Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. PAPERCLIP.

Epigenetics across the evolutionary tree: New paradigms from non-model animals.

All animals have evolved solutions to manage their genomes, enabling the efficient organization of meters of DNA strands in the nucleus and allowing for nuanced regulation of gene expression while keeping transposable elements suppressed. Epigenetic modifications are central to accomplishing all these. Recent advances in sequencing technologies and the development of techniques that profile epigenetic marks and chromatin accessibility using reagents that can be used in any species has catapulted epigenomic studies in diverse animal species, shedding light on the multitude of epigenomic mechanisms utilized across the evolutionary tree. Now, comparative epigenomics is a rapidly growing field that is uncovering mechanistic aspects of epigenetic modifications and chromatin organization in non-model invertebrates, ranging from octopus to sponges. This review puts recent discoveries in the epigenetics of non-model invertebrates in historical context, and describes new insight into the patterning and functions of DNA methylation and other highly conserved epigenetic modifications.

Antimicrobial and cytotoxic activities of flavonoid and phenolics extracted from Sepia pharaonis ink (Mollusca: Cephalopoda).

BACKGROUND: Several studies have been reported previously on the bioactivities of different extracts of marine molluscs. Therefore, we decided to evaluate the cytotoxic and antimicrobial activities of S. pharaonis ink as a highly populated species in the Red Sea. We extracted the flavonoids from the ink and analyzed their composition. Then we evaluated systematically the cytotoxic and antimicrobial properties of this extract. A pharmacokinetic study was also conducted using SwissADME to assess the potential of the identified flavonoids and phenolic compounds from the ink extract to be orally active drug candidates. RESULTS: Cytotoxic activity was evaluated against 5 cell lines (MCF7, Hep G2, A549, and Caco2) at different concentrations (0.4 µg/mL, 1.6 µg/mL, 6.3 µg/mL, 25 µg/mL, 100 µg/mL). The viability of examined cells was reduced by the extract in a concentration-dependent manner. The highest cytotoxic effect of the extract was recorded against A549 and Hep G2 cancer cell lines cells with IC50 = 2.873 and 7.1 µg/mL respectively. The mechanistic analysis by flow cytometry of this extract on cell cycle progression and apoptosis induction indicated that the extract arrests the cell cycle at the S phase in Hep G2 and MCF7, while in A549 cell arrest was recorded at G1 phase. However, it causes G1 and S phase arrest in Caco2 cancer cell line. Our data showed that the extract has significant antimicrobial activity against all tested human microbial pathogens. However, the best inhibitory effect was observed against Candida albicans ATCC 10,221 with a minimum inhibitory concentration (MIC) of 1.95 µg/mL. Pharmacokinetic analysis using SwissADME showed that most flavonoids and phenolics compounds have high drug similarity as they satisfy Lipinski's criteria and have WLOGP values below 5.88 and TPSA below 131.6 Å2. CONCLUSION: S. pharaonis ink ethanolic extract showed a promising cytotoxic potency against various cell lines and a remarkable antimicrobial action against different pathogenic microbial strains. S. pharaonis ink is a novel source of important flavonoids that could be used in the future in different applications as a naturally safe and feasible alternative of synthetic drugs.

The glow of the night: The tapetum lucidum as a co-adaptation for the inverted retina.

The vertebrate retina is said to be inverted because the photoreceptors are oriented in the posterior direction and are thus unable to maximize photodetection under conditions of low illumination. The tapetum lucidum is a photoreflective structure located posterior to the photoreceptors in the eyes of some fish and terrestrial animals. The tapetum reflects light forward, giving incident photons a "second chance" to collide with a photoreceptor, substantially enhancing retinal photosensitivity in dim light. Across vertebrates (and arthropods), there are a wide variety of tapeta that vary in structure, chemical composition, and even tissue architecture, indicating repeated convergent evolution. To date, the tapetum has not been observed in any cephalopod, however, which also possess a camera-like eye, but with the retinal photoreceptors oriented in the anterior direction. We therefore hypothesize that the tapetum lucidum is a compensatory adaptation for the suboptimal design of the inverted retina of vertebrates.

