Molecular motor traffic with a slow binding site.

We discuss how the presence of a slow binding site in molecular motor traffic gives rise to defect-induced "traffic jams" that have properties different from those of the well-studied boundary-induced jams that originate from an imbalance between initiation and termination. To this end we analyze in detail the stationary distribution of a lattice gas model for traffic of molecular motors with a defect. In particular, we obtain analytically the exact spatial distribution of motors, the probability distribution of the random position of the molecular traffic jam and we report unexpected spatial anticorrelations between local molecular motor densities near the defect.

Coherent Excitation of Heterosymmetric Spin Waves with Ultrashort Wavelengths.

In the emerging field of magnonics, spin waves are foreseen as signal carriers for future spintronic information processing and communication devices, owing to both the very low power losses and a high device miniaturization potential predicted for short-wavelength spin waves. Yet, the efficient excitation and controlled propagation of nanoscale spin waves remains a severe challenge. Here, we report the observation of high-amplitude, ultrashort dipole-exchange spin waves (down to 80 nm wavelength at 10 GHz frequency) in a ferromagnetic single layer system, coherently excited by the driven dynamics of a spin vortex core. We used time-resolved x-ray microscopy to directly image such propagating spin waves and their excitation over a wide range of frequencies. By further analysis, we found that these waves exhibit a heterosymmetric mode profile, involving regions with anti-Larmor precession sense and purely linear magnetic oscillation. In particular, this mode profile consists of dynamic vortices with laterally alternating helicity, leading to a partial magnetic flux closure over the film thickness, which is explained by a strong and unexpected mode hybridization. This spin-wave phenomenon observed is a general effect inherent to the dynamics of sufficiently thick ferromagnetic single layer films, independent of the specific excitation method employed.

RNA Polymerase interactions and elongation rate.

We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and cooperation, we introduce a stochastic model that allows for the exact analytical computation of the stationary properties of transcription elongation as a function of RNAP density, their interaction strength, nucleoside triphosphate concentration, and rate of pyrophosphate release. Cooperative pushing, i.e., an enhancement of the average RNAP velocity and elongation rate, arises due to stochastic pushing which cannot be explained by steric hindrance alone. The cooperative effect requires a molecular repulsion in excess of a critical strength and disappears beyond a critical RNAP density, above which jamming due to collisions takes over. For strong repulsion and at the same time strong stochastic blocking, cooperative pushing at low RNAP densities is suppressed, but a reentrance regime at higher densities appears.

Three-dimensional localization microscopy using deep learning.

Single molecule localization microscopy (SMLM) is one of the fastest evolving and most broadly used super-resolving imaging techniques in the biosciences. While image recordings could take up to hours only ten years ago, scientists are now reaching for real-time imaging in order to follow the dynamics of biology. To this end, it is crucial to have data processing strategies available that are capable of handling the vast amounts of data produced by the microscope. In this article, we report on the use of a deep convolutional neural network (CNN) for localizing particles in three dimensions on the basis of single images. In test experiments conducted on fluorescent microbeads, we show that the precision obtained with a CNN can be comparable to that of maximum likelihood estimation (MLE), which is the accepted gold standard. Regarding speed, the CNN performs with about 22k localizations per second more than three orders of magnitude faster than the MLE algorithm of ThunderSTORM. If only five parameters are estimated (3D position, signal and background), our CNN implementation is currently slower than the fastest, recently published GPU-based MLE algorithm. However, in this comparison the CNN catches up with every additional parameter, with only a few percent extra time required per additional dimension. Thus it may become feasible to estimate further variables such as molecule orientation, aberration functions or color. We experimentally demonstrate that jointly estimating Zernike mode magnitudes for aberration modeling can significantly improve the accuracy of the estimates.

Conformal Invariance in Driven Diffusive Systems at High Currents.

