Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Decision making at a subcellular level determines the outcome of bacteriophage infection.

ABSTRACT: When the process of cell-fate determination is examined at single-cell resolution, it is often observed that individual cells undergo different fates even when subject to identical conditions. This "noisy" phenotype is usually attributed to the inherent stochasticity of chemical reactions in the cell. Here we demonstrate how the observed single-cell heterogeneity can be explained by a cascade of decisions occurring at the subcellular level. We follow the postinfection decision in bacteriophage lambda at single-virus resolution, and show that a choice between lysis and lysogeny is first made at the level of the individual virus. The decisions by all viruses infecting a single cell are then integrated in a precise (noise-free) way, such that only a unanimous vote by all viruses leads to the establishment of lysogeny. By detecting and integrating over the subcellular "hidden variables," we are able to predict the level of noise measured at the single-cell level.

SUBMITTER: Zeng L

PROVIDER: S-EPMC2873970 | biostudies-other | 2010 May

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Decision making at a subcellular level determines the outcome of bacteriophage infection.

Zeng Lanying L Skinner Samuel O SO Zong Chenghang C Sippy Jean J Feiss Michael M Golding Ido I

Cell 20100501 4

When the process of cell-fate determination is examined at single-cell resolution, it is often observed that individual cells undergo different fates even when subject to identical conditions. This "noisy" phenotype is usually attributed to the inherent stochasticity of chemical reactions in the cell. Here we demonstrate how the observed single-cell heterogeneity can be explained by a cascade of decisions occurring at the subcellular level. We follow the postinfection decision in bacteriophage l ...[more]

PMID: 20478257

Similar Datasets

Pupil-linked arousal determines variability in perceptual decision making.

Project description:Decision making between several alternatives is thought to involve the gradual accumulation of evidence in favor of each available choice. This process is profoundly variable even for nominally identical stimuli, yet the neuro-cognitive substrates that determine the magnitude of this variability are poorly understood. Here, we demonstrate that arousal state is a powerful determinant of variability in perceptual decision making. We measured pupil size, a highly sensitive index of arousal, while human subjects performed a motion-discrimination task, and decomposed task behavior into latent decision making parameters using an established computational model of the decision process. In direct contrast to previous theoretical accounts specifying a role for arousal in several discrete aspects of decision making, we found that pupil diameter was uniquely related to a model parameter representing variability in the rate of decision evidence accumulation: Periods of increased pupil size, reflecting heightened arousal, were characterized by greater variability in accumulation rate. Pupil diameter also correlated trial-by-trial with specific patterns of behavior that collectively are diagnostic of changing accumulation rate variability, and explained substantial individual differences in this computational quantity. These findings provide a uniquely clear account of how arousal state impacts decision making, and may point to a relationship between pupil-linked neuromodulation and behavioral variability. They also pave the way for future studies aimed at augmenting the precision with which people make decisions.

| S-EPMC4168983 | biostudies-literature

Negative decision outcomes are more common among people with lower decision-making competence: an item-level analysis of the Decision Outcome Inventory (DOI).

Project description:Most behavioral decision research takes place in carefully controlled laboratory settings, and examination of relationships between performance and specific real-world decision outcomes is rare. One prior study shows that people who perform better on hypothetical decision tasks, assessed using the Adult Decision-Making Competence (A-DMC) measure, also tend to experience better real-world decision outcomes, as reported on the Decision Outcomes Inventory (DOI). The DOI score reflects avoidance of outcomes that could result from poor decisions, ranging from serious (e.g., bankruptcy) to minor (e.g., blisters from sunburn). The present analyses go beyond the initial work, which focused on the overall DOI score, by analyzing the relationships between specific decision outcomes and A-DMC performance. Most outcomes are significantly more likely among people with lower A-DMC scores, even after taking into account two variables expected to produce worse real-world decision outcomes: younger age and lower socio-economic status. We discuss the usefulness of DOI as a measure of successful real-world decision-making.

| S-EPMC4387469 | biostudies-literature

Proteome integral solubility alteration assay combined with multi-criteria decision-making analysis for developing adverse outcome pathways

Project description:To simplify chemical risk assessment, the adverse outcome pathway (AOP) method has arisen as a framework to predict the impact of chemical exposure on human and environmental health. The development of this predictive tool requires knowledge of the molecular interaction between chemicals and protein targets. Here, we demonstrate that the identification and selection of a target candidate to develop adverse outcome pathways can be obtained by applying high-throughput identification of chemical targets by proteome integral solubility alteration (PISA) assay, followed by selecting the priority target candidate by an analytical hierarchy process. From 8 identified protein targets for TCDD from a soluble proteome extracted from hepatocytes, we selected the priority target for developing AOPs. Our combined methodologies provide identification of a molecular initiating event, essential knowledge to link molecular interaction to impact on health. The identification of chemical targets following a systematic analysis of chemical protein interaction by proteomics increases the high-throughput and reduces the traditional bias. The target selection eliminates conflicting criteria by applying a multiple-criteria decision-making analysis.

