Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Kalman-like Self-Tuned Sensitivity in Biophysical Sensing.

ABSTRACT: Living organisms need to be sensitive to a changing environment while also ignoring uninformative environmental fluctuations. Here, we argue that living cells can navigate these conflicting demands by dynamically tuning their environmental sensitivity. We analyze the circadian clock in Synechococcus elongatus, showing that clock-metabolism coupling can detect mismatch between clock predictions and the day-night light cycle, temporarily raise the clock's sensitivity to light changes, and thus re-entraining faster. We find analogous behavior in recent experiments on switching between slow and fast osmotic-stress-response pathways in yeast. In both cases, cells can raise their sensitivity to new external information in epochs of frequent challenging stress, much like a Kalman filter with adaptive gain in signal processing. Our work suggests a new class of experiments that probe the history dependence of environmental sensitivity in biophysical sensing mechanisms.

SUBMITTER: Husain K

PROVIDER: S-EPMC10170658 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Kalman-like Self-Tuned Sensitivity in Biophysical Sensing.

Husain Kabir K Pittayakanchit Weerapat W Pattanayak Gopal G Rust Michael J MJ Murugan Arvind A

Cell systems 20190925 5

Living organisms need to be sensitive to a changing environment while also ignoring uninformative environmental fluctuations. Here, we argue that living cells can navigate these conflicting demands by dynamically tuning their environmental sensitivity. We analyze the circadian clock in Synechococcus elongatus, showing that clock-metabolism coupling can detect mismatch between clock predictions and the day-night light cycle, temporarily raise the clock's sensitivity to light changes, and thus re- ...[more]

PMID: 31563474

Similar Datasets

Auditory sensitivity provided by self-tuned critical oscillations of hair cells.

Project description:We introduce the concept of self-tuned criticality as a general mechanism for signal detection in sensory systems. In the case of hearing, we argue that active amplification of faint sounds is provided by a dynamical system that is maintained at the threshold of an oscillatory instability. This concept can account for the exquisite sensitivity of the auditory system and its wide dynamic range as well as its capacity to respond selectively to different frequencies. A specific model of sound detection by the hair cells of the inner ear is discussed. We show that a collection of motor proteins within a hair bundle can generate oscillations at a frequency that depends on the elastic properties of the bundle. Simple variation of bundle geometry gives rise to hair cells with characteristic frequencies that span the range of audibility. Tension-gated transduction channels, which primarily serve to detect the motion of a hair bundle, also tune each cell by admitting ions that regulate the motor protein activity. By controlling the bundle's propensity to oscillate, this feedback automatically maintains the system in the operating regime where it is most sensitive to sinusoidal stimuli. The model explains how hair cells can detect sounds that carry less energy than the background noise.

| S-EPMC16213 | biostudies-literature

A biophysical limit for quorum sensing in biofilms.

Project description:Bacteria grow on surfaces in complex immobile communities known as biofilms, which are composed of cells embedded in an extracellular matrix. Within biofilms, bacteria often interact with members of their own species and cooperate or compete with members of other species via quorum sensing (QS). QS is a process by which microbes produce, secrete, and subsequently detect small molecules called autoinducers (AIs) to assess their local population density. We explore the competitive advantage of QS through agent-based simulations of a spatial model in which colony expansion via extracellular matrix production provides greater access to a limiting diffusible nutrient. We note a significant difference in results based on whether AI production is constitutive or limited by nutrient availability: If AI production is constitutive, simple QS-based matrix-production strategies can be far superior to any fixed strategy. However, if AI production is limited by nutrient availability, QS-based strategies fail to provide a significant advantage over fixed strategies. To explain this dichotomy, we derive a biophysical limit for the dynamic range of nutrient-limited AI concentrations in biofilms. This range is remarkably small (less than 10-fold) for the realistic case in which a growth-limiting diffusible nutrient is taken up within a narrow active growth layer. This biophysical limit implies that for QS to be most effective in biofilms AI production should be a protected function not directly tied to metabolism.

| S-EPMC8166027 | biostudies-literature

Modeling time-varying brain networks with a self-tuning optimized Kalman filter.

