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Fig. 3 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook

Fig. 3. Significant KEGG pathway enrichment analysis in tissues from aerial organs (leaf & Stem) and bulb. The green colour enrichment indicates higher expression in aerial tissue while pink represents higher enrichment in bulb. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook

Fig. 4. Transcriptional protein-protein interactome (PPIN) prediction in F. roylei along the network statistics. (A) Overall prediction of PPI network based on significantly differential expressed transcripts. Spatial PPI network prediction of significantly enriched transcripts in (B) Bulb, (C) Leaf and (D) Stem.

Fig. 1 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook

Fig. 1. Summary of organ specific spatial transcriptome sequencing in F. roylei. (A): Overall quality filtering of sequenced reads; (B): Tissue specific high quality filtered reads obtained after removing low quality/adaptor contaminated sequences; (C): Assembly statistics details; (D): Venn diagram representing functional annotation with six different public protein databases.

Fig. 8 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook

Fig. 8. Representation of isosteroidal alkaloid biosynthesis pathway in F. roylei and heat map representing expression of genes in Stem, Leaf and Bulb tissue using red-blue scale (red: positive enrichment and Blue: negative enrichment of transcripts). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook

Fig. 2. Clustering of 2488 significant differentially expressed transcripts in leaf, stem and bulb in F. roylei (A) sub-cluster 1 represent transcripts with significant higher expression in bulb; (B): Sub-cluster 2 in Stem and (C): Sub-cluster 3 in leaf; (D): Pearson's correlation of organ specific significant differentially expressed clustered transcripts in leaf, stem and bulb tissues.

opennotspecifiedNov 2021View details →

Fig. 2 in The esterification of xanthophylls in Solanum lycopersicum (tomato) chromoplasts; the role of a non-specific acyltransferase

Fig. 2. Example chromatograms showing the effect of the pyp mutation on azygous and ketocarotenoid fruit. 1) Astaxanthin, 2) Lutein, 3) Phoenicoxanthin, 4) Canthaxanthin, 5) 3′OH Echinenone, 6) 3OH Echinenone, 7) Echinenone, 8 and 8′) Lycopene, 9) Esterified carotenoid, 10) γ-Carotene, 11) Esterified carotenoid, 12) β-Carotene.

opennotspecifiedNov 2021View details →

Fig. 1 in The esterification of xanthophylls in Solanum lycopersicum (tomato) chromoplasts; the role of a non-specific acyltransferase

Fig. 1. Workflow for the generation, screening and phenotypic observations of the four genotypes created. Blue circles indicate number of genotypes detected from the total pool used.

opennotspecifiedNov 2021View details →

Fig. 3 in The esterification of xanthophylls in Solanum lycopersicum (tomato) chromoplasts; the role of a non-specific acyltransferase

Fig. 3. Biosynthetic pathway of ketocarotenoids and ketocarotenoid esters. CRTZ and CRTW are the bacterial carotenoid hydroxylase and oxygenase enzymes respectively. The PYP gene facilitates the esterification with fatty acids to generate ketocarotenoid esters. Phoenicoxanthin and astaxanthin accumulate within the genotypes assessed and esterified forms of these have been observed in this work.

opencc-by-4.0Aug 2023View details →

Collection of Object-Centric Event Logs (OCEL 1.0 format; JSON-OCEL specification)

We provide some realistic examples of logs in the OCEL standard. The logs have originally been published at https://www.ocel-standard.org/

openother-openDec 2022View details →

Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"

This archive contains the code and datasets generated in the associated manuscript: "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits". We provide instructions, environments and scripts to reproduce the presented analyses.

opencc-by-4.0Dec 2022View details →

High risk clear cell renal cell carcinoma microenvironments contain protumour immunophenotypes lacking specific immune checkpoints.

Final Seurat file (rds) produced from the immune cell analysis performed in "High risk clear cell renal cell carcinoma microenvironments contain protumour immunophenotypes lacking specific immune checkpoints."

opencc-by-4.0May 2023View details →

Characterization of signal and transit peptides based on motif composition and taxon-specific patterns

These files contain data, sequences and supplementary information for the article entitled 'Characterization of signal and transit peptides based on motif composition and taxon-specific patterns'. Contents <ol> <li>Raw_data.zip - contains raw data and sequences downloaded from UniProt and other databases. These files were used to create datasets used for described analyses.</li> <li>Datasets.zip - presequence and peptide datasets obtained from raw data and used for all subsequent analyses.</li> <li>Motif_analysis_reports_presequences_AMP.zip - HTML reports with detailed analyses of motif composition of presequences and AMPs</li> <li>Motif_analysis_reports_presequences_encoded.zip - HTML reports with detailed analyses of motif composition of presequences using reduced alphabets</li> <li>Motif_analysis_reports_presequences_taxonomy.zip - HTML reports with detailed analyses of motif composition of presequences for different taxons</li> <li>Motif_analysis_reports_SP_taxonomy.zip - HTML reports with detailed analyses of motif composition of signal peptides on different taxonomic levels</li> <li>Motif_analysis_reports_presequences_counts.zip - HTML reports with detailed analyses of motifs occuring more than once in presequences and AMPs</li> </ol>   Abstract Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum (ER), and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed a comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution.

opennotspecifiedFeb 2020View details →

Fig. 2 in Terpenoid profiles of resin in the genus Dracaena are species specific

Fig. 2. Heat map of 20 terpenic volatiles (columns) identified by SPME-GC × GC-MS analyses in five species (rows) of the Dracaena spp. The dendrograms were created using correlation-based distances and the Ward method of hierarchical clustering (P <0.05). Columns are coloured according to chemical class (light orange = monoterepenes M1-8, dark orange = sesquiterpenes S1-12, Table 1). Key: C – Dracaena draco subsp. draco from Canary Islands; E − D. ombet from Ethiopia; M – D. draco subsp. ajgal from Marocco; O – D. serrulata from Oman; S – D. cinnabari from Socotra. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedFeb 2020View details →

