Biology subjects

Strand, E.

Publications and source records attributed to Strand, E..

10 recordsLinked to original sources

bioRxiv2025

Building an epigenetic clock: Utilizing whole genome DNA methylation patterns to predict age in haddock, Melanogrammus aeglefinus

Age-based population models are a gold standard approach to estimate stock size and sustainable catch recommendations for effective fisheries management. Traditional ageing by counting annuli on their ear stones (otoliths), is labor-intensive, lethal, and can be inaccurate for long-lived fishes. In this study, we present an accurate, non-lethal epigenetic clock method for predicting age in haddock, Melanogrammus aeglefinus, one of the most valuable commercial fisheries in the north Atlantic Ocean. Pectoral fin tissue (n=140 individuals) was collected during Fall 2022 and Spring 2023 bottom trawl surveys in the Georges Bank-Gulf of Maine region, and whole-genome bisulfite sequencing was conducted to measure CpG loci DNA methylation levels. The most age-predictive loci were identified using a three-step modeling approach: a Bayesian generalized linear mixed model with length and sex as random factors followed by machine learning models with a 70/30 train-test split. The final model used 111 loci to predict age within 1-year at 93% accuracy. Hypo- and hyper-methylated age-related loci were found throughout the genome and were enriched in intragenic regions with functions related to immunity, transcriptional regulation, and signal transduction. This study provides an accurate, cost-effective, and scalable epigenetic tool for fisheries management to predict the age of haddock.

genomics↗

bioRxiv2025

NucleoBench: A Large-Scale Benchmark of Neural Nucleic Acid DesignAlgorithms

We introduce GrAdaBeam, a hybrid model-based optimization algorithm that combines gradient-derived attention maps with an adaptive beam search to navigate complex nucleic acid fitness landscapes. By unifying the broad exploration of evolutionary methods with the precise guidance of gradient descent, GrAdaBeam overcomes a central limitation of existing approaches: no single optimization strategy performs robustly across the full spectrum of genomic design tasks. We rigorously evaluate GrAdaBeam and seven other design algorithms using NucleoBench, a novel benchmark covering 17 diverse genomic tasks that introduces a paired-start-sequence design for superior statistical comparisons. GrAdaBeam statistically outperforms all other algorithms across over 600,000 experiments, never ranking lower than second across all 17 benchmark tasks, while baseline methods often struggle on large models or long sequences. Critically, GrAdaBeam sequences generalize most reliably to independent predictive models and recover canonical transcription factor binding motifs de novo, providing evidence of biological signal capture beyond the optimization target. GrAdaBeam and NucleoBench are freely available as an open-source package.

genomics↗

bioRxiv2025

Genetics in the ocean's twilight zone: Population structure of the Mueller's pearlside across its distribution range

The large estimates of mesopelagic fish biomass have fuelled harvesting interests in the relatively untouched oceans twilight zone. The Muellers pearlside, one of the most abundant species inhabiting the north Atlantic mesopelagic layer, is a candidate to such fisheries despite its enormous ecological importance and the insufficient knowledge about its population genetic structure. To shed light on the latter, 863 individuals sampled across the North Atlantic and Mediterranean were genotyped using 170 genome-wide SNPs. Analyses revealed habitat-driven differentiation in three units: Mediterranean Sea, oceanic samples, and Norwegian fjords. These groups were not completely isolated to each other as a cline of Mediterranean admixture was detected in the Eastern Atlantic facade up to 47{degrees}N in an otherwise genetically homogeneous oceanic cluster. Temperature seemed to modulate the differentiation patterns, and in the Mediterranean added to the complicated topography of the Greek Seas to shape genetic structure. In the Norwegian coastline, sills did not hamper genetic exchange among fjords ranging 200 km apart, probably due to the position of the species in the water column together with its swimming capacity. This genetic information should be combined with demographic properties to outline the management of this species prior to any eventual fishery attempt.

genetics↗

bioRxiv2024

Coral larvae employ nitrogen sequestration mechanisms to stabilize carbon provisioning from algal symbionts under increased temperature

Rising sea surface temperatures are increasingly causing breakdown in the nutritional relationship between corals and algal endosymbionts (Symbiodiniaceae), threatening the basis of coral reef ecosystems and highlighting the critical role of coral reproduction in reef maintenance. The effects of thermal stress on metabolic exchange (i.e., transfer of fixed carbon photosynthates from symbiont to host) during sensitive early life stages, however, remains understudied. We exposed symbiotic Montipora capitata coral larvae in Hawaii to high temperature (+2.5{degrees}C for 3 days), assessed rates of photosynthesis and respiration, and used stable isotope tracing (4mM 13C sodium bicarbonate; 4.5 h) to quantify metabolite exchange. While larvae did not show any signs of bleaching and did not experience declines in survival and settlement, metabolic depression was significant under high temperature, indicated by a 19% reduction in respiration rates, but with no change in photosynthesis. Larvae exposed to high temperature showed evidence for maintained translocation of a major photosynthate, glucose, from the symbiont, but there was reduced metabolism of glucose through central carbon metabolism (i.e., glycolysis). The larval host invested in nitrogen cycling by increasing ammonium assimilation, urea metabolism, and sequestration of nitrogen into dipeptides, a mechanism that may support the maintenance of glucose translocation under thermal stress. Host nitrogen assimilation via dipeptide synthesis appears to be used for nitrogen limitation to the Symbiodiniaceae, with the outcome of reduced symbiont population growth and retention of fixed carbon, effectively simulating photosynthate translocation to the host. Collectively, our findings indicate that although these larvae are susceptible to metabolic stress under high temperature, they can combat bleaching by diverting energy to nitrogen assimilation to maintain symbiont population density, photosynthesis, and carbon translocation.

