Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica).

Ocean acidification (OA) is a major stressor threatening marine calcifiers, including the eastern oyster (Crassostrea virginica). In this paper, we provide insight into the molecular mechanisms associated with resilience to OA, with the dual intentions of probing both acclimation and adaptation potential in this species. C. virginica were spawned, and larvae were reared in control or acidified conditions immediately after fertilization. RNA samples were collected from larvae and juveniles, and DNA samples were collected from juveniles after undergoing OA-induced mortality and used to contrast gene expression (RNAseq) and SNP (ddRADseq) profiles from animals reared under both conditions. Results showed convergence of evidence from both approaches, particularly in genes involved in biomineralization that displayed significant changes in variant frequencies and gene expression levels among juveniles that survived acidification as compared to controls. Downregulated genes were related to immune processes, supporting previous studies demonstrating a reduction in immunity from exposure to OA. Acclimation to OA via regulation of gene expression might confer short-term resilience to immediate threats; however, the costs may not be sustainable, underscoring the importance of selection of resilient genotypes. Here, we identified SNPs associated with survival under OA conditions, suggesting that this commercially and ecologically important species might have the genetic variation needed for adaptation to future acidification. The identification of genetic features associated with OA resilience is a highly-needed step for the development of marker-assisted selection of oyster stocks for aquaculture and restoration activities.

Molecular Features Associated with Resilience to Ocean Acidification in the Northern Quahog, Mercenaria mercenaria.

The increasing concentration of CO2 in the atmosphere and resulting flux into the oceans will further exacerbate acidification already threatening coastal marine ecosystems. The subsequent alterations in carbonate chemistry can have deleterious impacts on many economically and ecologically important species including the northern quahog (Mercenaria mercenaria). The accelerated pace of these changes requires an understanding of how or if species and populations will be able to acclimate or adapt to such swift environmental alterations. Thus far, studies have primarily focused on the physiological effects of ocean acidification (OA) on M. mercenaria, including reductions in growth and survival. However, the molecular mechanisms of resilience to OA in this species remains unclear. Clam gametes were fertilized under normal pCO2 and reared under acidified (pH ~ 7.5, pCO2 ~ 1200 ppm) or control (pH ~ 7.9, pCO2 ~ 600 ppm) conditions before sampled at 2 days (larvae), 32 days (postsets), 5 and 10 months (juveniles) and submitted to RNA and DNA sequencing to evaluate alterations in gene expression and genetic variations. Results showed significant shift in gene expression profiles among clams reared in acidified conditions as compared to their respective controls. At 10 months of exposure, significant shifts in allele frequency of single nucleotide polymorphisms (SNPs) were identified. Both approaches highlighted genes coding for proteins related to shell formation, bicarbonate transport, cytoskeleton, immunity/stress, and metabolism, illustrating the role these pathways play in resilience to OA.

Criminality labelling influences reactions to others' pain.

Disparities in healthcare for underrepresented and stigmatized groups are well documented. Current understanding is that these inequalities arise, at least in part, from psychosocial factors such as stereotypes and in-group/out-group categorization. Pain management, perhaps because of the subjective nature of pain, is one area of research that has spearheaded these efforts. We investigated how observers react to the pain of individuals labelled as criminals. Face models expressing pain of different levels of intensity were portrayed as having committed a crime or not (control group). A sample of n = 327 college students were asked to estimate the intensity of the pain expressed by face models as well as their willingness to help them. Trait empathy was also measured. Data was analyzed using regression, mediation and moderation analyses. We show for the first time that observers were less willing to help individuals with a criminal history. Moreover, a moderation effect was observed whereby empathic participants were more willing to help control face models compared to less empathic participants. However, criminality history did not influence participant's pain estimation. We conclude that negative stereotypes associated with criminality can reduce willingness to help individuals in pain even when pain signals are accurately perceived.

Two parallel chromosome-level reference genomes to support restoration and aquaculture of European flat oyster Ostrea edulis.

This volume of Evolutionary Applications sees the publication of two genomes for the European native flat oyster Ostrea edulis, a species of significant evolutionary, ecological and commercial value. Each is a highly contiguous chromosome-level assembly from individuals of different genetic backgrounds, which have been benchmarked against one another. This situation has resulted from the serendipitous discovery that two independent research groups were both deep into the process of building, annotating and investigating separately produced assemblies. Due to constraints with funder requirements and the need to recognize early career researchers for their work, alongside the technical challenge of integrating assemblies from two very different genomes, there was limited capacity to merge the sequences into one publication at the stage of discovery. This issue is likely to become very common over the next few years until the technologies for working with multiple genomes at once, for example, graph genomes, become commonplace in nonmodel species. Consequently, both of our teams have decided to collaborate rather than compete, recognizing the benefit to copublishing two separate genome resources for the research community, each with distinct scientific investigations, and working collaboratively to benchmark the assemblies.

Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture.

The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species in the foreshore, obtaining a reference genome becomes essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio, Illumina, 10X linked, and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein-coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.

Chromosome-level reference genome for European flat oyster (Ostrea edulis L.).

The European flat oyster (Ostrea edulis L.) is a bivalve naturally distributed across Europe, which was an integral part of human diets for centuries, until anthropogenic activities and disease outbreaks severely reduced wild populations. Despite a growing interest in genetic applications to support population management and aquaculture, a reference genome for this species is lacking to date. Here, we report a chromosome-level assembly and annotation for the European Flat oyster genome, generated using Oxford Nanopore, Illumina, Dovetail OmniC™ proximity ligation and RNA sequencing. A contig assembly (N50: 2.38 Mb) was scaffolded into the expected karyotype of 10 pseudochromosomes. The final assembly is 935.13 Mb, with a scaffold-N50 of 95.56 Mb, with a predicted repeat landscape dominated by unclassified elements specific to O. edulis. The assembly was verified for accuracy and completeness using multiple approaches, including a novel linkage map built with ddRAD-Seq technology, comprising 4016 SNPs from four full-sib families (eight parents and 163 F1 offspring). Annotation of the genome integrating multitissue transcriptome data, comparative protein evidence and ab-initio gene prediction identified 35,699 protein-coding genes. Chromosome-level synteny was demonstrated against multiple high-quality bivalve genome assemblies, including an O. edulis genome generated independently for a French O. edulis individual. Comparative genomics was used to characterize gene family expansions during Ostrea evolution that potentially facilitated adaptation. This new reference genome for European flat oyster will enable high-resolution genomics in support of conservation and aquaculture initiatives, and improves our understanding of bivalve genome evolution.

Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks.

BACKGROUND: The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for resource restoration or aquaculture activities. Significant mortality events have been reported in the species throughout its native range as a result of diseases (microbial infections, leukemia) and acute environmental stress. In this context, the characterization of the hard clam genome can provide highly needed resources to enable basic (e.g., oncogenesis and cancer transmission, adaptation biology) and applied (clam stock enhancement, genomic selection) sciences. RESULTS: Using a combination of long and short-read sequencing technologies, a 1.86 Gb chromosome-level assembly of the clam genome was generated. The assembly was scaffolded into 19 chromosomes, with an N50 of 83 Mb. Genome annotation yielded 34,728 predicted protein-coding genes, markedly more than the few other members of the Venerida sequenced so far, with coding regions representing only 2% of the assembly. Indeed, more than half of the genome is composed of repeated elements, including transposable elements. Major chromosome rearrangements were detected between this assembly and another recent assembly derived from a genetically segregated clam stock. Comparative analysis of the clam genome allowed the identification of a marked diversification in immune-related proteins, particularly extensive tandem duplications and expansions in tumor necrosis factors (TNFs) and C1q domain-containing proteins, some of which were previously shown to play a role in clam interactions with infectious microbes. The study also generated a comparative repertoire highlighting the diversity and, in some instances, the specificity of LTR-retrotransposons elements, particularly Steamer elements in bivalves. CONCLUSIONS: The diversity of immune molecules in M. mercenaria may allow this species to cope with varying and complex microbial and environmental landscapes. The repertoire of transposable elements identified in this study, particularly Steamer elements, should be a prime target for the investigation of cancer cell development and transmission among bivalve mollusks.

Does the environmental history of mussels have an effect on the physiological response to additional stress under experimental conditions?

Expected effects on marine biota of the ongoing elevation of water temperature and high latitudes is of major concern when considering the reliability of coastal ecosystem production. To compare the capacity of coastal organisms to cope with a temperature increase depending on their environmental history, responses of adult blue mussels (Mytilus spp.) taken from two sites differentially exposed to chemical pollution were investigated during an experimental exposure to a thermal stress. Immune parameters were notably altered by extreme warming and transcriptional changes for a broad selection of genes were associated to the temperature increase following a two-step response pattern. Site-specific responses suggested an influence of environmental history and support the possibility of a genetic basis in the physiological response. However no meaningful difference was detected between the response of hybrids and M galloprovincialis. This study brings new information about the capacity of mussels to cope with the ongoing elevation of water temperature in these coastal ecosystems.

Measurement of individual differences in face-identity processing abilities in older adults.

