By the combination of peptide nucleic acid (PNA) with single-stranded DNA specific nucleases, alteration of a single base to another in DNA has been detected with high accuracy. Only the DNAs in DNA/PNA duplexes involving a mismatch are efficiently hydrolyzed by these enzymes, whereas fully matching sequences are kept intact. This difference is visually scored by adding 3,3'-diethylthiadicarbocyanine, which changes its color from blue to purple upon binding to DNA/PNA duplexes. These findings are applied to the convenient and straightforward detection of single nucleotide polymorphisms (SNPs). When the target site in the sample DNA is completely complementary with the PNA, a notable amount of DNA/PNA duplex remains and thus the solution exhibits purple color. In the presence of even one mismatch between PNA and DNA, however, the DNA is completely digested by the enzyme and therefore the dye shows its intrinsic blue color. The SNPs in the apolipoprotein E gene of human DNA have been successfully genotyped by this method.

Mesozoic marine reptiles and modern marine mammals are often considered ecological analogs, but the extent of their similarity is largely unknown. Particularly important is the presence/absence of deep-diving suction feeders among Mesozoic marine reptiles because this would indicate the establishment of mesopelagic cephalopod and fish communities in the Mesozoic. A recent study suggested that diverse suction feeders, resembling the extant beaked whales, evolved among ichthyosaurs in the Triassic. However, this hypothesis has not been tested quantitatively. We examined four osteological features of jawed vertebrates that are closely linked to the mechanism of suction feeding, namely hyoid corpus ossification/calcification, hyobranchial apparatus robustness, mandibular bluntness, and mandibular pressure concentration index. Measurements were taken from 18 species of Triassic and Early Jurassic ichthyosaurs, including the presumed suction feeders. Statistical comparisons with extant sharks and marine mammals of known diets suggest that ichthyosaurian hyobranchial bones are significantly more slender than in suction-feeding sharks or cetaceans but similar to those of ram-feeding sharks. Most importantly, an ossified hyoid corpus to which hyoid retractor muscles attach is unknown in all but one ichthyosaur, whereas a strong integration of the ossified corpus and cornua of the hyobranchial apparatus has been identified in the literature as an important feature of suction feeders. Also, ichthyosaurian mandibles do not narrow rapidly to allow high suction pressure concentration within the oral cavity, unlike in beaked whales or sperm whales. In conclusion, it is most likely that Triassic and Early Jurassic ichthyosaurs were ‘ram-feeders’, without any beaked-whale-like suction feeder among them. When combined with the inferred inability for dim-light vision in relevant Triassic ichthyosaurs, the fossil record of ichthyosaurs does not suggest the establishment of modern-style mesopelagic animal communities in the Triassic. This new interpretation matches the fossil record of coleoids, which indicates the absence of soft-bodied deepwater species in the Triassic.

The great white shark (Carcharodon carcharias) exhibits viviparous and oophagous reproduction. A 4950 mm total length (TL) gravid female accidentally caught by fishermen in the Okinawa Prefecture, Southern Japan carried six embryos (543-624 mm TL, three in each uterus). Both uteri contained copious amounts of yellowish viscous uterine fluid (over 79.2 litres in the left uterus), nutrient eggs and broken egg cases. The embryos had yolk stomachs that had ruptured, the mean volume of which was approximately 197.9 ml. Embryos had about 20 rows of potentially functional teeth in the upper and lower jaws. Periodic acid Schiff (PAS)-positive substances were observed on the surface and in the cytoplasm of the epithelial cells, and large, secretory, OsO4-oxidized lipid droplets of various sizes were distributed on the surface of the villous string epithelium on the uterine wall. Histological examination of the uterine wall showed it to consist of villi, similar to the trophonemata of Dasyatidae rays, suggesting that the large amount of fluid found in the uterus of the white shark was likely required for embryo nutrition. We conclude that: (1) the lipid-rich fluid is secreted from the uterine epithelium only in early gestation before the onset of oophagy, (2) the embryos probably use the abundant uterine fluid and encased nutrient eggs for nutrition at this stage of their development, and (3) the uterine fluid is the major source of embryonic nutrition before oophagy onset. This is the first record of the lipid histotrophy of reproduction among all shark species.

A monophosphate group was attached to the terminus of pseudo-complementary peptide nucleic acid (pcPNA), and two of thus modified pcPNAs were combined with Ce(IV)/EDTA for site-selective hydrolysis of double-stranded DNA. The site-selective DNA scission was notably accelerated by this chemical modification of pcPNAs. These second-generation artificial restriction DNA cutters (ARCUTs) differentiated the target sequence so strictly that no scission occurred even when only one DNA base-pair was altered to another. By using two of the activated ARCUTs simultaneously, DNA substrate was selectively cut at two predetermined sites, and the desired fragment was clipped and cloned. The DNA scission by ARCUT was also successful even when the target site was methylated by methyltransferase and protected from the corresponding restriction enzyme. Furthermore, potentiality of ARCUT for manipulation of huge DNA has been substantiated by site-selective scission of genomic DNA of Escherichia coli (composed of 4,600,000 bp) at the target site. All these results indicate promising applications of ARCUTs for versatile purposes.

