Higher-order temporal network effects through triplet evolution.
Ontology highlight
ABSTRACT:
SUBMITTER: Yao Q
PROVIDER: S-EPMC8322211 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:It is increasingly being recognized that physical interactions between distant chromosomal loci influence the expressivity of the genome. Thus, multiple enhancers may converge on a single gene promoter 1,2 and a single enhancer can stochastically loop to multiple promoters 3. Regulatory elements from neighboring domains or from other chromosomes may interact to generate chromatin structures poised for transcription4-8 or repression 9-11. However, a broader perspective on the formation and function of such networks remains largely unexplored. Using the high-resolution 4C (Circular Chromosome Conformation Capture) analysis, we identify here a genome-wide physical network between genomically imprinted domains impinging H19 imprinting control region (ICR). Sequences interacting with the H19 ICR constitutively map at or within most of known imprinted domains both in mouse embryonic stem cells and in vitro-derived embryoid bodies, despite distinct differences in chromatin environments. Moreover, all-to-all 3D DNA FISH analyses revealed that imprinted domains from 7 different chromosomes co-localize with each other in pair-wise patterns, highlighting the dynamic nature of these interactions. The observed interaction network is dependent on CTCF binding sites within the maternally inherited H19 ICR allele and delays reprogramming of epigenetic features at imprinted domains during male germline development. As other imprinted regions can interact with each other in an H19 ICR-dependent manner, the H19 ICR emerges as an organizer of chromosomal networks by specifically recognizing and reconfiguring imprinted domains. We propose that an ancient key regulatory region, such as the H19 ICR, gradually impacted epigenetic modifications via long-range interactions in the germline to facilitate the recruitment of imprinted genes and their formation in clusters during mammalian radiation. Furthermore, the perspective of epigenetic lesions de-stabilizing such chromosomal networks may advance our understanding of how quantitative traits influence human diseases, such as cancer.
2009-12-14 | GSE14074 | GEO
Project description:The introduction and establishment of nonindigenous species (NIS) through global ship movements poses a significant threat to marine ecosystems and economies. While ballast-vectored invasions have been partly addressed by some national policies and an international agreement regulating the concentrations of organisms in ballast water, biofouling-vectored invasions remain largely unaddressed. Development of additional efficient and cost-effective ship-borne NIS policies requires an accurate estimation of NIS spread risk from both ballast water and biofouling. We demonstrate that the first-order Markovian assumption limits accurate modeling of NIS spread risks through the global shipping network. In contrast, we show that higher-order patterns provide more accurate NIS spread risk estimates by revealing indirect pathways of NIS transfer using Species Flow Higher-Order Networks (SF-HON). Using the largest available datasets of non-indigenous species for Europe and the United States, we then compare SF-HON model predictions against those from networks that consider only first-order connections and those that consider all possible indirect connections without consideration of their significance. We show that not only SF-HONs yield more accurate NIS spread risk predictions, but there are important differences in NIS spread via the ballast and biofouling vectors. Our work provides information that policymakers can use to develop more efficient and targeted prevention strategies for ship-borne NIS spread management, especially as management of biofouling is of increasing concern.
| S-EPMC7394518 | biostudies-literature
Project description:Bird songs often display musical acoustic features such as tonal pitch selection, rhythmicity, and melodic contouring. We investigated higher-order musical temporal structure in bird song using an experimental method called "music scrambling" with human subjects. Recorded songs from a phylogenetically diverse group of 20 avian taxa were split into constituent elements ("notes" or "syllables") and recombined in original and random order. Human subjects were asked to evaluate which version sounded more "musical" on a per-species basis. Species identity and stimulus treatment were concealed from subjects, and stimulus presentation order was randomized within and between taxa. Two recordings of human music were included as a control for attentiveness. Participants varied in their assessments of individual species musicality, but overall they were significantly more likely to rate bird songs with original temporal sequence as more musical than those with randomized temporal sequence. We discuss alternative hypotheses for the origins of avian musicality, including honest signaling, perceptual bias, and arbitrary aesthetic coevolution.
