Three-dimensional measurement for spherical and nonspherical shapes of contact lenses.

In recent years, with the development of precise lathe-cutting equipment, special shaped contact lenses (CL) have been crafted. However, while it is possible to manufacture such a lens, its shape evaluation has not been well-established. We conducted a basic optical experiment using special lenses to measure a spherical lens and nonspherical mold. As the measurement sample, a metal ball, special CL, and a toric-shaped mold were adopted. In order to accurately measure those real shapes, we proposed an algorithm in which the probe light is vertically incident to the sample surface within a numerical aperture of the optical probe. For this algorithm, we developed the specialized time-domain optical coherence tomography (TD-OCT), which was designed to conduct circular scanning while maintaining vertical incidence by driving a two-axis (vertical and horizontal) micro-electromechanical system mirror with a phase difference of 90°. The shape, thickness distribution, and curvature radii of both front and back surfaces of a CL were estimated with this OCT signal analysis and sphere fitting. The shape and curvature radius were evaluated by using the simulated data under the same experimental conditions. They were sufficiently accurate based on the resolution of this OCT. Also, a toric-shaped mold was evaluated by comparing the relationship between each coordinate and intensity of the interference signal. As a result, it is confirmed that the experimental result and the simulated matched well.

Measurement algorithm for real front and back curved surfaces of contact lenses.

The optical measurement algorithm for the real front and back surfaces of contact lenses from their center to periphery accurately and simultaneously is proposed. It is an algorithm that makes light incident vertically along the curved surfaces of contact lenses under the condition that the difference of curvature radii between the front and back surfaces is small enough within the NA of the optical probe. For this purpose, we adopted time-domain optical coherence tomography (OCT) with translation and rotation mechanisms. The shape, thickness distribution, and curvature radii of both surfaces were estimated with OCT signal analysis and circular approximation. The measured results were compared with the designed values and the measured data from a conventional shape measurement device. The curved shape of both surfaces and thickness were well matched with the designed values from lens center to periphery. In a curvature radius of the front surface, there was a proportional bias with a limit of agreement of -0.77% to -2.09%, and the correlation coefficient was 0.57. On the back surface, there was no systematic bias, and minimal detectable change was 0.178 mm, in a range of 95% confidential interval. The proposed algorithm well visualized the real shape and optical characteristics of the contact lens with enough accuracy to the design.

De Novo Assembly of the Transcriptome of Turritopsis, a Jellyfish that Repeatedly Rejuvenates.

In most animals, aging is an irreversible process; however the species Turritopsis sp. has been observed to undergo a rejuvenation process as many as 14 times. In the present study, we used multiplexed RNA libraries to obtain the transcriptome from four developmental stages (St) of Turritopsis sp., including (I) immature medusa, (II) dumpling, (III) dumpling with a short stolon, and (IV) polyp, which had recently rejuvenated. A total of 4.02 billion paired-end reads were assembled de novo, yielding 90,327 contigs. Our analyses revealed that significant blast hits were recovered for 74% of the assembled contigs, and 19% were successfully annotated with gene ontology (GO) terms. A BLAST search demonstrated that 32% of the contigs were most similar to Hydra vulgarissequences. Raw reads from each sample were mapped against the contigs to find St-specific genes. This represents the first comprehensive set of de novo transcriptome data for this species, which may provide clues toward a better understanding of cyclical rejuvenation in multicellular animals.

Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii.

Only two hydromedusan species, Turritopsis dohrnii and T. sp., have exhibited experimental multiple-repeat life cycle reversion in the laboratory, which can be artificially induced by various means such as incubation with CsCl, heat shock, and mechanical damage with needles. In the present study, we constructed a genome assembly of T. dohrnii using Pacific Biosciences long-reads and Illumina short-reads, for which the genome DNA was extracted from 1,500 young medusae originated from a single clone. The total length of the draft genome sequence of T. dohrnii was 435.9 Mb (N50 length 747.2 kb). We identified 23,314 high-confidence genes and found the characteristics of RNA expression amongst developmental stages. Our genome assembly and transcriptome data provide a key model system resource that will be useful for understanding cyclical rejuvenation.

Evolutionary meaning of non-synchronous medusa release and spawning in the most advanced bivalve-inhabiting hydrozoan, Eugymnanthea japonica.

