Correction: Proteomics of intracellular freezing survival.

[This corrects the article DOI: 10.1371/journal.pone.

Proteomics of intracellular freezing survival.

Panagrolaimus sp. DAW1, a nematode cultured from the Antarctic, has the extraordinary physiological ability to survive total intracellular freezing throughout all of its compartments. While a few other organisms, all nematodes, have subsequently also been found to survive freezing in this manner, P.

Estradiol and genistein effects on the sea bass () scales: Transcriptome dataset.

Fish scales are mineralized structures that play important roles in protection and mineral homeostasis. This tissue expresses multiple estrogen receptor subtypes and can be targeted by estrogens or estrogenic endocrine-disrupting compounds, but their effects are poorly explored. The transcriptome data here presented support the findings reported in the research article "" [1].

Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes.

Most animal species reproduce sexually and fully parthenogenetic lineages are usually short lived in evolution. Still, parthenogenesis may be advantageous as it avoids the cost of sex and permits colonization by single individuals. Panagrolaimid nematodes have colonized environments ranging from arid deserts to Arctic and Antarctic biomes.

Genistein and estradiol have common and specific impacts on the sea bass (Dicentrarchus labrax) skin-scale barrier.

Teleost fish scales play important roles in animal protection and homeostasis. They can be targeted by endogenous estrogens and by environmental estrogenic endocrine disruptors. The phytoestrogen genistein is ubiquitous in the environment and in aquaculture feeds and is a disruptor of estrogenic processes in vertebrates.

Molecular mechanisms underpinning transgenerational plasticity in the green sea urchin Psammechinus miliaris.

The pre-conditioning of adult marine invertebrates to altered conditions, such as low pH, can significantly impact offspring outcomes, a process which is often referred to as transgenerational plasticity (TGP). This study describes for the first time, the gene expression profiles associated with TGP in the green sea urchin Psammechinus miliaris and evaluates the transcriptional contribution to larval resilience. RNA-Seq was used to determine how the expression profiles of larvae spawned into low pH from pre-acclimated adults differed to those of larvae produced from adults cultured under ambient pH.

Investigating trehalose synthesis genes after cold acclimation in the Antarctic nematode sp. DAW1.

sp. DAW1 is a freeze-tolerant Antarctic nematode which survives extensive intracellular ice formation. The molecular mechanisms of this extreme adaptation are still poorly understood.

Beyond connectedness: why pairwise metrics cannot capture community stability.

The connectedness of species in a trophic web has long been a key structural characteristic for both theoreticians and empiricists in their understanding of community stability. In the past decades, there has been a shift from focussing on determining the number of interactions to taking into account their relative strengths. The question is: How do the strengths of the interactions determine the stability of a community? Recently, a metric has been proposed which compares the stability of observed communities in terms of the strength of three- and two-link feedback loops (cycles of interaction strengths).

Molecular snapshot of an intracellular freezing event in an Antarctic nematode.

The Antarctic nematode, Panagrolaimus sp. DAW1 (formerly called Panagrolaimus davidi), is the best documented example of an organism able to survive intracellular ice formation in all of its compartments. Not only is it able to survive such extreme physiological disruption, but it is able to produce progeny once thawed from such a state.

Establishing RNAi in a Non-Model Organism: The Antarctic Nematode Panagrolaimus sp. DAW1.

The Antarctic nematode Panagrolaimus sp. DAW1 is one of the only organisms known to survive extensive intracellular freezing throughout its tissues. Although the physiological mechanisms of this extreme adaptation are partly understood, the molecular mechanisms remain largely unknown.

Extremophiles in an Antarctic Marine Ecosystem.

Recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. However, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. In addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique.

Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.

Background: Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context.

Biodiversity in marine invertebrate responses to acute warming revealed by a comparative multi-omics approach.

Understanding species' responses to environmental change underpins our abilities to make predictions on future biodiversity under any range of scenarios. In spite of the huge biodiversity in most ecosystems, a model species approach is often taken in environmental studies. To date, we still do not know how many species we need to study to input into models and inform on ecosystem-level responses to change.

Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomics.

Background: The capacity of marine species to survive chronic heat stress underpins their ability to survive warming oceans as a result of climate change. In this study RNA-Seq and 2-DE proteomics were employed to decipher the molecular response of the sub-tidal bivalve Pecten maximus, to elevated temperatures.