cell biology↗

bioRxiv2024

DNA methylation modulates transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)

Ocean acidification significantly affects marine calcifiers like oysters, warranting the study of molecular mechanisms like DNA methylation that contribute to adaptive plasticity in response to environmental change. However, a consensus has not been reached on the extent to which methylation modules gene expression, and in turn plasticity, in marine invertebrates. In this study, we investigated the impact of pCO2 on gene expression and DNA methylation in the eastern oyster, Crassostrea virginica. After a 30-day exposure to control (572 ppm) or elevated pCO2 (2,827 ppm), whole genome bisulfite sequencing (WGBS) and RNA-Seq data were generated from adult female gonad tissue and male sperm samples. Although differentially methylated loci (DML) were identified in females (89) and males (2,916), there were no differentially expressed genes, and only one differentially expressed transcript in females. However, gene body methylation impacted other forms of gene activity in sperm, such as the maximum number of transcripts expressed per gene and changes in the predominant transcript expressed. Elevated pCO2 exposure increased gene expression variability (transcriptional noise) in males but decreased noise in females, suggesting a sex-specific role of methylation in gene expression regulation. Functional annotation of genes with changes in transcript-level expression or containing DML revealed several enriched biological processes potentially involved in elevated pCO2 response, including apoptotic pathways and signal transduction, as well as reproductive functions. Taken together, these results suggest that DNA methylation may regulate gene expression variability to maintain homeostasis in elevated pCO2 conditions and could play a key role in environmental resilience in marine invertebrates.

physiology↗

bioRxiv2023

Coral species-specific loss and physiological legacy effects are elicited by extended marine heatwave

Marine heatwaves are increasing in frequency and intensity, with potentially catastrophic consequences for marine ecosystems such as coral reefs. An extended heatwave and recovery time-series that incorporates multiple stressors and is environmentally realistic can provide enhanced predictive capacity for performance under climate change conditions. We exposed common reef-building corals in Hawai i, Montipora capitata and Pocillopora acuta, to a 2-month period of high temperature and high pCO2 conditions or ambient conditions in a factorial design, followed by 2 months of ambient conditions. High temperature, rather than high pCO2, drove multivariate physiology shifts through time in both species, including decreases in respiration rates and endosymbiont densities. Pocillopora acuta exhibited more significantly negatively altered physiology, and substantially higher bleaching and mortality than M. capitata. The sensitivity of P. acuta appears to be driven by higher baseline rates of photosynthesis paired with lower host antioxidant capacity, creating an increased sensitivity to oxidative stress. Thermal tolerance of M. capitata may be partly due to harboring a mixture of Cladocopium and Durusdinium spp., whereas P. acuta was dominated by other distinct Cladocopium spp. Only M. capitata survived the experiment, but physiological state in heatwave exposed M. capitata remained significantly diverged at the end of recovery relative to individuals that experienced ambient conditions. In future climate scenarios, particularly marine heatwaves, our results indicate a species-specific loss of corals that is driven by baseline host and symbiont physiological differences as well as Symbiodiniaceae community compositions, with the surviving species experiencing physiological legacies that are likely to influence future stress responses.

physiology↗

bioRxiv2023

Multi-omic analysis of coral development elucidates the metabolic transitions from parental provisioning to endosymbiotic nutritional exchange

Climate change accelerates coral reef decline and jeopardizes recruitment essential for ecosystem recovery. Adult corals rely on a vital nutritional exchange with their symbiotic algae (Symbiodiniaceae), but the dynamics and sensitivity of this reliance from fertilization to recruitment are understudied. We investigated the physiological, metabolomic, and transcriptomic changes across 13 developmental stages of Montipora capitata, a coral in Hawai i that inherits symbionts from parent to egg. We found that embryonic development depends on maternally provisioned mRNAs and lipids, with a rapid shift to symbiont-derived nutrition in swimming larvae. Symbiont density and photosynthesis peak once swimming to fuel pelagic larval dispersal. In contrast, respiratory demand increases significantly during metamorphosis, settlement, and calcification, reflecting this energy-intensive morphological reorganization. Symbiont ontogenetic proliferation is driven by symbiont ammonium assimilation with little evidence of nitrogen metabolism in the coral host. As development progresses, the host enhances nitrogen sequestration, regulating symbiont populations, and ensuring the transfer of fixed carbon to support metamorphosis, with both metabolomic and transcriptomic indicators of increased carbohydrate availability. Although algal symbiont communities remained stable, bacterial communities shifted with ontogeny, associated with holobiont metabolic reorganization. Our study reveals extensive metabolic changes during development, increasingly reliant on symbiont nutrition. Metamorphosis and settlement emerge as the most critical periods of energetic vulnerability to projected climate scenarios that destabilize symbiosis. This highly detailed elucidation of symbiotic nutritional exchange relative to sensitive early life stages provides essential knowledge for understanding and forecasting nutritional symbiosis integration, and specifically, coral survival and recruitment in a future of climate change.

