@misc{8930, abstract = {Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.}, author = {Kavcic, Bor}, keywords = {Escherichia coli, antibiotic combinations, translation, growth laws, drug interactions, bacterial physiology, translation inhibitors}, publisher = {Institute of Science and Technology Austria}, title = {{Analysis scripts and research data for the paper "Minimal biophysical model of combined antibiotic action"}}, doi = {10.15479/AT:ISTA:8930}, year = {2020}, } @misc{8951, abstract = {Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.}, author = {Nagy-Staron, Anna A}, keywords = {Gene regulatory networks, Gene expression, Escherichia coli, Synthetic Biology}, publisher = {Institute of Science and Technology Austria}, title = {{Sequences of gene regulatory network permutations for the article "Local genetic context shapes the function of a gene regulatory network"}}, doi = {10.15479/AT:ISTA:8951}, year = {2020}, } @misc{7383, abstract = {Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.}, author = {Grah, Rok}, keywords = {Matlab scripts, analysis of microfluidics, mathematical model}, publisher = {Institute of Science and Technology Austria}, title = {{Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation}}, doi = {10.15479/AT:ISTA:7383}, year = {2020}, } @misc{9222, author = {Katsaros, Georgios}, publisher = {Institute of Science and Technology Austria}, title = {{Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling}}, doi = {10.15479/AT:ISTA:9222}, year = {2020}, } @misc{8375, abstract = {Supplementary movies showing the following sequences for spatio-temporarily programmed shells: input geometry and actuation time landscape; comparison of morphing processes from a camera recording and a simulation; final actuated shape.}, author = {Guseinov, Ruslan}, publisher = {Institute of Science and Technology Austria}, title = {{Supplementary data for "Computational design of curved thin shells: from glass façades to programmable matter"}}, doi = {10.15479/AT:ISTA:8375}, year = {2020}, } @misc{7689, abstract = {These are the supplementary research data to the publication "Zero field splitting of heavy-hole states in quantum dots". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file. }, author = {Katsaros, Georgios}, publisher = {Institute of Science and Technology Austria}, title = {{Supplementary data for "Zero field splitting of heavy-hole states in quantum dots"}}, doi = {10.15479/AT:ISTA:7689}, year = {2020}, } @misc{8761, author = {Guseinov, Ruslan}, publisher = {Institute of Science and Technology Austria}, title = {{Supplementary data for "Computational design of cold bent glass façades"}}, doi = {10.15479/AT:ISTA:8761}, year = {2020}, } @misc{8563, abstract = {Supplementary data provided for the provided for the publication: Igor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife.}, author = {Csicsvari, Jozsef L and Gridchyn, Igor and Schönenberger, Philipp}, publisher = {Institute of Science and Technology Austria}, title = {{Optogenetic alteration of hippocampal network activity}}, doi = {10.15479/AT:ISTA:8563}, year = {2020}, } @misc{14592, abstract = {Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.}, author = {Schur, Florian KM}, publisher = {Institute of Science and Technology Austria}, title = {{STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy}}, doi = {10.15479/AT:ISTA:14592}, year = {2020}, } @misc{7016, abstract = {Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.}, author = {Tomanek, Isabella}, keywords = {Escherichia coli, gene amplification, galactose, DOG, experimental evolution, Illumina sequence data, FACS data, microfluidics data}, publisher = {Institute of Science and Technology Austria}, title = {{Data for the paper "Gene amplification as a form of population-level gene expression regulation"}}, doi = {10.15479/AT:ISTA:7016}, year = {2019}, }