Computer-Aided Drug Design (CADD) to De-Orphanize Marine Molecules: Finding Potential Therapeutic Agents for Neurodegenerative and Cardiovascular Diseases

Computer-aided drug design (CADD) techniques allow the identification of compounds capable of modulating protein functions in pathogenesis-related pathways, which is a promising line on drug discovery. Marine natural products (MNPs) are considered a rich source of bioactive compounds, as the oceans are home to much of the planet’s biodiversity. Biodiversity is directly related to chemodiversity, which can inspire new drug discoveries. Therefore, natural products (NPs) in general, and MNPs in particular, have been used for decades as a source of inspiration for the design of new drugs. However, NPs present both opportunities and challenges. These difficulties can be technical, such as the need to dive or trawl to collect the organisms possessing the compounds, or biological, due to their particular marine habitats and the fact that they can be uncultivable in the laboratory. For all these difficulties, the contributions of CADD can play a very relevant role in simplifying their study, since, for example, no biological sample is needed to carry out an in-silico analysis. Therefore, the amount of natural product that needs to be used in the entire preclinical and clinical study is significantly reduced. Here, we exemplify how this combination between CADD and MNPs can help unlock their therapeutic potential. In this study, using a set of marine invertebrate molecules, we elucidate their possible molecular targets and associated therapeutic potential, establishing a pipeline that can be replicated in future studies.

Non-marine invertebrate trace fossils from the Tertiary Calatayud-Teruel basin, NE Spain

Relatively diverse trace fossils made by insects, other arthropods and oligochaete worms occur in the Miocene lacustrine and marginal lacustrine deposits of the Calatayud-Teruel basin (NE Spain). They include the ichnospecies Celliforma isp., Celliforma? isp. A and B, Celliforma? aff. habari, Rosellichnus cf. arabicus, Spongeliomorpha isp., Labyrintichnus terrerensis n. igen. et isp., Taenidium barreti, Beaconites filiformis n. isp. and Polykladichnus aragonensis n. isp. Their taxonomic and ethologic interpretations and cross-cutting relationships permit to envisage new lines of evidence for reconstructing transitions from dry-ground terrestrial to moist-ground and subaqueous environments, related to episodic floodings in lacustrine ponds. These environmental transitions (related to external controls) are characterized by benthic community replacements, evinced by vertical successions of Termitichnus, Scoyenia and Mermia-like ichnofacies.

Marine Invertebrate Peptides: Antimicrobial Peptides

Antimicrobial peptides are an important component of many organisms’ innate immune system, with a good inhibitory or killing effect against the invading pathogens. As a type of biological polypeptide with natural immune activities, antimicrobial peptides have a broad spectrum of antibacterial, antiviral, and antitumor activities. Nevertheless, these peptides cause no harm to the organisms themselves. Compared with traditional antibiotics, antimicrobial peptides have the advantage of not producing drug resistance and have a unique antibacterial mechanism, which has attracted widespread attention. In this study, marine invertebrates were classified into arthropods, annelids, mollusks, cnidarians, and tunicata. We then analyzed the types, sources and antimicrobial activities of the antimicrobial peptides in each group. We also reviewed the immune mechanism from three aspects: membrane-targeted direct killing effects, non-membrane targeting effects and immunomodulatory effects. Finally, we discussed their applications and the existing problems facing antimicrobial peptides in actual production. The results are expected to provide theoretical support for future research and applications of antimicrobial peptides in marine invertebrates.

