Project description:Telomerase plays a vital role in cancer and aging, and telomerase activity detection has drawn great attention recently. However, a feasible in situ imaging system for intracellular telomerase is still a challenge. Here, we develop a novel approach to image intracellular telomerase activity using DNA-based computation. A cascade nucleic acid logic gate that responded to intracellular telomerase was constructed. A telomerase substrate (TS) probe, extended by intracellular telomerase, worked as an input to initiate computation cascades. In this way, intracellular telomerase could be clearly indicated by fluorophore labeled nucleic acids as the output. Through one-step incubation, evaluation of the intracellular telomerase activity for a HeLa cell line and the ability to differentiate cancer cells from normal cells could be realized. Furthermore, the response of intracellular telomerase activity to a telomerase-inhibiting model drug was observed using the proposed method. Thus, this intracellular telomerase computation device will allow improvements in studying the relationship between telomerase and cancer, and may help to develop telomerase inhibitors. This finding also expands the applications of DNA computational techniques in cells.
Project description:The self-assembly of nanoparticles driven by small molecules or ions may produce colloidal superlattices with features and properties reminiscent of those of metals or semiconductors. However, to what extent the properties of such supramolecular crystals actually resemble those of atomic materials often remains unclear. Here, we present coarse-grained molecular simulations explicitly demonstrating how a behavior evocative of that of semiconductors may emerge in a colloidal superlattice. As a case study, we focus on gold nanoparticles bearing positively charged groups that self-assemble into FCC crystals via mediation by citrate counterions. In silico ohmic experiments show how the dynamically diverse behavior of the ions in different superlattice domains allows the opening of conductive ionic gates above certain levels of applied electric fields. The observed binary conductive/nonconductive behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular level, crossing the "band gap" requires a sufficient electrostatic stimulus to break the intermolecular interactions and make ions diffuse throughout the superlattice's cavities.
Project description:Mechano-sensitive channels are ubiquitous membrane proteins that activate in response to increasing tension in the lipid membrane. They facilitate a sudden, nonselective release of solutes and water that safeguards the integrity of the cell in hypo- or hyper-osmotic shock conditions. We have simulated the rapid release of content from a pressurized liposome through a particular mechano-sensitive protein channel, MscL, embedded in the liposomal membrane. We show that a single channel is able to relax the liposome, stressed to the point of bursting, in a matter of microseconds. We map the full activation-deactivation cycle of MscL in near-atomic detail and are able to quantify the rapid decrease in liposomal stress as a result of channel activation. This provides a computational tool that opens the way to contribute to the rational design of functional nano-containers.
Project description:Aquaporin 0 (AQP0), the major intrinsic protein of the eye lens, plays a vital role in maintaining lens clarity by facilitating the transport of water across lens fiber cell membranes. AQP0 reduces its osmotic water permeability constant (Pf) in response to increases in the external calcium concentration, an effect that is mediated by an interaction with the calcium-binding messenger protein, calmodulin (CaM), and phosphorylation of the CaM-binding site abolishes calcium sensitivity. Despite recent structural characterization of the AQP0-CaM complex, the mechanism by which CaM modulates AQP0 remains poorly understood. By combining atomistic molecular dynamics simulations and oocyte permeability assays, we conclude that serine phosphorylation of AQP0 does not inhibit CaM binding to the whole AQP0 protein. Instead, AQP0 phosphorylation alters calcium sensitivity by modifying the AQP0-CaM interaction interface, particularly at an arginine-rich loop that connects the fourth and fifth transmembrane helices. This previously unexplored loop, which sits outside of the canonical CaM-binding site on the AQP0 cytosolic face, mechanically couples CaM to the pore-gating residues of the second constriction site. We show that this allosteric loop is vital for CaM regulation of the channels, facilitating cooperativity between adjacent subunits and regulating factors such as serine phosphorylation. Similar allosteric interactions may also mediate CaM modulation of the properties of other CaM-regulated proteins.
Project description:Spinal cord dorsal horn inhibition is critical to the processing of sensory inputs, and its impairment leads to mechanical allodynia. How this decreased inhibition occurs and whether its restoration alleviates allodynic pain are poorly understood. Here, we show that a critical step in the loss of inhibitory tone is the change in the firing pattern of inhibitory parvalbumin (PV)-expressing neurons (PVNs). Our results show that PV, a calcium-binding protein, controls the firing activity of PVNs by enabling them to sustain high-frequency tonic firing patterns. Upon nerve injury, PVNs transition to adaptive firing and decrease their PV expression. Interestingly, decreased PV is necessary and sufficient for the development of mechanical allodynia and the transition of PVNs to adaptive firing. This transition of the firing pattern is due to the recruitment of calcium-activated potassium (SK) channels, and blocking them during chronic pain restores normal tonic firing and alleviates chronic pain. Our findings indicate that PV is essential for controlling the firing pattern of PVNs and for preventing allodynia. Developing approaches to manipulate these mechanisms may lead to different strategies for chronic pain relief.
