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opencc-by-4.0Jul 2023View details →

Dataset: The Main Evolutionary Pathways of Massive Hierarchical Triple Stars

This is a reproduction package for the paper "The Main Evolutionary Pathways of Massive Hierarchical Triple Stars" by Kummer et al. (2023). It aims to provide the most important data products and reproduce the Figures of the paper.

opencc-by-4.0Oct 2024View details →

Interactions between methylerythritol phosphate (MEP) pathway metabolites and Escherichia coli K-12 fatty acid biosynthesis enzymes

Raw data files from native mass spectrometry analyses examining the interactions between methylerythritol phosphate (MEP) pathway metabolites and Escherichia coli K-12 fatty acid biosynthesis enzymes. Recorded in positive mode direct injection.

Fig. 4. S in Regulation of M1/M2 macrophage polarization by Sutherlandia frutescens via NFkB and MAPK signaling pathways

Fig. 4. S. frutescens inhibits LPS-induced HMOX-1 upregulation in RAW 264.7 cells. Data represent mean ± SEM of three independent experiments, each conducted in duplicate, +++ = p <0.001 compared to DMSO control; *** = p <0.001 compared to LPS control; ## = p <0.01 ethanolic extract compared to hot aqueous extract.

Fig. 5 in Regulation of M1/M2 macrophage polarization by Sutherlandia frutescens via NFkB and MAPK signaling pathways

Fig. 5. Effect of S. frutescens on A) CD86 (M1) and B) CD206 (M2) expression in LPS-induced RAW 264.7 cells. Data represent mean ± SEM of three independent experiments, each conducted in triplicate++ = p <0.05, +++ = p <0.001 compared to DMSO control; * = p <0.05, ** = p <0.01, *** = p <0.001 compared to LPS control; # = p <0.05 ethanolic extract compared to hot aqueous extract.

Fig. 3. S in Regulation of M1/M2 macrophage polarization by Sutherlandia frutescens via NFkB and MAPK signaling pathways

Fig. 3. S. frutescens modulated the expression of pro-inflammatory cytokines in LPS-induced Raw 264.7 cells. Data represent mean ± SEM of three independent experiments, ++ = p <0.05, +++ = p <0.001 compared to DMSO control; * = p <0.05, ** = p <0.01, *** = p <0.001 compared with LPS control; ### = p <0.001 ethanolic extract compared to hot aqueous extract.

Fig. 1. S in Regulation of M1/M2 macrophage polarization by Sutherlandia frutescens via NFkB and MAPK signaling pathways

Fig. 1. S.frutescens reduces (A) NO and (B) ROS production in LPS-induced RAW 264.7 cells. 10 μM Curcumin was used as an anti-inflammatory control. Data represent mean ± SEM of three independent experiments,each conducted in triplicate, +++ = p <0.001 compared to DMSO control; * = p <0.05,** = p <0.01,*** = p <0.001 compared to LPS control; # = p <0.05 ethanolic extract compared to hot aqueous extract.

Fig. 2. S in Regulation of M1/M2 macrophage polarization by Sutherlandia frutescens via NFkB and MAPK signaling pathways

Fig. 2. S. frutescens reduces (A) iNOS and (B) COX-2 expression in LPS-induced RAW 264.7 cells. Data represent mean ± SEM of three independent experiments, each conducted in triplicate, +++ = p <0.001 compared to DMSO control; * = p <0.05, ** = p <0.01, *** = p <0.001 compared to LPS control; # = p <0.05 ethanolic extract compared to hot aqueous extract.

Fig. 6. S in Regulation of M1/M2 macrophage polarization by Sutherlandia frutescens via NFkB and MAPK signaling pathways