We consider space-time correlations in driven diffusive systems which undergo a fluctuation into a regime with an atypically large current or dynamical activity. For a single conserved mass we show that the spatiotemporal density correlations in one space dimension are fully determined by conformal field theory with central charge c=1, corresponding to a ballistic universality class with dynamical exponent z=1. The full phase diagram for general atypical behavior exhibits the conformally invariant regime and, for atypically low current or activity, a region of phase separation. The phase transition line between these two regimes corresponds to typical behavior and the dynamics belongs to the Kardar-Parisi-Zhang universality class with dynamical exponent z=3/2, except for a diffusive point with z=2. The exact universal dynamical structure function is obtained in explicit form from the one-dimensional asymmetric simple exclusion process with periodic and open boundaries in the limit of maximal current.

Energy saving in WWTP: Daily benchmarking under uncertainty and data availability limitations.

Efficient management of Waste Water Treatment Plants (WWTPs) can produce significant environmental and economic benefits. Energy benchmarking can be used to compare WWTPs, identify targets and use these to improve their performance. Different authors have performed benchmark analysis on monthly or yearly basis but their approaches suffer from a time lag between an event, its detection, interpretation and potential actions. The availability of on-line measurement data on many WWTPs should theoretically enable the decrease of the management response time by daily benchmarking. Unfortunately this approach is often impossible because of limited data availability. This paper proposes a methodology to perform a daily benchmark analysis under database limitations. The methodology has been applied to the Energy Online System (EOS) developed in the framework of the project "INNERS" (INNovative Energy Recovery Strategies in the urban water cycle). EOS calculates a set of Key Performance Indicators (KPIs) for the evaluation of energy and process performances. In EOS, the energy KPIs take in consideration the pollutant load in order to enable the comparison between different plants. For example, EOS does not analyse the energy consumption but the energy consumption on pollutant load. This approach enables the comparison of performances for plants with different loads or for a single plant under different load conditions. The energy consumption is measured by on-line sensors, while the pollutant load is measured in the laboratory approximately every 14 days. Consequently, the unavailability of the water quality parameters is the limiting factor in calculating energy KPIs. In this paper, in order to overcome this limitation, the authors have developed a methodology to estimate the required parameters and manage the uncertainty in the estimation. By coupling the parameter estimation with an interval based benchmark approach, the authors propose an effective, fast and reproducible way to manage infrequent inlet measurements. Its use enables benchmarking on a daily basis and prepares the ground for further investigation.

A single-molecule approach to explore binding, uptake and transport of cancer cell targeting nanotubes.

In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity.

Quest for the golden ratio universality class.

Using mode-coupling theory, the conditions for all allowed dynamical universality classes for the conserved modes in one-dimensional driven systems are presented in closed form as a function of the stationary currents and their derivatives. With an eye on the search for the golden ratio universality class, the existence of some families of microscopic models is ruled out a priori by using an Onsager-type macroscopic current symmetry. In particular, if the currents are symmetric or antisymmetric under the interchange of the conserved densities, then at equal mean densities the golden modes can only appear in the antisymmetric case and if the conserved quantities are correlated, but not in the symmetric case where at equal densities one mode is always diffusive and the second may be either Kardar-Parisi-Zhang (KPZ), modified KPZ, 3/2-Lévy, or also diffusive. We also show that the predictions of mode-coupling theory for a noisy chain of harmonic oscillators are exact.

Exact matrix product solution for the boundary-driven Lindblad XXZ chain.

We demonstrate that the exact nonequilibrium steady state of the one-dimensional Heisenberg XXZ spin chain driven by boundary Lindblad operators can be constructed explicitly with a matrix product ansatz for the nonequilibrium density matrix where the matrices satisfy a quadratic algebra. This algebra turns out to be related to the quantum algebra U(q)[SU(2)]. Coherent state techniques are introduced for the exact solution of the isotropic Heisenberg chain with and without quantum boundary fields and Lindblad terms that correspond to two different completely polarized boundary states. We show that this boundary twist leads to nonvanishing stationary currents of all spin components. Our results suggest that the matrix product ansatz can be extended to more general quantum systems kept far from equilibrium by Lindblad boundary terms.

Disruption of the glucocorticoid receptor gene in the nervous system results in reduced anxiety.

