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

The mechanical response of fire ant rafts

Fire ants (Solenopsis invicta) cohesively aggregate via the formation of voluntary ant-to-ant attachments when under confinement or exposed to water. Once formed, these aggregations act as viscoelastic solids due to dynamic bond exchange between neighboring ants as demonstrated by rate-dependent mechanical response of 3D aggregations, confined in rheometers. We here investigate the mechanical response of 2D, planar ant rafts roughly as they form in nature. Specifically, we load rafts under uniaxial tension to failure, as well as to 50% strain for two cycles with various recovery times between. We do so while measuring raft reaction force (to estimate network-scale stress), as well as the networks' instantaneous velocity fields and topological damage responses to elucidate the ant-scale origins of global mechanics. The rafts display brittle-like behavior even at slow strain rates (relative to the unloaded bond detachment rate) for which Transient Network Theory predicts steady-state creep. This provides evidence that loaded ant-to-ant bonds undergo mechanosensitive bond stabilization or act as \say{catch bonds}. This is further supported by the coalescence of voids that nucleate due to biaxial stress conditions and merge due to bond dissociation. The characteristic timescales of void coalescence due to chain dissociation provide evidence that the local detachment of stretched bonds is predominantly strain- (as opposed to bond lifetime-) dependent, even at slow strain rates, implying that bond detachment rates diminish significantly under stretch. Significantly, when the voids are closed by restoring the rafts to unstressed conditions, mechanical recovery occurs, confirming the presence of concentration-dependent bond association that - combined with force-diminished dissociation - could further bolster network cohesion under certain stress states

The Electronic Spectrum of Fullerenes from the Dirac Equation

The electronic spectrum of sheets of graphite (plane honeycomb lattice) folded into regular polihedra is studied. A continuum limit valid for sufficiently large molecules and based on a tight binding approximation is derived. It is found that a Dirac equation describes the flat graphite lattice. Curving the lattice by insertion of odd numbered rings can be mimicked by coupling effective gauge fields. In particular the $C_{60}$ and related molecules are well described by the Dirac equation on the surface of a sphere coupled to a color monopole sitting at its center.Comment: 29 pages, 7 figures. IASSNS-HEP-92/5

Tops and Writhing DNA

The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's "local writhe expression" which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations.Comment: 17 pages two figure

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient.

While it is well established that microbial composition and diversity shift along environmental gradients, how interactions among microbes change is poorly understood. Here, we tested how community structure and species interactions among diverse groups of soil microbes (bacteria, fungi, non-fungal eukaryotes) change across a fundamental ecological gradient, succession. Our study system is a high-elevation alpine ecosystem that exhibits variability in successional stage due to topography and harsh environmental conditions. We used hierarchical Bayesian joint distribution modeling to remove the influence of environmental covariates on species distributions and generated interaction networks using the residual species-to-species variance-covariance matrix. We hypothesized that as ecological succession proceeds, diversity will increase, species composition will change, and soil microbial networks will become more complex. As expected, we found that diversity of most taxonomic groups increased over succession, and species composition changed considerably. Interestingly, and contrary to our hypothesis, interaction networks became less complex over succession (fewer interactions per taxon). Interactions between photosynthetic microbes and any other organism became less frequent over the gradient, whereas interactions between plants or soil microfauna and any other organism were more abundant in late succession. Results demonstrate that patterns in diversity and composition do not necessarily relate to patterns in network complexity and suggest that network analyses provide new insight into the ecology of highly diverse, microscopic communities

Domestic Queensware in Kensington-Fishtown: Excavating Philadelphia\u27s Waterfront Neighborhoods

Ongoing archaeological excavation undertaken by URS/AECOM along the I-95 corridor in Kensington-Fishtown in Philadelphia have brought to light 18th and 19th century domestic and industrial life along a three-mile section of the Delaware River waterfront. Excavation has revealed over 400 shaft features, yard deposits, and industrial foundations yielding over one million artifacts from a three mile section of the Delaware River waterfront. A small quantity of domestic queensware has been recovered from barrel and wood-lined box privies and from an early 19th century drain feature. The recovery of domestic queensware in Kensington-Fishtown has revealed that this ware had become part of the domestic fabric of early 19th century consumers in this part of the city