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704 results for “nucleotides”
FIGURE 6 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 6. Phylogenetic tree of four sequenced assassin bugs. Bayesian inference and Maximum likelihood analysis inferred from all genes recovered the same topological structure. Bootstrap values and Bayesian posterior probabilities are indicated at each node.
FIGURE 3 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 3. Predicted secondary structure of the rrnL in S. flavipes. Regions in red indicate the high variability in the four assassin bugs. Roman numerals denote the conserved domain structure. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.
FIGURE 2 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 2. Inferred secondary structures of 22 tRNAs of S. flavipes. The tRNAs are labeled with the abbreviations of their corresponding amino acids. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.
FIGURE 4 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 4. Predicted secondary structure of the rrnS in S. flavipes. Regions in red indicate the high variability in the four assassin bugs. Roman numerals denote the conserved domain structure. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.
FIGURE 5 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 5. (A) The conserved region of the mitochondrial control region of S. flavipes, A. dohrni, T. dimidiata and V. hoffmanni. (B) The structural organization of the mitochondrial control region of S. flavipes. The control region flanking genes rrnS, trnI (I), trnQ (Q), and trnM (M) are represented in purple and green boxes. The light blue boxes with roman numerals indicate the tandem repeat region. "G+C" indicates high G+C content region. "A+T" indicates high A+T content region. The black box indicates G element.
FIGURE 1 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 1. Map of the mtochondrial genome of S. flavipes. Direction of gene transcription is indicated by the arrows. PCGs are shown as blue arrows, rRNA genes as purple arrows, tRNA genes as red arrows and large non-coding regions (>100 bp) as cyan rectangles. tRNA genes are labeled according to single-letter IUPAC-IUB abbreviations (L1: UUR; L2:CUN; S1:AGN; S2:UCN). The GC content is plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC Skew is plotted as the deviation from the average GC skew of the entire sequence. Ticks in the inner cycle indicate the sequence length.
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description. in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description.
Figure 3 in Nucleotide sequence data confirm diagnosis and local endemism of variable morphospecies of Andean astroblepid catfishes (Siluriformes: Astroblepidae)
Figure 3. Results of the phylogenetic analysis of astroblepid morphospecies obtained from maximum likelihood analysis of the combined DNA sequence data set. Numerals at nodes represent bootstrap proportions (values less than 50% not shown); stars represent nodes supported by bootstrap values of 80% or greater. Sample numbers correspond with materials listed in Table 1. Letters designate morphospecies; shaded boxes denote monophyletic assemblages of population samples.
Figure 1 in Nucleotide sequence data confirm diagnosis and local endemism of variable morphospecies of Andean astroblepid catfishes (Siluriformes: Astroblepidae)
Figure 1. Variation in pigmentation in Astroblepus morphospecies A–I. A, morphospecies A, ANSP (Academy of Natural Sciences of Philadelphia) 180586 (4793), 51.6 mm standard length (SL), Araza River. B, morphospecies B, ANSP 180587 (4779), 75 mm SL, Araza River. C, morphospecies B, ANSP 180582 (4801), 80.4 mm SL, Araza drainage (Dr.) D, morphospecies B, ANSP 180582 (4800), 54.5 mm SL, Araza Dr. E, morphospecies C, ANSP 180581 (4805), 27.2 mm SL, Araza Dr. F, morphospecies C, ANSP 180586 (4794), 58 mm SL, Araza River. G, morphospecies D, ANSP 180599 (4822), 51.7 mm SL, Urubamba Dr. H, morphospecies D, ANSP 180602 (4499), 85 mm SL, Urubamba Dr. I, morphospecies H, ANSP 180618 (4423), 46.3 mm SL, Apurimac Dr. J, morphospecies H, ANSP 180616 (4436), 79.2 mm SL, Apurimac Dr. K, morphospecies E, ANSP 180595 (4785), 61.3 mm SL, Urubamba Dr. L, morphospecies E, ANSP 180605 (4490), 110.5 mm SL, Apurimac Dr. M, morphospecies F, ANSP 180606 (4487), 75.7 mm SL, Apurimac Dr. N, morphospecies F, ANSP 180601 (4759), 52.6 mm SL, Urubamba Dr. O, morphospecies G, ANSP 180588 (4787), 59.5 mm SL, Urubamba Dr. P, morphospecies I, ANSP 180607 (4477), 39.4 mm SL, Apurimac Dr. Photo in (A) by S. A. S.; photos in (B–P) by M. H. S. P.
Figure 2 in Nucleotide sequence data confirm diagnosis and local endemism of variable morphospecies of Andean astroblepid catfishes (Siluriformes: Astroblepidae)
Figure 2. Distribution of astroblepid morphospecies and study region. Circled letters correspond with the morphospecies designations (Table 1) and may represent more than one lot or collection locality.
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site.