Results: Individuals were maintained at three different temperatures (15, 21 and 25 °C) for 56 days, representing control conditions, maximum environmental temperature and extreme warming, with individuals sampled at seven time points.

Variability among individuals is generated at the gene expression level.

Selection acts on individuals, specifically on their differences. To understand adaptation and responses to change therefore requires knowledge of how variation is generated and distributed across traits. Variation occurs on different biological scales, from genetic through physiological to morphological, yet it is unclear which of these carries the most variability.

Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana.

The Brazilian oyster Crassostrea brasiliana was challenged to three common environmental contaminants: phenanthrene, diesel fuel water-accommodated fraction (WAF) and domestic sewage. Total RNA was extracted from the gill and digestive gland, and cDNA libraries were sequenced using the 454 FLX platform. The assembled transcriptome resulted in ̃20,000 contigs, which were annotated to produce the first de novo transcriptome for C.

Transcriptome of the Antarctic brooding gastropod mollusc Margarella antarctica.

454 RNA-Seq transcriptome data were generated from foot tissue of the Antarctic brooding gastropod mollusc Margarella antarctica. A total of 6195 contigs were assembled de novo, providing a useful resource for researchers with an interest in Antarctic marine species, phylogenetics and mollusc biology, especially shell production.

Transcriptomic response to shell damage in the Antarctic clam, Laternula elliptica: time scales and spatial localisation.

Mollusc shell is built-up by secretion from the mantle and is the result of a controlled biological process termed biomineralisation. In general mollusc shells are well characterised however, the molecular mechanisms used by molluscs to produce shell remain largely unknown. One tractable method to study molecular biomineralisation mechanisms are shell damage-repair experiments, which stimulate calcification pathways.

Adult acclimation to combined temperature and pH stressors significantly enhances reproductive outcomes compared to short-term exposures.

This study examined the effects of long-term culture under altered conditions on the Antarctic sea urchin, Sterechinus neumayeri. Sterechinus neumayeri was cultured under the combined environmental stressors of lowered pH (-0.3 and -0.

Molecular analysis of the cold tolerant Antarctic nematode, Panagrolaimus davidi.

Isolated and established in culture from the Antarctic in 1988, the nematode Panagrolaimus davidi has proven to be an ideal model for the study of adaptation to the cold. Not only is it the best-documented example of an organism surviving intracellular freezing but it is also able to undergo cryoprotective dehydration. As part of an ongoing effort to develop a molecular understanding of this remarkable organism, we have assembled both a transcriptome and a set of genomic scaffolds.

Deep sequencing of the mantle transcriptome of the great scallop Pecten maximus.

RNA-Seq transcriptome data were generated from mantle tissue of the great scallop, Pecten maximus. The consensus data were produced from a time course series of animals subjected to a 56-day thermal challenge at 3 different temperatures. A total of 26,064 contigs were assembled de novo, providing a useful resource for both the aquaculture community and researchers with an interest in mollusc shell production.

Limpet feeding rate and the consistency of physiological response to temperature.

Thermal reaction norms are fundamental relationships for geographic comparisons of organism response to temperature. They are shaped by an organism's environmental history and provide insights into both the global patterns of thermal sensitivity and the physiological mechanisms underlying temperature response. In this study we conducted the first measure of the thermal reaction norm for feeding, comparing the radula rasping rate of two tropical and one polar limpet species.

Interaction strengths in balanced carbon cycles and the absence of a relation between ecosystem complexity and stability.

The strength of interactions is crucial to the stability of ecological networks. However, the patterns of interaction strengths in mathematical models of ecosystems have not yet been based upon independent observations of balanced material fluxes. Here we analyse two Antarctic ecosystems for which the interaction strengths are obtained: (1) directly, from independently measured material fluxes, (2) for the complete ecosystem and (3) with a close match between species and 'trophic groups'.

High-throughput sequencing reveals inbreeding depression in a natural population.

Proxy measures of genome-wide heterozygosity based on approximately 10 microsatellites have been used to uncover heterozygosity fitness correlations (HFCs) for a wealth of important fitness traits in natural populations. However, effect sizes are typically very small and the underlying mechanisms remain contentious, as a handful of markers usually provides little power to detect inbreeding. We therefore used restriction site associated DNA (RAD) sequencing to accurately estimate genome-wide heterozygosity, an approach transferrable to any organism.