@misc{14705, abstract = {Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.}, author = {Elkrewi, Marwan N}, keywords = {sex chromosome evolution, genome assembly, dosage compensation}, publisher = {Institute of Science and Technology Austria}, title = {{Data from "Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation"}}, doi = {10.15479/AT:ISTA:14705}, year = {2024}, } @misc{12820, abstract = {Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. This data repository contains NMR data presented in the associated manuscript}, author = {Schanda, Paul}, publisher = {Institute of Science and Technology Austria}, title = {{Research data of the publication "Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR"}}, doi = {10.15479/AT:ISTA:12820}, year = {2023}, } @misc{12945, abstract = {basic data for use in code for experimental data analysis for manuscript under revision: Dynamic pathogen detection and social feedback shape collective hygiene in ants Casillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S}, author = {Cremer, Sylvia}, keywords = {collective behavior, host-pathogen interactions, social immunity, epidemiology, social insects, probabilistic modeling}, publisher = {Institute of Science and Technology Austria}, title = {{Data from: "Dynamic pathogen detection and social feedback shape collective hygiene in ants" }}, doi = {10.15479/AT:ISTA:12945}, year = {2023}, } @misc{12370, abstract = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. }, author = {Gupta, Divyansh and Sumser, Anton L and Jösch, Maximilian A}, publisher = {Institute of Science and Technology Austria}, title = {{Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields}}, doi = {10.15479/AT:ISTA:12370}, year = {2023}, } @misc{12949, abstract = {The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.}, author = {Barton, Nicholas H}, keywords = {Quantitative genetics, infinitesimal model}, publisher = {Institute of Science and Technology Austria}, title = {{The infinitesimal model with dominance}}, doi = {10.15479/AT:ISTA:12949}, year = {2023}, } @misc{12869, abstract = {We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. }, author = {Klausen, Frederik Ravn and Lauritsen, Asbjørn Bækgaard}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for: A stochastic cellular automaton model of culture formation}}, doi = {10.15479/AT:ISTA:12869}, year = {2023}, } @misc{14562, abstract = {Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration. }, author = {Schur, Florian KM}, publisher = {Institute of Science and Technology Austria}, title = {{Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning"}}, doi = {10.15479/AT:ISTA:14562}, year = {2023}, } @misc{14472, abstract = {Data related to the following paper: "Stress granules plug and stabilize damaged endolysosomal membranes" (https://doi.org/10.1038/s41586-023-06726-w) Abstract: Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in "Stress granules plug and stabilize damaged endolysosomal membranes", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.}, author = {Vanhille-Campos, Christian Eduardo and Šarić, Anđela}, publisher = {Institute of Science and Technology Austria}, title = {{Stress granules plug and stabilize damaged endolysosomal membranes}}, doi = {10.15479/AT:ISTA:14472}, year = {2023}, } @misc{12693, abstract = {See Readme File for further information.}, author = {Cremer, Sylvia}, publisher = {Institute of Science and Technology Austria}, title = {{Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males }}, doi = {10.15479/AT:ISTA:12693}, year = {2023}, } @misc{12933, abstract = {Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster".}, author = {Puixeu Sala, Gemma}, publisher = {Institute of Science and Technology Austria}, title = {{Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster}}, doi = {10.15479/AT:ISTA:12933}, year = {2023}, }