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Data from: Photoacclimation and induction of light-enhanced calcification in the mesophotic coral Euphyllia paradivisa

Corals and their photosymbionts experience inherent changes in light along depth gradients, leading them to have evolved several well-investigated photoacclimation strategies. As coral calcification is influenced by light (a process described as LEC-"light enhanced calcification"), studies have sought to determine the link between photosynthesis and calcification, but many puzzling aspects still persist. Here we examine the physiology of Euphyllia paradivisa, a coral species found at a wide range of depths but that is strictly mesophotic in the Red Sea; and also examines the coupling between photosynthesis and light-enhanced calcification by investigating the response of the coral under several controlled light regimes during a long-term experiment. E. paradivisa specimens were collected from 40-50 m depth and incubated under three light conditions for a period of one year: full-spectrum shallow-water light (~3 m, e.g. shallow-light treatment); blue deep-water light (~40 m, e.g. mesophotic-light treatment); or total darkness (e.g. dark treatment). Net photosynthesis remained similar in the shallow-light treated corals compared to the mesophotic-light treated corals, under both low and high light. However, calcification increased dramatically with increasing light intensity in the shallow-light treated corals suggesting a decoupling between these processes. Photoacclimation to shallow-water conditions was indicated by enhanced respiration, a higher density of zooxanthellae per polyp, and lower chlorophyll a content per cell. The dark-treated corals became completely bleached but did not lower their metabolism below that of the mesophotic-light treated corals. No Symbiodinium clade shift was found following the year-long light treatments. We conclude that E. paradivisa, and its original symbiont clade, can adapt to various light conditions by controlling its metabolic rate and growth energy investment, and consequently induce LEC.

Data from: Rituximab vs placebo induction prior to glatiramer acetate monotherapy in multiple sclerosis

Objective: To examine whether rituximab induction followed by glatiramer acetate (GA) monotherapy is more effective than GA alone for the treatment of relapsing MS with active disease. Methods: This was a single center, double-blind, placebo-controlled study(NCT01569451). Fifty-five participants were randomly assigned (1:1ratio) to either rituximab (R-GA) or placebo induction (P-GA), followed by all participants initiating GA therapy. Participants were followed up to 3-years. The primary endpoint was the number of participants with no evidence of disease activity (NEDA) (those without relapse, new MRI lesions and sustained change in disability. Results: Twenty-eight and 27 participants received rituximab and placebo induction, respectively, with one participant in each arm withdrawing prior to 6-month MRI. There were no significant differences in baseline characteristics. At end of study, 44.44% of R-GA participants demonstrated NEDA, vs 19.23% of P-GA participants (p = 0.049). A smaller proportion of R-GA participants failed treatment (37.04%R-GA vs 69.23%P-GA, p=0.019), and time to treatment failure was longer (23.32 monthsR-GA vs 11.29 monthsP-GA, p=0.027). Fewer participants in the R-GA arm had new lesions (25.93%R-GA vs 61.54%P-GA, p=0.009), and there were fewer new T2 lesions (0.48R-GA vs 1.96P-GA vs, p=0.027). Probability of demonstrating NEDA in the R-GA arm returned to baseline within the study period. There were no differences in adverse events. Conclusions: Induction therapy with rituximab followed by GA may provide superior efficacy in the short term to GA alone in relapsing MS, but this benefit appears to wane within the study period. Larger studies are needed to assess sustainability of results.

opencc-zeroOct 2019View details →

Data from: Rapid induction of the heat hardening response in an Arctic insect

<a name="_Hlk16601098">The ability to cope with increasing and more variable temperatures, due to predicted climate changes, through plastic and/or evolutionary responses will be crucial for the persistence of Arctic species. </a>Here, we investigate plasticity of heat tolerance of the Greenlandic seed bug Nysius groenlandicus, which inhabits areas with widely fluctuating temperatures. We test the heat resistance and hardening capacity (plasticity) of N. groenlandicus using both static (heat knock down time, HKDT) and dynamic (critical thermal maximum, CTmax) assays. We find that N. groenlandicus is able to tolerate short-term exposure to temperatures up to almost 50°C and that it can quickly increase heat resistance following heat hardening. Further, we find that this hardening response is reversible within hours after hardening. These findings contrast with common observations from temperate and tropical insects and suggest that more attention should be given to species in extreme and thermally variable environments such as Arctic and subarctic regions.

