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829 results for “Evolvability”
Data and code for: Male-mediated maturation unlikely to evolve via adaptive evolution
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Data from: Neuronal function and dopamine signaling evolve at high temperature in Drosophila
<p>Neuronal activity is temperature sensitive and affects behavioral traits important for individual fitness, such as locomotion and courtship. Yet, we do not know enough about the evolutionary response of neuronal phenotypes in new temperature environments. Here, we use long-term experimental evolution of <em>Drosophila simulans</em> populations exposed to novel temperature regimes. Here, we demonstrate a direct relationship between thermal selective pressure and the evolution of neuronally expressed molecular and behavioral phenotypes. Several essential neuronal genes evolve lower expression at high temperatures and higher expression at low temperatures, with dopaminergic neurons standing out by displaying the most consistent expression change across independent replicates. We functionally validate the link between evolved gene expression and behavioral changes by pharmacological intervention in the experimentally evolved <em>D. simulans</em> populations as well as by genetically triggered expression changes of key genes in <em>D. melanogaster</em>. As natural temperature clines confirm our results for <em>Drosophila</em> and <em>Anopheles</em>populations, we conclude that neuronal dopamine evolution is a key factor for temperature adaptation.</p>
Data for: Viral receptor-binding protein evolves new function through mutations that cause trimer instability and functional heterogeneity
<p>When proteins evolve new activity, a concomitant decrease in stability is often observed because the mutations that confer new activity can destabilize the native fold. In the conventional model of protein evolution, reduced stability is considered a purely deleterious cost of molecular innovation because unstable proteins are prone to aggregation and are sensitive to environmental stressors. However, recent work has revealed that non-native, often unstable protein conformations play an important role in mediating evolutionary transitions, raising the question of whether instability can itself potentiate the evolution of new activity. We explored this question in a bacteriophage receptor binding protein (RBP) during host-range evolution. We studied the properties of the RBP of bacteriophage before and after host-range evolution and demonstrated that the evolved protein is relatively unstable and may exist in multiple conformations with unique receptor preferences. Through a combination of structural modeling and in vitro oligomeric state analysis, we found that the instability arises from mutations that interfere with trimer formation. This study raises the intriguing possibility that protein instability might play a previously unrecognized role in mediating host-range expansions in viruses.</p>
mRNA prime–boost evolves precursors toward VRC01-like broadly neutralizing antibodies in preclinical humanized mouse models
<p>Germline-targeting (GT) protein immunogens to induce VRC01-class broadly neutralizing antibodies (bnAbs) to the CD4 binding site (CD4bs) of the HIV Envelope have shown promise in clinical trials. Here, we preclinically validated the mRNA-LNP delivery of one such immunogen, eOD-GT8, as a soluble self-assembling 60mer nanoparticle in humanized mouse models. In a model with three humanized B cell lineages bearing distinct VRC01-precursor B cell receptors (BCRs) with similar affinities for eOD-GT8, all lineages could be simultaneously primed and undergo diversification and affinity maturation with no sign of exclusionary competition. Boosts drove precursor B cell participation in germinal centers, the accumulation of somatic hypermutations, including in key VRC01-class positions, and affinity maturation to boost and native-like antigens in two of the three precursor lineages. We have preclinically validated a prime-boost regimen of soluble self-assembling nanoparticles delivered by mRNA-LNP, demonstrating that multiple lineages can be primed, boosted, and diversify along the bnAb pathway.</p>
Data for: Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster
<p>Tremendous plant metabolic diversity arises from phylogenetically-restricted specialized metabolic pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing in biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and the role of BGCs in pathway evolution remain underappreciated. In this study, we investigated the mechanisms driving acylsugar evolution in the Solanaceae. Previously thought to be restricted to glandular trichomes, acyl sugars were recently discovered in cultivated tomato roots. We demonstrated that acyl sugars in cultivated tomato roots and trichomes have different sugar cores, identified root-enriched paralogs of trichome acyl sugar pathway genes, and characterized a key paralog required for root acyl sugar biosynthesis, <em>SlASAT1-LIKE</em> (<em>SlASAT1-L</em>), which is nested within a previously-reported trichome acyl sugar BGC. Finally, we provided evidence that <em>ASAT1-L</em> arose through duplication of its paralog, <em>ASAT1</em>, and was trichome-expressed before acquiring root-specific expression in the <em>Solanum</em> genus. Our results illuminate the genomic context and molecular mechanisms underpinning metabolic diversity in plants.</p>
Fitness landscape of substrate-adaptive mutations in evolved APC transporters
<p>Growth rate calculations:</p> <p>Single colonies of <em>S. cerevisiae</em> Δ10AA pADHXC3GH-<em>GOI</em> were inoculated in YB media supplemented with 4 mm NH<sub>4</sub><sup>+</sup> and 0.1 mg/ml ampicillin, and grown until late logarithmic phase. The cultures were pelleted at 750 × <em>g</em> for 10 min at 30 °C and washed with YB media. The wells in the microplate were filled with the amino acids of interest to a final concentration of 2 mM and with culture cells to a final OD<sub>600</sub> of 0.04, to a final total well volume of 200 µl. Sterile water was added in the space between the wells to avoid evaporation. The prepared microplates included three biological replicates of the strains with the plasmid containing the gene of interest (GOI) and one biological replicate of the strain with the empty vector. The absorbance in each well was measured at 600 nm in 30 min intervals without shaking of the microplate, at 30 °C for 72 h in a SpectraMax ABS Plus plate reader. The data sets (CSV files) are the raw optical density readings from the growth assays, along with plate layout metadata (CSV files). The growth rates were derived based on the Baranyi growth model, using the <em>growthrates</em> package in <em>R</em>.</p> <p>Included transporter genes:</p> <p>Mutated transporters (script growth_rates_mutants_Baranyi2.r)</p> <p><em>AGP1</em>, <em>AGP1</em>-N, <em>AGP1</em>-V,<em> AGP1</em>-NV, <em>AGP1</em>-G, <em>AGP1</em>-T, <em>PUT4</em>, <em>PUT4</em>-S</p> <p>Wild-type transporters (script growth_rates_wild_types_Baranyi2.r)</p> <p><em>AGP1</em>, <em>BAP2</em>, <em>CAN1</em>, <em>HIP1</em>, <em>LYP1</em>, <em>MMP1</em>, <em>PUT4</em></p> <p> </p> <p>Plasmid sequences (Genbank files):</p> <p>pADHXC3GH-AGP1, pADHXC3GH-BAP2, pADHXC3GH-CAN1, pADHXC3GH-HIP1, pADHXC3GH-LYP1, pADHXC3GH-MMP1, pADHXC3GH-PUT4-S L207S, pADHXC3GH-PUT4, pADHXC3GH</p> <p> </p> <p>Measureing relative membrane fluorescence (all transporters in this study have C-terminal GFP tags):</p> <p>Micrographs were analyzed with ImageJ using the script analyse_cell_perimeter.ijm</p>
Beyond the Hype: Benchmarking LLM-Evolved Heuristics for Bin Packing - Data
<p>This repository contains the data and additional information for the paper 'Beyond the Hype: Benchmarking LLM-Evolved Heuristics for Bin Packing'. </p> <p>The following files are included:</p> <ul> <li>heatmaps.zip: heatmaps showing heuristic performance per dataset for 3 metrics;</li> <li>heuristic_perf.zip: raw results files for each datasets;</li> <li>tuning.zip: tuning log files;</li> <li>ts_features_evolved.csv and ts_features_evolved_10_features_excess_bins.csv : full and selected time-series features computed on the evolved datasets;</li> <li>BPinstances.csv : raw bin packing instances from all datasets: independent and evolved.</li> </ul>
Dataset used in "Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector"
