@article{665, abstract = {The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria.}, author = {Bergmiller, Tobias and Andersson, Anna M and Tomasek, Kathrin and Balleza, Enrique and Kiviet, Daniel and Hauschild, Robert and Tkacik, Gasper and Guet, Calin C}, issn = {00368075}, journal = {Science}, number = {6335}, pages = {311 -- 315}, publisher = {American Association for the Advancement of Science}, title = {{Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity}}, doi = {10.1126/science.aaf4762}, volume = {356}, year = {2017}, } @misc{5571, abstract = {This folder contains all the data used in each of the main figures of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures. }, author = {Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Data for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}}, doi = {10.15479/AT:ISTA:78}, year = {2017}, } @misc{5559, abstract = {Strong amplifiers of natural selection}, author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak , Martin}, keywords = {natural selection}, publisher = {Institute of Science and Technology Austria}, title = {{Strong amplifiers of natural selection}}, doi = {10.15479/AT:ISTA:51}, year = {2017}, } @misc{5572, abstract = {Code described in the Supplementary Methods of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.)}, author = {Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Code for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}}, doi = {10.15479/AT:ISTA:79 }, year = {2017}, } @article{946, abstract = {Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.}, author = {Von Wangenheim, Daniel and Hauschild, Robert and Fendrych, Matyas and Barone, Vanessa and Benková, Eva and Friml, Jirí}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Live tracking of moving samples in confocal microscopy for vertically grown roots}}, doi = {10.7554/eLife.26792}, volume = {6}, year = {2017}, } @article{1078, abstract = {One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. }, author = {Von Wangenheim, Daniel and Hauschild, Robert and Friml, Jirí}, journal = {Journal of visualized experiments JoVE}, number = {119}, publisher = {Journal of Visualized Experiments}, title = {{Light sheet fluorescence microscopy of plant roots growing on the surface of a gel}}, doi = {10.3791/55044}, volume = {2017}, year = {2017}, } @misc{5565, abstract = {One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. The Video is licensed under a CC BY NC ND license. }, author = {Von Wangenheim, Daniel and Hauschild, Robert and Friml, Jirí}, publisher = {Institute of Science and Technology Austria}, title = {{Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel}}, doi = {10.15479/AT:ISTA:66}, year = {2017}, } @misc{5566, abstract = {Current minimal version of TipTracker}, author = {Hauschild, Robert}, keywords = {tool, tracking, confocal microscopy}, publisher = {Institute of Science and Technology Austria}, title = {{Live tracking of moving samples in confocal microscopy for vertically grown roots}}, doi = {10.15479/AT:ISTA:69}, year = {2017}, } @inbook{424, abstract = {We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b, d) such that the following holds. If F is a finite family of subsets of Rd such that βi(∩G)≤b for any G⊊F and every 0 ≤ i ≤ [d/2]-1 then F has Helly number at most h(b, d). Here βi denotes the reduced Z2-Betti numbers (with singular homology). These topological conditions are sharp: not controlling any of these [d/2] first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map C*(K)→C*(Rd).}, author = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, booktitle = {A Journey through Discrete Mathematics: A Tribute to Jiri Matousek}, editor = {Loebl, Martin and Nešetřil, Jaroslav and Thomas, Robin}, isbn = {978-331944479-6}, pages = {407 -- 447}, publisher = {Springer}, title = {{Bounding helly numbers via betti numbers}}, doi = {10.1007/978-3-319-44479-6_17}, year = {2017}, } @article{463, abstract = {We investigate transient behaviors induced by magnetic fields on the dynamics of the flow of a ferrofluid in the gap between two concentric, independently rotating cylinders. Without applying any magnetic fields, we uncover emergence of flow states constituted by a combination of a localized spiral state (SPIl) in the top and bottom of the annulus and different multi-cell flow states (SPI2v, SPI3v) with toroidally closed vortices in the interior of the bulk (SPIl+2v = SPIl + SPI2v and SPIl+3v = SPIl + SPI3v). However, when a magnetic field is presented, we observe the transient behaviors between multi-cell states passing through two critical thresholds in a strength of an axial (transverse) magnetic field. Before the first critical threshold of a magnetic field strength, multi-stable states with different number of cells could be observed. After the first critical threshold, we find the transient behavior between the three- and two-cell flow states. For more strength of magnetic field or after the second critical threshold, we discover that multi-cell states are disappeared and a localized spiral state remains to be stimulated. The studied transient behavior could be understood by the investigation of various quantities including a modal kinetic energy, a mode amplitude of the radial velocity, wavenumber, angular momentum, and torque. In addition, the emergence of new flow states and the transient behavior between their states in ferrofluidic flows indicate that richer and potentially controllable dynamics through magnetic fields could be possible in ferrofluic flow.