2023-03-11 | PXD033056 | Pride

Group personality during collective decision-making: a multi-level approach.

Project description:Collective decision-making processes emerge from social feedback networks within a group. Many studies on collective behaviour underestimate the role of individual personality and, as a result, personality is rarely analysed in the context of collective dynamics. Here, we show evidence of sheltering behaviour personality in a gregarious insect (Periplaneta americana), which is characterized by a collective personality at the group level. We also highlight that the individuals within groups exhibited consistent personality traits in their probability of sheltering and total time sheltered during the three trials over one week. Moreover, the group personality, which arises from the synergy between the distribution of behaviour profiles in the group and social amplifications, affected the sheltering dynamics. However, owing to its robustness, personality did not affect the group probability of reaching a consensus. Finally, to prove social interactions, we developed a new statistical method that will be helpful for future research on personality traits and group behaviour. This approach will help to identify the circumstances under which particular group compositions may improve the fitness of individuals in gregarious species.

| S-EPMC4344149 | biostudies-literature

Implications of response shift for micro-, meso-, and macro-level healthcare decision-making using results of patient-reported outcome measures.

Project description:PurposeResults of patient-reported outcome measures (PROMs) are increasingly used to inform healthcare decision-making. Research has shown that response shift can impact PROM results. As part of an international collaboration, our goal is to provide a framework regarding the implications of response shift at the level of patient care (micro), healthcare institute (meso), and healthcare policy (macro).MethodsEmpirical evidence of response shift that can influence patients' self-reported health and preferences provided the foundation for development of the framework. Measurement validity theory, hermeneutic philosophy, and micro-, meso-, and macro-level healthcare decision-making informed our theoretical analysis.ResultsAt the micro-level, patients' self-reported health needs to be interpreted via dialogue with the clinician to avoid misinterpretation of PROM data due to response shift. It is also important to consider the potential impact of response shift on study results, when these are used to support decisions. At the meso-level, individual-level data should be examined for response shift before aggregating PROM data for decision-making related to quality improvement, performance monitoring, and accreditation. At the macro-level, critical reflection on the conceptualization of health is required to know whether response shift needs to be controlled for when PROM data are used to inform healthcare coverage.ConclusionGiven empirical evidence of response shift, there is a critical need for guidelines and knowledge translation to avoid potential misinterpretations of PROM results and consequential biases in decision-making. Our framework with guiding questions provides a structure for developing strategies to address potential impacts of response shift at micro-, meso-, and macro-levels.

| S-EPMC8602130 | biostudies-literature

Impact of uncertainty and ambiguous outcome phrasing on moral decision-making.

Project description:The literature has shown that different types of moral dilemmas elicit discrepant decision patterns. The present research investigated the role of uncertainty in contributing to these decision patterns. Two studies were conducted to examine participants' choices in commonly used dilemmas. Study 1 showed that participants' perceived outcome probabilities were significantly associated with their moral choices, and that these associations were independent from the dilemma type. Study 2 revealed that participants had significantly less preference for killing the individual when the outcome probabilities were stated using the modal verb 'will' than when they were stated using the numerical phrasing of '100%'. Our findings illustrate a discord between experimenter and participant in the interpretation of task instructions.

| S-EPMC7250437 | biostudies-literature

A design principle of group-level decision making in cell populations.

