Nucleotide substitution
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Red deer with very pale coat colour are observed sporadically. In the red deer (Cervus elaphus) population of Reinhardswald in Germany, about 5% of animals have a white coat colour that is not associated with albinism. In order to facilitate the conservation of the animals, it should be determined whether and to what extent brown animals carry the white gene.
9p vihagrid 30-01-2023 8 3 Download
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The coat colour of fallow deer is highly variable and even white animals can regularly be observed in game farming and in the wild. Affected animals do not show complete albinism but rather some residual pigmentation resembling a very pale beige dilution of coat colour.
8p vihagrid 30-01-2023 8 3 Download
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Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear.
24p vigalileogalilei 27-02-2022 14 1 Download
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Base editing installs a precise nucleotide change in specific gene loci without causing a double-strand break. Its efficiency in human embryos is generally low, limiting its utility in functional genetic studies.
7p vigalileogalilei 27-02-2022 11 1 Download
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Millions of nucleotide variants are identified through cancer genome sequencing and it is clinically important to identify the pathogenic variants among them. By introducing base substitutions at guide RNA target regions in the genome, CRISPR-Cas9-based base editors provide the possibility for evaluating a large number of variants in their genomic context.
25p viarchimedes 26-01-2022 11 0 Download
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Sequences of the mitochondrial cytochrome oxidase I (COI) gene of one Greek and 25 Turkish Myzus cerasi (Fabricus) (Hemiptera: Aphididae) populations collected from Prunus avium and Prunus cerasus were analyzed. The partial coding region of COI studied is 605 bp for all the populations, from which 565 nucleotides were conserved, 40 were variable, 37 were singleton, and 3 were parsimony-informative. Four haplotypes were identified based on nucleotide substitutions and the mean of intraspecific divergence was calculated to be 0.3%.
10p dolomite36 30-12-2021 19 0 Download
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Hedysarum alamutense, a new species in the tribe Hedysareae DC. (Fabaceae), is described and illustrated. It belongs to the traditionally recognized Hedysarum L. section Multicaulia (Boiss.) B.Fedtsch., which extends over the West Alborz Mountains in northern Iran. This species is characterized by greenish stems and corolla persisting in fruiting stage and has mostly 1–2-jointed, unarmed, biconvex pods with short hairs becoming bald early, and flattened margins. Phylogenetic analyses of molecular data clearly unite this species with H. formosum Fisch. & C.A.Mey. ex Basin.
9p tudichquannguyet 29-11-2021 10 1 Download
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Genetic testing identifies the potential risk of multiple endocrine neoplasia in a Vietnamese family
In this study, we reported a rare case of a 44-year-old man from Vietnam with medullary thyroid carcinoma and pheochromocytoma as the symptom of MEN2A. Genetic testing indicated a nucleotide substitution located in exon 11 of the RET proto-oncogene (c.1900T>C, p.C634R), which was reported as a known pathogenic mutation of MEN2A. Further genetic tests on the other family members found the same mutation in his daughter (currently 14 years-old) and his son (currently 8 years-old). A
7p spiritedaway36 25-11-2021 10 1 Download
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Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets.
13p vibeauty 23-10-2021 8 1 Download
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Temperature adaptation of biological molecules is fundamental in evolutionary studies but remains unsolved. Fishes living in cold water are adapted to low temperatures through adaptive modification of their biological molecules, which enables their functioning in extreme cold. To study nucleotide and amino acid preference in cold-water fishes, we investigated the substitution asymmetry of codons and amino acids in protein-coding DNA sequences between cold-water fishes and tropical fishes.
10p vibeauty 23-10-2021 8 1 Download
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The examined factors include genes, codon position, a CpG indicator, directionality, nucleotide, amino acid, codon, and context (neighboring nucleotides), in addition to other site based factors. Partitioning a model by a factor’s value results in several sub-models (one for each value), where the likelihoods of the sub-models can be combined to form a score for the entire model. Eventually, the leading models are considered as viable candidates for explaining mtDNA substitution rates.
13p vitzuyu2711 29-09-2021 12 1 Download
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At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality).
13p visilicon2711 20-08-2021 15 1 Download
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The C:G > T:A substitution at the CpG dinucleotide contexts is the most frequent substitution type in genome evolution. The mutational process is obviously ongoing in the human germline; however, its impact on common and rare genomic polymorphisms has not been comprehensively investigated yet.
11p vijeeni2711 24-07-2021 11 0 Download
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Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored.
15p vijichea2711 28-05-2021 11 1 Download
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Calvin cycle plays a crucial role in carbon fixation which provides the precursors of organic macromolecules for plant growth and development. Currently, no gene involved in Calvin cycle has been identified in monocotyledonous plants through mutant or/and map-based cloning approach.
14p vijichea2711 28-05-2021 7 1 Download
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The algorithm uses a Complementary table with four values corresponding with data bits ‘00’, ‘01’, ‘10’, and ‘11’, so that, we can embed two bits for each nucleotide. Moreover, with four levels of Complementary values, the algorithm shows that the proposed method also improve the security for hidden data.
5p chauchaungayxua11 23-03-2021 9 1 Download
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In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all 203 possible nucleotide substitution models in the Maximum Likelihood (ML) setting under the common Akaike, corrected Akaike, and Bayesian information criteria.
13p vioklahoma2711 19-11-2020 14 1 Download
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Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a method to reliably calculate the occurrence probabilities of sequence alignments via evolutionary processes on an entire sequence.
21p vioklahoma2711 19-11-2020 18 2 Download
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Amino acid substitutions due to DNA nucleotide replacements are frequently disease-causing because of affecting functionally important sites. If the substituting amino acid does not fit into the protein, it causes structural alterations that are often harmful.
8p viconnecticut2711 29-10-2020 9 2 Download
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Duplex sequencing is the most accurate approach for identification of sequence variants present at very low frequencies. Its power comes from pooling together multiple descendants of both strands of original DNA molecules, which allows distinguishing true nucleotide substitutions from PCR amplification and sequencing artifacts.
10p vicolorado2711 22-10-2020 10 0 Download