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https://www.readbyqxmd.com/read/28092810/expectation-and-futurity-the-remarkable-success-of-genetic-determinism
#1
Maurizio Esposito
Genetic determinism is nowadays largely questioned and widely criticized. However, if we look at the history of biology in the last one hundred years, we realize that genetic determinism has always been controversial. Why, then, did it acquire such relevance in the past despite facing longstanding criticism? Through the analysis of some of the ambitious expectations of future scientific applications, this article explores the possibility that part of the historical success of genetic determinism lies in the powerful rhetorical strategies that have connected the germinal matter with alluring bio-technological visions...
January 13, 2017: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/28092571/machine-learned-replacement-of-n-labels-for-basecalled-sequences-in-dna-barcoding
#2
Eddie Ma, Sujeevan Ratnasingham, Stefan Kremer
This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label...
August 11, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28090565/thbs2-is-a-candidate-modifier-of-liver-disease-severity-in-alagille-syndrome
#3
Ellen A Tsai, Melissa A Gilbert, Christopher M Grochowski, Lara A Underkoffler, He Meng, Xiaojie Zhang, Michael M Wang, Hailu Shitaye, Kurt D Hankenson, David Piccoli, Henry Lin, Binita M Kamath, Marcella Devoto, Nancy B Spinner, Kathleen M Loomes
BACKGROUND & AIMS: Alagille syndrome is an autosomal-dominant, multisystem disorder caused primarily by mutations in JAG1, resulting in bile duct paucity, cholestasis, cardiac disease, and other features. Liver disease severity in Alagille syndrome is highly variable, however, factors influencing the hepatic phenotype are unknown. We hypothesized that genetic modifiers may contribute to the variable expressivity of this disorder. METHODS: We performed a genome-wide association study in a cohort of Caucasian subjects with known pathogenic JAG1 mutations, comparing patients with mild vs severe liver disease, followed by functional characterization of a candidate locus...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28090405/transcriptomic-analysis-of-diplomonad-parasites-reveals-a-trans-spliced-intron-in-a-helicase-gene-in-giardia
#4
Scott William Roy
BACKGROUND: The mechanisms by which DNA sequences are expressed is the central preoccupation of molecular genetics. Recently, ourselves and others reported that in the diplomonad protist Giardia lamblia, the coding regions of several mRNAs are produced by ligation of independent RNA species expressed from distinct genomic loci. Such trans-splicing of introns was found to affect nearly as many genes in this organism as does classical cis-splicing of introns. These findings raised questions about the incidence of intron trans-splicing both across the G...
2017: PeerJ
https://www.readbyqxmd.com/read/28089792/pharmacological-inhibition-of-pkc%C3%AE-counteracts-muscle-disease-in-a-mouse-model-of-duchenne-muscular-dystrophy
#5
V Marrocco, P Fiore, A Benedetti, S Pisu, E Rizzuto, A Musarò, L Madaro, B Lozanoska-Ochser, M Bouché
: Inflammation plays a considerable role in the progression of Duchenne Muscular Dystrophy (DMD), a severe muscle disease caused by a mutation in the dystrophin gene. We previously showed that genetic ablation of Protein Kinase C θ (PKCθ) in mdx, the mouse model of DMD, improves muscle healing and regeneration, preventing massive inflammation. To establish whether pharmacological targeting of PKCθ in DMD can be proposed as a therapeutic option, in this study we treated young mdx mice with the PKCθ inhibitor Compound 20 (C20)...
