Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Probing the limits to positional information.

ABSTRACT: The reproducibility and precision of biological patterning is limited by the accuracy with which concentration profiles of morphogen molecules can be established and read out by their targets. We consider four measures of precision for the Bicoid morphogen in the Drosophila embryo: the concentration differences that distinguish neighboring cells, the limits set by the random arrival of Bicoid molecules at their targets (which depends on absolute concentration), the noise in readout of Bicoid by the activation of Hunchback, and the reproducibility of Bicoid concentration at corresponding positions in multiple embryos. We show, through a combination of different experiments, that all of these quantities are approximately 10%. This agreement among different measures of accuracy indicates that the embryo is not faced with noisy input signals and readout mechanisms; rather, the system exerts precise control over absolute concentrations and responds reliably to small concentration differences, approaching the limits set by basic physical principles.

SUBMITTER: Gregor T

PROVIDER: S-EPMC2253670 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Probing the limits to positional information.

Gregor Thomas T Tank David W DW Wieschaus Eric F EF Bialek William W

Cell 20070701 1

The reproducibility and precision of biological patterning is limited by the accuracy with which concentration profiles of morphogen molecules can be established and read out by their targets. We consider four measures of precision for the Bicoid morphogen in the Drosophila embryo: the concentration differences that distinguish neighboring cells, the limits set by the random arrival of Bicoid molecules at their targets (which depends on absolute concentration), the noise in readout of Bicoid by ...[more]

PMID: 17632062

Similar Datasets

Probing Limits of Information Spread with Sequential Seeding.

Project description:We consider here information spread which propagates with certain probability from nodes just activated to their not yet activated neighbors. Diffusion cascades can be triggered by activation of even a small set of nodes. Such activation is commonly performed in a single stage. A novel approach based on sequential seeding is analyzed here resulting in three fundamental contributions. First, we propose a coordinated execution of randomized choices to enable precise comparison of different algorithms in general. We apply it here when the newly activated nodes at each stage of spreading attempt to activate their neighbors. Then, we present a formal proof that sequential seeding delivers at least as good spread coverage as the single stage seeding does. Moreover, we also show that, under modest assumptions, sequential seeding performs provably better than the single stage seeding using the same number of seeds and node ranking. Finally, we present experimental results comparing single stage and sequential approaches on directed and undirected graphs to the well-known greedy approach to provide the objective measure of the sequential seeding benefits. Surprisingly, applying sequential seeding to a simple degree-based selection leads to higher coverage than achieved by the computationally expensive greedy approach currently considered to be the best heuristic.

| S-EPMC6143613 | biostudies-literature

Grid Cells Encode Local Positional Information.

Project description:The brain has an extraordinary ability to create an internal spatial map of the external world [1]. This map-like representation of environmental surroundings is encoded through specific types of neurons, located within the hippocampus and entorhinal cortex, which exhibit spatially tuned firing patterns [2, 3]. In addition to encoding space, these neurons are believed to be related to contextual information and memory [4-7]. One class of such cells is the grid cells, which are located within the entorhinal cortex, presubiculum, and parasubiculum [3, 8]. Grid cell firing forms a hexagonal array of firing fields, a pattern that is largely thought to reflect the operation of intrinsic self-motion-related computations [9-12]. If this is the case, then fields should be relatively uniform in size, number of spikes, and peak firing rate. However, it has been suggested that this is not in fact the case [3, 13]. The possibility exists that local spatial information also influences grid cells, which-if true-would greatly change the way in which grid cells are thought to contribute to place coding. Accordingly, we asked how discriminable the individual fields of a given grid cell are by looking at the distribution of field firing rates and reproducibility of this distribution across trials. Grid fields were less uniform in intensity than expected, and the pattern of strong and weak fields was spatially stable and recurred across trials. The distribution remained unchanged even after arena rescaling, but not after remapping. This suggests that additional local information is being overlaid onto the global hexagonal pattern of grid cells.

| S-EPMC5558037 | biostudies-literature

Probing the efficiency of proteolytic events by positional proteomics.

Project description:Several mass spectrometry-driven techniques allow to map the substrate repertoires and specificities of proteases. These techniques typically yield long lists of protease substrates and processed sites with (potential) physiological relevance, but in order to understand the primary function of a protease, it is important to discern bystander substrates from critical substrates. Because the former are generally processed with lower efficiency, data on the actual substrate cleavage efficiency could assist in categorizing protease substrates. In this study, quantitative mass spectrometry following metabolic proteome labeling (SILAC), combined with the isolation of N-terminal peptides by Combined Fractional Diagonal Chromatography, was used to monitor fluxes in the concentration of protease-generated neo-N-termini. In our experimental setup, a Jurkat cell lysate was treated with the human serine protease granzyme B (hGrB) for three different incubation periods. The extensive list of human granzyme B substrates previously catalogued by N-terminal Combined Fractional Diagonal Chromatography (1) was then used to assign 101 unique hGrB-specific neo-N-termini in 86 proteins. In this way, we were able to define several sites as getting efficiently cleaved in vitro and consequently recognize potential physiologically more relevant substrates. Among them the well-known hGrB substrate Bid was confirmed as being an efficient hGrB substrate next to several other potential regulators of hGrB induced apoptosis such as Bnip2 and Akap-8. Several of our proteomics results were further confirmed by substrate immunoblotting and by using peptide substrates incubated with human granzyme B.

| S-EPMC3033678 | biostudies-literature

Positional information drives distinct traits in transcriptomically identified neuronal types

Project description:We transcriptionally profiled the neuronal types of the zebrafish larvae optic tectum and matched them with their functional and morphological properties.