<p><strong>[Figs 1 and S2]</strong></p> <p> </p> <p><strong>00_cloned_NRC123.fasta</strong></p> <p> </p> <p>FASTA file containing NRC1, NRC2 and NRC3 sequences tested in HR cell death assay.</p> <p> </p> <p><strong>01_NRCX0123_4species.fasta</strong></p> <p> </p> <p>FASTA file containing NRC0, NRC1, NRC2, NRC3 and NRCX of <em>N. benthamiana</em>, <em>C. annuum</em> (pepper), <em>S. tuberosum</em> (potato) and <em>S. lycopersicum</em> (tomato). In addition to a previously published dataset (Selvaraj et al., 2023), we included the NbNRC2, CaNRC3 and StNRC3 sequences from 00_cloned_NRC123.fasta.</p> <p> </p> <p><strong>02_NRCX0123_4species.local_aln.fasta</strong></p> <p> </p> <p>FASTA file containing the protein sequence alignment of 01_NRCX0123_4species.fasta. We used MAFFT for the alignment (Katoh & Standley, 2013).</p> <p> </p> <p><strong>03_NRCX0123_4species.local_aln.clip.fasta</strong></p> <p> </p> <p>FASTA file containing the trimmed protein sequence alignment of 02_NRCX0123_4species.local_aln.fasta. We used ClipKIT for trimming (Steenwyk et al., 2020).</p> <p> </p> <p><strong>04_NRCX0123_4species.local_aln.clip.fasta.treefile</strong></p> <p><strong> </strong></p> <p>Newick file containing the phylogenetic tree reconstructed based on 03_NRCX0123_4species.local_aln.clip.fasta. We used IQ-TREE to create a phylogenetic tree (Minh et al., 2020).</p> <p> </p> <p><strong>[Fig 2B]</strong></p> <p><strong> </strong></p> <p><strong>05_cloned_NRC123.local_aln.fasta</strong></p> <p><strong> </strong></p> <p>FASTA file containing the protein sequence alignment of 00_cloned_NRC123.fasta. We used MAFFT for the alignment (Katoh & Standley, 2013).</p> <p> </p> <p><strong>[Fig 5 and Table S1]</strong></p> <p> </p> <p><strong>06_NRCH_cds_23-06-20.min2400max2800.fasta</strong></p> <p><strong> </strong></p> <p>FASTA file containing the nucleotide sequences of helper NRC sequences from 124 Solanaceae genomes (Sugihara et al., 2023; Huang et al., 2023). We filtered out sequences shorter than 2,400 or longer than 2,800 bases, resulting in 1,748 sequences.</p> <p> </p> <p><strong>07_NRCH_cds_23-06-20.min2400max2800.aa.fasta</strong></p> <p> </p> <p>FASTA file of the amino acid sequences translated from 06_NRCH_cds_23-06-20.min2400max2800.fasta.</p> <p> </p> <p><strong>08_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.fasta</strong></p> <p> </p> <p>FASTA file containing the amino acid sequences of NB-ARC module corresponding to the sequences in 07_NRCH_cds_23-06-20.min2400max2800.aa.fasta.</p> <p> </p> <p><strong>09_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta</strong></p> <p> </p> <p>FASTA file containing the trimmed protein sequence alignment of 02_NRCX0123_4species.local_aln.fasta. We used MAFFT and ClipKIT for the alignment and trimming, respectively (Katoh & Standley, 2013; Steenwyk et al., 2020).</p> <p> </p> <p><strong>10_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta.treefile</strong></p> <p> </p> <p>Newick file containing the phylogenetic tree reconstructed based on 09_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta. We used IQ-TREE to create a phylogenetic tree (Minh et al., 2020).</p> <p> </p> <p><strong>11_NRCX123_cds_23-06-20.min2400max2800.fasta</strong></p> <p> </p> <p>FASTA file containing the the nucleotide sequences of NRC1/2/3X clades identified based on 10_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta.treefile.</p> <p> </p> <p><strong>12_NRCX123_nt_codon_ancseq_v1.2.1.zip</strong></p> <p> </p> <p>Results of ancestral sequence reconstruction. We used ancseq to perform ancestral sequence reconsturction (Sugihara, 2024). "NRCX123_cds_23-06-20.min2400max2800.nt_codon.local_aln.manual.clip.uniq.rm_4sp.fasta" is an input alignment and "NRCX123_cds_23-06-20.min2400max2800.nt_codon.local_aln.manual.clip.uniq.rm_4sp.fasta.treefile" is a tree file. Regarding the output files for ancseq, please refer to the <a href="https://github.com/YuSugihara/ancseq?tab=readme-ov-file#outputs">GitHub repository</a>.</p> <p> </p> <p><strong>[Fig S7]</strong></p> <p> </p> <p><strong>13_logo_plot.zip</strong></p> <p> </p> <p>Sequence alignments and script used in Fig S7. To generate the consensus sequence shown in Fig S7, we concatenated interfaces 1, 2 and 3 with SS15 and visualized the results using logomaker (Tareen and Kinney, 2020).</p> <p> </p> <p><strong>References</strong></p> <p> </p> <p>Huang C-Y, Huang Y-S, Sugihara Y, Wang H-Y, Huang L-T, Lopez-Agudelo JC, Chen Y-F, Lin K-Y, Chiang B-J, Toghani A, Kourelis J, Derevnina L, Wu C-H. 2023. Functional divergence shaped the network architecture of plant immune receptors. <em>bioRxiv</em>. 2023:2023.12.12.571219. DOI: 10.1101/2023.12.12.571219.</p> <p>Katoh K, Standley DM. 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. <em>Molecular Biology and Evolution</em> 30:772–780. DOI: 10.1093/molbev/mst010.