Uncertainty and Cooperation: Analytical Results and a Simulated Agent Society

Uncertainty is an important factor that influences social evolution in natural and artificial environments. Here we distinguish between three aspects of uncertainty. Environmental uncertainty is the variance of resources in the environment, perceived uncertainty is the variance of the resource distribution as perceived by the organism and effective uncertainty is the variance of resources effectively enjoyed by individuals. We show analytically that perceived uncertainty is larger than environmental uncertainty and that effective uncertainty is smaller than perceived uncertainty, when cooperation is present. We use an agent society simulation in a two dimensional world for the generation of simulation data as one realisation of the analytical results. Together with our earlier theoretical work, results here show that cooperation can buffer the detrimental effects of uncertainty on the organism. The proposed conceptualisation of uncertainty can help in understanding its effects on social evolution and in designing artificial social environments.Agent-Based Modelling, Cooperation, Social Interaction Simulation, Uncertainty

Environmental Effects On Drosophila Brain Development And Learning

Brain development and behavior are sensitive to a variety of environmental influences including social interactions and physicochemical stressors. Sensory input in situ is a mosaic of both enrichment and stress, yet little is known about how multiple environmental factors interact to affect brain anatomical structures, circuits and cognitive function. In this study, we addressed these issues by testing the individual and combined effects of sub-adult thermal stress, larval density and early-adult living spatial enrichment on brain anatomy and olfactory associative learning in adult Drosophila melanogaster. In response to heat stress, the mushroom bodies (MBs) were the most volumetrically impaired among all of the brain structures, an effect highly correlated with reduced odor learning performance. However, MBs were not sensitive to either larval culture density or early-adult living conditions. Extreme larval crowding reduced the volume of the antennal lobes, optic lobes and central complex. Neither larval crowding nor early-adult spatial enrichment affected olfactory learning. These results illustrate that various brain structures react differently to environmental inputs, and that MB development and learning are highly sensitive to certain stressors (pre-adult hyperthermia) and resistant to others (larval crowding). © 2018. Published by The Company of Biologists Ltd

Wilson Line Picture of Levin-Wen Partition Functions

Levin and Wen [Phys. Rev. B 71, 045110 (2005)] have recently given a lattice Hamiltonian description of doubled Chern-Simons theories. We relate the partition function of these theories to an expectation of Wilson loops that form a link in 2+1 dimensional spacetime known in the mathematical literature as Chain-Mail. This geometric construction gives physical interpretation of the Levin-Wen Hilbert space and Hamiltonian, its topological invariance, exactness under coarse-graining, and how two opposite chirality sectors of the doubled theory arise.Comment: Final published version; Appendix adde

Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Venkataraman, Y. R., White, S. J., & Roberts, S. B. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics, 23(1), (2022): 556, https://doi.org/10.1186/s12864-022-08781-5.Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation.This work was funded by National Science Foundation award 1634167 to SBR. The Hall Conservation Genetics Research Fund (YRV) supported sequencing for this project

Occurrence and diversity of Xanthomonas campestris pv. campestris in vegetable brassica fields in Nepal

Black rot caused by Xanthomonas campestris pv. campestris was found in 28 sampled cabbage fields in five major cabbage-growing districts in Nepal in 2001 and in four cauliflower fields in two districts and a leaf mustard seed bed in 2003. Pathogenic X. campestris pv. campestris strains were obtained from 39 cabbage plants, 4 cauliflower plants, and 1 leaf mustard plant with typical lesions. Repetitive DNA polymerase chain reaction-based fingerprinting (rep-PCR) using repetitive extragenic palindromic, enterobacterial repetitive intergenic consensus, and BOX primers was used to assess the genetic diversity. Strains were also race typed using a differential series of Brassica spp. Cabbage strains belonged to five races (races 1, 4, 5, 6, and 7), with races 4, 1, and 6 the most common. All cauliflower strains were race 4 and the leaf mustard strain was race 6. A dendrogram derived from the combined rep-PCR profiles showed that the Nepalese X. campestris pv. campestris strains clustered separately from other Xanthomonas spp. and pathovars. Race 1 strains clustered together and strains of races 4, 5, and 6 were each split into at least two clusters. The presence of different races and the genetic variability of the pathogen should be considered when resistant cultivars are bred and introduced into regions in Nepal to control black rot of brassicas

The Effects of Age and Lifetime Flight Behavior on Flight Capacity in Drosophila Melanogaster

The Effects of Flight Behavior on Physiology and Senescence May Be Profound in Insects Because of the Extremely High Metabolic Costs of Flight. Flight Capacity in Insects Decreases with Age; in Contrast, Limiting Flight Behavior Extends Lifespan and Slows the Age-Related Loss of Antioxidant Capacity and Accumulation of Oxidative Damage in Flight Muscles. in This Study, We Tested the Effects of Age and Lifetime Flight Behavior on Flight Capacity by Measuring Wingbeat Frequency, the Ability to Fly in a Hypo-Dense Gas Mixture, and Metabolic Rate in Drosophila Melanogaster. Specifically, 5-Day-Old Adult Flies Were Separated into Three Life-Long Treatments: (1) Those Not Allowed to Fly (No Flight), (2) Those Allowed - But Not Forced - to Fly (Voluntary Flight) and (3) Those Mechanically Stimulated to Fly (Induced Flight). Flight Capacity Senesced Earliest in Flies from the No-Flight Treatment, Followed by the Induced-Flight Group and Then the Voluntary Flight Group. Wingbeat Frequency Senesced with Age in All Treatment Groups, But Was Most Apparent in the Voluntary- and Induced-Flight Groups. Metabolic Rate during Agitated Flight Senesced Earliest and Most Rapidly in the Induced Flight Group, and Was Low and Uniform throughout Age in the No-Flight Group. Early Senescence in the Induced-Flight Group Was Likely Due to the Acceleration of Deleterious Aging Phenomena Such as the Rapid Accumulation of Damage at the Cellular Level, While the Early Loss of Flight Capacity and Low Metabolic Rates in the No-Flight Group Demonstrate that Disuse Effects Can Also Significantly Alter Senescence Patterns of Whole-Insect Performance

Thermal Disruption of Mushroom Body Development and Odor Learning in Drosophila

Environmental stress (nutritive, chemical, electromagnetic and thermal) has been shown to disrupt central nervous system (CNS) development in every model system studied to date. However, empirical linkages between stress, specific targets in the brain, and consequences for behavior have rarely been established. The present study experimentally demonstrates one such linkage by examining the effects of ecologically-relevant thermal stress on development of the Drosophila melanogaster mushroom body (MB), a conserved sensory integration and associative center in the insect brain. We show that a daily hyperthermic episode throughout larval and pupal development (1) severely disrupts MB anatomy by reducing intrinsic Kenyon cell (KC) neuron numbers but has little effect on other brain structures or general anatomy, and (2) greatly impairs associative odor learning in adults, despite having little effect on memory or sensory acuity. Hence, heat stress of ecologically relevant duration and intensity can impair brain development and learning potential