Recruitment, settlement and ontogeny of the serpulid 'Spirobranchus cariniferus' (Gray, 1843)

<p>Serpulids are a globally represented group of polychaetes and can be found in many habitats from the intertidal fringe to the subtidal environment and even in deep-sea ecosystems. These tube-dwelling worms are often described as pioneer species in new or disturbed habitats. Serpulids secrete a calcareous tube and often occur in aggregations. These patches can range from several centimetres to several metres in diameter and may even form reef systems. Accumulations of tube-dwelling worms provide a new habitat for other species and, therefore, serpulids are considered bioengineers. Serpulid aggregations are known to enhance biodiversity and species abundance and may increase water quality through their filter activity. Despite their ecological importance, their ecology and ontogeny have received little attention. Spirobranchus cariniferus, a New Zealand endemic intertidal serpulid, is a substantial contributor to intertidal ecosystems. For this and other Serpulidae, the link between larval development and larval settlement is missing. However, this connection is essential to understand recruitment and ecology of tube-dwelling worms. Therefore, in this thesis, I describe the ontogeny of S. cariniferus from larval development to recruitment and reproduction. In the first data chapter, I present my findings on the recruitment of S. cariniferus in the field. This serpulid settles aggregatively in the field but not necessarily in response to the presence of adult conspecifics, as has been previously reported. Abiotic factors such as sunlight or wave disturbance have a more substantial effect on recruitment rather than the occurrence of adult individuals of the same or a competing species. Additionally, this chapter provides support for the hypothesis that larvae of S. cariniferus may accumulate near the substrate before settlement. Many sessile marine invertebrate taxa occur in either aggregations or as solitary individuals, with potential benefits and disadvantages associated with each configuration. For S. cariniferus, solitary and aggregative individuals can be found in the same habitat. Therefore, the second data chapter compares growth and mortality for individuals living alone or in aggregation. While solitary and aggregative individuals elongate their tubes at a similar rate, further correlations of body to tube sizes lead to the conclusion that solitary worms focus more of their energy on tube length growth rather than body size increment compared to aggregative conspecifics. Mortality is highly variable but does not differ between both configurations. However, individuals living in a patch have a better ability to recover from damage to their tubes. In the last two decades, the idea that gonochorism is the general reproductive pattern for Serpulidae has been challenged, and instead it has been suggested by some that protandry is the more common trait. Therefore, with my third data chapter, I explore maturation and sex ratio of S. cariniferus and whether it changes for individuals living alone vs. in aggregation or based on size. While maturation depends on size, sex does not, and neither maturation nor sex ratio are dependent on whether individuals live in aggregation or not. Further, the ratio of females to males did not favour either sex consistently. For the first time in this species I found evidence of possible hermaphroditism. Through spawning trials and histological sections, I identified nine individuals which simultaneously contained oocytes and sperm cells. I suggest therefore, that S. cariniferus has alternating sexes rather than protandry as a reproductive strategy. In the fourth and final data chapter, I describe the metamorphosis and settlement behaviour of S. cariniferus larvae. For this serpulid species, settlement and metamorphosis are separate and distinct steps that involve both behavioural and morphological changes to the larvae. Further, this entire process can be quite prolonged (i.e. over several days), and at some points can be reversed. It is therefore very important that observations last longer than 24–48 hours, when studying serpulid settlement. As far as I am aware, this is the first study on a serpulid species to examine aggregative settlement in the field in relation to the presence of adult conspecifics and abiotic factors, and also to explicitly test for consequences of solitary vs. group living on growth and mortality. It is also the first to show evidence of hermaphroditism in this species. I hope my research and this thesis stimulates a more inclusive and holistic investigation of serpulids in the future. Larval development, settlement patterns and ontogeny need to be studied in detail if we want to understand the evolution, ecology, impacts and benefits of these and other sessile marine invertebrates.</p>

Recruitment, settlement and ontogeny of the serpulid 'Spirobranchus cariniferus' (Gray, 1843)