</p> <p>Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. <em>Molecular Biology and Evolution</em> 37:1530–1534. DOI: 10.1093/molbev/msaa015.</p> <p>Selvaraj M, Toghani A, Pai H, Sugihara Y, Kourelis J, Yuen ELH, Ibrahim T, Zhao H, Xie R, Maqbool A, Concepcion JCD la, Banfield MJ, Derevnina L, Petre B, Lawson DM, Bozkurt TO, Wu C-H, Kamoun S, Contreras MP. 2023. Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome. <em>bioRxiv</em>. 2023:2023.12.17.572070. DOI: 10.1101/2023.12.17.572070.</p> <p>Steenwyk JL, Iii TJB, Li Y, Shen X-X, Rokas A. 2020. ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference. <em>PLOS Biology</em> 18:e3001007. DOI: 10.1371/journal.pbio.3001007.</p> <p>Sugihara Y. 2024. YuSugihara/ancseq: v1.2.1. <em>Zenodo</em>. DOI: 10.5281/zenodo.10808871.</p> <p>Sugihara Y, Toghani A, Kamoun S, Kourelis J. 2023. NLRome dataset from 124 genomes of plants in the Solanaceae family. <em>Zenodo</em>. DOI: 10.5281/zenodo.10354350.</p> <p>Tareen A, Kinney JB. 2020. Logomaker: beautiful sequence logos in Python. Bioinformatics 36:2272–2274. doi:10.1093/bioinformatics/btz921</p> <p> </p>
Obligate mutualistic cooperation limits evolvability
<p>Cooperative mutualisms are widespread and play fundamental roles in many ecosystems. Given that these interactions are often obligate, the Darwinian fitness of the participating individuals is not only determined by the information encoded in their own genomes, but also the traits and capabilities of their corresponding interaction partners. Thus, a major outstanding question is how obligate cooperative mutualisms affect the ability of organisms to adapt evolutionarily to changing environmental conditions. Here we address this issue using a mutualistic cooperation between two auxotrophic genotypes of Escherichia coli that reciprocally exchanged costly amino acids. Amino acid-supplemented monocultures and unsupplemented cocultures were exposed to stepwise increasing concentrations of different antibiotics. This selection experiment reveals that metabolically interdependent bacteria are generally less able to adapt to environmental stress than autonomously growing strains. Moreover, obligate cooperative mutualists frequently regain metabolic autonomy, resulting in a collapse of the mutualistic interaction. </p>
Obligate mutualistic cooperation limits evolvability
<p>Cooperative mutualisms are widespread and play fundamental roles in many ecosystems. Given that these interactions are often obligate, the Darwinian fitness of the participating individuals is not only determined by the information encoded in their own genomes, but also the traits and capabilities of their corresponding interaction partners. Thus, a major outstanding question is how obligate cooperative mutualisms affect the ability of organisms to adapt evolutionarily to changing environmental conditions. Here we address this issue using a mutualistic cooperation between two auxotrophic genotypes of Escherichia coli that reciprocally exchanged costly amino acids. Amino acid-supplemented monocultures and unsupplemented cocultures were exposed to stepwise increasing concentrations of different antibiotics. This selection experiment reveals that metabolically interdependent bacteria are generally less able to adapt to environmental stress than autonomously growing strains. Moreover, obligate cooperative mutualists frequently regain metabolic autonomy, resulting in a collapse of the mutualistic interaction. </p>
Loricarioid catfish evolved skin denticles that recapitulate teeth at the structural, developmental, and genetic levels (raw RNAseq reads)
<p>The first vertebrate mineralized skeleton was an external bony armor coated with dental structures. The subsequent emergence of a mineralized endoskeleton and of teeth are considered key innovations in the diversification of vertebrates. Although time clouds our understanding of the initial evolution of these mineralized structures, recent re-emergences may shed light on the underlying processes. Loricarioid catfishes are a lineage that, much like the ancestral vertebrates, bear denticle-clad bony armor from head to tail. Loricarioid denticles (LDs) and oral teeth are very similar in superstructure. We show here that other extra-oral dental structures are found as ancestral characters only in lineages that are distantly related to loricarioids such as sharks or coelacanth, indicating that LDs have independently re-emerged in loricarioid catfishes. We investigate whether