Fig. 6. S. frutescens inhibits NFKB and MAPK activation in LPS-induced RAW 264.7 cells. (A) Quantitative analysis of nuclear NFKB localization determined using the cell scoring analysis module on MetaXpress® software (Version 5.1) of the ImageXpress Micro XLS (Molecular Devices, USA), with expression recorded as percentage of LPS induction. Changes in phosphorylation level of (B) p-p65 NFKB, (C) p-ERK 1/2 and (D) p-p38 detected by flow cytometry analysis, with expression recoded as percentage of untreated control. Data represents mean ± SEM of three independent experiments, each conducted in triplicate, +++ = p <0.001 compared to DMSO control; * = p <0.05, ** = p <0.01, *** = p <0.001 compared to LPS control; # = p <0.05 ethanolic extract compared to hot aqueous extract. Corresponding immunofluorescence images of control cells (Ei), LPS induced cells (Eii), LPS induced cells co-treated with 50 μg mL −1 and 200 μg mL −1 hot aqueous S. frutescens extract (Eiii, Eiv), LPS induced cells co-treated with 50 μg mL −1 and 200 μg mL −1 ethanolic S. frutescens extract (Ev, Evi). Cells were stained with anti-p65 NFKB antibody and co-stained with DAPI. Increased nuclear localization and increased cytoplasmic expression is seen following LPS treatment (Eii), which is reduced following co-treatment with S. frutescens (Eiii-Evi). Scale bar = 50 μm.

opencc-zeroDec 2017View details →

Data from: Functional traits and environmental conditions predict community isotopic niches and energy pathways across spatial scales

1. Despite ongoing research in food web ecology and functional biogeography, the links between food-web structure, functional traits and environmental conditions across spatial scales remain poorly understood. Trophic niches, defined as the amount of energy and elemental space occupied by species and food webs, may help bridge this divide. 2. Here, we ask how the functional traits of species, the environmental conditions of habitats and the spatial scale of analysis jointly determine the characteristics of trophic niches. We used isotopic niches as a proxy of trophic niches, and conducted analyses at spatial scales ranging from local food webs and metacommunities to geographically distant sites. 3. We sampled aquatic macroinvertebrates from 104 tank bromeliads distributed across five sites from Central to South America, and compiled the macroinvertebrates' functional traits and stable isotope values (δ15N and δ13C). We assessed how isotopic niches within each bromeliad were influenced by the functional trait composition of their associated invertebrates and environmental conditions (i.e., habitat size, canopy cover, and detrital concentration). We then evaluated whether the diet of dominant predators and, consequently, energy pathways within food webs, reflected functional and environmental changes among bromeliads across sites. Finally, we determined the extent to which the isotopic niches of macroinvertebrates within each bromeliad contributed to the metacommunity isotopic niches within each site, and compared these metacommunity-level niches over biogeographic scales. 4. At the bromeliad level, isotopic niches increased with the functional richness of species in the food web and the detrital concentration in the bromeliad. The diet of top predators tracked shifts in prey biomass along gradients of canopy cover and detrital concentration. Bromeliads that grew under heterogeneous canopy cover displayed less trophic redundancy and therefore combined to form larger metacommunity isotopic niches. Finally, the size of metacommunity niches depended on within-site heterogeneity in canopy cover. 5. Our results suggest that the trophic niches occupied by food webs can predictably scale from local food webs to metacommunities to biogeographic regions. This scaling process is determined by both the functional traits of species and heterogeneity in environmental conditions.

opencc-zeroOct 2019View details →

Data from: Complete loss of the MHC II pathway in an anglerfish, Lophius piscatorius

Genome studies in fish provide evidence for the adaptability of the vertebrate immune system, revealing alternative immune strategies. The reported absence of the major compatibility complex (MHC) class II pathway components in certain species of pipefish (genus Syngnathus) and cod-like fishes (order Gadiformes) is of particular interest. The MHC II pathway is responsible for immunization and defence against extracellular threats through the presentation of exogenous peptides to T helper cells. Here we demonstrate the absence of all genes encoding MHC II components (CD4, CD74 A/B, and both classical and non-classical MHC II α/β) in the genome of an anglerfish, Lophius piscatorius, indicating loss of the MHC II pathway. In contrast, it has previously been reported that another anglerfish, Antennarius striatus, retains all MHC II genes, placing the loss of MHC II in the Lophius clade to their most recent common ancestor. In the three taxa where MHC II loss has occurred, the gene loss has been restricted to four or five core MHC II components, suggesting that, in teleosts, only these genes have functions that are restricted to the MHC II pathway.

opencc-zeroDec 2017View details →

Data from: The convergent evolution of snake-like forms by divergent evolutionary pathways in squamate reptiles