<p>Serpulids are a globally represented group of polychaetes and can be found in many habitats from the intertidal fringe to the subtidal environment and even in deep-sea ecosystems. These tube-dwelling worms are often described as pioneer species in new or disturbed habitats. Serpulids secrete a calcareous tube and often occur in aggregations. These patches can range from several centimetres to several metres in diameter and may even form reef systems. Accumulations of tube-dwelling worms provide a new habitat for other species and, therefore, serpulids are considered bioengineers. Serpulid aggregations are known to enhance biodiversity and species abundance and may increase water quality through their filter activity. Despite their ecological importance, their ecology and ontogeny have received little attention. Spirobranchus cariniferus, a New Zealand endemic intertidal serpulid, is a substantial contributor to intertidal ecosystems. For this and other Serpulidae, the link between larval development and larval settlement is missing. However, this connection is essential to understand recruitment and ecology of tube-dwelling worms. Therefore, in this thesis, I describe the ontogeny of S. cariniferus from larval development to recruitment and reproduction. In the first data chapter, I present my findings on the recruitment of S. cariniferus in the field. This serpulid settles aggregatively in the field but not necessarily in response to the presence of adult conspecifics, as has been previously reported. Abiotic factors such as sunlight or wave disturbance have a more substantial effect on recruitment rather than the occurrence of adult individuals of the same or a competing species. Additionally, this chapter provides support for the hypothesis that larvae of S. cariniferus may accumulate near the substrate before settlement. Many sessile marine invertebrate taxa occur in either aggregations or as solitary individuals, with potential benefits and disadvantages associated with each configuration. For S. cariniferus, solitary and aggregative individuals can be found in the same habitat. Therefore, the second data chapter compares growth and mortality for individuals living alone or in aggregation. While solitary and aggregative individuals elongate their tubes at a similar rate, further correlations of body to tube sizes lead to the conclusion that solitary worms focus more of their energy on tube length growth rather than body size increment compared to aggregative conspecifics. Mortality is highly variable but does not differ between both configurations. However, individuals living in a patch have a better ability to recover from damage to their tubes. In the last two decades, the idea that gonochorism is the general reproductive pattern for Serpulidae has been challenged, and instead it has been suggested by some that protandry is the more common trait. Therefore, with my third data chapter, I explore maturation and sex ratio of S. cariniferus and whether it changes for individuals living alone vs. in aggregation or based on size. While maturation depends on size, sex does not, and neither maturation nor sex ratio are dependent on whether individuals live in aggregation or not. Further, the ratio of females to males did not favour either sex consistently. For the first time in this species I found evidence of possible hermaphroditism. Through spawning trials and histological sections, I identified nine individuals which simultaneously contained oocytes and sperm cells. I suggest therefore, that S. cariniferus has alternating sexes rather than protandry as a reproductive strategy. In the fourth and final data chapter, I describe the metamorphosis and settlement behaviour of S. cariniferus larvae. For this serpulid species, settlement and metamorphosis are separate and distinct steps that involve both behavioural and morphological changes to the larvae. Further, this entire process can be quite prolonged (i.e. over several days), and at some points can be reversed. It is therefore very important that observations last longer than 24–48 hours, when studying serpulid settlement. As far as I am aware, this is the first study on a serpulid species to examine aggregative settlement in the field in relation to the presence of adult conspecifics and abiotic factors, and also to explicitly test for consequences of solitary vs. group living on growth and mortality. It is also the first to show evidence of hermaphroditism in this species. I hope my research and this thesis stimulates a more inclusive and holistic investigation of serpulids in the future. Larval development, settlement patterns and ontogeny need to be studied in detail if we want to understand the evolution, ecology, impacts and benefits of these and other sessile marine invertebrates.</p>

The Sizes, Growth and Reproduction of Arrow Worms (Chaetognatha) in Light of the Gill-Oxygen Limitation Theory (GOLT)