The glucocorticoid receptor (Gr, encoded by the gene Grl1) controls transcription of target genes both directly by interaction with DNA regulatory elements and indirectly by cross-talk with other transcription factors. In response to various stimuli, including stress, glucocorticoids coordinate metabolic, endocrine, immune and nervous system responses and ensure an adequate profile of transcription. In the brain, Gr has been proposed to modulate emotional behaviour, cognitive functions and addictive states. Previously, these aspects were not studied in the absence of functional Gr because inactivation of Grl1 in mice causes lethality at birth (F.T., C.K. and G.S., unpublished data). Therefore, we generated tissue-specific mutations of this gene using the Cre/loxP -recombination system. This allowed us to generate viable adult mice with loss of Gr function in selected tissues. Loss of Gr function in the nervous system impairs hypothalamus-pituitary-adrenal (HPA)-axis regulation, resulting in increased glucocorticoid (GC) levels that lead to symptoms reminiscent of those observed in Cushing syndrome. Conditional mutagenesis of Gr in the nervous system provides genetic evidence for the importance of Gr signalling in emotional behaviour because mutant animals show an impaired behavioural response to stress and display reduced anxiety.

Ferromagnetic order controlled by the magnetic interface of LaNiO3/La2/3Ca1/3MnO3 superlattices.

Interface engineering in complex oxide superlattices is a growing field, enabling manipulation of the exceptional properties of these materials, and also providing access to new phases and emergent physical phenomena. Here we demonstrate how interfacial interactions can induce a complex charge and spin structure in a bulk paramagnetic material. We investigate a superlattice (SLs) consisting of paramagnetic LaNiO3 (LNO) and highly spin-polarized ferromagnetic La2/3Ca1/3MnO3 (LCMO), grown on SrTiO3 (001) substrate. We observed emerging magnetism in LNO through an exchange bias mechanism at the interfaces in X-ray resonant magnetic reflectivity. We find non-symmetric interface induced magnetization profiles in LNO and LCMO which we relate to a periodic complex charge and spin superstructure. High resolution scanning transmission electron microscopy images reveal that the upper and lower interfaces exhibit no significant structural variations. The different long range magnetic order emerging in LNO layers demonstrates the enormous potential of interfacial reconstruction as a tool for tailored electronic properties.

Brain activation during fear conditioning in humans depends on genetic variations related to functioning of the hypothalamic-pituitary-adrenal axis: first evidence from two independent subsamples.

BACKGROUND: Enhanced acquisition and delayed extinction of fear conditioning are viewed as major determinants of anxiety disorders, which are often characterized by a dysfunctional hypothalamic-pituitary-adrenal (HPA) axis. METHOD: In this study we employed cued fear conditioning in two independent samples of healthy subjects (sample 1: n=60, sample 2: n=52). Two graphical shapes served as conditioned stimuli and painful electrical stimulation as the unconditioned stimulus. In addition, guided by findings from published animal studies on HPA axis-related genes in fear conditioning, we examined variants of the glucocorticoid receptor and corticotropin-releasing hormone receptor 1 genes. RESULTS: Variation in these genes showed enhanced amygdala activation during the acquisition and reduced prefrontal activation during the extinction of fear as well as altered amygdala-prefrontal connectivity. CONCLUSIONS: This is the first demonstration of the involvement of genes related to the HPA axis in human fear conditioning.

Magnetic vortex core reversal by excitation with short bursts of an alternating field.

The vortex state, characterized by a curling magnetization, is one of the equilibrium configurations of soft magnetic materials and occurs in thin ferromagnetic square and disk-shaped elements of micrometre size and below. The interplay between the magnetostatic and the exchange energy favours an in-plane, closed flux domain structure. This curling magnetization turns out of the plane at the centre of the vortex structure, in an area with a radius of about 10 nanometres--the vortex core. The vortex state has a specific excitation mode: the in-plane gyration of the vortex structure about its equilibrium position. The sense of gyration is determined by the vortex core polarization. Here we report on the controlled manipulation of the vortex core polarization by excitation with small bursts of an alternating magnetic field. The vortex motion was imaged by time-resolved scanning transmission X-ray microscopy. We demonstrate that the sense of gyration of the vortex structure can be reversed by applying short bursts of the sinusoidal excitation field with amplitude of about 1.5 mT. This reversal unambiguously indicates a switching of the out-of-plane core polarization. The observed switching mechanism, which can be understood in the framework of micromagnetic theory, gives insights into basic magnetization dynamics and their possible application in data storage.