Unusual Evolution of Cephalopod Tryptophan Indole-Lyases.

Tryptophan indole-lyase (TIL), a pyridoxal-5-phosphate-dependent enzyme, catalyzes the hydrolysis of L-tryptophan (L-Trp) to indole and ammonium pyruvate. TIL is widely distributed among bacteria and bacterial TILs consist of a D2-symmetric homotetramer. On the other hand, TIL genes are also present in several metazoans. Cephalopods have two TILs, TILα and TILß, which are believed to be derived from a gene duplication that occurred before octopus and squid diverged. However, both TILα and TILß individually contain disruptive amino acid substitutions for TIL activity, and neither was active when expressed alone. When TILα and TILß were coexpressed, however, they formed a heterotetramer that exhibited low TIL activity. The loss of TIL activity of the heterotetramer following site-directed mutagenesis strongly suggests that the active heterotetramer contains the TILα/TILß heterodimer. Metazoan TILs generally have lower kcat values for L-Trp than those of bacterial TILs, but such low TIL activity may be rather suitable for metazoan physiology, where L-Trp is in high demand. Therefore, reduced activity may have been a less likely target for purifying selection in the evolution of cephalopod TILs. Meanwhile, the unusual evolution of cephalopod TILs may indicate the difficulty of post-gene duplication evolution of enzymes with catalytic sites contributed by multiple subunits, such as TIL.

Biomechanics, motor control and dynamic models of the soft limbs of the octopus and other cephalopods.

Muscular hydrostats are organs composed entirely of packed arrays of incompressible muscles and lacking any skeletal support. Found in both vertebrates and invertebrates, they are of great interest for comparative biomechanics from engineering and evolutionary perspectives. The arms of cephalopods (e.g. octopus and squid) are particularly interesting muscular hydrostats because of their flexibility and ability to generate complex behaviors exploiting elaborate nervous systems. Several lines of evidence from octopus studies point to the use of both brain and arm-embedded motor control strategies that have evolved to simplify the complexities associated with the control of flexible and hyper-redundant limbs and bodies. Here, we review earlier and more recent experimental studies on octopus arm biomechanics and neural motor control. We review several dynamic models used to predict the kinematic characteristics of several basic motion primitives, noting the shortcomings of the current models in accounting for behavioral observations. We also discuss the significance of impedance (stiffness and viscosity) in controlling the octopus's motor behavior. These factors are considered in light of several new models of muscle biomechanics that could be used in future research to gain a better understanding of motor control in the octopus. There is also a need for updated models that encompass stiffness and viscosity for designing and controlling soft robotic arms. The field of soft robotics has boomed over the past 15 years and would benefit significantly from further progress in biomechanical and motor control studies on octopus and other muscular hydrostats.

Improving the biological realism of predator-prey size relationships in food web models alters ecosystem dynamics.

Body-size relationships between predators and prey exhibit remarkable diversity. However, the assumption that predators typically consume proportionally smaller prey often underlies size-dependent predation in ecosystem models. In reality, some animals can consume larger prey or exhibit limited changes in prey size as they grow larger themselves. These distinct predator-prey size relationships challenge the conventional assumptions of traditional size-based models. Cephalopods, with their diverse feeding behaviours and life histories, offer an excellent case study to investigate the impact of greater biological realism in predator-prey size relationships on energy flow within a size-structured ecosystem model. By categorizing cephalopods into high and low-activity groups, in line with empirically derived, distinct predator-prey size relationships, we found that incorporating greater biological realism in size-based feeding reduced ecosystem biomass and production, while simultaneously increasing biomass stability and turnover. Our results have broad implications for ecosystem modelling, since distinct predator-prey size relationships extend beyond cephalopods, encompassing a wide array of major taxonomic groups from filter-feeding fishes to baleen whales. Incorporating a diversity of size-based feeding in food web models can enhance their ecological and predictive accuracy when studying ecosystem dynamics.

Epigenetic machinery is functionally conserved in cephalopods.

