Millisecond-scale behaviours of plankton quantified in vitro and in situ using the Event-based Vision Sensor.

The Event-based Vision Sensor (EVS) is a bio-inspired sensor that captures detailed motions of objects, aiming to become the 'eyes' of machines like self-driving cars. Compared to conventional frame-based image sensors, the EVS has an extremely fast motion capture equivalent to 10,000-fps even with standard optical settings, plus high dynamic ranges for brightness and also lower consumption of memory and energy. Here, we developed 22 characteristic features for analysing the motions of aquatic particles from the EVS raw data and tested the applicability of the EVS in analysing plankton behaviour. Laboratory cultures of six species of zooplankton and phytoplankton were observed, confirming species-specific motion periodicities up to 41 Hz. We applied machine learning to automatically classify particles into four categories of zooplankton and passive particles, achieving an accuracy up to 86%. At the in situ deployment of the EVS at the bottom of Lake Biwa, several particles exhibiting distinct cumulative trajectory with periodicities in their motion (up to 16 Hz) were identified, suggesting that they were living organisms with rhythmic behaviour. We also used the EVS in the deep sea, observing particles with active motion and periodicities over 40 Hz. Our application of the EVS, especially focusing on its millisecond-scale temporal resolution and wide dynamic range, provides a new avenue to investigate organismal behaviour characterised by rapid and periodical motions. The EVS will likely be applicable in the near future for the automated monitoring of plankton behaviour by edge computing on autonomous floats, as well as quantifying rapid cellular-level activities under microscopy.

The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae).

This study presents the complete mitochondrial genome sequence of Gammarus nipponensis, a freshwater crustacean found in the western regions of Honshu, Shikoku and Kyushu in Japan. The entire genome is 16,429 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, as well as the putative control regions. The mitochondrial genome of G. nipponensis is characterized by a high concentration of A and T nucleotides (67.1%). Notably, the mitogenome contains long TATTTTA repeats in the control region 2 at 686 bp long. This newly available genome information will be useful for studying the evolutionary relationships within the genus Gammarus and for understanding diversification among G. nipponensis populations.

Tropomyosin induces the synthesis of magnesian calcite in sea urchin spines.

Calcium carbonate is present in many biominerals, including in the exoskeletons of crustaceans and shells of mollusks. High Mg-containing calcium carbonate was synthesized by high temperatures, high pressures or high molecular organic matter. For example, biogenic high Mg-containing calcite is synthesized under strictly controlled Mg concentration at ambient temperature and pressure. The spines of sea urchins consist of calcite, which contain a high percentage of magnesium. In this study, we investigated the factors that increase the magnesium content in calcite from the spines of the sea urchin, Heliocidaris crassispina. X-ray diffraction and inductively coupled plasma mass spectrometry analyses showed that sea urchin spines contain about 4.8% Mg. The organic matrix extracted from the H. crassispina spines induced the crystallization of amorphous phase and synthesis of magnesium-containing calcite, while amorphous was synthesized without SUE (sea urchin extract). In addition, aragonite was synthesized by SUE treated with protease-K. HC tropomyosin was specifically incorporated into Mg precipitates. Recombinant HC-tropomyosin induced calcite contained 0.1-2.5% Mg synthesis. Western blotting of sea urchin spine extracts confirmed that HC tropomyosin was present in the purple sea urchin spines at a protein weight ratio of 1.5%. These results show that HC tropomyosin is one factor that increases the magnesium concentration in the calcite of H. crassispina spines.

Preliminary assessment of genetic variation in the Japanese endemic freshwater crab, Geothelphusadehaani, based on mitochondrial DNA sequences.

Geothelphusadehaani, a freshwater crab species endemic to Japan, has the largest distribution range amongst the 19 known species in the country. Due to its low dispersal capability and restricted habitat to freshwater, it serves as an excellent model for understanding gene flow between geographically isolated populations. In this study, we analysed the genetic relationships of 26 G.dehaani populations collected from different locations in the Japanese archipelago using two mitochondrial DNA regions - cytochrome oxidase subunit I (COI) and cytochrome b (cytB). Our results from the analysis of molecular variance (AMOVA) revealed high genetic variation amongst populations and the phylogenetic analysis identified four geographical groups: Clade I - Honshu and Shikoku, Clade II - north-eastern Kyushu, Clade III - southern Kyushu and Clade IV - north-western Kyushu. Notably, Clade IV exhibited the highest genetic distance amongst the observed groupings. These findings highlight the need for further examination of G.dehaani in Kyushu, including morphological and behavioural traits, to better understand the observed diversity within the species in the region.

The Germline Marker Piwi Expressed in the Skin Layer of the Polychaete Perinereis wilsoni After Injury.