The Chaetognatha are a marine invertebrate phylum including 132 extant, carnivorous species in nine families and two orders, but with unclear protostomian affinities in the animal kingdom. We document the gradual recognition of the distinctiveness of chaetognaths by early taxonomists, with some emphasis on the often-overlooked studies by Chinese marine biologists. The carnivorous arrow worms are understudied relative to their importance in the marine zooplankton, where they rank second in abundance after the herbivorous copepods. Although arrow worms lack gills or other dedicated respiratory organs, we show that the Gill-Oxygen Limitation Theory (GOLT) can be used to explain how temperature and respiration affect their growth and related life-history traits. Notably, we present a reappraisal of evidence for size–temperature relationships between and within chaetognath species, and for the relationship between their temperature-mediated oxygen demand and their growth patterns. Von Bertalanffy weight growth curves of Ferosagitta hispida (family: Sagittidae) based on earlier aquarium experiments by various authors are presented, which suggest (a) a good fit and (b) that the life span of chaetognaths is much lower than suggested by the authors of several published growth curves drawn onto length–frequency samples from the wild. In addition, we show that chaetognaths attain first maturity at a fraction of the maximum length they can attain that is similar to the corresponding fraction in fishes. Overall, we suggest that the manner in which the oxygen they require enters the body of small marine invertebrates, although often neglected, is a crucial aspect of their biology. In addition, based on our result that arrow worms conform to the GOLT, we suggest that this theory may provide the theoretical framework for the study of growth in the other water-breathing ectotherms lacking gills.

Whole body regeneration and developmental competition in two botryllid ascidians

Background Botryllid ascidians are a group of marine invertebrate chordates that are colonial and grow by repeated rounds of asexual reproduction to form a colony of individual bodies, called zooids, linked by a common vascular network. Two distinct processes are responsible for zooid regeneration. In the first, called blastogenesis, new zooids arise from a region of multipotent epithelium from a pre-existing zooid. In the second, called whole body regeneration (WBR), mobile cells in the vasculature coalesce and are the source of the new zooid. In some botryllid species, blastogenesis and WBR occur concurrently, while in others, blastogenesis is used exclusively for growth, while WBR only occurs following injury or exiting periods of dormancy. In species such as Botrylloides diegensis, injury induced WBR is triggered by the surgical isolation of a small piece of vasculature. However, Botryllus schlosseri has unique requirements that must be met for successful injury induced WBR. Our goal was to understand why there would be different requirements between these two species. Results While WBR in B. diegensis was robust, we found that in B. schlosseri, new zooid growth following injury is unlikely due to circulatory cells, but instead a result of ectopic development of tissues leftover from the blastogenic process. These tissues could be whole, damaged, or partially resorbed developing zooids, and we defined the minimal amount of vascular biomass to support ectopic regeneration. We did find a common theme between the two species: a competitive process exists which results in only a single zooid reaching maturity following injury. We utilized this phenomenon and found that competition is reversible and mediated by circulating factors and/or cells. Conclusions We propose that WBR does not occur in B. schlosseri and that the unique requirements defined in other studies only serve to increase the chances of ectopic development. This is likely a response to injury as we have discovered a vascular-based reversible competitive mechanism which ensures that only a single zooid completes development. This competition has been described in other species, but the unique response of B. schlosseri to injury provides a new model to study resource allocation and competition within an individual.

Morphometry of cellular behavior of coelomocytes from starfish Asterias amurensis

A comprehensive statistical analysis using a wide range of linear and non-linear morphological parameters enabled identification of the main stages in the in vitro dynamics of cell behavior of immune cells of the marine invertebrate Asterias amurensis (Echinodermata, Asteroidea). Three stages may be distinguished in the cell behavior, which are characterized by the differences in complexity of the cell boundary microsculpture as well as by the size and asymmetry of the cell and convex hull of the cell. The first stage (5 min after placing cells onto a substrate) is characterized by more complex cell morphology and an increase in the process number and spreading area. The second stage (15 min) is characterized by simplification of cell morphology, retraction of some processes, and rounding of cells upon continued cell spreading. At the third stage (60 min), new large processes with rounded contours emerge due to partial retraction of the flattened cell surface. Each stage is characterized by statistically significant differences in several linear and nonlinear parameters of the external morphology for all cell types.