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Figure 3 in Assessing structure and seasonal variations of a temperate shallow water fish assemblage through Snorkel Visual Census

Figure 3. – Correlation between temperature and species richness compared between diurnal and nocturnal counts. Dotted trendlines show the quadratic and linear relationships between species richness and temperature at diurnal and nocturnal counts respectively.

Figure 3 in Infraspecific genetic variation and population structure of Salvia nemorosa L. (Lamiaceae) in Iran

Figure 3. PCoA plot of the studied populations based on ISSR data (population numbers are according to Table 1).

Figure 2 in Infraspecific genetic variation and population structure of Salvia nemorosa L. (Lamiaceae) in Iran

Figure 2. MDS plot of the studied populations based on ISSR data (population numbers are according to Table 1).

Figure 4 in Infraspecific genetic variation and population structure of Salvia nemorosa L. (Lamiaceae) in Iran

Figure 4. NJ tree of S. nemorosa populations based on ISSR results (population numbers are according to Table 1).

opencc-by-4.0Jan 2019View details →

Data sets for modeling double strand break susceptibility and interrogating structural variation in cancer

This is data used and produced for the study of "Modeling double strand break susceptibility to interrogate structural variation in cancer".  Background: Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs). Results: We used experimentally quantified DSB frequencies in cell lines with matched chromatin and sequence features to derive the first quantitative genome-wide models of DSB susceptibility. These models are accurate and provide novel insights into the mutational mechanisms generating DSBs. Models trained in one cell type can be successfully applied to others, but a substantial proportion of DSBs appear to reflect cell type specific processes. Using model predictions as a proxy for susceptibility to DSBs in tumours, many SV-enriched regions appear to be poorly explained by selectively neutral mutational bias alone. A substantial number of these regions show unexpectedly high SV breakpoint frequencies given their predicted susceptibility to mutation and are therefore credible targets of positive selection in tumours. These putatively positively selected SV hotspots are enriched for genes previously shown to be oncogenic. In contrast, several hundred regions across the genome show unexpectedly low levels of SVs, given their relatively high susceptibility to mutation. These novel coldspot regions appear to be subject to purifying selection in tumours and are enriched for active promoters and enhancers. Conclusions: We conclude that models of DSB susceptibility offer a rigorous approach to the inference of SVs putatively subject to selection in tumours.

opencc-by-4.0Nov 2015View details →

Fig. 2 in Spatial variation of dung beetle assemblages associated with forest structure in remnants of southern Brazilian Atlantic Forest

Fig. 2. Principal coordinates analysis (PCoA) of dung beetle species based on Bray–Curtis similarity and environmental variables based on Euclidean distance. The analysis was performed using presence–absence (a), abundance (b) and biomass (c) data of dung beetles, and 15 environmental variables (d). ANH: Anhatomirim Environmental Protection Area; ITA: Permanent Protection Areas of Itapema; PER: Peri Lagoon Municipal Park; RAT: Permanent Protection Areas of Ratones.

opencc-by-4.0Dec 2014View details →

Text-fig. 7. Cercidiphyllaceae 1–3. Trochodendroides genetrix (NEWBERRY) comb. nov. and associated reproductive structures (4, 5) from Killpecker Cr., Rock Springs, Wyoming (UF loc. 18126). 1. Twig with three attached leaves, showing variation in leaf shape and serration; composite figure assembled from images of both counterparts, UF 35427. 2. Complete leaf including petiole, UF 13243. 3. Same as 2, detail of venation. 4. Nyssidium arcticum (HEER) ILJINSKAYA fruits on an incomplete axis, UF 35454. 5. Dispersed winged seed, UF 35479. Scale = 3 cm in 1, 2; 1 cm in 3, 4; 0.5 cm in 5. in Revisions To Roland Brown'S North American Paleocene Flora

Text-fig. 7. Cercidiphyllaceae 1–3. Trochodendroides genetrix (NEWBERRY) comb. nov. and associated reproductive structures (4, 5) from Killpecker Cr., Rock Springs, Wyoming (UF loc. 18126). 1. Twig with three attached leaves, showing variation in leaf shape and serration; composite figure assembled from images of both counterparts, UF 35427. 2. Complete leaf including petiole, UF 13243. 3. Same as 2, detail of venation. 4. Nyssidium arcticum (HEER) ILJINSKAYA fruits on an incomplete axis, UF 35454. 5. Dispersed winged seed, UF 35479. Scale = 3 cm in 1, 2; 1 cm in 3, 4; 0.5 cm in 5.

opencc-by-4.0Apr 2015View details →

Figure 2 in Monthly variations in the shell structure of two freshwater ostracod (Crustacea) species in Karapınar Spring (Bolu, Turkey)

Figure 2. SEM photos of (A) Potamocypris similis, left valve inner view; and (B) Psychrodromus olivaceus, carapace right valve external view. Scale bar = 100 µm.

opencc-by-4.0Apr 2015View details →

Date Figure 4 in Monthly variations in the shell structure of two freshwater ostracod (Crustacea) species in Karapınar Spring (Bolu, Turkey)

Date Figure 4. Sr/Ca ratio in the valves of P. similis (PS) and P. olivaceus (PO) from Karapınar Spring. Note that the far left point in the circle is an outlier.