Convergent evolution of phenotypes is considered evidence that evolution is deterministic. Establishing if such convergent phenotypes arose through convergent evolutionary pathways is a stronger test of determinism. We studied the evolution of snake-like body shapes in six clades of lizards, each containing species ranging from short-bodied and pentadactyl to long-bodied and limbless. We tested whether body shapes that evolved in each clade were convergent, and whether clades evolved snake-like body shapes following convergent evolutionary pathways. Our analyses showed that indeed species with the same numbers of digits in each clade evolved convergent body shapes. We then compared evolutionary pathways among clades by considering patterns of evolutionary integration and shape of relationship among body parts, patterns of vertebral evolution, and models of digit evolution. We found that all clades elongated their bodies through the addition, not elongation, of vertebrae, and had similar patterns of integration. However, patterns of integration, the body parts that were related by a linear or a threshold model, and patterns of digit evolution differed among clades. These results showed that clades followed different evolutionary pathways. This suggests an important role of historical contingency as opposed to determinism in the convergent evolution of snake-like body shapes.

opencc-zeroDec 2016View details →

Data from: Disentangling the pathways of land use impacts on the functional structure of fish assemblages in Amazon streams

Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the Amazon to date, examining functional responses of fish assemblages to land use. We sampled fish assemblages from two large human-modified regions, and characterized stream conditions by physical habitat attributes and key landscape-change variables, including density of road crossings (i.e. riverscape fragmentation), deforestation, and agricultural intensification. Fish species were functionally characterized using ecomorphological traits describing feeding, locomotion, and habitat preferences, and these traits were used to derive indices that quantitatively describe the functional structure of the assemblages. Using structural equation modeling, we disentangled multiple drivers operating at different spatial scales, identifying causal pathways that significantly affect stream condition and the structure of the fish assemblages. Deforestation at catchment and riparian network scales altered the channel morphology and the stream bottom structure, changing the functional identity of assemblages. Local deforestation reduced the functional evenness of assemblages (i.e. increased dominance of specific trait combinations) mediated by expansion of aquatic vegetation cover. Riverscape fragmentation reduced functional richness, evenness and divergence, suggesting a trend toward functional homogenization and a reduced range of ecological niches within assemblages following the loss of regional connectivity. These results underscore the often-unrecognized importance of different land use changes, each of which can have marked effects on stream biodiversity. We draw on the relationships observed herein to suggest priorities for the improved management of stream systems in the multiple-use landscapes that predominate in human-modified tropical forests.

opencc-zeroDec 2014View details →

Data from: Plant defenses against ants provide a pathway to social parasitism in butterflies

Understanding the chemical cues and gene expressions that mediate herbivore–host-plant and parasite–host interactions can elucidate the ecological costs and benefits accruing to different partners in tight-knit community modules, and may reveal unexpected complexities. We investigated the exploitation of sequential hosts by the phytophagous–predaceous butterfly Maculinea arion, whose larvae initially feed on Origanum vulgare flowerheads before switching to parasitize Myrmica ant colonies for their main period of growth. Gravid female butterflies were attracted to Origanum plants that emitted high levels of the monoterpenoid volatile carvacrol, a condition that occurred when ants disturbed their roots: we also found that Origanum expressed four genes involved in monoterpene formation when ants were present, accompanied by a significant induction of jasmonates. When exposed to carvacrol, Myrmica workers upregulated five genes whose products bind and detoxify this biocide, and their colonies were more tolerant of it than other common ant genera, consistent with an observed ability to occupy the competitor-free spaces surrounding Origanum. A cost is potential colony destruction by Ma. arion, which in turn may benefit infested Origanum plants by relieving their roots of further damage. Our results suggest a new pathway, whereby social parasites can detect successive resources by employing plant volatiles to simultaneously select their initial plant food and a suitable sequential host.

opencc-zeroJul 2019View details →

Data from: Alternative functional strategies and altered carbon pathways facilitate broad depth ranges in coral-obligate reef fishes