Studies of the megamouth shark, one of three planktivorous sharks, can provide information about their evolutionary history. Megamouth shark feeding has never been observed in life animals, but two alternative hypotheses on biomechanics suggest either feeding, i.e., ram feeding or suction feeding. In this study, the second moment of area of the ceratohyal cartilages, which is an indicator of the flexural stiffness of the cartilages, is calculated for 21 species of ram- and suction-feeding sharks using computed tomography. The results indicate that suction-feeding sharks have ceratohyal cartilages with a larger second moment of area than ram-feeding sharks. The result also indicates that the ram-suction index, which is an indicator of relative contribution of ram and suction behavior, is also correlated with the second moment of area of the ceratohyal. Considering that large bending stresses are expected to be applied to the ceratohyal cartilage during suction, the larger second moment of area of the ceratohyal of suction-feeding sharks can be interpreted as an adaptation for suction feeding. Based on the small second moment of area of the ceratohyal cartilage of the megamouth shark, the feeding mode of the megamouth shark is considered to be ram feeding, similar to the planktivorous basking shark. From these results, an evolutionary scenario of feeding mechanics of three species of planktivorous sharks can be suggested. In this scenario, the planktivorous whale shark evolved ram feeding from a benthic suction-feeding ancestor. Ram feeding in the planktivorous megamouth shark and the basking shark evolved from ram feeding swimming-type ancestors and that both developed their unique filtering system to capture small-sized prey.

Unlike most viviparous vertebrates, lamniform sharks develop functional teeth during early gestation. This feature is considered to be related to their unique reproductive mode where the embryo grows to a large size via feeding on nutritive eggs in utero. However, the developmental process of embryonic teeth is largely uninvestigated. We conducted X-ray microcomputed tomography to observe the dentitions of early-, mid-, and full-term embryos of the white shark Carcharodon carcharias (Lamniformes, Lamnidae). These data reveal the ontogenetic change of embryonic dentition of the species for the first time. Dentition of the early-term embryos (∼45 cm precaudal length, PCL) is distinguished from adult dentition by 1) the presence of microscopic teeth in the distalmost region of the paratoquadrate, 2) a fang-like crown morphology, and 3) a lack of basal concavity of the tooth root. The "intermediate tooth" of early-term embryos is almost the same size as the adjacent teeth, suggesting that lamnoid-type heterodonty (lamnoid tooth pattern) has not yet been established. We also discovered that mid-term embryos (∼80 cm PCL) lack functional dentition. Previous studies have shown that the maternal supply of nutritive eggs in lamnoid sharks ceases during mid- to late-gestation. Thus, discontinuation of functional tooth development is likely associated with the completion of the oophagous (egg-eating) phase. Replacement teeth in mid-term embryos include both embryonic and adult-type teeth, suggesting that the embryo to adult transition in dental morphology occurs during this period. J. Morphol. 278:215-227, 2017. © 2016 Wiley Periodicals,Inc.

Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA) sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes) species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi, Chlamydoselachus anguineus (frilled shark) is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved as Chlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus, H. nakamurai))). Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks.

Background In the darkness of the ocean, an impressive number of taxa have evolved the capability to emit light. Many mesopelagic organisms emit a dim ventral glow that matches with the residual environmental light in order to camouflage themselves (counterillumination function). Sharks use their luminescence mainly for this purpose. Specific lateral marks have been observed in Etmopteridae sharks (one of the two known luminous shark families) suggesting an inter/intraspecific recognition. Conversely, dorsal luminescence patterns are rare within these deep-sea organisms. Results Here we report evidence that Etmopterus spinax, Etmopterus molleri and Etmopterus splendidus have dorsal luminescence patterns. These dorsal patterns consist of specific lines of luminous organs, called photophores, on the rostrum, dorsal area and at periphery of the spine. This dorsal light seems to be in contrast with the counterilluminating role of ventral photophores. However, skin photophores surrounding the defensive dorsal spines show a precise pattern supporting an aposematism function for this bioluminescence. Using in situ imaging, morphological and histological analysis, we reconstructed the dorsal light emission pattern on these species, with an emphasis on the photogenic skin associated with the spine. Analyses of video footage validated, for the first time, the defensive function of the dorsal spines. Finally, we did not find evidence that Etmopteridae possess venomous spine-associated glands, present in Squalidae and Heterondontidae, via MRI and CT scans. Conclusion This work highlights for the first time a species-specific luminous dorsal pattern in three deep-sea lanternsharks. We suggest an aposematic use of luminescence to reveal the presence of the dorsal spines. Despite the absence of venom apparatus, the defensive use of spines is documented for the first time in situ by video recordings. Electronic supplementary material The online version of this article (10.1186/s40851-019-0126-2) contains supplementary material, which is available to authorized users.