History-dependent domain and skyrmion formation in 2D van der Waals magnet Fe3GeTe2.

The discovery of two-dimensional magnets has initiated a new field of research, exploring both fundamental low-dimensional magnetism, and prospective spintronic applications. Recently, observations of magnetic skyrmions in the 2D ferromagnet Fe3GeTe2 (FGT) have been reported, introducing further application possibilities. However, controlling the exhibited magnetic state requires systematic knowledge of the history-dependence of the spin textures, which remains largely unexplored in 2D magnets. In this work, we utilise real-space imaging, and complementary simulations, to determine and explain the thickness-dependent magnetic phase diagrams of an exfoliated FGT flake, revealing a complex, history-dependent emergence of the uniformly magnetised, stripe domain and skyrmion states. The results show that the interplay of the dominant dipolar interaction and strongly temperature dependent out-of-plane anisotropy energy terms enables the selective stabilisation of all three states at zero field, and at a single temperature, while the Dzyaloshinksii-Moriya interaction must be present to realise the observed Néel-type domain walls. The findings open perspectives for 2D devices incorporating topological spin textures.

Toggle-like current-induced Bloch point dynamics of 3D skyrmion strings in a room temperature nanowire.

Research into practical applications of magnetic skyrmions, nanoscale solitons with interesting topological and transport properties, has traditionally focused on two dimensional (2D) thin-film systems. However, the recent observation of novel three dimensional (3D) skyrmion-like structures, such as hopfions, skyrmion strings (SkS), skyrmion bundles, and skyrmion braids, motivates the investigation of new designs, aiming to exploit the third spatial dimension for more compact and higher performance spintronic devices in 3D or curvilinear geometries. A crucial requirement of such device schemes is the control of the 3D magnetic structures via charge or spin currents, which has yet to be experimentally observed. In this work, we utilise real-space imaging to investigate the dynamics of a 3D SkS within a nanowire of Co8Zn9Mn3 at room temperature. Utilising single current pulses, we demonstrate current-induced nucleation of a single SkS, and a toggle-like positional switching of an individual Bloch point at the end of a SkS. The observations highlight the possibility to locally manipulate 3D topological spin textures, opening up a range of design concepts for future 3D spintronic devices.

Improved localization of cellular membrane receptors using combined fluorescence microscopy and simultaneous topography and recognition imaging.

The combination of fluorescence microscopy and atomic force microscopy has a great potential in single-molecule-detection applications, overcoming many of the limitations coming from each individual technique. Here we present a new platform of combined fluorescence and simultaneous topography and recognition imaging (TREC) for improved localization of cellular receptors. Green fluorescent protein (GFP) labeled human sodium-glucose cotransporter (hSGLT1) expressed Chinese Hamster Ovary (CHO) cells and endothelial cells (MyEnd) from mouse myocardium stained with phalloidin-rhodamine were used as cell systems to study AFM topography and fluorescence microscopy on the same surface area. Topographical AFM images revealed membrane features such as lamellipodia, cytoskeleton fibers, F-actin filaments and small globular structures with heights ranging from 20 to 30 nm. Combined fluorescence and TREC imaging was applied to detect density, distribution and localization of YFP-labeled CD1d molecules on alpha-galactosylceramide (alphaGalCer)-loaded THP1 cells. While the expression level, distribution and localization of CD1d molecules on THP1 cells were detected with fluorescence microscopy, the nanoscale distribution of binding sites was investigated with molecular recognition imaging by using a chemically modified AFM tip. Using TREC on the inverted light microscope, the recognition sites of cell receptors were detected in recognition images with domain sizes ranging from approximately 25 to approximately 160 nm, with the smaller domains corresponding to a single CD1d molecule.

Real-space imaging of confined magnetic skyrmion tubes.