January 7, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28089252/practical-approaches-for-whole-genome-sequence-analysis-of-heart-and-blood-related-traits
#6
Alanna C Morrison, Zhuoyi Huang, Bing Yu, Ginger Metcalf, Xiaoming Liu, Christie Ballantyne, Josef Coresh, Fuli Yu, Donna Muzny, Elena Feofanova, Navin Rustagi, Richard Gibbs, Eric Boerwinkle
Whole-genome sequencing (WGS) allows for a comprehensive view of the sequence of the human genome. We present and apply integrated methodologic steps for interrogating WGS data to characterize the genetic architecture of 10 heart- and blood-related traits in a sample of 1,860 African Americans. In order to evaluate the contribution of regulatory and non-protein coding regions of the genome, we conducted aggregate tests of rare variation across the entire genomic landscape using a sliding window, complemented by an annotation-based assessment of the genome using predefined regulatory elements and within the first intron of all genes...
January 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28088213/glycine-alanine-dipeptide-repeat-protein-contributes-to-toxicity-in-a-zebrafish-model-of-c9orf72-associated-neurodegeneration
#7
Yu Ohki, Andrea Wenninger-Weinzierl, Alexander Hruscha, Kazuhide Asakawa, Koichi Kawakami, Christian Haass, Dieter Edbauer, Bettina Schmid
BACKGROUND: The most frequent genetic cause of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) is the expansion of a GGGGCC hexanucleotide repeat in a non-coding region of the chromosome 9 open reading frame 72 (C9orf72) locus. The pathological hallmarks observed in C9orf72 repeat expansion carriers are the formation of RNA foci and deposition of dipeptide repeat (DPR) proteins derived from repeat associated non-ATG (RAN) translation. Currently, it is unclear whether formation of RNA foci, DPR translation products, or partial loss of C9orf72 predominantly drive neurotoxicity in vivo...
January 14, 2017: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/28088192/nucleotide-diversity-inflation-as-a-genome-wide-response-to-experimental-lifespan-extension-in-drosophila-melanogaster
#8
Pawel Michalak, Lin Kang, Pernille M Sarup, Mads F Schou, Volker Loeschcke
BACKGROUND: Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often reach intermediate population frequencies due to balancing selection, an elusive process when sought out empirically. Alternatively, genetic diversity may increase as a result of positive frequency-dependent selection and genetic purging in bottlenecked populations. RESULTS: While experimental evolution systems with directional phenotypic selection typically result in at least local heterozygosity loss, we report that selection for increased lifespan in Drosophila melanogaster leads to an extensive genome-wide increase of nucleotide diversity in the selected lines compared to replicate control lines, pronounced in regions with no or low recombination, such as chromosome 4 and centromere neighborhoods...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28087634/genome-wide-identification-of-regulatory-elements-in-sertoli-cells
#9
Danielle M Maatouk, Anirudh Natarajan, Yoichiro Shibata, Lingyun Song, Gregory E Crawford, Uwe Ohler, Blanche Capel
A current goal of molecular biology is to identify transcriptional networks regulating cell differentiation. However, identifying functional gene regulatory elements has been challenging in the context of developing tissues where material is limited and cell types are mixed. To identify regulatory sites during sex determination, we subjected Sertoli cells from mouse fetal testes to DNaseI-seq and ChIP-seq for H3K27ac. DNaseI-seq identified putative regulatory sites around Sertoli- and pregranulosa-enriched genes; however, active enhancers marked by H3K27ac were enriched proximal only to Sertoli-enriched genes...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28087495/comparative-analysis-of-variation-and-selection-in-the-hcv-genome
#10
Juan Ángel Patiño-Galindo, Fernando González-Candelas
Genotype 1 of the hepatitis C virus (HCV) is the most prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and CD8), and secondary protein structure...
January 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28087155/population-genetic-data-of-38-insertion-deletion-markers-in-six-populations-of-the-northern-fringe-of-the-iberian-peninsula
#11
Sergio Cardoso, Rubén Sevillano, David Gamarra, Ana Santurtún, Begoña Martínez-Jarreta, Marian M de Pancorbo
Insertion-deletions have been reported very useful markers for forensic purposes. To further deepen in this matter, 38 non-coding bi-allelic autosomal indels were analyzed in 575 individuals representing six populations from the northern fringe of the Iberian Peninsula. Autochthonous populations from the Basque Country, northern Navarre, the Pas Valley in Cantabria and Aragon were analyzed, together with non-autochthonous populations from the Basque Country and northern Navarre. At the intra-population level, all loci analyzed were in Hardy-Weinberg equilibrium except for marker rs33917182 in autochthonous Basques...
