Single-cell profiling screen identifies microtubule-dependent reduction of variability in signaling

Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell-to-cell variability in signal strength and cellular response. Here, we screened 1,141 non-essential genes to identify 50 “variability genes”. Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct “axes” of system behavior. Three genes affected cytoplasmic microtubule function: BIM1, GIM2, and GIM4. We used genetic and chemical perturbations to show that, without microtubules, PRS output is reduced but variability is unaffected, while, when microtubules are present but their function is perturbed, output is sometimes lowered, but its variability is always high. The increased variability caused by microtubule perturbations required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the membrane-localized scaffold to which Fus3 must bind to be activated. Visualization of Ste5 localization dynamics demonstrated that perturbing microtubules destabilized Ste5 at the membrane signaling site. The fact that such microtubule perturbations cause aberrant fate and polarity decisions in mammals suggests that microtubule-dependent signal stabilization might also operate throughout metazoans.Fil: Pesce, Gustavo C.. Abalone Bio, Inc; Estados UnidosFil: Zdraljevic, Stefan. Northwestern University; Estados UnidosFil: Peria, William J.. Fred Hutchinson Cancer Research Center; Estados UnidosFil: Bush, Alan. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Repetto, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Rockwell, Daniel. Abalone Bio Inc; Estados UnidosFil: Yu, Richard C.. Abalone Bio Inc; Estados UnidosFil: Colman Lerner, Alejandro Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Brent, Roger. Fred Hutchinson Cancer Research Center; Estados Unido

Electronic and magnetic phase diagrams of Kitaev quantum spin liquid candidate Na2_2Co2_2TeO6_6

The 3$d^7$ Co$^{2+}$-based insulating magnet \NCTO{} has recently been reported to have strong Kitaev interactions on a honeycomb lattice, and is thus being considered as a Kitaev quantum spin liquid candidate. However, due to the existence of other types of interactions, a spontaneous long-range magnetic order occurs. This order is suppressed by applied magnetic fields leading to a succession of phases and ultimately saturation of the magnetic moments. The precise phase diagram, the nature of the phases, and the possibility that one of the field-induced phases is a Kitaev quantum spin liquid phase are still a matter of debate. Here we measured an extensive set of physical properties to build the complete temperature-field phase diagrams to magnetic saturation at 10 T for magnetic fields along the $a$- and $a^*$-axes, and a partial phase diagram up to 60 T along $c$. We probe the phases using magnetization, specific heat, magnetocaloric effect, magnetostriction, dielectric constant, and electric polarization, which is a symmetry-sensitive probe. With these measurements we identify all the previously incomplete phase boundaries and find new high-field phase boundaries. We find strong magnetoelectric coupling in the dielectric constant and moderate magnetostrictive coupling at several phase boundaries. Furthermore, we detect the symmetry of the magnetic order using electrical polarization measurements under magnetic fields. Based on our analysis, the absence of electric polarization under zero or finite magnetic field in any of the phases or after...Comment: LA-UR-22-3257

Set Pseudophasors to Stun for Flow Cytometry

Study of signal transduction in live cells benefits from the ability to visualize and quantify light emitted by fluorescent proteins (XFPs) fused to different signaling proteins. However, because cell signaling proteins are often present in small numbers, and because the XFPs themselves are poor fluorophores, the amount of emitted light, and the observable signal in these studies, is often small. An XFP's fluorescence lifetime contains additional information about the immediate environment of the fluorophore that can augment the information from its weak light signal. Here, we constructed and expressed in Saccharomyces cerevisiae variants of Teal Fluorescent Protein (TFP) and Citrine that were isospectral but had shorter fluorescence lifetimes, ∼ 1.5 ns vs ∼ 3 ns. We modified microscopic and flow cytometric instruments to measure fluorescence lifetimes in live cells. We developed digital hardware and a measure of lifetime called a "pseudophasor" that we could compute quickly enough to permit sorting by lifetime in flow. We used these abilities to sort mixtures of cells expressing TFP and the short-lifetime TFP variant into subpopulations that were respectively 97% and 94% pure. This work demonstrates the feasibility of using information about fluorescence lifetime to help quantify cell signaling in living cells at the high throughput provided by flow cytometry. Moreover, it demonstrates the feasibility of isolating and recovering subpopulations of cells with different XFP lifetimes for subsequent experimentation

Push-Pull and Feedback Mechanisms Can Align Signaling System Outputs with Inputs

Many cell signaling systems, including the yeast pheromone response system, exhibit “dose-response alignment” (DoRA), in which output of one or more downstream steps closely matches the fraction of occupied receptors. DoRA can improve the fidelity of transmitted dose information. Here, we searched systematically for biochemical network topologies that produced DoRA. Most networks, including many containing feedback and feedforward loops, could not produce DoRA. However, networks including “push-pull” mechanisms, in which the active form of a signaling species stimulates downstream activity and the nominally inactive form reduces downstream activity, enabled perfect DoRA. Networks containing feedbacks enabled DoRA, but only if they also compared feedback to input and adjusted output to match. Our results establish push-pull as a non-feedback mechanism to align output with variable input and maximize information transfer in signaling systems. They also suggest genetic approaches to determine whether particular signaling systems use feedback or push-pull control.Fil: Andrews, Steven S.. Fred Hutchinson Cancer Research Center; Estados Unidos. The Molecular Sciences Institute; Estados UnidosFil: Peria, William J.. Fred Hutchinson Cancer Research Center; Estados UnidosFil: Yu, Richard C.. The Molecular Sciences Institute; Estados UnidosFil: Colman Lerner, Alejandro Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Brent, Roger. The Molecular Sciences Institute; Estados Unidos. Fred Hutchinson Cancer Research Center; Estados Unido

Data from: Single‐cell profiling screen identifies microtubule‐dependent reduction of variability in signaling

Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell‐to‐cell variability in signal strength and cellular response. Here, we screened 1,141 non‐essential genes to identify 50 “variability genes”. Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct “axes” of system behavior. Three genes affected cytoplasmic microtubule function: BIM1, GIM2, and GIM4. We used genetic and chemical perturbations to show that, without microtubules, PRS output is reduced but variability is unaffected, while, when microtubules are present but their function is perturbed, output is sometimes lowered, but its variability is always high. The increased variability caused by microtubule perturbations required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the membrane‐localized scaffold to which Fus3 must bind to be activated. Visualization of Ste5 localization dynamics demonstrated that perturbing microtubules destabilized Ste5 at the membrane signaling site. The fact that such microtubule perturbations cause aberrant fate and polarity decisions in mammals suggests that microtubule‐dependent signal stabilization might also operate throughout metazoans

Fluorescent proteins.

<p>A) Body plan of fluorescent proteins. DarkCitrine is fused to the N terminus of TFP and Citrine with a GSGG linker (black bar). B) Emission spectra from yeast expressing each XFP excited by a 458 nm laser and emission collected from 460–650 nm. (Double-headed arrows indicate wavelength bands used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109940#pone-0109940-g002" target="_blank">Figure 2</a>)</p

Yeast Strains.

<p>Yeast Strains.</p