BACKGROUND: Epigenetic regulatory mechanisms are divergent across the animal kingdom, yet these mechanisms are not well studied in non-model organisms. Unique features of cephalopods make them attractive for investigating behavioral, sensory, developmental, and regenerative processes, and recent studies have elucidated novel features of genome organization and gene and transposon regulation in these animals. However, it is not known how epigenetics regulates these interesting cephalopod features. We combined bioinformatic and molecular analysis of Octopus bimaculoides to investigate the presence and pattern of DNA methylation and examined the presence of DNA methylation and 3 histone post-translational modifications across tissues of three cephalopod species. RESULTS: We report a dynamic expression profile of the genes encoding conserved epigenetic regulators, including DNA methylation maintenance factors in octopus tissues. Levels of 5-methyl-cytosine in multiple tissues of octopus, squid, and bobtail squid were lower compared to vertebrates. Whole genome bisulfite sequencing of two regions of the brain and reduced representation bisulfite sequencing from a hatchling of O. bimaculoides revealed that less than 10% of CpGs are methylated in all samples, with a distinct pattern of 5-methyl-cytosine genome distribution characterized by enrichment in the bodies of a subset of 14,000 genes and absence from transposons. Hypermethylated genes have distinct functions and, strikingly, many showed similar expression levels across tissues while hypomethylated genes were silenced or expressed at low levels. Histone marks H3K27me3, H3K9me3, and H3K4me3 were detected at different levels across tissues of all species. CONCLUSIONS: Our results show that the DNA methylation and histone modification epigenetic machinery is conserved in cephalopods, and that, in octopus, 5-methyl-cytosine does not decorate transposable elements, but is enriched on the gene bodies of highly expressed genes and could cooperate with the histone code to regulate tissue-specific gene expression.

Structural and Functional Characterization of Orcokinin B-like Neuropeptides in the Cuttlefish (Sepia officinalis).

The cuttlefish (Sepia officinalis) is a Cephalopod mollusk that lives in the English Channel and breeds in coastal spawning grounds in spring. A previous work showed that the control of egg-laying is monitored by different types of regulators, among which neuropeptides play a major role. They are involved in the integration of environmental cues, and participate in the transport of oocytes in the genital tract and in the secretion of capsular products. This study addresses a family of neuropeptides recently identified and suspected to be involved in the control of the reproduction processes. Detected by mass spectrometry and immunocytochemistry in the nerve endings of the accessory sex glands of the females and ovary, these neuropeptides are also identified in the hemolymph of egg-laying females demonstrating that they also have a hormone-like role. Released in the hemolymph by the sub-esophageal mass, a region that innervates the genital tract and the neurohemal area of the vena cava, in in vitro conditions these neuropeptides modulated oocyte transport and capsular secretion. Finally, in silico analyses indicated that these neuropeptides, initially called FLGamide, had extensive structural homology with orcokinin B, which motivated their name change.

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.

Microbes have been critical drivers of evolutionary innovation in animals. To understand the processes that influence the origin of specialized symbiotic organs, we report the sequencing and analysis of the genome of Euprymna scolopes, a model cephalopod with richly characterized host-microbe interactions. We identified large-scale genomic reorganization shared between E. scolopes and Octopus bimaculoides and posit that this reorganization has contributed to the evolution of cephalopod complexity. To reveal genomic signatures of host-symbiont interactions, we focused on two specialized organs of E. scolopes: the light organ, which harbors a monoculture of Vibrio fischeri, and the accessory nidamental gland (ANG), a reproductive organ containing a bacterial consortium. Our findings suggest that the two symbiotic organs within E. scolopes originated by different evolutionary mechanisms. Transcripts expressed in these microbe-associated tissues displayed their own unique signatures in both coding sequences and the surrounding regulatory regions. Compared with other tissues, the light organ showed an abundance of genes associated with immunity and mediating light, whereas the ANG was enriched in orphan genes known only from E. scolopes Together, these analyses provide evidence for different patterns of genomic evolution of symbiotic organs within a single host.