January 3, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28081453/intertypic-recombination-of-human-parechovirus-4-isolated-from-infants-with-sepsis-like-disease
#12
Pekka Kolehmainen, Anu Siponen, Teemu Smura, Hannimari Kallio-Kokko, Olli Vapalahti, Anne Jääskeläinen, Sisko Tauriainen
BACKGROUND: Human parechoviruses (HPeVs) (family Picornaviridae), are common pathogens in young children. Despite their high prevalence, research on their genetic identity, diversity and evolution have remained scarce. OBJECTIVES: Complete coding regions of three previously reported HPeV-4 isolates from Finnish children with sepsis-like disease were sequenced in order to elucidate the phylogenetic relationships and potential recombination events during the evolution of these isolates...
January 3, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28081242/genetic-and-clinical-analyses-of-doa-and-lhon-in-304-chinese-patients-with-suspected-childhood-onset-hereditary-optic-neuropathy
#13
Yadi Li, Jie Li, Xiaoyun Jia, Xueshan Xiao, Shiqiang Li, Xiangming Guo
Leber hereditary optic neuropathy (LHON) and dominant optic atrophy (DOA), the most common forms of hereditary optic neuropathy, are easily confused, and it is difficult to distinguish one from the other in the clinic, especially in young children. The present study was designed to survey the mutation spectrum of common pathogenic genes (OPA1, OPA3 and mtDNA genes) and to analyze the genotype-phenotype characteristics of Chinese patients with suspected childhood-onset hereditary optic neuropathy. Genomic DNA and clinical data were collected from 304 unrelated Chinese probands with suspected hereditary optic neuropathy with an age of onset below 14 years...
2017: PloS One
https://www.readbyqxmd.com/read/28080992/microevolutionary-traits-and-comparative-population-genomics-of-the-emerging-pathogenic-fungus-cryptococcus-gattii
#14
Rhys A Farrer, Kerstin Voelz, Daniel A Henk, Simon A Johnston, Matthew C Fisher, Robin C May, Christina A Cuomo
Emerging fungal pathogens cause an expanding burden of disease across the animal kingdom, including a rise in morbidity and mortality in humans. Yet, we currently have only a limited repertoire of available therapeutic interventions. A greater understanding of the mechanisms of fungal virulence and of the emergence of hypervirulence within species is therefore needed for new treatments and mitigation efforts. For example, over the past decade, an unusual lineage of Cryptococcus gattii, which was first detected on Vancouver Island, has spread to the Canadian mainland and the Pacific Northwest infecting otherwise healthy individuals...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28079883/cysteamine-re-establishes-the-clearance-of-pseudomonas-aeruginosa-by-macrophages-bearing-the-cystic-fibrosis-relevant-f508del-cftr-mutation
#15
Eleonora Ferrari, Romina Monzani, Valeria R Villella, Speranza Esposito, Francesca Saluzzo, Federica Rossin, Manuela D'Eletto, Antonella Tosco, Fabiola De Gregorio, Valentina Izzo, Maria C Maiuri, Guido Kroemer, Valeria Raia, Luigi Maiuri
Cystic fibrosis (CF), the most common lethal monogenic disease in Caucasians, is characterized by recurrent bacterial infections and colonization, mainly by Pseudomonas aeruginosa, resulting in unresolved airway inflammation. CF is caused by mutations in the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR) protein, which functions as a chloride channel in epithelial cells, macrophages, and other cell types. Impaired bacterial handling by macrophages is a feature of CF airways, although it is still debated how defective CFTR impairs bacterial killing...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28079472/polymorphisms-of-rps6kb1-and-cd86-associates-with-susceptibility-to-multiple-sclerosis-in-iranian-population
#16
Rasoul Abdollah Zadeh, Nazanin Jalilian, Mohammad Ali Sahraian, Zeinab Kasraian, Mohammad Reza Noori-Daloii
OBJECTIVE:  Multiple sclerosis (MS) is the most prevalent disorder of nervous system inflammation which involves demyelination of spinal cord; this process depends on both environmental and genetic susceptibility factors. In the present study, we examined the association between two SNPs in RPS6KB1 (rs180515) and CD86 (rs9282641) with MS in Iranian population. RPS6KB1gene encodes p70S6K1 protein which plays a key role in mTOR signaling pathway, while CD86 gene codes a membrane protein type I which belongs to immunoglobulin super family act on co-stimulation signaling pathway...