Magnetic skyrmions are topologically nontrivial particles with a potential application as information elements in future spintronic device architectures. While they are commonly portrayed as two dimensional objects, in reality magnetic skyrmions are thought to exist as elongated, tube-like objects extending through the thickness of the host material. The study of this skyrmion tube state (SkT) is vital for furthering the understanding of skyrmion formation and dynamics for future applications. However, direct experimental imaging of skyrmion tubes has yet to be reported. Here, we demonstrate the real-space observation of skyrmion tubes in a lamella of FeGe using resonant magnetic x-ray imaging and comparative micromagnetic simulations, confirming their extended structure. The formation of these structures at the edge of the sample highlights the importance of confinement and edge effects in the stabilisation of the SkT state, opening the door to further investigation into this unexplored dimension of the skyrmion spin texture.

Hepatocyte differentiation in vitro: initiation of tyrosine aminotransferase expression in cultured fetal rat hepatocytes.

A fetal rat hepatocyte culture system has been used to study the molecular mechanisms of tyrosine aminotransferase (TAT) gene expression during development. It has previously been shown that TAT activity can be detected in 19-d, but not 15-d, gestation hepatocytes on the first day of culture (Yeoh, G. C. T., F. A. Bennett, and I. T. Oliver. 1979. Biochem. J. 180:153-160). In this study enzyme activity, synthesis, and mRNA levels were determined in hepatocytes isolated from 13-, 15-, and 19-d gestation rats maintained in culture for 1, 2, or 3 d and exposed to dexamethasone. TAT expression is barely detectable in 13-d gestation hepatocytes even after 3 d in culture. Hepatocytes isolated from 15-d gestation fetuses have undetectable levels of enzyme activity and synthesis on the first day of culture; both can be assayed by days 2 and 3. TAT mRNA levels in these hepatocytes, measured by hybridization with a specific cDNA, increase substantially during culture. TAT activity, synthesis, and mRNA are evident on the first and subsequent days of culture in 19-d gestation hepatocytes. Transcription measurements in isolated nuclei indicate that the increase in TAT mRNA in 15- and 19-d gestation hepatocytes is associated with an increase in transcription of the gene. Immunocytochemical studies demonstrated that the increase in TAT expression correlated with an increase in the proportion of hepatocytes expressing the enzyme, rather than a simultaneous increase in all hepatocytes. These results support the proposal that a subpopulation of 15-d fetal hepatocytes undergo differentiation in culture with respect to TAT.

The DNA binding-independent function of the glucocorticoid receptor mediates repression of AP-1-dependent genes in skin.

The glucocorticoid receptor (GR) mediates the biological effects of glucocorticoids (GCs) through activation or repression of gene expression, either by DNA binding or via interaction with other transcription factors, such as AP-1. Work in tissue culture cells on the regulation of AP-1-dependent genes, such as collagenase (MMP-13) and stromelysin (MMP-3) has suggested that the antitumor and antiinflammatory activity of GCs is mediated, at least in part, by GR-mediated downmodulation of AP-1. Here, we have identified phorbol ester-induced expression of MMP-3 and MMP-13 in mouse skin as the first example of an in vivo system to measure negative interference between AP-1 and GR in the animal. Cell type-specific induction of these genes by tumor promoters is abolished by GCs. Importantly, this is also the case in GR(dim) mice expressing a DNA binding-defective mutant version of GR. In contrast, the newly identified target genes in skin, plasma glutathione peroxidase and HSP-27, were induced by GC in wild-type, but not in GR(dim) mice. Thus, these data suggest that the DNA binding-independent function of the GR is dispensable for repression of AP-1 activity in vivo and responsible for the antitumor promoting activity of GCs.

Resetting of circadian time in peripheral tissues by glucocorticoid signaling.

In mammals, circadian oscillators reside not only in the suprachiasmatic nucleus of the brain, which harbors the central pacemaker, but also in most peripheral tissues. Here, we show that the glucocorticoid hormone analog dexamethasone induces circadian gene expression in cultured rat-1 fibroblasts and transiently changes the phase of circadian gene expression in liver, kidney, and heart. However, dexamethasone does not affect cyclic gene expression in neurons of the suprachiasmatic nucleus. This enabled us to establish an apparent phase-shift response curve specifically for peripheral clocks in intact animals. In contrast to the central clock, circadian oscillators in peripheral tissues appear to remain responsive to phase resetting throughout the day.