Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc

Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves

DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas)

<p>Abstract</p> <p>Background</p> <p>DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (<it>Crassostrea gigas</it>).</p> <p>Results</p> <p>Methylation sensitive PCR and bisulfite sequencing PCR approaches were used to identify CpG methylation in <it>C. gigas </it>genes and demonstrated that this species possesses intragenic methylation. <it>In silico </it>analysis of CpGo/e ratios in publicly available sequence data suggests that DNA methylation is a common feature of the <it>C. gigas </it>genome, and that specific functional categories of genes have significantly different levels of methylation.</p> <p>Conclusions</p> <p>The Pacific oyster genome displays intragenic DNA methylation and contains genes necessary for DNA methylation in animals. Results of this investigation suggest that DNA methylation has regulatory functions in <it>Crassostrea gigas</it>, particularly in gene families that have inducible expression, including those involved in stress and environmental responses.</p

Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates?

There is a significant amount of variation in DNA methylation characteristics across organisms. Likewise, the biological role of DNA methylation varies across taxonomic lineages. The complexity of DNA methylation patterns in invertebrates has only recently begun to be characterized in-depth. In some invertebrate species that have been examined to date, methylated DNA is found primarily within coding regions and patterning is closely associated with gene function. Here we provide a perspective on the potential role of DNA methylation in these invertebrates with a focus on how limited methylation may contribute to increased phenotypic plasticity in highly fluctuating environments. Specifically, limited methylation could facilitate a variety of transcriptional opportunities including access to alternative transcription start sites, increasing sequence mutations, exon skipping, and transient methylation

Characterization of EST derived SSRs from the bay scallop, Argopecten irradians

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Blackwell Publishing for personal use, not for redistribution. The definitive version was published in Molecular Ecology Notes 5 (2005): 567-568, doi:10.1111/j.1471-8286.2005.00996.x.Interest in bay scallop conservation has resulted in organized stock enhancement efforts and increased attention to fisheries management issues. Genetic markers can facilitate the monitoring of enhancement efforts, characterization of wild populations, and optimize hatchery practices. We have identified eight polymorphic simple sequence repeat markers including one dinucleotide, six trinucleotide and one compound dinucleotide repeats, in expressed sequence tags generated from multiple bay scallop cDNA libraries. The numbers of alleles range from two to five. The expected and observed heterozygosities range from 0.093 to 0.720 and 0.095 to 0.600, respectively.This project was supported by National Research Initiative Competitive Grant no. 2003-35206-12834 from the USDA Cooperative State Research, Education, and Extension Service and by a grant from the County of Barnstable Massachusetts, USA (both to SBR)

Development and validation of a real-time quantitative PCR assay for the detection and quantification of Perkinsus marinus in the Eastern oyster, Crassostrea virginica

Author Posting. © National Shellfisheries Association, 2009. This article is posted here by permission of National Shellfisheries Association for personal use, not for redistribution. The definitive version was published in Journal of Shellfish Research 28 (2009): 459-464, doi:10.2983/035.028.0306.Perkinus marinus causes a devastating disease, known as Dermo, in the Eastern oyster Crassostrea virginica. Routine detection of the disease is traditionally accomplished by the use of the Ray/Makin assay, using Fluid Thioglycollate Medium (RFTM). A simple real-time quantitative PCR assay was developed as a diagnostic tool to detect and quantify P. marinus, to complement and serve as an alternate to the RFTM method. Using a dual-labeled probe approach, a sensitive assay was designed to accurately detect a range of one to several thousand P. marinus organisms present in oyster tissues. A simple extraction method was used to increase throughput of the assay. Cultured P. marinus cells were quantified prior to DNA extraction, generating a standard curve and allowing cell counts to be derived from PCR cycle threshold values. Direct comparison of the RFTM and real-time PCR methods was accomplished by using tissue samples from the same oyster for both tests. Plotting cycle threshold values against the known Mackin index value generated a standard curve with a coefficient of regression of 0.9. Our results indicate that correlations could be made between this molecular based approach and traditional methods, allowing results generated from the PCR assay to be easily translated into the understood Mackin scale

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

Searching for physics beyond the Standard Model through the dipole interaction

The magnetic dipole interaction played a central role in the development of QED, and continued in that role for the Standard Model. The muon anomalous magnetic moment has served as a benchmark for models of new physics, and the present experimental value is larger than the standard-model value by more than three standard deviations. The electric dipole moment (EDM) violates parity ({$P$}) and time-reversal ({$T$}) symmetries, and in the context of the $CPT$ theorem, the combination of charge conjugation and parity ($CP$). Since a new source of {$CP$} violation outside of that observed in the $K$ and $B$ meson systems is needed to help explain the baryon asymmetry of the universe, searches for EDMs are being carried out worldwide on a number of systems. The standard-model value of the EDM is immeasurably small, so any evidence for an EDM would signify the observation of new physics. Unique opportunities exist for EDM searches using polarized proton, deuteron or muon beams in storage rings. This talk will provide an overview of the theory of dipole moments, and the relevant experiments. The connection to the transition dipole moment that could produce lepton flavor violating interactions such as $\mu^+ \rightarrow e^+ \gamma$ is also mentioned.Comment: Invited Plenary talk at the 19th International Spin Physics Symposium, Juelic