The first report of a parasitic 'turbellarian' from a cephalopod mollusc, with description of Octopoxenus antarcticus gen. nov., sp. nov. (Platyhelminthes: Fecampiida: Notenteridae).

Parasitic 'turbellarians' are known from various animals such as echinoderms, crustaceans, annelids, bivalve and gastropod molluscs. So far, however, no 'turbellarians' have been reported from cephalopods. In this paper we report a parasitic 'turbellarian' from the giant Antarctic octopus, Megaleledone setebos. We dissected two specimens of M. setebos caught in the Ross Sea (Antarctica) and found numerous worms in their intestine and liver. The worms were spherical or oblong and had two morphologically different poles. The frontal pole bears a small conical protrusion containing large elongated pear-shaped frontal glands and large polygonal cells. The ducts of the frontal glands open terminally to form the frontal organ. The caudal pole has an opening shaped as a folded tube connected by the genital pore with a common genital atrium, which continues into a canal with a muscular sheath. The worms were identified as 'turbellarians' from the family Notenteridae (Fecampiida). This family contains only one species, Notentera ivanovi, reported from the gut of a polychaete at the White Sea. The worms that we found in the gastrointestinal tract of the octopuses were morphologically similar to N. ivanovi but differed from it in several important respects. Phylogenetic analysis based on 28S rDNA gene showed that the newly found worm clustered together with other fecampiids in a highly supported clade and was closely related to N. ivanovi. On the basis of these morphological and molecular data, we described a new species, Octopoxenus antarcticus gen. nov., sp. nov. (Fecampiida: Notenteridae), establishing a new genus to accommodate it and provided an updated diagnosis of the family Notenteridae. This is the first report of a parasitic 'turbellarian' from a cephalopod mollusc.

Shaping and Reshaping Transcriptome Plasticity during Evolution.

Transcriptome plasticity, usually associated with alternative isoform generation, is recognised as a key mechanism driving proteomic diversity and biological complexity. Recent findings of Liscovitch-Brauer et al. and Ma et al. suggest that RNA base modifications are an additional central mode of transcriptome malleability that have the potential to determine evolutionary outcomes.

Persistent Organic Pollutants Burden, Trophic Magnification and Risk in a Pelagic Food Web from Coastal NW Mediterranean Sea.

The storage capacity, trophic magnification and risk of sixty-two POPs have been evaluated in a well-characterized pelagic food web (including phytoplankton, zooplankton, six fish, and two cephalopods species) from an impacted area in NW Mediterranean Sea. Our results show the high capacity of the planktonic compartment for the storage of polybrominated diphenyl ethers (PBDEs) and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), consistent with their estimated low trophic magnification factors (TMF) of 0.2-2.0 (PBDEs) and of 0.3-1.1 (PCDD/Fs). ∑PBDEs dominated in the zooplankton size-class 200-1000 µm (∼330 ng g-1 lw, median), whereas ∑PCDD/Fs accumulated preferentially in phytoplankton size-class 0.7-200 µm (875 pg g-1 lw, median). In contrast, polychlorinated biphenyls (PCBs) were preferentially bioaccumulated in the higher trophic levels (six fish species and two cephalopods) with TMFs = 0.8-3.9, reaching median concentrations of 4270 and 3140 ng g-1 lw (∑PCBs) in Atlantic bonito (Sarda sarda) and chub mackerel (Scomber colias), respectively. For these edible species, the estimated weekly intakes of dioxin-like POPs for humans based on national consumption standards overpassed the EU tolerable weekly intake. Moreover, the concentrations of nondioxin-like PCBs in S. sarda were above the EU maximum levels in foodstuffs, pointing to a risk. No risk evidence was found due to consumption of all other edible species studied, neither for PBDEs. The integrated burden of POPs in the food web reached ∼18 µg g-1 lw, representing a dynamic stock of toxic organic chemicals in the study area. We show that the characterized food web could be a useful and comprehensive "bioindicator" of the chemical pollution status of the study area, opening new perspectives for the monitoring of toxic chemicals in Mediterranean coastal waters.

Do animals dream?