| S-EPMC8044833 | biostudies-literature
Project description:The assembly and maintenance of microbial diversity in natural communities, despite the abundance of toxin-based antagonistic interactions, presents major challenges for biological understanding. A common framework for investigating such antagonistic interactions involves cyclic dominance games with pairwise interactions. The incorporation of higher-order interactions in such models permits increased levels of microbial diversity, especially in communities in which antibiotic-producing, sensitive, and resistant strains coexist. However, most such models involve a small number of discrete species, assume a notion of pure cyclic dominance, and focus on low mutation rate regimes, none of which well represent the highly interlinked, quickly evolving, and continuous nature of microbial phenotypic space. Here, we present an alternative vision of spatial dynamics for microbial communities based on antagonistic interactions-one in which a large number of species interact in continuous phenotypic space, are capable of rapid mutation, and engage in both direct and higher-order interactions mediated by production of and resistance to antibiotics. Focusing on toxin production, vulnerability, and inhibition among species, we observe highly divergent patterns of diversity and spatial community dynamics. We find that species interaction constraints (rather than mobility) best predict spatiotemporal disturbance regimes, whereas community formation time, mobility, and mutation size best explain patterns of diversity. We also report an intriguing relationship among community formation time, spatial disturbance regimes, and diversity dynamics. This relationship, which suggests that both higher-order interactions and rapid evolution are critical for the origin and maintenance of microbial diversity, has broad-ranging links to the maintenance of diversity in other systems.
| S-EPMC8740587 | biostudies-literature
Project description:Naturally occurring signals in audition and touch can be complex and marked by temporal variations in frequency and amplitude. Auditory frequency sweep processing has been studied extensively; however, much less is known about sweep processing in touch because studies have primarily focused on the perception of simple sinusoidal vibrations. Given the extensive interactions between audition and touch in the frequency processing of pure tone signals, we reasoned that these senses might also interact in the processing of higher-order frequency representations like sweeps. In a series of psychophysical experiments, we characterized the influence of auditory distractors on the ability of participants to discriminate tactile frequency sweeps. Auditory frequency sweeps systematically biased the tactile perception of sweep direction. Importantly, auditory cues exerted little influence on tactile sweep direction perception when the sounds and vibrations occupied different absolute frequency ranges or when the sounds consisted of intensity sweeps. Thus, audition and touch interact in frequency sweep perception in a frequency- and feature-specific manner. Our results demonstrate that audio-tactile interactions are not constrained to the processing of simple sinusoids. Because higher-order frequency representations may be synthesized from simpler representations, our findings imply that multisensory interactions in the temporal frequency domain span multiple hierarchical levels in sensory processing. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
| S-EPMC6472995 | biostudies-literature
Project description:Human social interactions in local settings can be experimentally detected by recording the physical proximity and orientation of people. Such interactions, approximating face-to-face communications, can be effectively represented as time varying social networks with links being unceasingly created and destroyed over time. Traditional analyses of temporal networks have addressed mostly pairwise interactions, where links describe dyadic connections among individuals. However, many network dynamics are hardly ascribable to pairwise settings but often comprise larger groups, which are better described by higher-order interactions. Here we investigate the higher-order organizations of temporal social networks by analyzing five publicly available datasets collected in different social settings. We find that higher-order interactions are ubiquitous and, similarly to their pairwise counterparts, characterized by heterogeneous dynamics, with bursty trains of rapidly recurring higher-order events separated by long periods of inactivity. We investigate the evolution and formation of groups by looking at the transition rates between different higher-order structures. We find that in more spontaneous social settings, group are characterized by slower formation and disaggregation, while in work settings these phenomena are more abrupt, possibly reflecting pre-organized social dynamics. Finally, we observe temporal reinforcement suggesting that the longer a group stays together the higher the probability that the same interaction pattern persist in the future. Our findings suggest the importance of considering the higher-order structure of social interactions when investigating human temporal dynamics.