BACKGROUND: Face-identity processing declines with age. Few studies have examined whether face-identity processing abilities can be measured independently from general cognitive abilities in older adults (OA). This question has practical implications for the assessment of face-identity processing abilities in OA and theoretical implications for the notion of face processing as a specific ability. The present study examined the specificity of face memory and face matching abilities in OA aged 50 + . METHODS: Performance of younger adults (YA) and OA was measured on face tasks: Cambridge Face Memory Task (CFMT), the Glasgow Face Matching Task (GFMT), holistic processing; and tasks of general cognition: fluid intelligence, selective attention, and mental rotation. Data were analyzed using multiple regression models encompassing (i) the CFMT/GFMT and measures of general cognition; and (ii) all face processing tasks. RESULTS: Across the two age groups, models encompassing all face tasks were significant and accounted for more variance in the data than models encompassing the CFMT/GFMT and measures of general cognition. General cognitive abilities accounted for 17% of variance for the GFMT (p < 0.01) and 3% for the CFMT (p > 0.05). DISCUSSION: Our results suggest that face memory can be measured independently from general cognition using the CFMT in OA. Implications for the notion of a general face processing factor across the adult lifespan are discussed.

Different measures of holistic face processing tap into distinct but partially overlapping mechanisms.

Holistic processing, which includes the integration of facial features and analysis of their relations to one another, is a hallmark of what makes faces 'special'. Various experimental paradigms purport to measure holistic processing but these have often produced inconsistent results. This has led researchers to question the nature and structure of the mechanism(s) underlying holistic processing. Using an individual differences approach, researchers have examined relations between various measures of holistic processing in an attempt to resolve these questions. In keeping with this, we examined relationships between four commonly used measures of holistic face processing in a large group of participants (N = 223): (1) The Face Inversion Effect, (2) the Part Whole Effect (PWE), (3) the Composite Face Effect, and (4) the Configural Featural Detection Task (CFDT). Several novel methodological and analytical elements were introduced, including the use of factor analysis and the inclusion of control conditions to confirm the face specificity of all of the effects measured. The four indexes of holistic processing derived from each measure loaded onto two factors, one encompassing the PWE and the CFDT, and one encompassing the CE. The 16 conditions tested across the four tasks loaded onto four factors, each factor corresponding to a different measure. These results, together with those of other studies, suggest that holistic processing is a multifaceted construct and that different measures tap into distinct but partially overlapping elements of it.

Identification of variants associated with hard clam, Mercenaria mercenaria, resistance to Quahog Parasite Unknown disease.

Severe losses in aquacultured and wild hard clam (Mercenaria mercenaria) stocks have been previously reported in the northeastern United States due to a protistan parasite called QPX (Quahog Parasite Unknown). Previous work demonstrated that clam resistance to QPX is under genetic control. This study identifies single nucleotide polymorphism (SNP) associated with clam survivorship from two geographically segregated populations, both deployed in an enzootic site. The analysis contrasted samples collected before and after undergoing QPX-related mortalities and relied on a robust draft clam genome assembly. ~200 genes displayed significant variant enrichment at each sampling point in both populations, including 18 genes shared between both populations. Markers from both populations were identified in genes related to apoptosis pathways, protein-protein interaction, receptors, and signaling. This research begins to identify genetic markers associated with clam resistance to QPX disease, leading the way for the development of resistant clam stocks through marker-assisted selection.

Perceptual Similarity Can Drive Age-Related Elevation of False Recognition.

Older adults consistently show elevated rates of false recognition of new items that are related to studied items. This finding has been largely attributed to a greater tendency for older adults to rely on conceptual gist during memory recognition tasks. However, perceptual factors may also be implicated considering that related items are not only conceptually but also perceptually similar. While some findings do suggest that age-related increases in false recognitions can be driven by perceptual factors, little is known about the nature and circumstances under which these factors operate. To address this gap, we measured basic visual ability as well as false recognition for four different image categories (upright faces, inverted faces, chairs, houses) in younger (n = 34) and older (n = 34) adults. Each image category represented different levels of variability in perceptual similarity and pre-experimental exposure. Perceptual similarity was objectively defined on the basis of the low-level properties of the images. We found evidence that perceptual similarity can contribute to elevated rates of false recognition in older adults. Our results also suggest that declines in basic visual abilities influence elevated false recognition in older adults for perceptually similar but not perceptually dissimilar items. We conclude that both perceptual and conceptual similarity can drive age-related differences in false recognition.

Age Differences in Face Processing: The Role of Perceptual Degradation and Holistic Processing.