The understanding of biological functions of sleep has improved recently, including an understanding of the deep evolutionary roots of sleep among animals. However, dreaming as an element of sleep may be particularly difficult to address in non-human animals because in humans dreaming involves a non-wakeful form of awareness typically identified through verbal report. Here, we argue that parallels that exist between the phenomenology, physiology, and sleep behaviors during human dreaming provide an avenue to investigate dreaming in non-human animals. We review three alternative measurements of human dreaming - neural correlates of dreaming, 'replay' of newly-acquired memories, and dream-enacting behaviors - and consider how these may be applied to non-human animal models. We suggest that while animals close in brain structure to humans (such as mammals and birds) may be optimal models for the first two of these measurements, cephalopods, especially octopuses, may be particularly good candidates for the third.

The ammonite septum is not an adaptation to deep water: re-evaluating a centuries-old idea.

The shells of ammonoid cephalopods are among the most recognizable fossils, whose fractally folded, internal walls (septa) have inspired many hypotheses on their adaptive value. The enduring explanation for their iterative evolution is that they strengthen the shell against pressure at increasing water depths. The fossil record does not definitively support this idea and much of the theoretical mechanical work behind it has suffered from inaccurate testing geometries and conflicting results. By using a different set of mathematical methods compared with previous studies, I generate a system of finite-element models that explore how different parameters affect the shell's response to water pressure. Increasing the number of initial folds of the septa ultimately has little to no effect on the resulting stress in the shell wall or the septum itself. The introduction of higher-order folds does reduce the tensile stress in the shell wall; however, this is coupled with a higher rate of increase of tensile stress in the septum itself. These results reveal that the increase in complexity should not be expected to have a significant effect on the shell's strength and suggests that the evolution of ammonitic septa does not reflect a persistent trend towards deeper-water habitats.

Cuttlefish show flexible and future-dependent foraging cognition.

Some animals optimize their foraging activity by learning and memorizing food availability, in terms of quantity and quality, and adapt their feeding behaviour accordingly. Here, we investigated whether cuttlefish flexibly adapt their foraging behaviour according to the availability of their preferred prey. In Experiment 1, cuttlefish switched from a selective to an opportunistic foraging strategy (or vice versa) when the availability of their preferred prey at night was predictable versus unpredictable. In Experiment 2, cuttlefish exhibited day-to-day foraging flexibility, in response to experiencing changes in the proximate future (i.e. preferred prey available on alternate nights). In Experiment 1, the number of crabs eaten during the day decreased when shrimp (i.e. preferred food) were predictably available at night, while the consumption of crabs during the day was maintained when shrimp availability was unpredictable. Cuttlefish quickly shifted from one strategy to the other, when experimental conditions were reversed. In Experiment 2, cuttlefish only reduced their consumption of crabs during the daytime when shrimps were predictably available the following night. Their daytime foraging behaviour appeared dependent on shrimps' future availability. Overall, cuttlefish can adopt dynamic and flexible foraging behaviours including selective, opportunistic and future-dependent strategies, in response to changing foraging conditions.

Evidence of learning and memory in the juvenile dwarf cuttlefish Sepia bandensis.

Measuring behavior in the form of numerical data is difficult, especially for studies involving complex actions. DanioVision is a closed-chamber system that utilizes subject tracking to comprehensively record behavior, while also mitigating the influence of environmental conditions. We used DanioVision to record activity of juvenile dwarf cuttlefish (Sepia bandensis) during the inaccessible prey (IP) procedure, a memory experiment in which cuttlefish learn to inhibit capture attempts towards inaccessible prey. By quantifying total movement and orientation of the body, we found that cuttlefish show memory by selectively inhibiting tentacle strikes without reducing total movement, or orientation towards the prey. We show that DanioVision can be used to assess multiple components of dynamic responses that are not measurable by direct observation alone and provide new evidence that strike inhibition is the product of learning, and not motor fatigue.

Mercury bioaccumulation in the long-fin squid Loligo forbesi near the Mid-Atlantic Ridge: Implications to human exposure.