Spatial refuges in peripheral habitats will become increasingly important for species persistence as climate change and other disturbances progressively impact habitat quality and assemblage compositions. However, the capacity for persistence will be determined in part by species‐specific abilities to absorb costs related to altered or decreased quantities and quality of resources at range peripheries. We compared variations in dietary strategies and energy acquisition trade‐offs along depth gradients in two obligate corallivores that differ in level of diet specialization. We also assessed depth‐related changes in energy pathways and energy content of their mixotrophic prey. We found no changes in feeding effort or total resource availability (total coral cover) towards deep range margins, but availability of the preferred resource (Acropora coral) decreased. While both species selectively targeted Acropora, the more specialized species (Chaetodon baronessa) exhibited limited feeding plasticity along the depth gradient. The degree of selectivity towards the preferred coral increased rather than decreased with depth, being 40 times greater than expected, given availability, at their range periphery. In contrast, the generalist's diet (Chaetodon octofasciatus) varied greatly in response to changes in resource availability with depth. Unexpectedly, the energy content of Acropora did not decline with depth, likely due to increased coral heterotrophy in deeper water, indicated by shifts in their molecular isotope geochemistry. This shift was accompanied by a 20% increase in plankton‐sourced carbon in the muscle tissue of deep‐resident fish, despite no observations of direct feeding on plankton food sources. Our results indicate that deep ranges in coral‐obligate reef fishes are supported by multiple mechanisms of trophic versatility in both the fish and corals. This nutritional plasticity likely serves a compensatory role in the resilience and eventual adaptation of organisms at their range peripheries. For species vulnerable to increasing anthropogenic impacts at range cores, variable and multi‐trophic functional responses can act to buffer against costs and increase the refuge potential of range peripheries. Specialist consumers may also be supported indirectly at range margins via trophic plasticity within their preferred prey.

opencc-zeroApr 2020View details →

Data from: Genomic regions underlying metabolic and neuronal signaling pathways are temporally consistent outliers in a moving avian hybrid zone

The study of hybrid zones can provide insight into the genetic basis of species differences that are relevant for the maintenance of reproductive isolation. Hybrid zones can also provide insight into climate change, species distributions, and evolution. The hybrid zone between black-capped chickadees (Poecile atricapillus) and Carolina chickadees (P. carolinensis) is shifting northward in response to increasing winter temperatures but is not increasing in width. This pattern indicates strong selection against chickadees with admixed genomes. Using high-resolution genomic data, we identified regions of the genomes that are outliers in both time points and do not introgress between the species; these regions may be involved in the maintenance of reproductive isolation. Genes involved in metabolic regulation processes were overrepresented in this dataset. Several gene ontology categories were also temporally consistent—including glutamate signaling, synaptic transmission, and catabolic processes—but the nucleotide variants leading to this pattern were not. Our results support recent findings that hybrids between black-capped and Carolina chickadees have higher basal metabolic rates than either parental species and suffer spatial memory and problem-solving deficits. Metabolic breakdown, as well as spatial memory and problem-solving, in hybrid chickadees may act as strong postzygotic isolation mechanisms in this moving hybrid zone.

opencc-by-4.0Jul 2021View details →

Rewiring of endogenous signaling pathways to genomic targets for therapeutic cell reprogramming