Circadial spawning times of medusa of the bivalve-inhabiting hydrozoans Eugymnanthea japonica Kubota and Eutima japonica Uchida are confirmed to be morning (possibly sunrise) for the former species and night for the latter. Eugymnanthea, with small, short-lived, univoltine medusae, seems to have evolved from a form similar to Eutima japonica, with larger, longer-lived, multivoltine medusae; the morning spawning of medusae in Eugymnanthea may therefore be a newly evolved trait. Medusa release from polyps and spawning of medusae are not synchronous in Eugymnanthea japonica. This non-synchrony may represent an evolutionarily transitional state leading to the most advanced state, synchrony of these two reproductive events, as in certain other ephemeral hydrozoan medusae.

Distribution of Symbiobacterium thermophilum and related bacteria in the marine environment.

We study the ecological distribution of a unique syntrophic bacterium, Symbiobacterium thermophilum, and related bacteria. In this study, we found that they were frequently obtained from seashells and several marine samples. Symbiobacterium also grew from sterilized oyster shells incubated undersea for 2 or 3 months on the coast of Shimoda, Shizuoka, Japan. 16S rRNA gene-based phylogeny of the clones obtained from the Symbiobacterium-positive cultures demonstrated the potential diversity of this bacterial group, which constitutes a distinct clade between Actinobacteria and Firmicutes. We successfully isolated two new Symbiobacterium strains from oyster shells. 16S rRNA gene-based phylogeny indicated that one belongs to S. thermophilum, and that the other is affiliated with a different species. We also isolated Ureibacillius spp., which showed activity supporting the growth of S. thermophilum.

Early Cambrian pentamerous cubozoan embryos from South China.

BACKGROUND: Extant cubozoans are voracious predators characterized by their square shape, four evenly spaced outstretched tentacles and well-developed eyes. A few cubozoan fossils are known from the Middle Cambrian Marjum Formation of Utah and the well-known Carboniferous Mazon Creek Formation of Illinois. Undisputed cubozoan fossils were previously unknown from the early Cambrian; by that time probably all representatives of the living marine phyla, especially those of basal animals, should have evolved. METHODS: Microscopic fossils were recovered from a phosphatic limestone in the Lower Cambrian Kuanchuanpu Formation of South China using traditional acetic-acid maceration. Seven of the pre-hatched pentamerous cubozoan embryos, each of which bears five pairs of subumbrellar tentacle buds, were analyzed in detail through computed microtomography (Micro-CT) and scanning electron microscopy (SEM) without coating. RESULTS: The figured microscopic fossils are unequivocal pre-hatching embryos based on their spherical fertilization envelope and the enclosed soft-tissue that has preserved key anatomical features arranged in perfect pentaradial symmetry, allowing detailed comparison with modern cnidarians, especially medusozoans. A combination of features, such as the claustrum, gonad-lamella, suspensorium and velarium suspended by the frenula, occur exclusively in the gastrovascular system of extant cubozoans, indicating a cubozoan affinity for these fossils. Additionally, the interior anatomy of these embryonic cubozoan fossils unprecedentedly exhibits the development of many new septum-derived lamellae and well-partitioned gastric pockets unknown in living cubozoans, implying that ancestral cubozoans had already evolved highly specialized structures displaying unexpected complexity at the dawn of the Cambrian. The well-developed endodermic lamellae and gastric pockets developed in the late embryonic stages of these cubozoan fossils are comparable with extant pelagic juvenile cubomedusae rather than sessile cubopolyps, whcih indicates a direct development in these fossil taxa, lacking characteristic stages of a typical cnidarian metagenesis such as planktonic planula and sessile polyps.

Tiny sea anemone from the Lower Cambrian of China.

BACKGROUND: Abundant fossils from the Ediacaran and Cambrian showing cnidarian grade grossly suggest that cnidarian diversification occurred earlier than that of other eumetazoans. However, fossils of possible soft-bodied polyps are scanty and modern corals are dated back only to the Middle Triassic, although molecular phylogenetic results support the idea that anthozoans represent the first major branch of the Cnidaria. Because of difficulties in taxonomic assignments owing to imperfect preservation of fossil cnidarian candidates, little is known about forms ancestral to those of living groups. METHODS AND FINDINGS: We have analyzed the soft-bodied polypoid microfossils Eolympia pediculata gen. et sp. nov. from the lowest Cambrian Kuanchuanpu Formation in southern China by scanning electron microscopy and computer-aided microtomography after isolating fossils from sedimentary rocks by acetic acid maceration. The fossils, about a half mm in body size, are preserved with 18 mesenteries including directives bilaterally arranged, 18 tentacles and a stalk-like pedicle. The pedicle suggests a sexual life cycle, while asexual reproduction by transverse fission also is inferred by circumferential grooves on the body column. CONCLUSIONS: The features found in the present fossils fall within the morphological spectrum of modern Hexacorallia excluding Ceriantharia, and thus Eolympia pediculata could be a stem member for this group. The fossils also demonstrate that basic features characterizing modern hexacorallians such as bilateral symmetry and the reproductive system have deep roots in the Early Cambrian.