the similarities between LDs and teeth extend to their developmental and genetic context, and how their development compares to that of other vertebrate integument structures. Our detailed study of the development of LDs, and gene expression analyses through in situ hybridization confirm that all 12 genes from the tooth-forming gene regulatory network (oGRN) are expressed in developing LDs in a similar way as they are expressed in developing teeth. We then compare the developmental, structural, and genetic aspects of LD and teeth with that of other integument appendages such as fish scales, shark dermal denticles, feathers and hairs. We find that LDs share all developmental cues with teeth and, to a lesser extent, with the other vertebrate integument structures. Taken together, our results indicate that denticles have re-emerged on the trunk of loricarioid catfishes through the ectopic co-option of the oGRN rather than the resurrection of an ancestral trunk-specific denticle genetic pathway.</p>
No major cost of evolved survivorship in Drosophila melanogaster populations coevolving with Pseudomonas entomophila
<p><span>Rapid exaggeration of host and pathogen traits via arms race dynamics is one possible outcome of host-pathogen coevolution. However, the exaggerated traits are expected to incur costs in terms of resource investment in other life-history traits. The current study investigated the costs associated with evolved traits in a host-pathogen coevolution system. We used the <em>Drosophila melanogaster</em> (host)-<em>Pseudomonas entomophila</em> (pathogen) system to experimentally derive two selection regimes, one where the host and pathogen both coevolved, and the other, where only the host evolved against a non-evolving pathogen. After 17 generations of selection, we found that hosts from both selected populations had better post-infection survivorship than controls. Even though the coevolving populations tended to have better survivorship post-infection, we found no clear evidence that the two selection regimes were significantly different from each other.. There was weak evidence for the coevolving pathogens being more virulent than the ancestral pathogen. We found no major cost of increased post-infection survivorship. The costs were not different between the coevolving hosts and the hosts evolving against a non-evolving pathogen. We found no evolved costs in the coevolving pathogens. Thus, our results suggest that increased host immunity and pathogen virulence may not be costly.</span></p>
The phenotypic plasticity of an evolving digital organism
<p>Data set and R code used in the analysis reported in the manuscript entitled "<em>The phenotypic plasticity of an evolving digital organism</em>", which has been accepted in Proc. R. Open. Sci. for publication.</p>
Data from: Loss-of-heterozygosity facilitates a fitness valley crossing in experimentally evolved multicellular yeast
<p>These data sets are generated to investigate a simple evolutionary landscape that arises from underdominance at a single locus where the fitness valley consists of only one less-fit genotype. We make use of an experimental system previous evolved in the laboratory, the S<em>accharomyces cerevisiae</em> snowflake system. This system was experimentally selected resulting in a significant evolutionary shift, the transition from uni-to-multicellularity in asexual diploid populations. We carried out the phenotypic and fitness characterization of the strains. Additionally, we observed a rapid loss of heterozygosity (LOH) events in the heterozygote strains. Experimental evolution starting with the heterozygote strains suggests that LOH is common both under selection and without selection. LOH event drive adaptation that may enable rapid evolution in diploid yeast. </p>
Olfactory receptor alignments for: Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats
<p>While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. In phyllostomid bats, an ecologically diverse clade that evolved plant-visiting from an insectivorous ancestor, the evolution of novel food detection mechanisms is suggested to be a key innovation, as plant-visiting species rely strongly on olfaction, supplementarily using echolocation. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration are coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants — a potential ecological constraint on sensory evolution.</p>