Data underlying the figures in the publication “Rewiring of endogenous signaling pathways to genomic targets for therapeutic cell reprogramming”, published in Nat Commun, 2020, 11, 608. <a href="https://www.nature.com/articles/s41467-020-14397-8">https://www.nature.com/articles/s41467-020-14397-8</a> Table of contents: 1. Source Data; Excel file with the data for Figures 2, 3b, 3d, 3c, 4a, 4b, 4c, 5 as well as S2, S3, S4, S5, S6, S7a, S7b, S8, S9, S10, S11, S12, S13a and S13b. Data 1 – Transgene expression by SEAP Data for Figures 2, S2, S4, S5, S7a, S8, S9, S12 and S13b. SEAP (human placental secreted alkaline phosphatase) levels were profiled in cell culture supernatants using a colorimetric assay. 100 µL 2x SEAP assay buffer (20 mM homoarginine, 1 mM MgCl2, 21% diethanolamine, pH 9.8) was mixed with 80 µL heat-inactivated (30 min at 65 °C) cell culture supernatant. After the addition of 20 µL substrate solution (120 mM p-nitrophenyl phosphate; cat. no. AC128860100, Thermo Fisher Scientific, Waltham, MA, USA), the absorbance time course was recorded at 405 nm and 37 °C using a Tecan Genios PRO plate reader (cat. no. P97084; Tecan Group AG, Maennedorf, Switzerland) and the SEAP levels were determined as follows: first, absorbance change over time (slope) was calculated. According to the Beer–Lambert’s law, absorbance is proportional to the concentration of a colored compound and depends on the light path length (d) and extinction coefficient (ε) (ε for p-nitrophenyl (εpNP) = 18.600 M−1 cm−1). Enzymatic activity EA [U/L] was calculated from the equation: EA = slope × dilution factor × εpNP−1 × d−1 Values in the file present determined SEAP levels. Data 2 – Endogenous gene expression by qPCR Data for Figures 3b, 3d, 4a, 4b, 5, S3, S6, S10, S11 and S13a. Total RNA of HEK293T cells was isolated using the Quick-RNA kit (Zymo Research, Irvine, CA, USA). Reverse transcription was performed using a High-Capacity cDNA Reverse Transcription Kit (cat. no. 4368814, Thermo Fisher Scientific, Waltham, MA, USA). Quantitative PCR was performed with the SsoAdvanced Universal SYBR® Green Supermix (cat. no. 1725270, Bio-Rad, Hercules, CA, USA). The Eppendorf Realplex Mastercycler (Eppendorf GmbH) was set to the following amplification parameters: 30 s at 95 °C and 40 cycles of 15 s at 95 °C followed by 30 s at X °C (X = 59 for insulin, 64 for IL-12, 59 or 64 for GAPDH). The relative threshold cycle (Ct) was determined and normalized to the endogenous glyceraldehyde 3-phosphate dehydrogenase (GAPDH) transcript. The fold change for each transcript relative to the control was calculated using the comparative Ct method. Values in the file present determined mRNA levels relative to GAPDH. Data 3 – Secreted protein level by ELISA Data for Figures 3c and 4c. Human Insulin was quantified with the Mercodia Insulin ELISA (cat. no. 10-1113-01, Mercodia, Uppsala, Sweden). IL-12 was quantified with the human IL-12 (p40) ELISA Kit (cat. no. KAC1561, Thermo Fisher Scientific, Waltham, MA, USA). Values in the file present protein levels as determined by ELISA kit. Data 4 – Nanoluc luciferase Data for Figure S7b. NanoLuc® luciferase was quantified in cell culture supernatants using the Nano-Glo® Luciferase Assay System (cat. no. N1110; Promega, Duebendorf, Switzerland). In brief, 7.5 µL of cell culture supernatant was added per well of a black 384-well plate and mixed with 7.5 µL substrate-containing assay buffer. Total luminescence was quantified using a Tecan Genios PRO plate reader (Tecan Group AG). Values in the file present luminescence as measured.

opencc-by-4.0Jul 2021View details →

Data set of the article "Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation"

Data set of the article "Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation"

opencc-zeroJul 2021View details →

Molecular evolution of phototransduction pathway genes in nocturnal and diurnal fireflies (Coleoptera: Lampyridae)

Most organisms are dependent on sensory cues from their environment for survival and reproduction. Fireflies (Coleoptera: Lampyridae) represent an ideal system for studying sensory niche adaptation due to many species relying on bioluminescent communication, as well as a diversity of ecology. Here we examine the phototransduction pathway in this non-model organism, and provide some of the first evidence for positive selection in the PT pathway in insects. Duplications are found in calmodulin, inactivation no afterpotential C, inactivation no afterpotential D, and transient receptor potential. We also find strong support for positive selection in arrestin-2, inactivation no afterpotential D, and transient receptor potential, with weak support for positive selection in guanine nucleotide-binding protein G(q) subunit alpha and neither inactivation nor afterpotential C. This represents an exciting new avenue of study as we seek to further understand these molecular players.

opencc-zeroJul 2021View details →

Transcriptome dataset to: Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development

This collection contains RNA-seq data obtained from young flower buds of Silene latifolia for each sample in the main manuscript in triplicate (male, female, two generations of hermaphrodites). The RNA was isolated from adult plants of U15 population and two subsequent generations, made by full-sib mating (U15=15 generations, U16=16 generations, U17=17 generations). The petals and sepals were removed before RNA-isolation. To avoid the bias made by sampling of old flower buds, only the first flowers were always sampled. The deposited RNA-seq data were not processed.