Occurrence and detrimental effects of the bivalve-inhabiting hydroid Eutima japonica on juveniles of the Japanese scallop Mizuhopecten yessoensis in Funka Bay, Japan: relationship to juvenile massive mortality in 2003.

In November 2003, we first observed prevalent occurrence of a hydroid, Eutima japonica, on soft body tissues of age zero Japanese scallop (Mizuhopecten yessoensis) juveniles cultured in large areas of Funka Bay, Hokkaido. The occurrence coincided with massive death of juvenile scallops. A major objective was to clarify ecological relationships between the symbionts, and to infer the relationship between symbiosis and the massive mortality. To do this, we investigated distributions of association rates of hydroids with juvenile scallops at 15-34 sites over 3 years (2003-2005), with age one adult scallops at 24 sites in 2003, and with mussels at 13 sites in 2004. We studied seasonal changes in association rates with juvenile scallops, and numbers of polyps per juvenile scallop at three sites from November 2003 to June 2004. We also quantified the hydroid impacts on juvenile scallop shell length growth and triglyceride accumulation in the digestive gland. The association rate of E. japonica polyps with juvenile scallops was high in large areas of Funka Bay in 2003, and overlapped the distribution of mussels bearing polyps. Association rates with age one adult scallops were very low in November 2003, even at the sites where polyps were very common on juvenile scallops. Levels of hydroid occurrence in juvenile scallops varies by year. We found that hydroids presence in juvenile scallops declined drastically in 2004 and 2005. The association rates with juvenile scallops, and numbers of polyps per juvenile scallop declined during winter, until they disappeared completely in the following June. Since polyps were rare in adult scallops, we believe that infection of juvenile scallops was probably initiated from the planulae produced by medusae released from polyps growing on Mytilus spp., especially M. galloprovincialis. Subsequently, the inhabitation spread intraspecifically and interspecifically. In juvenile scallops, inhabitation of polyps reduced shell length growth by 43%, and triglyceride accumulation in digestive glands by 24-47%. Inhabitation of E. japonica on juvenile scallop is best regarded as parasitism, rather than inquilinism or commensalism. Occurrence of polyps was probably not a direct lethal factor for juvenile scallops, because there were some sites where association rates were high, but mortalities were low. Massive mortalities in 2003 may have resulted from simultaneous impacts of heavy polyp load and stresses caused by the way in which the animals were handled (transferred from cages for pre-intermediate culture to cages for intermediate culture), because the massive mortality occurred within a month of the transfer. The presence of polyps in juvenile scallops does not affect the quality of the product in Funka Bay, because market size scallops are hydroid-free.

The olfactory receptor gene repertoires in secondary-adapted marine vertebrates: evidence for reduction of the functional proportions in cetaceans.

An olfactory receptor (OR) multigene family is responsible for the well-developed sense of smell possessed by terrestrial tetrapods. Mammalian OR genes had diverged greatly in the terrestrial environment after the fish-tetrapod split, indicating their importance to land habitation. In this study, we analysed OR genes of marine tetrapods (minke whale Balaenoptera acutorostrata, dwarf sperm whale Kogia sima, Dall's porpoise Phocoenoides dalli, Steller's sea lion Eumetopias jubatus and loggerhead sea turtle Caretta caretta) and revealed that the pseudogene proportions of OR gene repertoires in whales were significantly higher than those in their terrestrial relative cattle and also in sea lion and sea turtle. On the other hand, the pseudogene proportion of OR sequences in sea lion was not significantly higher compared with that in their terrestrial relative (dog). It indicates that secondary perfectly adapted marine vertebrates (cetaceans) have lost large amount of their OR genes, whereas secondary-semi-adapted marine vertebrates (sea lions and sea turtles) still have maintained their OR genes, reflecting the importance of terrestrial environment for these animals.