physiology↗

bioRxiv2022

Long-read RNA Sequencing Improves the Annotation of the Equine Transcriptome

1A high-quality reference genome assembly, a biobank of diverse equine tissues from the Functional Annotation of the Animal Genome (FAANG) initiative, and incorporation of long-read sequencing technologies, have enabled efforts to build a comprehensive and tissue-specific equine transcriptome. The equine FAANG transcriptome reported here provides up to 45% improvement in transcriptome completeness across tissue types when compared to either RefSeq or Ensembl transcriptomes. This transcriptome also provides major improvements in the identification of alternatively spliced isoforms, novel noncoding genes, and 3 transcription termination site (TTS) annotations. The equine FAANG transcriptome will empower future functional studies of important equine traits while providing future opportunities to identify allele-specific expression and differentially expressed genes across tissues.

genomics↗

bioRxiv2021

Developmental series of gene expression clarifies maternal mRNA provisioning and maternal-to-zygotic transition in the reef-building coral Montipora capitata

BackgroundMaternal mRNA provisioning of oocytes regulates early embryogenesis. Maternal transcripts are degraded as zygotic genome activation (ZGA) intensifies, a phenomenon known as the maternal-to-zygotic transition (MZT). Here, we examine gene expression over nine developmental stages in the Pacific rice coral, Montipora capitata, from eggs and embryos at 1, 4, 9, 14, 22, and 36 hours-post-fertilization (hpf), as well as swimming larvae (9d), and adult colonies. ResultsWeighted Gene Coexpression Network Analysis revealed four expression peaks, identifying the maternal complement, two waves of the MZT, and adult expression. Gene ontology enrichment revealed maternal mRNAs are dominated by cell division, methylation, biosynthesis, metabolism, and protein/RNA processing and transport functions. The first MZT wave occurs from [~]4-14 hpf and is enriched in terms related to biosynthesis, methylation, cell division, and transcription. In contrast, functional enrichment in the second MZT wave, or ZGA, from 22 hpf-9dpf, includes ion/peptide transport and cell signaling. Finally, adult expression is enriched for functions related to signaling, metabolism, and ion/peptide transport. Our proposed MZT timing is further supported by expression of enzymes involved in zygotic transcriptional repression (Kaiso) and activation (Sox2), which peak at 14 hpf and 22 hpf, respectively. Further, DNA methylation writing (DNMT3a) and removing enzymes (TET1) peak and remain stable past [~]4 hpf, indicating that methylome programming occurs before 4 hpf. ConclusionsOur high-resolution insight into the coral maternal mRNA and MZT provides essential information regarding setting the stage for, and the sensitivity of, developmental success and parental carryover effects under increasing environmental stress.

developmental biology↗

bioRxiv2020

A genome-wide scan for candidate lethal variants in Thoroughbred horses.

Recessive lethal variants often segregate at low frequencies in animal populations, such that two randomly selected individuals are unlikely to carry the same mutation. However, the likelihood of an individual inheriting two copies of a recessive lethal mutation is dramatically increased by inbreeding events. Such occurrences are particularly common in domestic animal populations, which are often characterised by high rates of inbreeding and low effective population sizes. To date there have been no published investigations into the presence of specific variants at high frequencies in domestic horse populations. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we scanned genotype data from Thoroughbred horses (n = 526) for adjacent single nucleotide polymorphisms (SNPs) at high heterozygote frequencies, but with a complete absence of homozygotes. Two SNPs that matched these criteria were mapped to an intronic region in the LY49B gene, indicating that a closely linked mutation may cause lethality in homozygous state. Despite a complete absence of homozygotes, almost 35% of Thoroughbreds included in these analyses were heterozygous for both SNPs. A similar loss or absence of homozygotes was observed in genotype data from other domestic horse breeds (n = 2030). Variant analysis of whole-genome sequence data (n = 90) identified two SNPs in the 3UTR region of the LY49B gene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed that LY49B is expressed in the trophoblast during placentation stage of development. In this study, a region in the LY49B gene was identified as a strong candidate for harbouring a variant causing lethality in homozygous state. These findings suggest that LY49B may have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations. Author SummaryRecessive lethal mutations may reach high frequencies in livestock populations due to selective breeding practices, resulting in reduced fertility rates. In this study, we characterise recessive lethal mutations at high frequencies in the Thoroughbred horse population, a breed with high rates of inbreeding and low genetic diversity. We identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Two 3UTR variants were identified as most likely to cause loss of function in the LY49B gene, resulting in lethality. This finding provides novel insights into the potential importance of LY49B in equine development. Additionally, this study may assist with breeding strategies to improve fertility rates in the Thoroughbred and other domestic horse breeds.

bioinformatics↗