Are shark teeth proxies for functional traits? A framework to infer ecology from the fossil record.

Modern sharks have an evolutionary history of at least 250 million years and are known to play key roles in marine systems, from controlling prey populations to connecting habitats across oceans. These ecological roles can be quantified based on their functional traits, which are typically morphological (e.g., body size) or behavioural (e.g., feeding and diet). Nonetheless, the understanding of such roles of extinct sharks is limited due to the inherent incompleteness of their fossil record, which consists mainly of isolated teeth. As such, establishing links between tooth morphology and ecological traits in living sharks could provide a useful framework to infer sharks' ecology from the fossil record. Here, based on extant sharks from which morphological and behavioural characteristics are known, the authors assess the extent to which isolated teeth can serve as proxies for functional traits. To do so, they first review the scientific literature on extant species to evaluate the use of shark dental characters as proxies for ecology to then perform validation analyses based on an independent data set collected from museum collections. Their results reveal that 12 dental characters have been used in shark literature as proxies for three functional traits: body size, prey preference and feeding mechanism. From all dental characters identified, tooth size and cutting edge are the most widely used. Validation analyses suggest that seven dental characters - crown height, crown width, cutting edge, lateral cusplets, curvature, longitudinal outline and cross-section outline - are the best proxies for the three functional traits. In particular, tooth size (crown height and width) was found to be a reliable proxy of all three traits; the presence of serrations on the cutting edge was one of the best proxies for prey preference; and tooth shape (longitudinal outline) and the presence of lateral cusplets were among the best indicators of feeding mechanism. Overall, the authors' results suggest that in the absence of directly measurable traits in the fossil record, these seven dental characters (and different combinations of them) can be used to quantify the ecological roles of extinct sharks. This information has the potential to provide key insights into how shark functional diversity has changed through time, including their ecological responses to extinction events.

The extinct shark Otodus megalodon was a transoceanic superpredator: Inferences from 3D modeling.

Although shark teeth are abundant in the fossil record, their bodies are rarely preserved. Thus, our understanding of the anatomy of the extinct Otodus megalodon remains rudimentary. We used an exceptionally well-preserved fossil to create the first three-dimensional model of the body of this giant shark and used it to infer its movement and feeding ecology. We estimate that an adult O. megalodon could cruise at faster absolute speeds than any shark species today and fully consume prey the size of modern apex predators. A dietary preference for large prey potentially enabled O. megalodon to minimize competition and provided a constant source of energy to fuel prolonged migrations without further feeding. Together, our results suggest that O. megalodon played an important ecological role as a transoceanic superpredator. Hence, its extinction likely had large impacts on global nutrient transfer and trophic food webs.

Single Stranded Fully Modified-Phosphorothioate Oligonucleotides can Induce Structured Nuclear Inclusions, Alter Nuclear Protein Localization and Disturb the Transcriptome In Vitro.

Oligonucleotides and nucleic acid analogues that alter gene expression are now showing therapeutic promise in human disease. Whilst the modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, such modifications may also confer unexpected physicochemical and biological properties. Gapmer mixed-modified and DNA oligonucleotides on a phosphorothioate backbone can bind non-specifically to intracellular proteins to form a variety of toxic inclusions, driven by the phosphorothioate linkages, but also influenced by the oligonucleotide sequence. Recently, the non-antisense or other off-target effects of 2' O- fully modified phosphorothioate linkage oligonucleotides are becoming better understood. Here, we report chemistry-specific effects of oligonucleotides composed of modified or unmodified bases, with phosphorothioate linkages, on subnuclear organelles and show altered distribution of nuclear proteins, the appearance of highly stable and strikingly structured nuclear inclusions, and disturbed RNA processing in primary human fibroblasts and other cultured cells. Phosphodiester, phosphorodiamidate morpholino oligomers, and annealed complimentary phosphorothioate oligomer duplexes elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of transfected fibroblasts exhibiting such disruption. Our data add to the growing body of evidence of off-target effects of some phosphorothioate nucleic acid drugs in primary cells and suggest alternative approaches to mitigate these effects.

NEAT1 polyA-modulating antisense oligonucleotides reveal opposing functions for both long non-coding RNA isoforms in neuroblastoma.

Many long non-coding RNAs (lncRNA) are highly dysregulated in cancer and are emerging as therapeutic targets. One example is NEAT1, which consists of two overlapping lncRNA isoforms, NEAT1_1 (3.7 kb) and NEAT1_2 (23 kb), that are functionally distinct. The longer NEAT1_2 is responsible for scaffolding gene-regulatory nuclear bodies termed paraspeckles, whereas NEAT1_1 is involved in paraspeckle-independent function. The NEAT1 isoform ratio is dependent on the efficient cleavage and polyadenylation of NEAT1_1 at the expense of NEAT1_2. Here, we developed a targeted antisense oligonucleotide (ASO) approach to sterically block NEAT1_1 polyadenylation processing, achieving upregulation of NEAT1_2 and abundant paraspeckles. We have applied these ASOs to cells of the heterogeneous infant cancer, neuroblastoma, as we found higher NEAT1_1:NEAT1_2 ratio and lack of paraspeckles in high-risk neuroblastoma cells. These ASOs decrease NEAT1_1 levels, increase NEAT1_2/paraspeckles and concomitantly reduce cell viability in high-risk neuroblastoma specifically. In contrast, overexpression of NEAT1_1 has the opposite effect, increasing cell proliferation. Transcriptomic analyses of high-risk neuroblastoma cells with altered NEAT1 ratios and increased paraspeckle abundance after ASO treatment showed an upregulation of differentiation pathways, as opposed to the usual aggressive neuroblastic phenotype. Thus, we have developed potential anti-cancer ASO drugs that can transiently increase growth-inhibiting NEAT1_2 RNA at the expense of growth-promoting NEAT1_1 RNA. These ASOs, unlike others that degrade lncRNAs, provide insights into the importance of altering lncRNA polyadenylation events to suppress tumorigenesis as a strategy to combat cancer.

Body dimensions of the extinct giant shark Otodus megalodon: a 2D reconstruction.

Inferring the size of extinct animals is fraught with danger, especially when they were much larger than their modern relatives. Such extrapolations are particularly risky when allometry is present. The extinct giant shark †Otodus megalodon is known almost exclusively from fossilised teeth. Estimates of †O. megalodon body size have been made from its teeth, using the great white shark (Carcharodon carcharias) as the only modern analogue. This can be problematic as the two species likely belong to different families, and the position of the †Otodus lineage within Lamniformes is unclear. Here, we infer †O. megalodon body dimensions based on anatomical measurements of five ecologically and physiologically similar extant lamniforms: Carcharodon carcharias, Isurus oxyrinchus, Isurus paucus, Lamna ditropis and Lamna nasus. We first assessed for allometry in all analogues using linear regressions and geometric morphometric analyses. Finding no evidence of allometry, we made morphological extrapolations to infer body dimensions of †O. megalodon at different sizes. Our results suggest that a 16 m †O. megalodon likely had a head ~ 4.65 m long, a dorsal fin ~ 1.62 m tall and a tail ~ 3.85 m high. Morphometric analyses further suggest that its dorsal and caudal fins were adapted for swift predatory locomotion and long-swimming periods.