2024-11-13 | GSE269232 | GEO

Probing the ultimate limits of plasmonic enhancement.

Project description:Metals support surface plasmons at optical wavelengths and have the ability to localize light to subwavelength regions. The field enhancements that occur in these regions set the ultimate limitations on a wide range of nonlinear and quantum optical phenomena. We found that the dominant limiting factor is not the resistive loss of the metal, but rather the intrinsic nonlocality of its dielectric response. A semiclassical model of the electronic response of a metal places strict bounds on the ultimate field enhancement. To demonstrate the accuracy of this model, we studied optical scattering from gold nanoparticles spaced a few angstroms from a gold film. The bounds derived from the models and experiments impose limitations on all nanophotonic systems.

| S-EPMC3649871 | biostudies-literature

Positional information generated by spatially distributed signaling cascades.

Project description:The temporal and stationary behavior of protein modification cascades has been extensively studied, yet little is known about the spatial aspects of signal propagation. We have previously shown that the spatial separation of opposing enzymes, such as a kinase and a phosphatase, creates signaling activity gradients. Here we show under what conditions signals stall in the space or robustly propagate through spatially distributed signaling cascades. Robust signal propagation results in activity gradients with long plateaus, which abruptly decay at successive spatial locations. We derive an approximate analytical solution that relates the maximal amplitude and propagation length of each activation profile with the cascade level, protein diffusivity, and the ratio of the opposing enzyme activities. The control of the spatial signal propagation appears to be very different from the control of transient temporal responses for spatially homogenous cascades. For spatially distributed cascades where activating and deactivating enzymes operate far from saturation, the ratio of the opposing enzyme activities is shown to be a key parameter controlling signal propagation. The signaling gradients characteristic for robust signal propagation exemplify a pattern formation mechanism that generates precise spatial guidance for multiple cellular processes and conveys information about the cell size to the nucleus.

| S-EPMC2654021 | biostudies-literature

Coding design of positional information for robust morphogenesis.

Project description:Robust positioning of cells in a tissue against unavoidable noises is important for achieving normal and reproducible morphogenesis. The position in a tissue is represented by morphogen concentrations, and cells read them to recognize their spatial coordinates. From the engineering viewpoint, these positioning processes can be regarded as an information coding. Organisms are conjectured to adopt good coding designs with high reliability for a given number of available morphogen species and their chemical properties. To answer, quantitatively, the questions of how good coding is adopted, and subsequently when, where, and to what extent each morphogen contributes to positioning, we need a way to evaluate the goodness of coding. In this article, by introducing basic concepts of computer science, we mathematically formulate coding processes in morphogen-dependent positioning, and define some key concepts such as encoding, decoding, and positional information and its precision. We demonstrate the best designs for pairs of encoding and decoding rules, and show how those designs can be biologically implemented by using some examples. We also propose a possible procedure of data analysis to validate the coding optimality formulated here.

| S-EPMC3218323 | biostudies-literature

Positional information modulates transient regeneration-activated cell states during vertebrate appendage regeneration.

Project description:Injury is a common occurrence in the life of most if not all organisms. Because injury and the extent of damage inflicted are not predictable events, pre-existing tissues must somehow determine how much tissue needs to be restored. It has been known for over a century that amputation position along a proximal-distal (P/D) axis determines the regeneration speed of amputated limbs in regeneration-competent animals1. Yet, it is not clear how an injured limb conveys positional information during regeneration to faithfully restore pre-existing morphologies and functions. Here, we profiled millimetric caudal fins regenerating proximal and distal amputations in the African killifish (Nothobranchius furzeri). We report position-specific, differential modulation of the spatial distribution, duration, and magnitude of proliferation, and the possibility to predict blastema sizes. Regenerating fins profiled by single cell RNA sequencing identified a Transient Regeneration-Activated Cell State (TRACS) enriched in extracellular matrix (ECM) components and modifiers that is proportionally amplified to match a given amputation position. We located this transient cell state to the basal epidermis by gene expression and confocal microscopy, and propose a role for these cells in transducing positional information to the regeneration blastema. Understanding the temporal deployment of regenerative cell states may hold the key to set up a successful regeneration event in organisms with limited regenerative abilities such as humans.

2024-04-01 | GSE260629 | GEO

Wnt-regulated dynamics of positional information in zebrafish somitogenesis.

Project description:How signaling gradients supply positional information in a field of moving cells is an unsolved question in patterning and morphogenesis. Here, we ask how a Wnt signaling gradient regulates the dynamics of a wavefront of cellular change in a flow of cells during somitogenesis. Using time-controlled perturbations of Wnt signaling in the zebrafish embryo, we changed segment length without altering the rate of somite formation or embryonic elongation. This result implies specific Wnt regulation of the wavefront velocity. The observed Wnt signaling gradient dynamics and timing of downstream events support a model for wavefront regulation in which cell flow plays a dominant role in transporting positional information.

| S-EPMC3943186 | biostudies-literature

Probing the limits of Q-tag bioconjugation of antibodies.

Project description:Site-selective labelling of antibodies (Abs) can circumvent problems from heterogeneity of conventional conjugation. Here, we evaluate the industrially-applied chemoenzymatic 'Q-tag' strategy based on transglutaminase-mediated (TGase) amide-bond formation in the generation of 89Zr-radiolabelled antibody conjugates. We show that, despite previously suggested high regioselectivity of TGases, in the anti-Her2 Ab Herceptin™ more precise native MS indicates only 70-80% functionalization at the target site (Q298H), in competition with modification at other sites, such as Q3H critically close to the CDR1 region.

| S-EPMC6788405 | 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