Invasive plant species that experience lower herbivory pressure may evolve lower diversities of chemical defence compounds in the exotic range
<p><strong>ABSTRACT</strong></p> <p><strong>PREMISE</strong></p> <p>Invasive plant species often escape from specialist herbivore species and are likely to experience herbivory mostly from generalist herbivore species in the exotic range. Consequently, the Shifting Defence Hypothesis (SDH) predicts that invasive plants will express higher concentrations of qualitative defence compounds to deter dominant generalist herbivores in the exotic range. Here, I additionally propose a Reduced Chemical Diversity Hypothesis (RCDH), which predicts that reduced herbivory pressure will select for invasive plant genotypes that produce lower diversities of defence compounds in the exotic range.</p> <p><strong><span>METHODS</span></strong></p> <p>I tested whether: (1) Invasive <em>Brassica nigra</em> populations express a lower diversity and an overall higher concentration of glucosinolate compounds than native-range <em>B. nigra</em>; (2) <em>Brassica nigra</em> individuals that express high diversities and concentrations of glucosinolates are more attractive to specialist and deterrent to generalist herbivores; (3) Tissues of invasive <em>B. nigra </em>are less palatable to two generalist herbivores <em>Theba pisana</em> and <em>Helix aspersa</em> than tissues of native-range<em> B. nigra</em>.</p> <p><strong><span>RESULTS</span></strong></p> <p>Invasive <em>B. nigra </em>populations expressed a significantly lower diversity of glucosinolate compounds and a marginally higher concentration of total glucosinolate compounds. Leaf tissues of the invasive <em>B. nigra</em> were significantly less palatable to <em>T. pisana</em> and marginally less so to <em>H. aspersa</em>. <em>Brassica nigra</em> individuals that expressed high concentrations of total glucosinolate compounds were visited by a low diversity of generalist herbivore species in the field.</p> <p><strong><span>CONCLUSIONS</span></strong></p> <p>The biogeographical differences in glucosinolate profiles of invasive and native-range populations of <em>B. nigra</em> may be the result of differential herbivore selection pressures in the respective ranges.</p>
Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host
<p>Scripts and data used in the work "Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host".</p> <p><strong>Abstract: </strong>Although generalist insect herbivores can migrate and rapidly adapt to a broad range of host plants, they can face significant difficulties when accidentally migrating to novel and marginally-suitable hosts. What happens, at both the performance and transcriptional levels, if these marginally-suitable hosts must be used for multiple generations before migration to a suitable host can take place, largely remains unknown. In this study, we established multigenerational colonies of the whitefly <em>Bemisia tabaci</em>, a generalist phloem-feeding species, adapted to a marginally-suitable host (habanero pepper) or an optimal host (cotton). We used reciprocal host tests to estimate the differences in performance of the populations on both hosts under optimal (30 <sup>o</sup>C) and mild-stressful (24 <sup>o</sup>C) temperature conditions, and documented the associated transcriptomic changes. The habanero pepper-adapted population greatly improved its performance on habanero pepper but did not reach its performance level on cotton, the original host. It also showed reduced performance on cotton, relative to the non-adapted population, and an antagonistic effect of the lower-temperature stressor. The transcriptomic data revealed that most of the expression changes, associated with long-term adaptation to habanero pepper, can be categorized as “evolved” with no initial plastic response. Three molecular functions dominated: enhanced formation of cuticle structural constituents, enhanced activity of oxidation-reduction processes involved in neutralization of phytotoxins and reduced production of proteins from the cathepsin B family. Taken together, these findings indicate that generalist insects can adapt to novel host plants by modifying the expression of a relatively small set of specific molecular functions.</p>
Carbon and nitrogen abundances as indicators of material mixing in evolved stars