Data from: Context-dependent induction of allelopathy in plants under competition

Some plants use allelopathy to compete against neighbouring plants, and the ability to induce allelopathic compound production in response to competition is hypothesized to be adaptive, as plants can save costs of metabolite production in the absence of competitors. However, whether plants induce allelopathy has rarely been explored so far. We studied the inducibility of polyacetylenes—putative allelopathic compounds in Solidago altissima—in response to competition. Polyacetylenes were found in natural soil surrounding S. altissima patches within the range of concentration known to inhibit competitor growth. Individual S. altissima plants with higher polyacetylene concentration in roots suppressed the growth of the competitor plants more, suggesting that root polyacetylene levels proximate plants' allelopathic capacity. Competition induced polyacetylenes in a context-dependent manner: Whereas introduced Japanese and Australian populations of S. altissima had higher constitutive concentration of polyacetylenes than the native North American populations, inducibility was observed only in Australian plants, where the population is still at an early stage of invasion. Also, induction became more prominent under nutrient depletion, where enhanced allelopathy may be particularly beneficial for suppressing a competitor's exploitative capacity. Finally, we found weak evidence for a trade-off between constitutive and induced polyacetylenes. The observed patterns suggest that allelopathic plants could respond to competition by inducing allelochemical production, but the benefit of such plasticity may vary across time and space. Shifts in competitor communities in introduced range over time may shape plant's plastic responses to competition, while variation in resource availability may alter competitive environment to influence the degree to which plants induce allelopathy.

Data from: Water-borne defense induction of a rockweed in the wild

1. Laboratory-scale studies suggest that water-borne chemical cues released in grazing of marine macroalgae act as info-chemicals allowing the yet-undamaged conspecifics to increase their resistance before the actual herbivore attack. The relevance of this finding in natural populations has thus far remained unexplored. 2. We investigated spread of water-borne herbivore resistance in a field experiment using the littoral foundation species Fucus vesiculosus. We exposed algal genotypes for water-borne cues in the distances of 0.5 and 2 meters from the grazed cue-emitting genotypes. We measured herbivore resistance with preference experiments and recorded changes in the phlorotannin content. We recorded changes in biomass and length of the genotypes to test if water-borne resistance correlates with the grazing damage on the cue-emitter or incurs costs for the genotypes in terms of reduced growth. 3. In two of our four experimental blocks, induced resistance via water-borne cues took place and spread to undamaged neighbours that were two meters distance apart. This provides evidence of water-borne resistance induction in the wild as well as of small-scale spatial variation in the spread of induction. The undamaged neighbours induced resistance to a lesser extent than the directly grazed cue-emitters did, but resistance was consistently expressed among all 26 algal genotypes and independent of the amount of grazing damage on the cue-emitter. Herbivore resistance correlated negatively with the growth in the grazed cue-emitting genotypes while water-borne resistance was independent of the variation in growth. 4. Our results show, for the first time for marine macroalgae in a natural setting, that information about the increased risk of herbivory can be carried by water-borne cues and is used to prime or induce defences prior to an actual attack. The results we present furthermore indicate that water-borne resistance differs quantitatively and qualitatively from the resistance triggered by actively feeding herbivores. Ability to induce resistance prior the herbivore arrival may greatly influence the ability of littoral macroalgae to withstand the generally intense herbivory of marine benthic environments.

opencc-zeroDec 2013View details →

Data from: Diapause induction and relaxed selection on alternative developmental pathways in a butterfly

1. Seasonal phenotypic plasticity entails differential trait expression depending on the time of season. The facultative induction of winter diapause in temperate insects is a developmental switch mechanism often leading to differential expression in life history traits. However, when there is a latitudinal shift from a bivoltine to univoltine life cycle, selection for pathway-specific expression is disrupted, which may allow drift towards less optimal trait values within the non-selected pathway. 2. We use field- and experimental data from five Swedish populations of Pararge aegeria to investigate latitudinal variation in voltinism, local adaptation in the diapause switch, and footprints of selection on pathway-specific regulation of life history traits and sexual dimorphism in larval development. 3. Field data clearly illustrated how natural populations gradually shift from bivoltinism to univoltinism as latitude increases. This was supported experimentally as the decrease in direct development at higher latitudes was accompanied by increasing critical daylengths, suggesting local adaptation in the diapause switch. 4. The differential expression among developmental pathways in development time and growth rate was significantly less pronounced in univoltine populations. Univoltine populations showed no significant signs of protandry during larval development, suggesting that erosion of the direct development pathway under relaxed selection has led to the loss of its sex-specific modifications.

