26 papers · ranked by Valyu relevance
Saurabh Mahajan, Deepa Agashe, A Wong
Genomic GC (Guanine-Cytosine) content is a fundamental molecular trait linked with many key genomic features such as codon and amino acid use. Across bacteria, GC content is surprisingly diverse and has been studied for many decades; yet its evolution remains incompletely understood. Since it is difficult to observe GC…
Saurabh Mahajan, Deepa Agashe
Genomic GC content is a fundamental molecular trait linked with many key genomic features such as codon and amino acid use. Across bacteria, GC content is surprisingly diverse and has been studied for many decades; yet its evolution remains incompletely understood. Since it is difficult to observe GC content evolve on…
En-Ze Hu, Shen Sun, Deng-Ke Niu
Many environmental factors are associated with GC content evolution. However, the relationship between GC content and halophilicity has been poorly explored. Higher GC contents have been linked to halophiles because of a few solitary archaeal cases. The only previous statistical study on the relationship ignored the…
Yi Qiu, Yoon Mo Kang, Christopher Korfmann, Fanny Pouyet + 2 more
In vertebrates, most protein-coding genes have a peak of GC-content near their 5’ transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation of mRNAs. Despite the importance of GC-content for RNA metabolism, its general features, origin, and maintenance remain mysterious.…
Uberto Pozzoli, Giorgia Menozzi, Matteo Fumagalli, Matteo Cereda + 4 more
'Giacomo P Comi' 'Rachele Cagliani' 'Nereo Bresolin' 'Manuela Sironi'] Background Mammalian genomes consist of regions differing in GC content, referred to as isochores or GC-content domains. The scientific debate is still open as to whether such compositional heterogeneity is a selected or neutral trait. Results Here…
Yi Qiu, Yoon Mo Kang, Christopher Korfmann, Fanny Pouyet + 2 more
'Andrew Eckford' 'Alexander F. Palazzo'] Background In vertebrates, most protein-coding genes have a peak of GC-content near their 5′ transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation of mRNAs. Despite the importance of GC-content for RNA metabolism, its general…
Chowdhury Rafeed Rahman, Zhong Wee Poh, Anders Jacobsen Skanderup, Limsoon Wong
Cell-free DNA (cfDNA) analysis has wide-ranging clinical applications due to its non-invasive nature. However, cfDNA fragmentomics and copy number analysis can be complicated by GC bias. There is a lack of GC correction software based on rigorous cfDNA GC bias analysis. Furthermore, there is no standardized metric for…
Riccardo G. Kyriacou, Peter O. Mulhair, Peter W. H. Holland
The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome…
Lucio Aliperti Car, Gonzalo Farfañuk, Luciana L. Couso, Alfonso Soler‐Bistué + 2 more
'Alfonso Soler‐Bistué' 'Ariel A. Aptekmann' 'Ignacio E. Sánchez'] The GC content of prokaryotic genomes is species-specific and takes values from 16 to 77 percent. There are currently no accepted explanations for this diversity of selection for GC content. We analyzed the known correlations between GC content, genome…
Riccardo G. Kyriacou, Peter O. Mulhair, Peter W. H. Holland
The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome…
Franziska Weindel, Andreas L. Gimpel, Robert N. Grass, Reinhard Heckel
'Reinhard Heckel'] DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include constraints that avoid homopolymers (consecutive repeated…
Jon Bohlin, Lars Snipen, Simon P Hardy, Anja B Kristoffersen + 4 more
'Karin Lagesen' 'Torunn Dønsvik' 'Eystein Skjerve' 'David W Ussery'] Background Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly…
Nabil Bennenni, Kenza Guenda, T. Aaron Gulliver
Deoxyribonucleic acid (DNA) contains the genetic program for the biological development of life. DNA is formed by strands linked together and twisted in the shape of a double helix. Each strand is a sequence of four possible nucleotides, two purines, adenine A and guanine G, and two pyrimidines, thymine T and cytosine…
Sukhamoy Pattanayak, Abhay Kumar Singh
In this paper, we develop the theory for constructing DNA cyclic codes of odd length over R = Z 4 [ u ] / h u 2 − 1 i based on the deletion distance. Firstly, we relate DNA pairs with a special 16 elements of ring R. Cyclic codes of odd length over R satisfy the reverse constraint and the reverse-complement constraint…