<p>Carbon and nitrogen abundances are among most useful quantitative indicators of mixing processes in evolved stars. Because of the first dredge-up abundances of 12C decrease while abundances of 13C and 14N increase. These alterations become efficient again on the red giant branch when stars reach the so-called luminosity bump, and depend on stellar evolutionary stage, mass, metallicity, rotation, magnetic activity and other parameters and processes. An overview is provided on observational analyses of evolved low mass giants accomplished using the Nordic Optical Telescope.</p>
Data from: Extreme neck elongation evolved despite strong developmental constraints in bizarre Triassic reptiles – implication for neck modularity in archosaurs
<p>The Triassic radiation of vertebrates saw the emergence of the modern vertebrate groups, as well as numerous extinct animals exhibiting conspicuous, unique anatomical characteristics. Among these, members of Tanystropheidae (Reptilia: Archosauromorpha) displayed cervical vertebral elongation to an extent unparalleled in any other vertebrate. Tanystropheids were exceptionally ecologically diverse and had a wide spatial and temporal distribution. This may have been related to their neck anatomy, yet its evolution and functional properties remain poorly understood. We used geometric morphometrics to capture the intraspecific variation between the vertebrae comprising the cervical column among early archosauromorphs, to trace the evolutionary history of neck elongation in these animals. Our results show that the cervical series of these reptiles can be divided into modules corresponding to those of extant animals. Tanystropheids achieved neck elongation through somite elongation and a shift between cervical and thoracic regions, without presacral vertebrae count increase - contrary to crown archosaurs. This suggests a peculiar developmental constraint that strongly affected the evolution of tanystropheids. The data obtained just at the base of the archosauromorph phylogenetic tree is crucial for further studies on the modularity of vertebral columns of not only Triassic reptile groups but extant and other extinct animals as well.</p>
Dataset related to "High-frequency optimally windowed chirp rheometry for rapidly evolving viscoelastic materials: Application to a crosslinking thermoset"
<p>Knowledge of the evolution in the mechanical properties of a curing polymer matrix is of great importance in composite parts or structure<br>fabrication. Conventional rheometry, based on small amplitude oscillatory shear, is limited by long interrogation times. In rapidly evolving<br>materials, time sweeps can provide a meaningful measurement albeit at a single frequency. To overcome this constraint, we utilize a combined<br>frequency- and amplitude-modulated chirped strain waveform in conjunction with a homemade sliding plate piezo-operated rheometer (PZR)<br>and a dual-head commercial rotational rheometer (Anton Paar MCR 702) to probe the linear viscoelasticity of these time-evolving materials.<br>The direct controllability of the PZR, resulting from the absence of any kind of firmware and the microsecond actuator-sensor response<br>renders this device ideal for exploring the advantages of this technique. The high frequency capability allows us to extend the upper limits of<br>the accessible linear viscoelastic spectrum and, most importantly, to shorten the length of the interrogating strain signal (OWCh-PZR) to subsecond<br>scales, while retaining a high time-bandwidth product. This short duration ensures that the mutation number (NMu) is kept sufficiently<br>low, even in fast-curing resins. The method is validated via calibration tests in both instruments, and the corresponding limitations are discussed.<br>As a proof of concept, the technique is applied to a curing vinylester resin. The linear viscoelastic (LVE) spectrum is assessed every<br>20 s to monitor the rapid evolution in the time and frequency dependence of the complex modulus. Comparison of the chirp implementation,<br>based on parameters such as duration of the experiment, sampling frequency, and frequency range, in a commercial rotational rheometer with<br>the PZR provides further information on the applicability of this technique and its limitations. Finally, FTIR spectroscopy is utilized to gain<br>insights into the evolution of the chemical network, and the gap dependence of the evolving material properties in these heterogeneous<br>systems is also investigated</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.