Project description:One of the main challenges in building a quantum processor is to characterize the environmental noise. Noise characterization can be achieved by exploiting different techniques, such as randomization where several sequences of random quantum gates are applied to the qubit under test to derive statistical characteristics about the affecting noises. A scalable and robust algorithm able to benchmark the full set of Clifford gates using randomization techniques is called randomized benchmarking. In this study, we simulated randomized benchmarking protocols in a semiconducting all-electrical three-electron double-quantum dot qubit, i.e. hybrid qubit, under different error models, that include quasi-static Gaussian and the more realistic 1/f noise model, for the input controls. The average error of specific quantum computational gates is extracted through interleaved randomized benchmarking obtained including Clifford gates between the gate of interest. It provides an estimate of the fidelity as well as theoretical bounds for the average error of the gate under test.
Project description:Circadian clock circuitry intersects with a plethora of signaling pathways to adequately time physiological processes to occur at the most appropriate time of the day and year. However, our mechanistic understanding of how the clockwork is wired to its output is limited. Here we uncover mechanistic connections between the core clock component GIGANTEA (GI) and hormone signaling through the modulation of key components of the transduction pathways. Specifically, we show how GI modulates gibberellin (GA) signaling through the stabilization of the DELLA proteins, which act as negative components in the signaling of this hormone. GI function within the GA pathway is required to precisely time the permissive gating of GA sensitivity, thereby determining the phase of GA-regulated physiological outputs.
Project description:The ever-growing demand for faster and more efficient data transfer and processing has brought optical computation strategies to the forefront of research in next-generation computing. Here, we report a universal computing approach with the chirality degree of freedom. By exploiting the crystal symmetry-enabled well-known chiral selection rules, we demonstrate the viability of the concept in bulk silica crystals and atomically thin semiconductors and create ultrafast (<100-fs) all-optical chirality logic gates (XNOR, NOR, AND, XOR, OR, and NAND) and a half adder. We also validate the unique advantages of chirality gates by realizing multiple gates with simultaneous operation in a single device and electrical control. Our first demonstrations of logic gates using chiral selection rules suggest that optical chirality could provide a powerful degree of freedom for future optical computing.
Project description:Temperature has a major role in plant growth and survival, for example wheat yields decrease by about 6% for every 1°C rise in global temperature [1]. High temperatures induce the expression of protective chaperones and modulate growth responses. Key players in the heat protection response are transcription factors of the HEAT SHOCK FACTOR A1 (HSFA1) family [2]. However the pathways that activate the HSFA1 class TFs, and how these perceive temperature and integrate it with other environmental signals are not clear. Plants are exposed to considerable diurnal temperature variation, and have evolved pathways to anticipate likely future conditions. For example, the cold response pathway is gated by the circadian clock, enabling the degree of responsiveness to cold to be controlled in the context of the environment [3, 4] and genes promoting elongation growth and flowering in response to warm temperature are induced during the night via thermosensory phytochromes [5 ,6]. It is not known in Arabidopsis if the warm temperature protective pathways are gated. In this study we find that there is strong diurnal variation in the heat stress response of Arabidopsis, and we show that this correlates with the expression of HSP70 in the day night cycle. The dark to light transition is in fact sufficient to robustly induce expression of warm temperature protective genes such as HSP70. A forward genetic screen with a HSP70-Luciferase reporter line revealed genes necessary for controlling this process and identified a central role for chloroplast signalling in the warm temperature response that accounts for diurnal variation in thermotolerance.
Project description:Study objectivesSleep is under the control of homeostatic and circadian processes, which interact to determine sleep timing and duration, but the mechanisms through which the circadian system modulates sleep are largely unknown. We therefore used adult-specific, temporally controlled neuronal activation and inhibition to identify an interaction between the circadian clock and a novel population of sleep-promoting neurons in Drosophila.MethodsTransgenic flies expressed either dTRPA1, a neuronal activator, or Shibire(ts1), an inhibitor of synaptic release, in small subsets of neurons. Sleep, as determined by activity monitoring and video tracking, was assessed before and after temperature-induced activation or inhibition using these effector molecules. We compared the effect of these manipulations in control flies and in mutant flies that lacked components of the molecular circadian clock.ResultsAdult-specific activation or inhibition of a population of neurons that projects to the sleep-promoting dorsal Fan-Shaped Body resulted in bidirectional control over sleep. Interestingly, the magnitude of the sleep changes were time-of-day dependent. Activation of sleep-promoting neurons was maximally effective during the middle of the day and night, and was relatively ineffective during the day-to-night and night-to-day transitions. These time-ofday specific effects were absent in flies that lacked functional circadian clocks.ConclusionsWe conclude that the circadian system functions to gate sleep through active inhibition at specific times of day. These data identify a mechanism through which the circadian system prevents premature sleep onset in the late evening, when homeostatic sleep drive is high.