drug Design, Development and Therapy
Kamil Mikulášek, Kamil S Jaroň, Petr Kulhánek, Miroslava Bittová, Jan Havliš
We studied sequence-dependent retention properties of synthetic 5'-terminal phosphate absent trinucleotides containing adenine, guanine and thymine through reversed-phase liquid chromatography (RPLC) and QSRR modelling. We investigated the influence of separation conditions, namely mobile phase composition (ion interaction agent content, pH and organic constituent content), on sequence-dependent separation by means of ion-interaction RPLC (II-RPLC) using two types of models: experimental design-artificial neural networks (ED-ANN), and linear regression based on molecular dynamics data...
October 21, 2016: Journal of Chromatography. A
Marc Alexandre Duarte Gigonzac, Lilian Souza Teodoro, Lysa Berandes Minasi, Thaís Cidália Vieira, Aparecido Divino da Cruz
Fragile X Syndrome (FXS) is the most common cause of inherited intellectual disability. The most common etiology of the syndrome is expansion and methylation of a CGG trinucleotide at chromosome region Xq27.3 involving FMR1. This disorder is commonly underdiagnosed in children and adolescents, given the high clinical variability. In Brazil, molecular diagnosis of FXS by capillary electrophoresis does not exist in the public health system. The current standard for separation and identification of DNA fragment sizes is 50 cm capillary electrophoresis, which is uncommon in public genotyping laboratories...
September 26, 2016: Electrophoresis
Mohamed A M Atia, Gamal H Osman, Wael H Elmenofy
In this study, we undertook a survey to analyze the distribution and frequency of microsatellites or Simple Sequence Repeats (SSRs) in Spodoptera littoralis multiple nucleopolyhedrovirus (SpliMNPV) genome (isolate AN-1956). Out of the 55 microsatellite motifs, identified in the SpliMNPV-AN1956 genome using in silico analysis (inclusive of mono-, di-, tri- and hexa-nucleotide repeats), 39 were found to be distributed within coding regions (cSSRs), whereas 16 were observed to lie within intergenic or noncoding regions...
2016: Scientific Reports
Wen-Hua Qi, Chao-Chao Yan, Wu-Jiao Li, Xue-Mei Jiang, Guang-Zhou Li, Xiu-Yue Zhang, Ting-Zhang Hu, Jing Li, Bi-Song Yue
As the first systematic examination of simple sequence repeats (SSRs) and guanine-cytosine (GC) distribution in intragenic and intergenic regions of ten primates, our study showed that SSRs and GC displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation. Our results suggest that the majority of SSRs are distributed in non-coding regions, such as the introns, TEs, and intergenic regions. In these primates, trinucleotide perfect (P) SSRs were the most abundant repeats type in the 5'UTRs and CDSs, whereas, mononucleotide P-SSRs were the most in the intron, 3'UTRs, TEs, and intergenic regions...
September 16, 2016: Aging
Maxim V Gerashchenko, Vadim N Gladyshev
Ribosome profiling has emerged as a powerful method to assess global gene translation, but methodological and analytical challenges often lead to inconsistencies across labs and model organisms. A critical issue in ribosome profiling is nuclease treatment of ribosome-mRNA complexes, as it is important to ensure both stability of ribosomal particles and complete conversion of polysomes to monosomes. We performed comparative ribosome profiling in yeast and mice with various ribonucleases including I, A, S7 and T1, characterized their cutting preferences, trinucleotide periodicity patterns and coverage similarities across coding sequences, and showed that they yield comparable estimations of gene expression when ribosome integrity is not compromised...
September 15, 2016: Nucleic Acids Research
Min Ji Kang, Hye Bin Yim, Hyung Bin Hwang
We report two cases of myotonic dystrophy in one family; both diagnosed from genetic analysis following ophthalmic indications, but before the manifestation of systemic symptoms. A 39-year-old female visited our clinic for routine examination. Mild ptosis, sluggish pupillary response, and bilateral snowflake cataracts were found. Fundus examination revealed an increased cup-to-disc ratio (CDR) in both eyes and a defect in the retinal nerve fiber layer in the right eye. Intraocular pressure was low, but within the normal range in both eyes...
July 2016: Indian Journal of Ophthalmology
Nimrat Chatterjee, Yunfu Lin, John H Wilson
Almost 20 incurable neurodegenerative disorders are caused by trinucleotide repeat (TNR) expansion beyond a certain threshold, with disease time of onset and severity positively correlating with repeat length. Typically, long TNRs display a bias toward further expansion and repeats continue to expand not only during germline transmissions from parents to offspring, but also remain highly unstable in somatic tissues of patients. Hence, understanding TNR instability mechanisms sheds light on underlying disease pathology...
May 2016: Postdoc Journal: a Journal of Postdoctoral Research and Postdoctoral Affairs
Laila C Schenkel, Charles Schwartz, Cindy Skinner, David Rodenhiser, Peter Ainsworth, Guillaume Pare, Bekim Sadikovic
Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability. It is most frequently caused by an abnormal expansion of the CGG trinucleotide repeat (>200 repeats) located in the promoter of the fragile X mental retardation gene (FMR1), resulting in promoter DNA hypermethylation and gene silencing. Current clinical tests for FXS are technically challenging and labor intensive, and may involve use of hazardous chemicals or radioisotopes. We clinically validated the Illumina Infinium HumanMethylation450 DNA methylation array for FXS screening...
August 29, 2016: Journal of Molecular Diagnostics: JMD
Tomoko Fujino, Takeru Suzuki, Koudai Okada, Kanako Kogashi, Ken-Ichi Yasumoto, Kazuhiro Sogawa, Hiroyuki Isobe
A method for the synthesis of chimeric oligonucleotides was developed to incorporate purine nucleobases and multiple triazole linkers in natural, phosphate-linked structures of RNA. A solution-phase synthesis method for triazole-linked RNA oligomers via copper-catalyzed azide-alkyne cycloaddition reaction was optimized and tolerated purine nucleobases and protecting groups for further transformations. Three (TL)RNA trinucleotides with 5'-protected hydroxy and 3'-phosphoramidite groups were prepared, and one congener with a representative sequence was subjected to automated, solid-phase phosphoramidite synthesis...
October 7, 2016: Journal of Organic Chemistry
Natalia P Rocha, Fabiola M Ribeiro, Erin Furr-Stimming, Antonio L Teixeira
Huntington's disease (HD) is a neurodegenerative disorder characterized by selective loss of neurons in the striatum and cortex, which leads to progressive motor dysfunction, cognitive decline, and psychiatric disorders. Although the cause of HD is well described-HD is a genetic disorder caused by a trinucleotide (CAG) repeat expansion in the gene encoding for huntingtin (HTT) on chromosome 4p16.3-the ultimate cause of neuronal death is still uncertain. Apart from impairment in systems for handling abnormal proteins, other metabolic pathways and mechanisms might contribute to neurodegeneration and progression of HD...
2016: Mediators of Inflammation
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