Due to growing commercial interest as a fishing resource and its intermediate position in the marine trophic chains as both prey and predator, cephalopods can play an important role in mercury (Hg) transfer along the marine food webs, since they can bioaccumulate this metal in its tissues. Our study aims to analyze Hg accumulation in Loligo forbesi caught in the Azores Archipelago (Portugal) quantifying Hg in different tissues (mantle and stomach), as well in the squid stomach content, in order to evaluate the efficiency of Hg transfer from prey to predator. Hg data from the tissues was used to estimate the weekly tolerable Hg intake due to squid consumption. Overall data indicate that Hg measured in the stomach tissue (0.1 ± 0.01 µg g-1) was significantly higher than Hg levels found in the mantle (0.04 ± 0.001 µg g-1) and stomach contents (0.01 ± 0.001 µg g-1). BMF (bioaccumulation factor) was >1 for all the samples, indicating a biomagnification process from prey to predator. Hg concentration in the mantle tissue was correlated with mantle size; although females present higher Hg levels than males, the difference was found to be not related to gender but rather to the fact that females had larger bodies. Finally, considering the Hg concentration found in the mantle and the permitted Hg levels, it is advisable to consume up to 1050-1890g of squid per week, according to the regulatory agencies. Thus, our results indicate that, since these doses are respected, consumption of squids from the Azorean waters do not pose a risk to humans.

Linkage of A-to-I RNA Editing in Metazoans and the Impact on Genome Evolution.

The adenosine-to-inosine (A-to-I) RNA editomes have been systematically characterized in various metazoan species, and many editing sites were found in clusters. However, it remains unclear whether the clustered editing sites tend to be linked in the same RNA molecules or not. By adopting a method originally designed to detect linkage disequilibrium of DNA mutations, we examined the editomes of ten metazoan species and detected extensive linkage of editing in Drosophila and cephalopods. The prevalent linkages of editing in these two clades, many of which are conserved between closely related species and might be associated with the adaptive proteomic recoding, are maintained by natural selection at the cost of genome evolution. Nevertheless, in worms and humans, we only detected modest proportions of linked editing events, the majority of which were not conserved. Furthermore, the linkage of editing in coding regions of worms and humans might be overall deleterious, which drives the evolution of DNA sites to escape promiscuous editing. Altogether, our results suggest that the linkage landscape of A-to-I editing has evolved during metazoan evolution. This present study also suggests that linkage of editing should be considered in elucidating the functional consequences of RNA editing.

From synaptic input to muscle contraction: arm muscle cells of Octopus vulgaris show unique neuromuscular junction and excitation-contraction coupling properties.

The muscular-hydrostat configuration of octopus arms allows high manoeuvrability together with the efficient motor performance necessary for its multitasking abilities. To control this flexible and hyper-redundant system the octopus has evolved unique strategies at the various levels of its brain-to-body organization. We focus here on the arm neuromuscular junction (NMJ) and excitation-contraction (E-C) properties of the arm muscle cells. We show that muscle cells are cholinergically innervated at single eye-shaped locations where acetylcholine receptors (AChR) are concentrated, resembling the vertebrate neuromuscular endplates. Na+ and K+ contribute nearly equally to the ACh-activated synaptic current mediating membrane depolarization, thereby activating voltage-dependent L-type Ca2+ channels. We show that cell contraction can be mediated directly by the inward Ca2+ current and also indirectly by calcium-induced calcium release (CICR) from internal stores. Indeed, caffeine-induced cell contraction and immunohistochemical staining revealed the presence and close association of dihydropyridine (DHPR) and ryanodine (RyR) receptor complexes, which probably mediate the CICR. We suggest that the dynamics of octopus arm contraction can be controlled in two ways; motoneurons with large synaptic inputs activate vigorous contraction via activation of the two routs of Ca2+ induced contraction, while motoneurons with lower-amplitude inputs may regulate a graded contraction through frequency-dependent summation of EPSP trains that recruit the CICR. Our results thus suggest that these motoneuronal pools are likely to be involved in the activation of different E-C coupling modes, thus enabling a dynamics of muscles activation appropriate for various tasks such as stiffening versus motion generation.