Figure 6 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)

Figure 6. Secondary structure models of the highly variable proximal part of helix 43 (S6, Fig. 1) in Zygaeninae. All structures are based on thermodynamic folding by minimizing the free energy and have been calculated considering the entire nucleotide sequence of helix 43. The change in the Gibb's free energy (dG) refers to the S6 structure only. Applied ambiguity code: G/A = R, C/U = Y.

Figure 3 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)

Figure 3. Consensus structure and base pair probability matrix of helix E23-5 (S3, Fig. 1) in Lepidoptera. Nucleotides in circles indicate consistent and/or compensatory substitutions. The size of squares in the grid is proportional to the probability of a base pairing. Note that the species Z. centaureae, Z. laeta and Z. huguenini have been omitted from this analysis because of their deviating secondary structure (compare with Fig. 4).

Figure 2 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)

Figure 2. Distribution of pairwise tree edit distances between highly variable SSU rRNA secondary structure areas (S1–S6, Fig. 1) of Zygaenoidea excluding taxa of the subgenus Mesembrynus (top) and of Zygaena species belonging to the subgenus Mesembrynus only (bottom). The extreme values in the Zygaenoidea tree edit distance distribution on the right all involve Z. excelsa, a species showing a highly derived secondary structure in the area S6 (compare with Fig. 6).

Figure 1 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)

Figure 1. Secondary structure model of the SSU (18S) rRNA gene sequence of Zygaena (Mesembrynus) sarpedon lusitanica Reiss, 1936 (Lepidoptera: Zygaenidae; accession no. AJ830858) and structure variation in the helices E10-1 and E23-12 among species of the subfamily Zygaeninae. Nucleotides in the model are continuously numbered beginning at the 5′-end of the molecule; tick marks identify every tenth base. Light shading indicate helices numbered according to Wuyts et al. (2002). S1–S6 (dark shades) denote areas with variable secondary structure in the subfamily Zygaeninae. Roman numerals specify the domains I, II, III and IV. The following ambiguity code has been applied: A/C = M, C/U = Y, G/A = R.

Figure 7 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)

Figure 7. Neighbour-joining tree based on structural differences in the variable areas S1–S6 (compare with Fig. 1) of the small-subunit (18S) rRNA in taxa of the genus Zygaena. The topology is rooted with Reissita simonyi and Epizygaenella caschmirensis as outgroup. Taxa of the subgenus Mesembrynus are indicated by shading. Numbers in parentheses specify the number of species in a particular group.

Figure 5 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)

Figure 5. Consensus structure and base pair probability matrix of the proximal part of helix 43 (S6, Fig. 1) in Lepidoptera. Nucleotides in circles indicate consistent and/or compensatory substitutions. The size of squares in the grid is proportional to the probability of a base pairing. Note that the unpaired nucleotides C and G in the helix will most likely bind in individual structures having this specific nucleotide combination, but non-Watson–Crick pairings are too frequent in the alignment for assuming a generally nucleotide interaction at this position in the consensus structure.

opencc-by-4.0Sep 2009View details →

Fig. 2 in Microsatellite variation and population genetic structure of a neotropical endangered Bryconinae species Brycon insignis Steindachner, 1877: implications for its conservation and sustainable management

Fig. 2. UPGMA clustering of the Nei's genetic distance (1972) of the Brycon insignis sampling locations based on six microsatellite loci. Bootstrap values above 50% are shown above branches indicating percentage support in 5000 permutations. Power Company Hatchery (PCH), São João River (SJR), Paraíba do Sul River (PSR), Imbé River (IMR), Muriaé River (MUR) and Itabapoana River (ITR).

opencc-by-4.0Dec 2022View details →

Part 1: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'

Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory. The file Data.One.Focb-2.tar contains 22 files of paired-end reads from F. oxysporum f.sp. cubense tropical race 1 isolate N2 (SRA accession: SRR550150, SRR550151), and F. oxysporum f.sp. cubense TR4 isolates Hainan.B2 (SRR550152), My-1 (SRR7226877), La-2 (SRR7226878), Vn-2 (SRR7226879), Leb1.2C (SRR7226880), JV11 (SRR7226881), Phi2.6C (SRR7226882), Pak1.1A (SRR7226883), UK0001 (SRR9733598).

opencc-by-4.0Dec 2022View details →

Part 2: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'

Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory. The file Data.One.Focb.tar contains 16 files of paired-end reads from F. oxysporum f.sp. cubense TR4 isolates II-5 (SRA accession: SRR10054446), S1B8 (SRR10054447), JV14 (SRR10054448), FOC.TR4-5 (SRR10054449), FOC.TR4-1 (SRR10054450), Col2 (SRR10103605), Col4 (SRR10125423), Col17 (SRR10747097).