Project description:Brain networks are complex dynamical systems in which directed interactions between different areas evolve at the sub-second scale of sensory, cognitive and motor processes. Due to the highly non-stationary nature of neural signals and their unknown noise components, however, modeling dynamic brain networks has remained one of the major challenges in contemporary neuroscience. Here, we present a new algorithm based on an innovative formulation of the Kalman filter that is optimized for tracking rapidly evolving patterns of directed functional connectivity under unknown noise conditions. The Self-Tuning Optimized Kalman filter (STOK) is a novel adaptive filter that embeds a self-tuning memory decay and a recursive regularization to guarantee high network tracking accuracy, temporal precision and robustness to noise. To validate the proposed algorithm, we performed an extensive comparison against the classical Kalman filter, in both realistic surrogate networks and real electroencephalography (EEG) data. In both simulations and real data, we show that the STOK filter estimates time-frequency patterns of directed connectivity with significantly superior performance. The advantages of the STOK filter were even clearer in real EEG data, where the algorithm recovered latent structures of dynamic connectivity from epicranial EEG recordings in rats and human visual evoked potentials, in excellent agreement with known physiology. These results establish the STOK filter as a powerful tool for modeling dynamic network structures in biological systems, with the potential to yield new insights into the rapid evolution of network states from which brain functions emerge.

| S-EPMC7451990 | biostudies-literature

Biophysical principles of choanoflagellate self-organization.

Project description:Inspired by the patterns of multicellularity in choanoflagellates, the closest living relatives of animals, we quantify the biophysical processes underlying the morphogenesis of rosette colonies in the choanoflagellate Salpingoeca rosetta We find that rosettes reproducibly transition from an early stage of 2-dimensional (2D) growth to a later stage of 3D growth, despite the underlying variability of the cell lineages. Our perturbative experiments demonstrate the fundamental importance of a basally secreted extracellular matrix (ECM) for rosette morphogenesis and show that the interaction of the ECM with cells in the colony physically constrains the packing of proliferating cells and, thus, controls colony shape. Simulations of a biophysically inspired model that accounts for the size and shape of the individual cells, the fraction of ECM, and its stiffness relative to that of the cells suffices to explain our observations and yields a morphospace consistent with observations across a range of multicellular choanoflagellate colonies. Overall, our biophysical perspective on rosette development complements previous genetic perspectives and, thus, helps illuminate the interplay between cell biology and physics in regulating morphogenesis.

| S-EPMC6983409 | biostudies-literature

Insect odorant response sensitivity is tuned by metabotropically autoregulated olfactory receptors.

Project description:Insects possess one of the most exquisitely sensitive olfactory systems in the animal kingdom, consisting of three different types of chemosensory receptors: ionotropic glutamate-like receptors (IRs), gustatory receptors (GRs) and odorant receptors (ORs). Both insect ORs and IRs are ligand-gated ion channels, but ORs possess a unique configuration composed of an odorant-specific protein OrX and a ubiquitous coreceptor (Orco). In addition, these two ionotropic receptors confer different tuning properties for the neurons in which they are expressed. Unlike IRs, neurons expressing ORs are more sensitive and can also be sensitized by sub-threshold concentrations of stimuli. What is the mechanistic basis for these differences in tuning? We show that intrinsic regulation of Orco enhances neuronal response to odorants and sensitizes the ORs. We also demonstrate that inhibition of metabotropic regulation prevents receptor sensitization. Our results indicate that Orco-mediated regulation of OR sensitivity provides tunable ionotropic receptors capable of detecting odors over a wider range of concentrations, providing broadened sensitivity over IRs themselves.

| S-EPMC3595248 | biostudies-literature

Programming CAR T Cell Tumor Recognition: Tuned Antigen Sensing and Logic Gating.

Project description:The success of chimeric antigen receptor (CAR) T cells targeting B-cell malignancies propelled the field of synthetic immunology and raised hopes to treat solid tumors in a similar fashion. Antigen escape and the paucity of tumor-restricted CAR targets are recognized challenges to fulfilling this prospect. Recent advances in CAR T cell engineering extend the toolbox of chimeric receptors available to calibrate antigen sensitivity and combine receptors to create adapted tumor-sensing T cells. Emerging engineering strategies to lower the threshold for effective antigen recognition, when needed, and enable composite antigen recognition hold great promise for overcoming tumor heterogeneity and curbing off-tumor toxicities.SignificanceImproving the clinical efficacy of CAR T cell therapies will require engineering T cells that overcome heterogeneous and low-abundance target expression while minimizing reactivity to normal tissues. Recent advances in CAR design and logic gating are poised to extend the success of CAR T cell therapies beyond B-cell malignancies.

| S-EPMC10068450 | biostudies-literature

Self-powered high-sensitivity all-in-one vertical tribo-transistor device for multi-sensing-memory-computing.