FIGURE 1. Oxyurella singalensis Daday 1898 in Hormonal induction of males as a method for studying tropical cladocerans: description of males of four chydorid species (Cladocera: Anomopoda: Chydoridae)

FIGURE 1. Oxyurella singalensis Daday 1898, specimens from culture from Loeng Yai reservoir, Khon Kaen area: A–Cinstar I juvenile male: A—lateral view, B—antennule, C—distal portion of thoracic limb I; D–F—instar II juvenile male: Dlateral view, E—antennule, F—thoracic limb I; G–I—adult male: G—lateral view, H—antennule, I—thoracic limb I. Scale bars: 0.1 mm for A, D, G, 0.05 mm for B–C, E– F, H–I.

FIGURE 2. Oxyurella singalensis Daday 1898 in Hormonal induction of males as a method for studying tropical cladocerans: description of males of four chydorid species (Cladocera: Anomopoda: Chydoridae)

FIGURE 2. Oxyurella singalensis Daday 1898, specimens from culture from Loeng Yai reservoir, Khon Kaen area: A–Bpostabdomens of instar I and 2 juvenile males; C—postabdomen of adult male; D–E—distal denticles of adult male postabdomen. Scale bars 0.05 mm for A-C, 0.01 mm for D-E.

FIGURE 5 in Hormonal induction of males as a method for studying tropical cladocerans: description of males of four chydorid species (Cladocera: Anomopoda: Chydoridae)

FIGURE 5. Disparalona cf. hamata (Birge, 1810), adult male from culture from Loeng Yai reservoir, Khon Kaen area: A—lateral view, B—outline of postabdomen, C—distal part of postabdomen, D–E—antennule in different positions (aestheatascs omitted in E), F—thoracic limb I, G—copulatory hook and IDL of limb I. Scale bars: 0.1 mm for A and B, 0.05 mm for C–G.

FIGURE 4 in Hormonal induction of males as a method for studying tropical cladocerans: description of males of four chydorid species (Cladocera: Anomopoda: Chydoridae)

FIGURE 4. Leydigia cf. ciliata Gauthier, 1939, adult male from culture from pond near the highway Khon Kaen—Kalasin: A—lateral view, B–C—postabdomen, D—postabdominal claw, E—antennule, F—thoracic limb 1. Scale bars: 0.1 mm for A and B–C, 0.05 mm for D–F.

FIGURE 3 in Hormonal induction of males as a method for studying tropical cladocerans: description of males of four chydorid species (Cladocera: Anomopoda: Chydoridae)

FIGURE 3. Leberis diaphanus (King, 1853), adult male from culture from Loeng Yai reservoir, Khon Kaen area: A—lateral view, B—postabdomen, C—antennule, D —thoracic limb I, E—copulatory hook and IDL of limb I. Scale bars: 0.1 mm for A, 0.05 mm for B–E.

opencc-by-4.0Feb 2017View details →

General Terminology Induction: Two Corpora of Experimental Ontologies

Two corpora of ontologies that contain some data and hence can be used to evaluate ontology learning algorithms

opennotspecifiedDec 2017View details →

FIGURES 57–62. Sperm induction structures, females. 57 in Four new species of the subgenus Pachylaelaps (Longipachylaelaps) from Italy, with a new identification key to the known species (Acari: Pachylaelapidae)

FIGURES 57–62. Sperm induction structures, females. 57. Pachylaelaps (Longipachylaelaps) longisetis; 58. Pachylaelaps (Longipachylaelaps) brevipilis; 59. Pachylaelaps (Longipachylaelaps) longulus; 60. Pachylaelaps (Longipachylaelaps) distinctus; 61. Pachylaelaps (Longipachylaelaps) vicarius; 62. Pachylaelaps (Longipachylaelaps) carpathicus. Not scaled.

opengpl-3.0-or-laterDec 2023View details →

Scripts reproducing the analyses of the paper "HCMV exploits STING signaling and counteracts IFN and ISG induction to facilitate infection of dendritic cells" by Costa et al