| S-EPMC8007734 | biostudies-literature
Project description:A central question in genetics and evolution is the extent to which mutations have outcomes that change depending on the genetic context in which they occur. Pairwise interactions between mutations have been systematically mapped within and between genes, and contribute substantially to phenotypic variation amongst individuals. However, the extent to which genetic interactions themselves are stable or dynamic across genotypes is unclear. Here we quantify >45,000 genetic interactions between the same 87 pairs of mutations across >500 closely related genotypes of a yeast tRNA. Strikingly, all pairs of mutations interacted in at least 9% of genetic backgrounds and all pairs switched from interacting positively to interacting negatively in different genotypes (FDR<0.1). Higher order interactions are also abundant and dynamic across genotypes. The epistasis in this molecule means that all individual mutations switch from detrimental to beneficial in even closely-related genotypes. As a consequence, accurate genetic prediction requires mutation effects to be measured across different genetic backgrounds and the use of higher order epistatic terms.
2018-03-06 | GSE99418 | GEO
Project description:The evolution of complex signals may be favoured by hidden preferences or pre-existing sensory biases. Females of two species of grey treefrogs (Hyla chrysoscelis and Hyla versicolor) were tested with combinations of a conspecific advertisement call and acoustic appendages. Appendages consisted of aggressive calls and segments of advertisement calls from conspecific males and males of three other species and bursts of filtered noise. When a wide variety of these acoustic appendages followed the advertisement call, the resulting compound signal was often more attractive than the same advertisement call alone. When the same appendages led advertisement calls, however, the compound signal was never more attractive and sometimes less attractive. The order effect was especially strong in tests of H. versicolor in which advertisement-call duration was decreased. These results cannot be explained by a general pre-existing bias for extra stimulation per se. Rather, order and other effects may constrain the evolution and subsequent modification of complex and extravagant signals, examples of which have been reported for a wide range of taxa.
| S-EPMC2173945 | biostudies-literature
Project description:Synaptic connectivity between neocortical neurons is highly structured. The network structure of synaptic connectivity includes first-order properties that can be described by pairwise statistics, such as strengths of connections between different neuron types and distance-dependent connectivity, and higher order properties, such as an abundance of cliques of all-to-all connected neurons. The relative impact of first- and higher order structure on emergent cortical network activity is unknown. Here, we compare network structure and emergent activity in two neocortical microcircuit models with different synaptic connectivity. Both models have a similar first-order structure, but only one model includes higher order structure arising from morphological diversity within neuronal types. We find that such morphological diversity leads to more heterogeneous degree distributions, increases the number of cliques, and contributes to a small-world topology. The increase in higher order network structure is accompanied by more nuanced changes in neuronal firing patterns, such as an increased dependence of pairwise correlations on the positions of neurons in cliques. Our study shows that circuit models with very similar first-order structure of synaptic connectivity can have a drastically different higher order network structure, and suggests that the higher order structure imposed by morphological diversity within neuronal types has an impact on emergent cortical activity.
| S-EPMC7069066 | biostudies-literature
Project description:Synaptic strength depresses for low and potentiates for high activation of the postsynaptic neuron. This feature is a key property of the Bienenstock-Cooper-Munro (BCM) synaptic learning rule, which has been shown to maximize the selectivity of the postsynaptic neuron, and thereby offers a possible explanation for experience-dependent cortical plasticity such as orientation selectivity. However, the BCM framework is rate-based and a significant amount of recent work has shown that synaptic plasticity also depends on the precise timing of presynaptic and postsynaptic spikes. Here we consider a triplet model of spike-timing-dependent plasticity (STDP) that depends on the interactions of three precisely timed spikes. Triplet STDP has been shown to describe plasticity experiments that the classical STDP rule, based on pairs of spikes, has failed to capture. In the case of rate-based patterns, we show a tight correspondence between the triplet STDP rule and the BCM rule. We analytically demonstrate the selectivity property of the triplet STDP rule for orthogonal inputs and perform numerical simulations for nonorthogonal inputs. Moreover, in contrast to BCM, we show that triplet STDP can also induce selectivity for input patterns consisting of higher-order spatiotemporal correlations, which exist in natural stimuli and have been measured in the brain. We show that this sensitivity to higher-order correlations can be used to develop direction and speed selectivity.
| S-EPMC3228426 | biostudies-literature