OBJECTIVES: We simultaneously investigated the role of three hypotheses regarding age-related differences in face processing: perceptual degradation, impaired holistic processing, and an interaction between the two. METHODS: Young adults (YA) aged 20-33-year olds, middle-age adults (MA) aged 50-64-year olds, and older adults (OA) aged 65-82-year olds were tested on the context congruency paradigm, which allows measurement of face-specific holistic processing across the life span (Meinhardt-Injac, Persike & Meinhardt, 2014. Acta Psychologica, 151, 155-163). Perceptual degradation was examined by measuring performance with faces that were not filtered (FSF), with faces filtered to preserve low spatial frequencies (LSF), and with faces filtered to preserve high spatial frequencies (HSF). RESULTS: We found that reducing perceptual signal strength had a greater impact on MA and OA for HSF faces, but not LSF faces. Context congruency effects were significant and of comparable magnitude across ages for FSF, LSF, and HSF faces. By using watches as control objects, we show that these holistic effects reflect face-specific mechanisms in all age groups. DISCUSSION: Our results support the perceptual degradation hypothesis for faces containing only HSF and suggest that holistic processing is preserved in aging even under conditions of reduced signal strength.

Utility of the Hebb-Williams Maze Paradigm for Translational Research in Fragile X Syndrome: A Direct Comparison of Mice and Humans.

To generate meaningful information, translational research must employ paradigms that allow extrapolation from animal models to humans. However, few studies have evaluated translational paradigms on the basis of defined validation criteria. We outline three criteria for validating translational paradigms. We then evaluate the Hebb-Williams maze paradigm (Hebb and Williams, 1946; Rabinovitch and Rosvold, 1951) on the basis of these criteria using Fragile X syndrome (FXS) as model disease. We focused on this paradigm because it allows direct comparison of humans and animals on tasks that are behaviorally equivalent (criterion #1) and because it measures spatial information processing, a cognitive domain for which FXS individuals and mice show impairments as compared to controls (criterion #2). We directly compared the performance of affected humans and mice across different experimental conditions and measures of behavior to identify which conditions produce comparable patterns of results in both species. Species differences were negligible for Mazes 2, 4, and 5 irrespective of the presence of visual cues, suggesting that these mazes could be used to measure spatial learning in both species. With regards to performance on the first trial, which reflects visuo-spatial problem solving, Mazes 5 and 9 without visual cues produced the most consistent results. We conclude that the Hebb-Williams mazes paradigm has the potential to be utilized in translational research to measure comparable cognitive functions in FXS humans and animals (criterion #3).

Faces elicit different scanning patterns depending on task demands.

Eye movements were recorded while participants discriminated upright and inverted faces that differed with respect to either configural or featural information. Two hypotheses were examined: (1) whether featural and configural information processing elicit different scanning patterns; (2) whether fixations on a specific region of the face dominate scanning patterns. Results from two experiments were compared to examine whether participants' prior knowledge of the kind of information that would be relevant for the task (i.e., configural vs featural) influences eye movements. In Experiment 1, featural and configural discrimination trials were presented in random order such that participants were unaware of the information that would be relevant on any given trial. In Experiment 2, featural and configural discrimination trials were blocked and participants were informed of the nature of the discriminations. The results of both experiments suggest that faces elicit different scanning patterns depending on task demands. When participants were unaware of the nature of the information relevant for the task at hand, face processing was dominated by attention to the eyes. When participants were aware that relational information was relevant, scanning was dominated by fixations to the center of the face. We conclude that faces elicit scanning strategies that are driven by task demands.

From development to aging: Holistic face perception in children, younger and older adults.

Few published reports examine the development of holistic face processing across the lifespan such that face-specific processes are adequately differentiated from general developmental effects. To address this gap in the literature, we used the complete design of the composite paradigm (Richler & Gauthier, 2014) with faces and non-face control objects (watches) to investigate holistic processing in children (8-10years), young adults (20-32years) and older adults (65-78years). Several modifications to past research designs were introduced to improve the ability to draw conclusions about the development of holistic processing in terms of face-specificity, response bias, and age-related differences in attention. Attentional focus (narrow vs. wide focus at study) influenced the magnitude of the composite effect without eliminating holistic face processing in all age groups. Young adults showed large composite effects for faces, but none for watches. In contrast, older adults and children showed composite effects for both faces and watches, although the effects for faces were larger. Our findings suggest that holistic processing, as measured by the composite effect, might be moderated by less efficient attentional control in children and older adults. The study also underscores the importance of including comparable complex objects when investigating face processing across the lifespan.

On the particular vulnerability of face recognition to aging: a review of three hypotheses.