This is the code to reproduce the data analyses in the manuscript "HCMV exploits STING signaling and counteracts IFN and ISG induction to facilitate infection of dendritic cells". Required software and packages: R (4.2.1) circlize (0.4.15) ComplexHeatmap (2.12.1) cowplot (1.1.1) future (1.28.0) ggalluvial (0.12.5) ggpubr (0.4.0) ggrepel (0.9.1) GSVA (1.44.5) msigdbr (7.5.1) patchwork (1.1.2) plyr (1.8.7) presto (1.0.0) RColorBrewer (1.1-3) reshape2 (1.4.4) sctransform (0.3.5) Seurat (4.2.0) SeuratDisk (0.0.0.9020) SeuratWrappers (0.3.1) velocyto.R (0.6) Howto: Execute all scripts in order by first changing into the directory, and then executing the script: <pre><code>cd 00_QC; Rscript 00_QC.R; cd ..</code></pre>

Fig. 4 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 4. Transcript accumulation of genes associated with wound induced suberization. Transcript accumulation of known and putative genes encoding steps in suberin biosynthesis, from starch degradation to final assembly, over the wound-healing time course were retrieved from RNA-seq data. Heatmaps depict log2FPKM means for n = 3 biological replicates for each time point. Numbered pathway steps correspond to numbers in the suberin roadmap (Supplemental Fig. S4). Fumarase (step 63) is included as a step in the TCA pathway, but is shown in grey because its sequence did not have a corresponding PGSC gene identification number, and therefore transcript abundance could not be estimated in this study.

Fig. 6 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 6. Transcript accumulation of wound-induced CASP and GDSL genes. Transcript accumulation of known and putative CASP and GDSL genes, over the wound-healing time course were retrieved from RNA-seq data. Heatmaps depict log2FPKM means for n = 3 biological replicates for each time point.

Fig. 3. Network modules for suberin-associated metabolism genes. Expression profiles for 317 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 3. Network modules for suberin-associated metabolism genes. Expression profiles for 317 wound-induced and suberin-associated genes encompassing primary carbohydrate metabolism and the formation of suberin phenolic and aliphatic monomers were subjected to WGCNA. Genes belonging to carbohydrate (C), tricarboxylic acid cycle (TCA), shikimate pathway (S), phenolic metabolism (P), phenolic assembly (PA), fatty acid biosynthesis (FAB), fatty acid modification (FAM) and aliphatic assembly (AA) are colour-coded (see legend). (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 Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 2. Gene set enrichment analysis (GSEA) of biological processes across differentially expressed genes (DEGs). Time point comparison panels represent a union parametric analysis of gene set enrichment (PAGE) of biological process (BP) categorized gene ontology (GO) terms. Nodes represent gene sets and their size represents a range from 5 to 464 genes, and edges show overlapping genes between sets, with width representing ranges from 5 to 149 genes. Blue sets are downregulated, red are up-regulated, and grey nodes denote terms that were not detected as significantly differentially regulated (i.e. enriched) at that time point comparison. Labels denote assigned node numbers that correspond to Table 1 with associated GO ID, GO term and regulation overview. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 1. Global overview of the wound-healing transcriptome. A. Principle component analysis (PCA) of RNA-seq libraries. Colours represent biological replicate libraries generated from the same time point (gene log2FPKM space with scaling). B. Differentially expressed genes (DEGs) across time point comparisons. Genes were considered significantly up- or down-regulated if they met p ≤ 0.01 and |log2 (fold change)| (| LFC|) ≥ 2 significance cut-offs. Lists of significantly DEGs were generated using voom by applying these parameters with the Benjamini-Hochberg procedure to TMM-normalized HT-Seq count data. C. Venn diagram of DEGs significantly up- (red) or down-regulated (blue) over the wound-healing time course. Genes were considered significantly up- or down-regulated if they met p ≤ 0.01 and |LFC| ≥ 2 significance cut-offs. Lists of significantly DEGs were generated using voom by applying these parameters with the Benjamini-Hochberg procedure to TMM-normalized HT-Seq count data. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 5. Transcript accumulation of genes associated with wound induced ABA biosynthesis and degradation. Transcript accumulation of known and putative genes encoding steps in ABA biosynthesis and degradation, over the wound-healing time course were retrieved from RNA-seq data. Heatmaps depict log2FPKM means for n = 3 biological replicates for each time point. Numbered pathway steps correspond to numbers in the ABA metabolism pathway (Supplemental Fig. 6).