Metabolic recovery and compensatory shell growth of juvenile Pacific geoduck \u3cem\u3ePanopea generosa\u3c/em\u3e following short-term exposure to acidified seawater

While acute stressors can be detrimental, environmental stress conditioning can improve performance. To test the hypothesis that physiological status is altered by stress conditioning, we subjected juvenile Pacific geoduck, Panopea generosa, to repeated exposures of elevated pCO2 in a commercial hatchery setting followed by a period in ambient common garden. Respiration rate and shell length were measured for juvenile geoduck periodically throughout short-term repeated reciprocal exposure periods in ambient (~550 μatm) or elevated (~2400 μatm) pCO2 treatments and in common, ambient conditions, 5 months after exposure. Short-term exposure periods comprised an initial 10-day exposure followed by 14 days in ambient before a secondary 6-day reciprocal exposure. The initial exposure to elevated pCO2 significantly reduced respiration rate by 25% relative to ambient conditions, but no effect on shell growth was detected. Following 14 days in common garden, ambient conditions, reciprocal exposure to elevated or ambient pCO2 did not alter juvenile respiration rates, indicating ability for metabolic recovery under subsequent conditions. Shell growth was negatively affected during the reciprocal treatment in both exposure histories; however, clams exposed to the initial elevated pCO2 showed compensatory growth with 5.8% greater shell length (on average between the two secondary exposures) after 5 months in ambient conditions. Additionally, clams exposed to the secondary elevated pCO2 showed 52.4% increase in respiration rate after 5 months in ambient conditions. Early exposure to low pH appears to trigger carryover effects suggesting bioenergetic re-allocation facilitates growth compensation. Life stage-specific exposures to stress can determine when it may be especially detrimental, or advantageous, to apply stress conditioning for commercial production of this long-lived burrowing clam

Effect of body composition methodology on heritability estimation of body fatness

Heritability estimates of human body fatness vary widely and the contribution of body composition methodology to this variability is unknown. The effect of body composition methodology on estimations of genetic and environmental contributions to body fatness variation was examined in 78 adult male and female monozygotic twin pairs reared apart or together. Body composition was assessed by six methods - body mass index (BMI), dual energy x-ray absorptiometry (DXA), underwater weighing (UWW), total body water (TBW), bioelectric impedance (BIA), and skinfold thickness. Body fatness was expressed as percent body fat, fat mass, and fat mass/height2 to assess the effect of body fatness expression on heritability estimates. Model-fitting multivariate analyses were used to assess the genetic and environmental components of variance. Mean BMI was 24.5 kg/m2 (range of 17.8-43.4 kg/m2). There was a significant effect of body composition methodology (p<0.001) on heritability estimates, with UWW giving the highest estimate (69%) and BIA giving the lowest estimate (47%) for fat mass/height2. Expression of body fatness as percent body fat resulted in significantly higher heritability estimates (on average 10.3% higher) compared to expression as fat mass/height2 (p=0.015). DXA and TBW methods expressing body fatness as fat mass/height2 gave the least biased heritability assessments, based on the small contribution of specific genetic factors to their genetic variance. A model combining DXA and TBW methods resulted in a relatively low FM/ht2 heritability estimate of 60%, and significant contributions of common and unique environmental factors (22% and 18%, respectively). The body fatness heritability estimate of 60% indicates a smaller contribution of genetic variance to total variance than many previous studies using less powerful research designs have indicated. The results also highlight the importance of environmental factors and possibly genotype by environmental interactions in the etiology of weight gain and the obesity epidemic.R01 AR046124 - NIAMS NIH HHS; R01 MH065322 - NIMH NIH HHS; T32 HL069772 - NHLBI NIH HHS; R21 DK078867 - NIDDK NIH HHS; R37 DA018673 - NIDA NIH HHS; R01 DK076092 - NIDDK NIH HHS; R01 DK079003 - NIDDK NIH HHS; F32 DK009747 - NIDDK NIH HHS; R01 DA018673 - NIDA NIH HH

Design of Electromagnetic Cloaks and Concentrators Using Form-Invariant Coordinate Transformations of Maxwell's Equations

The technique of applying form-invariant, spatial coordinate transformations of Maxwell's equations can facilitate the design of structures with unique electromagnetic or optical functionality. Here, we illustrate the transformation-optical approach in the designs of a square electromagnetic cloak and an omni-directional electromagnetic field concentrator. The transformation equations are described and the functionality of the devices is numerically confirmed by two-dimensional finite element simulations. The two devices presented demonstrate that the transformation optic approach leads to the specification of complex, anisotropic and inhomogeneous materials with well directed and distinct electromagnetic behavior.Comment: submitted to "Photonics and Nanostructures", Special Issue "PECS VII", Elsevie