January 12, 2017: Neurological Research
https://www.readbyqxmd.com/read/28078570/micro-rna-expression-in-muscle-and-fiber-morphometry-in-myotonic-dystrophy-type-1
#17
Chiara Fritegotto, Chiara Ferrati, Valentina Pegoraro, Corrado Angelini
We aimed to explore the cellular action of micro-RNAs that are non-coding-RNAs modulating gene expression, whose expression is dysregulated in myotonic dystrophy (DM1). Basic procedure was to measure the levels of muscle-specific myo-miRNAs (miR-1, miR-133a/b, miR-206) in muscle of 12 DM1 patients. Muscle fiber morphometry and a new grading of histopathological severity score were used to compare specific myo-miRNA level and fiber atrophy. We found that the levels of miR-1 and miR-133a/b were significantly decreased, while miR-206 was significantly increased as compared to controls...
January 11, 2017: Neurological Sciences
https://www.readbyqxmd.com/read/28076858/non-coding-loss-of-function-variation-in-human-genomes
#18
Zachary Zappala, Stephen B Montgomery
Whole-genome and exome sequencing in human populations has revealed the tolerance of each gene for loss-of-function variation. By understanding this tolerance, it has become increasingly possible to identify genes that would make safe therapeutic targets and to identify rare genetic risk factors and phenotypes at the scale of individual genomes. To date, the vast majority of surveyed loss-of-function variants are in protein-coding regions of the genome mainly due to the focus on these regions by exome-based sequencing projects and their relative ease of interpretability...
2016: Human Heredity
https://www.readbyqxmd.com/read/28076288/transfer-rnas-with-novel-cloverleaf-structures
#19
Takahito Mukai, Oscar Vargas-Rodriguez, Markus Englert, H James Tripp, Natalia N Ivanova, Edward M Rubin, Nikos C Kyrpides, Dieter Söll
We report the identification of novel tRNA species with 12-base pair amino-acid acceptor branches composed of longer acceptor stem and shorter T-stem. While canonical tRNAs have a 7/5 configuration of the branch, the novel tRNAs have either 8/4 or 9/3 structure. They were found during the search for selenocysteine tRNAs in terabytes of genome, metagenome and metatranscriptome sequences. Certain bacteria and their phages employ the 8/4 structure for serine and histidine tRNAs, while minor cysteine and selenocysteine tRNA species may have a modified 8/4 structure with one bulge nucleotide...
October 5, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28075481/diagnosis-of-spinocerebellar-ataxias-caused-by-trinucleotide-repeat-expansions
#20
Joanne E Martindale
Spinocerebellar ataxias (SCAs) are a group of disorders that are both clinically and genetically heterogeneous. They usually demonstrate onset in adulthood, but some forms may have juvenile or infantile onset. There are many different types of SCA, demonstrating different modes of inheritance and types of mutation. The most common forms are due to dominantly inherited expansions in trinucleotide repeat sequences located within the coding region of the relevant genes, and these are readily identifiable by molecular genetic testing...
January 11, 2017: Current Protocols in Human Genetics
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