Age-related face recognition deficits are characterized by high false alarms to unfamiliar faces, are not as pronounced for other complex stimuli, and are only partially related to general age-related impairments in cognition. This paper reviews some of the underlying processes likely to be implicated in theses deficits by focusing on areas where contradictions abound as a means to highlight avenues for future research. Research pertaining to the three following hypotheses is presented: (i) perceptual deterioration, (ii) encoding of configural information, and (iii) difficulties in recollecting contextual information. The evidence surveyed provides support for the idea that all three factors are likely to contribute, under certain conditions, to the deficits in face recognition seen in older adults. We discuss how these different factors might interact in the context of a generic framework of the different stages implicated in face recognition. Several suggestions for future investigations are outlined.

Transcriptomic response of the hydrothermal mussel Bathymodiolus azoricus in experimental exposure to heavy metals is modulated by the Pgm genotype and symbiont content.

Hydrothermal vent mussels belonging to the genus Bathymodiolus dominate communities at hydrothermal sites of the Mid-Atlantic Ridge. The mussel Bathymodiolus azoricus harbors thiotrophic and methanotrophic symbiotic bacteria in its gills and evolves in naturally highly metal contaminated environments. In the context of investigations on metal tolerance/effect in B. azoricus, we focused our work on the short-term adaptive response (15days) of mussels to different metals exposure at a molecular level using metal concentrations chosen to mimic natural situations at three vents sites. The expression of a set of 38 genes involved in different steps of the metal uptake, detoxication and various metabolisms was analysed by qPCR. Mussels were also genotyped at 10 enzyme loci to explore the relationships among natural genetic variation and gene expression. Relation between symbiont content (both sulfur-oxidizing and methanogen bacteria) and gene expression was also analysed. Our study demonstrated the influence of metal cocktail composition and time exposure on the transcriptome regulation with a specific pattern of regulation observed for the three metal cocktail tested. We also evidenced the significant influence of some specific Pgm genotype on the global gene expression in our experimental populations and a general trend of a higher gene expression in individuals carrying a high symbiont content.

Configural and featural discriminations use the same spatial frequencies: a model observer versus human observer analysis.

Previous work has shown mixed results regarding the role of different spatial frequency (SF) ranges in featural and configural processing of faces. Some studies suggest no special role of any given band for either type of processing, while others suggest that low SFs principally support configural analysis. Here we attempt to put this issue on a more rigorous footing by comparing human performance when making featural and configural discriminations with that of a model observer algorithm carrying out the same task. The model uses a simple algorithm that calculates the dot product of a stimulus image with each available potential match image to find the maximally likely match. It thus provides a principled way of analyzing available image information. We find human accuracy peaks at around 10 cycles per face (cpf) regardless of whether featural or configural manipulations are being detected. We also find accuracy peaks in the same part of the spectrum regardless of which feature is manipulated (ie eyes, nose, or mouth). Conversely, model observer performance, measured in terms of white noise tolerance, peaks at approximately 5 cpf, and this value again remains roughly constant regardless of the type of manipulation and feature manipulated. The ratio of the model's noise tolerance to a derived equivalent noise tolerance value for humans peaks at around 10 cpf, similar to the accuracy data. These results provide evidence that the human performance maxima at 10 cpf are not due simply to the physical characteristics of face stimuli, but rather arise due to an interaction between the available information in face images and human perceptual processing.

Thermal limit for metazoan life in question: in vivo heat tolerance of the Pompeii worm.

The thermal limit for metazoan life, expected to be around 50°C, has been debated since the discovery of the Pompeii worm Alvinella pompejana, which colonizes black smoker chimney walls at deep-sea vents. While indirect evidence predicts body temperatures lower than 50°C, repeated in situ temperature measurements depict an animal thriving at temperatures of 60°C and more. This controversy was to remain as long as this species escaped in vivo investigations, due to irremediable mortalities upon non-isobaric sampling. Here we report from the first heat-exposure experiments with live A. pompejana, following isobaric sampling and subsequent transfer in a laboratory pressurized aquarium. A prolonged (2 hours) exposure in the 50-55°C range was lethal, inducing severe tissue damages, cell mortalities and triggering a heat stress response, therefore showing that Alvinella's upper thermal limit clearly is below 55°C. A comparison with hsp70 stress gene expressions of individuals analysed directly after sampling in situ confirms that Alvinella pompejana does not experience long-term exposures to temperature above 50°C in its natural environment. The thermal optimum is nevertheless beyond 42°C, which confirms that the Pompeii worm ranks among the most thermotolerant metazoans.