Eduardo P. C. Rocha, Edward J. Feil, Michael W. Nachman
In certain eukaryotes, BGC results from recombination between heterologous sequences preferentially removing AT polymorphisms . Contrary to sexual eukaryotes, allelic recombination in bacteria requires horizontal transfer. As a result, rates of recombination between, and even within, different bacterial species are…
Eran Elhaik, Tatiana V. Tatarinova
The variation in GC content along yeast chromosomes was first reported in S. cerevisiae (Sharp and Lloyd 1993) where GC3 ranged from 35% to 50% on chromosome III. Later observations confirmed similar patterns for the remaining chromosomes and linked the GC variation to recombination, that is, rich GC3 regions would…
Koen Van den Berge, Hsin-Jung Chou, Hector Roux de Bézieux, Kelly Street + 3 more
Modern assays have enabled high-throughput studies of epigenetic regulation of gene expression using DNA sequencing. In particular, the assay for transposase-accessible chromatin using sequencing (ATAC-seq) allows the study of chromatin configuration for an entire genome. Despite the gain in popularity of the assay…
Authors not listed
Based on electrostatic interactions and entropic gains from counterion release, DNA coacervates constitute an exciting example of associative assemblies due to high local DNA concentrations and possibility of their applications for drug and gene delivery. Because charge density is not affected by DNA sequence…
Federico Ruggeri, Eleonora Misino, Arianna Muti, Katerina Korre + 2 more
Annotation Methodology Authors: ['Federico Ruggeri' 'Eleonora Misino' 'Arianna Muti' 'Katerina Korre' 'Paolo Torroni' 'Alberto Barrón‐Cedeño'] We introduce the Guideline-Centered annotation process, a novel data annotation methodology focused on reporting the annotation guidelines associated with each data sample. We…
Peng Zhang, Baozhi Shi, Xiaobing Dai, Cancan Chen + 2 more
'Esmaiel Jabbari'] Geopolymer, as a sustainable, low-carbon gel binder, is regarded as a potential alternative to cement. Freeze-thaw (F-T) resistance, which has a profound influence on the service life of structures, is a crucial indicator for assessing the durability of geopolymer composites (GCs). Consequently…
Authors not listed
N-glycolylneuraminic acid (Neu5Gc) is a non-human sialic acid which is presented on the surface of human cells following uptake from dietary sources. This is widely hypothesised to drive the production of anti-Neu5Gc antibodies, which have implications for many aspects of human health. However, current methods to…
Authors not listed
Indigenous plant resources are valuable sources of therapeutics, but often lack detailed chemical characterization. This study employs Gas Chromatography-Mass Spectrometry (GC-MS) to provide a highly detailed comparative chemical profile of the non-polar bioactive constituents in the ethyl acetate extracts derived from…
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Despite the increasing use of gas chromatography coupled with electron ionization high resolution mass spectrometry (GC-EI-HRMS), only a limited amount of GC-EI-HRMS reference data is currently available. Such data are beneficial not only in combination with a GC-EI-HRMS instrument, but also for computational purposes…
Linxing Yao, Kaitlyn Maloley, Corey D. Broeckling, Steve Ensley + 2 more
Ethyl carbamate (EC) is a fermentation byproduct in foods and beverages and classified as a Group 2A probable human carcinogen. Each year greater than 40 million metric tons of fermentation co-products from the U.S. ethanol industry are fed to food animals. A GC-MS assay was developed to analyze EC extracted from…
Authors not listed
Grape seed extract (GSE) is widely utilized in functional foods and dietary supplements due to its antioxidant and anti-aging potential, with much of its bioactivity attributed to oligomeric proanthocyanidins (OPCs). However, current quality standards primarily rely on measurements of total proanthocyanidins or broad…
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Gas chromatography coupled with electron ionization and high-resolution mass spectrometry (GC-EI-HRMS) has been increasingly used in analytical chemistry in recent years. At the same time, there is currently relatively little specialized software for basic interpretation of such mass spectra, taking into account the…