Fig. 3 in Terpenoid profiles of resin in the genus Dracaena are species specific

Fig. 3. Principal component analyses (PCA) of transformed GC × GC-MS data of eight monoterpenes (M) identified in Dracaena spp. resin. (A) Variables factor map represents projection of variables (M1-8, Table 1) on the plane defined by the first two principal components. (B) Hierarchical clustering is score plot describing the species and their clustering. Coloured boxes indicate particular clusters. Key: C – Dracaena draco subsp. draco from Canary Islands; E − D. ombet from Ethiopia; M – D. draco subsp. ajgal from Marocco; O – D. serrulata from Oman; S – D. cinnabari from Socotra.

opennotspecifiedFeb 2020View details →

Fig. 1 in Terpenoid profiles of resin in the genus Dracaena are species specific

Fig. 1. Detail of SPME-GC × GC-MS analysis of Dracaena spp. terpenes. (A) Dracaena draco subsp. draco from Canary Islands, (B) D. draco subsp. ajgal from Marocco, (C) D. ombet from Ethiopia, (D) D. cinnabari from Socotra, (E) D. serrulata from Oman. Each dot represents one compound. The numbering corresponds to Table 1. The intensity of the signals is colour-coded from blue (zero) to red (maximum). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7 in Biosynthesis and tissue-specific partitioning of camphor and eugenol in Ocimum kilimandscharicum

Fig. 7. Schematic representation of the mechanisms underlying camphor and eugenol partitioning in O. kilimandscharicum revealed by integration of transcriptomics and metabolomics data. Partitioning of camphor to the aerial tissues was attributed to differential expression of camphor biosynthesis pathway genes (Mechanism 1), while partitioning of eugenol to the roots was attributed to transport from source (aerial tissues) to the sink (roots) (Mechanism 2) potentially mediated by ABC and MATE transporter proteins [geranyl diphosphate synthase (gpps), borneol dehydrogenase (bdh), eugenol synthase (egs), ATP-binding cassette (ABC) transporters, multidrug and toxic compound extrusion (MATE) transporters].

Fig. 6 in Biosynthesis and tissue-specific partitioning of camphor and eugenol in Ocimum kilimandscharicum

Fig. 6. Gene co-expression analysis. A whole genome co-expression network was constructed using our RNA-Seq data in CoExpNetViz to identify candidate genes putatively involved in eugenol biosynthesis and transportation. egs1 and 4cl4 were used as the bait genes (indicated using red font on the heat map representing digital gene expression of genes involved in phenylpropanoid pathway across different tissues). For heatmap analysis, the color scale for fold-change values is shown. The network was filtered to hold correlations with r-value cut-off corresponding to the top 95th percentile and bottom 5th percentile of all correlations measured (rvalue> 0.8 and r-value <−0.2, Pearson correlation coefficient). Red edges indicate negative correlation while green edges indicate positive correlation between genes. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Biosynthesis and tissue-specific partitioning of camphor and eugenol in Ocimum kilimandscharicum

Fig. 3. Agrobacterium-mediated transient silencing and overexpression of genes putatively involved in camphor biosynthesis in O. kilimandscharicum. GC-MS based metabolic profiling of (A) bdh silenced (RNAi_BDH) (B) gpps silenced (RNAi_GPPS) (C) bdh overexpressing (OE_BDH), and (D) gpps overexpressing (OE_GPPS) plants (where, "control" indicates uninduced plants). All experiments were repeated twice independently (number of plants per treatment, n = 6). Error bars represent the mean ± standard deviation. Data were statistically significant at p <0.0001 (indicated by "****"), p <0.001 (indicated by "***"), p <0.01 (indicated by "**"), and p <0.05 (indicated by "*").

Fig. 5 in Biosynthesis and tissue-specific partitioning of camphor and eugenol in Ocimum kilimandscharicum

Fig. 5. Integration of transcriptomics and metabolomics data for understanding eugenol biosynthesis in O. kilimandscharicum (Ok). (A) Pathway genes and intermediate metabolites in eugenol biosynthesis in O. kilimandscharicum. Transcripts for the genes marked in red were present in the Ok transcriptome. Metabolites marked in black were putatively identified; however, those marked in blue could not be detected on the LC-Orbitrap [phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), p-coumarate 3-hydroxylase (C3H), caffeic acid O-methyltransferse (COMT), 4-coumarate:CoA ligase (4CL), cinnamoyl-CoA reductase (CCR), cinnamyl alcohol dehydrogenase (CAD), alcohol acyltransferase (AAT), eugenol synthase (EGS)]. (B) Heat map analysis showing putatively identified intermediates detected on the LC-Orbitrap across different tissues [anther + pistil (A + P)]. All values represent an average of three biological replicates. The color scale for foldchange values is shown. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Biosynthesis and tissue-specific partitioning of camphor and eugenol in Ocimum kilimandscharicum

Fig. 2. Putative camphor biosynthesis pathway. Schematic representation of the putative camphor biosynthesis pathway in O. kilimandscharicum. Genes highlighted in red were cloned and functionally characterized [isopentynyl diphosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl diphosphate (GPP), bornyl diphosphate (BPP), geranyl diphosphate synthase (gpps), bornyl diphosphate synthase (bpps), bornyl diphosphate diphosphatase (bppd), borneol dehydrogenase (bdh)]. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)