Project description:Devices with sensing-memory-computing capability for the detection, recognition and memorization of real time sensory information could simplify data conversion, transmission, storage, and operations between different blocks in conventional chips, which are invaluable and sought-after to offer critical benefits of accomplishing diverse functions, simple design, and efficient computing simultaneously in the internet of things (IOT) era. Here, we develop a self-powered vertical tribo-transistor (VTT) based on MXenes for multi-sensing-memory-computing function and multi-task emotion recognition, which integrates triboelectric nanogenerator (TENG) and transistor in a single device with the simple configuration of vertical organic field effect transistor (VOFET). The tribo-potential is found to be able to tune ionic migration in insulating layer and Schottky barrier height at the MXene/semiconductor interface, and thus modulate the conductive channel between MXene and drain electrode. Meanwhile, the sensing sensitivity can be significantly improved by 711 times over the single TENG device, and the VTT exhibits excellent multi-sensing-memory-computing function. Importantly, based on this function, the multi-sensing integration and multi-model emotion recognition are constructed, which improves the emotion recognition accuracy up to 94.05% with reliability. This simple structure and self-powered VTT device exhibits high sensitivity, high efficiency and high accuracy, which provides application prospects in future human-mechanical interaction, IOT and high-level intelligence.

| S-EPMC9789038 | biostudies-literature

High-Sensitivity and Flexible Motion Sensing Enabled by Robust, Self-Healing Wood-Based Anisotropic Hydrogel Composites.

Project description:By integrating polyvinyl alcohol (PVA)-borate-tannic acid (TA)-sodium sulfate into cellulosic wood matrices, a novel wood-basedPVA-borate-TA-sodium sulfate (WPBTS) hydrogel is successfully synthesized. Through a multicomponent synergistic design combining natural lignocellulose, PVA, borax, TA, and sodium sulfate, multiple dynamic cross-linking mechanisms-dynamic borate bonding, hydrogen bonding, and metal-ligand interactions-are established, resulting in WPBTS hydrogels with exceptional mechanical properties and self-healing capabilities. The mechanical strength of the WPBTS hydrogel reached an impressive 19.8 MPa, a 45-fold increase compared to PVA-borax-tannic acid (PBTS) hydrogels. Furthermore, the assembled WPBTS hydrogel-based flexible sensor demonstrates a remarkably fast response time of just 20 ms and maintains excellent performance in challenging simulated saline environments. This innovation represents a significant advancement in sensor technology and highlights the potential for transformative applications in complex and demanding scenarios.

| S-EPMC11921998 | biostudies-literature

Sensing self and nonself circular RNAs

Project description:Circular RNAs (circRNAs) are single-stranded RNAs that are joined head to tail. Initially discovered as pathogen genomes such as hepatitis D virus (HDV) and plant viroids, circRNAs are recently recognized as a pervasive class of noncoding RNAs in eukaryotic cells, generated through back splicing. circRNAs have been postulated to function in cell-to-cell information transfer or memory due to their extraordinary stability. Whether and how circRNAs trigger immune recognition is not known. Here we show that exogenous circular RNAs potently stimulate immune signaling, and mammalian cells sense self vs. nonself circRNAs via circRNA biogenesis. Transfection of purified in vitro spliced circRNA into mammalian cells led to potent induction of innate immunity genes. The nucleic acid sensor RIG-I is necessary and sufficient to sense foreign circRNA, and RIG-I and foreign circRNA co-aggregate in cytoplasmic foci. CircRNA activation of innate immunity is independent of 5’ triphosphate, double-stranded RNA structure, or primary sequence of the foreign circRNA. Instead, self-nonself discrimination depends on the intron that programs the circRNA. Use of a human intron to express a foreign circRNA sequence abrogates immune activation, and the mature human circRNA is associated with diverse RNA binding proteins reflecting its endogenous splicing and biogenesis. These results reveal innate immune sensing of circRNA, a prevalent class of host and pathogen RNAs, and highlight introns—the predominant output of mammalian transcription—as unexpected arbiters of self-nonself identity in the RNA world.

2017-06-29 | GSE81345 | GEO

Self-sensing in Bacillus subtilis quorum-sensing systems.

Project description:Bacterial cell-cell signalling, or quorum sensing, is characterized by the secretion and groupwide detection of small diffusible signal molecules called autoinducers. This mechanism allows cells to coordinate their behaviour in a density-dependent manner. A quorum-sensing cell may directly respond to the autoinducers it produces in a cell-autonomous and quorum-independent manner, but the strength of this self-sensing effect and its impact on bacterial physiology are unclear. Here, we explore the existence and impact of self-sensing in the Bacillus subtilis ComQXP and Rap-Phr quorum-sensing systems. By comparing the quorum-sensing response of autoinducer-secreting and non-secreting cells in co-culture, we find that secreting cells consistently show a stronger response than non-secreting cells. Combining genetic and quantitative analyses, we demonstrate this effect to be a direct result of self-sensing and rule out an indirect regulatory effect of the autoinducer production genes on response sensitivity. In addition, self-sensing in the ComQXP system affects persistence to antibiotic treatment. Together, these findings indicate the existence of self-sensing in the two most common designs of quorum-sensing systems of Gram-positive bacteria.

| S-EPMC5739288 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data