FIGURE. DnaSP DNA polymorphism analysis - Nucleotide variability (Pi) comparison between Strobilanthes lupulina and S. glandulata. The window length and step size were set to 600bp and 200bp respectively. The most varying regions and the commonly used barcoding regions are listed against the base-pair differences found. in Strobilanthes glandulata (Acanthaceae), a new species from Sri Lanka based on the morphological and molecular evidences
FIGURE. DnaSP DNA polymorphism analysis - Nucleotide variability (Pi) comparison between Strobilanthes lupulina and S. glandulata. The window length and step size were set to 600bp and 200bp respectively. The most varying regions and the commonly used barcoding regions are listed against the base-pair differences found.
Phylogenomic data of Litsea complex based on genome-wide single-nucleotide variants (SNVs) and plastomes
<p>In this study, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of evergreen broadleaved forests (EBLFs) in East Asia to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) and plastomes. Finally, the dataset of phylogenomic matrices was generated, including five genome-wide SNVs dataset and plastomes matrix used for phylogenetic analysis.</p>
R notebooks to reproduce all analyses from the manuscript "grandR: a comprehensive package for nucleotide conversion sequencing data analysis"
<p>This package contains all R notebooks to reproduce the analyses from our manuscript "grandR: a comprehensive package for nucleotide conversion sequencing data analysis".</p> <p>In the zip file you find</p> <ul> <li>several rds files in the data folder: They contain grandR objects of both simulated and real SLAM-seq data sets. You can delete them and create them again by either just "knitting" the notebooks (which will generate all data necessary for this notebook and save it into the data folder), or by executing the generateAllDataFiles.R script ("Rscript generateAllDataFiles.R"), which will generate all rds files that do not exist).</li> <li>several R notebooks (Rmd): "Knitting" them will generate all figures from the manuscript. Without the data files (rds), this will be slow!</li> <li>knit_all.bash: Execute to "knit" all notebooks</li> <li>clean.bash: Clear the output of "knitting" the notebooks</li> </ul> <p> </p>
single-molecule measurements of nucleotides
<p>Current-time profiles of 4 nucleotides measured with a nanogap electrode fabricated using MCBJ.</p>
Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation
<p>„Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation”.</p> <p>In article, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ (U<sup>T</sup>) or 5′–GGGCGGG–3′ (G<sup>T</sup>) fragments. Using biophysical methods, the effect of covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif was studied. The sequence-guided o-BMVC G4-ligand acted as a quadruplex stabilizer but not duplex. The use of such conjugates (o-BMVC-RNA) creates the possibility of inducing and stabilizing the bimolecular quadruplexes on the G-rich mRNA template in a sequence-specific manner. The formation of QDH or Dss structures is dependent on a single nucleotide change in the target sequence, and the possibility to selectively stabilize the G-quadruplex domain by attaching the G4 ligand may become an attractive alternative therapy for patients with an EGFR-L858R mutation.</p> <p><a href="https://www.mdpi.com/2218-273X/11/8/1236">https://www.mdpi.com/2218-273X/11/8/1236</a>, <a href="https://doi.org/10.3390/biom11081236">https://doi.org/10.3390/biom11081236</a></p> <p>Files are available in original formats: .xlsx, .opi, bruker, MultiGauge raw-image file (.img), JPG file (.jpg), text document (.txt)</p>
indicate branches. above MrBayes numbers by inferred The . supports Ixodes of probability subgenera 22 posterior the of Inference 16 from Bayesian ticks of indicate genomes mitochondrial branches below 40 numbers of The sequences. RAxML nucleotide by the inferred from support inferred bootstrap Phylogenies Likelihood . 2 FIGURE Maximum in A new subgenus, Australixodes n. subgen. (Acari: Ixodidae), for the kiwi tick, Ixodes anatis Chilton, 1904, and validation of the subgenus Coxixodes Schulze, 1941 with a phylogeny of 16 of the 22 subgenera of Ixodes Latreille, 1795 from entire mitochondrial genome sequences
indicate branches. above MrBayes numbers by inferred The . supports Ixodes of probability subgenera 22 posterior the of Inference 16 from Bayesian ticks of indicate genomes mitochondrial branches below 40 numbers of The sequences. RAxML nucleotide by the inferred from support inferred bootstrap Phylogenies Likelihood . 2 FIGURE Maximum
Single Nucleotide Polymorph and location metadata for Turbo militaris from Eastern Australia
<p>Studies of population genomics have been increasingly used to identify climate change vulnerability and explore the potential resilience of harvested marine species. The turban snail, Turbo <em>militaris </em>is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades and continued climate change presents an ongoing challenge for sustainable fisheries management. This study investigates the likely resilience of Turbo <em>militaris</em> to future climate change effects using genotype-by-sequencing to explore patterns of gene flow and local adaptation across the entire species distribution. We provide evidence of a single admixed, and potentially panmictic, demographic unit with no evidence of genetic subdivision across the species range. Furthermore, significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation among sample locations. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation.</p>
The Expression of Immune Checkpoint CD28 rs1980422-related Single-nucleotide Polymorphisms in the Primary Immune Thrombocytopenia
ClinicalTrials.gov study NCT05468866. IPD Sharing: YES. Countries: 1. Publications: 4.
DNA Single Nucleotide Polymorphisms as Predictors of Toxicity
ClinicalTrials.gov study NCT02478476. IPD Sharing: Not stated. Countries: 1. Publications: 20.
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