}, author = {Altmeyer, Sebastian and Do, Younghae and Ryu, Soorok}, issn = {10541500}, journal = {Chaos}, number = {11}, publisher = {AIP Publishing}, title = {{Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow}}, doi = {10.1063/1.5002771}, volume = {27}, year = {2017}, } @article{996, abstract = {Iodine (I 2 ) molecules embedded in He nanodroplets are aligned by a 160 ps long laser pulse. The highest degree of alignment, occurring at the peak of the pulse and quantified by ⟨cos 2 θ 2D ⟩ , is measured as a function of the laser intensity. The results are well described by ⟨cos 2 θ 2D ⟩ calculated for a gas of isolated molecules each with an effective rotational constant of 0.6 times the gas-phase value, and at a temperature of 0.4 K. Theoretical analysis using the angulon quasiparticle to describe rotating molecules in superfluid helium rationalizes why the alignment mechanism is similar to that of isolated molecules with an effective rotational constant. A major advantage of molecules in He droplets is that their 0.4 K temperature leads to stronger alignment than what can generally be achieved for gas phase molecules -- here demonstrated by a direct comparison of the droplet results to measurements on a ∼ 1 K supersonic beam of isolated molecules. This point is further illustrated for more complex system by measurements on 1,4-diiodobenzene and 1,4-dibromobenzene. For all three molecular species studied the highest values of ⟨cos 2 θ 2D ⟩ achieved in He droplets exceed 0.96. }, author = {Shepperson, Benjamin and Chatterley, Adam and Søndergaard, Anders and Christiansen, Lars and Lemeshko, Mikhail and Stapelfeldt, Henrik}, issn = {00219606}, journal = {The Journal of Chemical Physics}, number = {1}, publisher = {AIP Publishing}, title = {{Strongly aligned molecules inside helium droplets in the near-adiabatic regime}}, doi = {10.1063/1.4983703}, volume = {147}, year = {2017}, } @article{912, abstract = {We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals. }, author = {Deuchert, Andreas}, issn = {00222488}, journal = { Journal of Mathematical Physics}, number = {8}, publisher = {AIP Publishing}, title = {{A lower bound for the BCS functional with boundary conditions at infinity}}, doi = {10.1063/1.4996580}, volume = {58}, year = {2017}, } @article{1029, abstract = {RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.}, author = {Lukacisin, Martin and Landon, Matthieu and Jajoo, Rishi}, issn = {19326203}, journal = {PLoS One}, number = {3}, publisher = {Public Library of Science}, title = {{Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast}}, doi = {10.1371/journal.pone.0174066}, volume = {12}, year = {2017}, } @article{664, abstract = {Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it.}, author = {Assen, Frank P and Sixt, Michael K}, issn = {10747613}, journal = {Immunity}, number = {4}, pages = {519 -- 520}, publisher = {Cell Press}, title = {{The dynamic cytokine niche}}, doi = {10.1016/j.immuni.2017.04.006}, volume = {46}, year = {2017}, } @article{682, abstract = {Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry.}, author = {Ukai, Hikari and Kawahara, Aiko and Hirayama, Keiko and Case, Matthew J and Aino, Shotaro and Miyabe, Masahiro and Wakita, Ken and Oogi, Ryohei and Kasayuki, Michiyo and Kawashima, Shihomi and Sugimoto, Shunichi and Chikamatsu, Kanako and Nitta, Noritaka and Koga, Tsuneyuki and Shigemoto, Ryuichi and Takai, Toshiyuki and Ito, Isao}, issn = {19326203}, journal = {PLoS One}, number = {6}, publisher = {Public Library of Science}, title = {{PirB regulates asymmetries in hippocampal circuitry}}, doi = {10.1371/journal.pone.0179377}, volume = {12}, year = {2017}, } @article{1028, abstract = {Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes.}, author = {Kainrath, Stephanie and Stadler, Manuela and Gschaider-Reichhart, Eva and Distel, Martin and Janovjak, Harald L}, issn = {14337851}, journal = {Angewandte Chemie - International Edition}, number = {16}, pages = {4608--4611}, publisher = {Wiley-Blackwell}, title = {{Green-light-induced inactivation of receptor signaling using cobalamin-binding domains}}, doi = {10.1002/anie.201611998}, volume = {56}, year = {2017}, } @article{1024, abstract = {The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges.}, author = {Hurny, Andrej and Benková, Eva}, issn = {10643745}, journal = {Auxins and Cytokinins in Plant Biology}, pages = {1 -- 29}, publisher = {Springer}, title = {{Methodological advances in auxin and cytokinin biology}}, doi = {10.1007/978-1-4939-6831-2_1}, volume = {1569}, year = {2017}, } @article{679, abstract = {Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections.}, author = {Ebner, Florian and Sedlyarov, Vitaly and Tasciyan, Saren and Ivin, Masa and Kratochvill, Franz and Gratz, Nina and Kenner, Lukas and Villunger, Andreas and Sixt, Michael K and Kovarik, Pavel}, issn = {00219738}, journal = {The Journal of Clinical Investigation}, number = {6}, pages = {2051 -- 2065}, publisher = {American Society for Clinical Investigation}, title = {{The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection}}, doi = {10.1172/JCI80631}, volume = {127}, year = {2017}, } @article{676, abstract = {The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation.}, author = {Krens, Gabriel and Veldhuis, Jim and Barone, Vanessa and Capek, Daniel and Maître, Jean-Léon and Brodland, Wayne and Heisenberg, Carl-Philipp J}, issn = {09501991}, journal = {Development}, number = {10}, pages = {1798 -- 1806}, publisher = {Company of Biologists}, title = {{Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation}}, doi = {10.1242/dev.144964}, volume = {144}, year = {2017}, } @article{704, abstract = {How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.}, author = {Steinrück, Magdalena and Guet, Calin C}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection}}, doi = {10.7554/eLife.25100}, volume = {6}, year = {2017}, }