Project description:Populations of cells often switch states as a group to cope with environmental changes such as nutrient availability and cell density. Although the gene circuits that underlie the switches are well understood at the level of single cells, the ways in which such circuits work in concert among many cells to support group-level switches are not fully explored. Experimental studies of microbial quorum sensing show that group-level changes in cellular states occur in either a graded or an all-or-none fashion. Here, we show through numerical simulations and mathematical analysis that these behaviors generally originate from two distinct forms of bistability. The choice of bistability is uniquely determined by a dimensionless parameter that compares the synthesis and the transport of the inducing molecules. The role of the parameter is universal, such that it not only applies to the autoinducing circuits typically found in bacteria but also to the more complex gene circuits involved in transmembrane receptor signaling. Furthermore, in gene circuits with negative feedback, the same dimensionless parameter determines the coherence of group-level transitions from quiescence to a rhythmic state. The set of biochemical parameters in bacterial quorum-sensing circuits appear to be tuned so that the cells can use either type of transition. The design principle identified here serves as the basis for the analysis and control of cellular collective decision making.

| S-EPMC3694814 | biostudies-literature

Low-level image statistics in natural scenes influence perceptual decision-making.

Project description:A fundamental component of interacting with our environment is gathering and interpretation of sensory information. When investigating how perceptual information influences decision-making, most researchers have relied on manipulated or unnatural information as perceptual input, resulting in findings that may not generalize to real-world scenes. Unlike simplified, artificial stimuli, real-world scenes contain low-level regularities that are informative about the structural complexity, which the brain could exploit. In this study, participants performed an animal detection task on low, medium or high complexity scenes as determined by two biologically plausible natural scene statistics, contrast energy (CE) or spatial coherence (SC). In experiment 1, stimuli were sampled such that CE and SC both influenced scene complexity. Diffusion modelling showed that the speed of information processing was affected by low-level scene complexity. Experiment 2a/b refined these observations by showing how isolated manipulation of SC resulted in weaker but comparable effects, with an additional change in response boundary, whereas manipulation of only CE had no effect. Overall, performance was best for scenes with intermediate complexity. Our systematic definition quantifies how natural scene complexity interacts with decision-making. We speculate that CE and SC serve as an indication to adjust perceptual decision-making based on the complexity of the input.

| S-EPMC7324621 | biostudies-literature

Changes in low-level neural properties underlie age-dependent visual decision making.

Project description:Aging typically slows down cognitive processes, specifically those related to perceptual decisions. However, the neurobiological mechanisms underlying these age-associated changes are still elusive. To address this, we studied the effect of aging on both perceptual and binocular rivalry in various presentation conditions. Two age groups of participants reported their spontaneous percept switches during continuous presentation and percept choices during intermittent presentation. We find no significant age effect on the mean and cumulative frequencies of percept switch durations under continuous presentation. However, the data show a significant age effect on coefficient of variation, ratio of standard deviation to mean of percept durations. Our results also reveal that the alternation rate for percept choices significantly declines at an older age under intermittent presentation. The latter effect is even more pronounced at shorter inter-stimulus durations. These results together with the predictions of existing neural models for bistable perception imply that age-dependency of visual perceptual decisions is caused by shifts in neural adaptation and noise, not by a change in inhibition strength. Thus, variation in the low-level neural properties, adaptation and noise, cause age-dependent properties in visual perceptual decisions.

| S-EPMC6050268 | biostudies-other

Centre-specific bacterial pathogen typing affects infection-control decision making.

Project description:Whole-genome sequencing is becoming the de facto standard for bacterial outbreak surveillance and infection prevention. This is accompanied by a variety of bioinformatic tools and needs bioinformatics expertise for implementation. However, little is known about the concordance of reported outbreaks when using different bioinformatic workflows. In this multi-centre proficiency testing among 13 major Dutch healthcare-affiliated centres, bacterial whole-genome outbreak analysis was assessed. Centres who participated obtained two randomized bacterial datasets of Illumina sequences, a Klebsiella pneumoniae and a Vancomycin-resistant Enterococcus faecium, and were asked to apply their bioinformatic workflows. Centres reported back on antimicrobial resistance, multi-locus sequence typing (MLST), and outbreak clusters. The reported clusters were analysed using a method to compare landscapes of phylogenetic trees and calculating Kendall-Colijn distances. Furthermore, fasta files were analysed by state-of-the-art single nucleotide polymorphism (SNP) analysis to mitigate the differences introduced by each centre and determine standardized SNP cut-offs. Thirteen centres participated in this study. The reported outbreak clusters revealed discrepancies between centres, even when almost identical bioinformatic workflows were used. Due to stringent filtering, some centres failed to detect extended-spectrum beta-lactamase genes and MLST loci. Applying a standardized method to determine outbreak clusters on the reported de novo assemblies, did not result in uniformity of outbreak-cluster composition among centres.

| S-EPMC8549354 | 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