Nereidid polychaete Perinereis wilsoni is a homonomous metameric worm with a complete septum between each segment. Each segment has germ cells localized in the distal area of the parapodia. Perinereis wilsoni is also known to have high abilities of tissue regeneration; however, it is still unclear whether germ cells can regenerate in the healing tissue. To address this, we surgically operated the parapodia of an adult worm to remove germ cells from the segments and observed the germ cell regeneration using the germ cell genetic marker Pw-piwi. At day 20 post-surgical operation of the parapodia in one side of the segment, we found that Pw-piwi was expressed in the regenerating parapodia. We surgically operated the parapodia on both sides of the segment to remove the germ cells completely and it gave a similar result. However, before the expression of this gene marker in the regenerating parapodia, we observed that Pw-piwi was expressed in cells in the skin layer of the worm just after surgical operations. These Pw-piwi-positive cells were not observed in the un-operated worm. Our observations showed that germ cells of Perinereis wilsoni can regenerate even after the complete removal of germ cells from the defined habitat. The Pw-piwipositive cells that appeared in the skin layer after the disappearance of germ cells may be involved in the regeneration of new germ cells.

Germ Cell Development in Male Perinereis nuntia and Gamete Spawning Mechanisms in Males and Females.

Perinereis nuntia is a fully segmented worm with complete intersegmental septa. A previous study of females revealed that germ cells of this animal originate in the tail end segment, called the pygidium. Germ cells were duplicated in the pygidium, transferred to a newly generated segment, and then settled in the parapodia. Within each segment, the settled germ cells proliferated in the parapodia and then migrated into a body cavity area to begin meiotic development. Currently, there is not much information about differences between male and female germ cell development. Therefore, we conducted monthly in situ hybridization analyses using the germ cell marker Pn-piwi and histological examinations. Germ cells detected by Pn-piwi initially settled in the distal areas of the parapodia on both sides of each segment, then formed a large germ cell cluster in each parapodium, and finally, small germ cell clusters were formed by the separation of the large clusters. The small clusters migrated to the deeper body cavity area during growth by segment addition. Until the female germ cells began vitellogenesis, the sex of germ cells could not be identified by morphological observation. Thus, male and female P. nuntia may have the same mechanism of germ cell provision to all segments. At the time of spawning, sperm were released from nephridiopores at the 2nd through 15th segments from the pygidium, while eggs were released through ruptures in the skin of 2-3 segments between the 10th and 30th segments from the tail.

Using environmental DNA analyses to assess the occurrence and abundance of the endangered amphidromous fish Plecoglossus altivelis ryukyuensis.

The Ryukyu ayu Plecoglossus altivelis ryukyuensis is an endangered amphidromous fish that inhabits rivers in the Ryukyu Archipelago (Japan). Populations of the species have declined dramatically. Consequently, the Ryukyu ayu has been registered as a natural monument in Japan and monitoring surveys with direct catching are restricted legally. This restriction, unfortunately, makes monitoring of population abundances difficult and creates a barrier to both advancing understanding of the species' status and the development of appropriate conservation plans. We developed a non-invasive monitoring methodology using eDNA analyses. We designed a specific quantitative PCR assay for the Ryukyu ayu using the mitochondrial ND4 region. Using this primer/probe set, we conducted eDNA analyses in three rivers on Amami-Ohshima Island. The DNA fragments were amplified from the eDNA extracted from natural water in each river. The numbers of DNA fragments detected were positively correlated with individual counts of fish obtained by visual snorkelling surveys. Our method does not contravene restrictions and facilitates abundance monitoring of this endangered fish species.

Photo images, 3D/CT data and mtDNA of the freshwater mussels (Bivalvia: Unionidae) in the Kyushu and Ryukyu Islands, Japan, with SEM/EDS analysis of the shell.

BACKGROUND: Freshwater mussels (Bivalvia: Unionidae), which are keystone species of freshwater ecosystems, are in global decline. In addition to ecological/genetic studies, morphological examinations are needed to help provide information for the development of additional freshwater mussel studies and eventually conservation efforts for freshwater ecosystems.The microscopic structure, which can be obtained by scanning electron microscopy (SEM) and elemental composition, which can be obtained with energy dispersive X-ray spectrometry (EDS), of mollusc shells are of interest to malacologists. However, information about freshwater mussels is still limited.Kyushu Island is the southernmost island of the four major islands of Japan. Kyushu Island is a hotspot of bitterling fishes in Japan, which simultaneously means that the island is a hotspot of freshwater mussels. The Ryukyu Islands stretch southwest from Kyushu Island to Taiwan; a freshwater mussel of unknown origin was reported from the Ryukyu Islands.Digital archiving for biology and ecology is a continuing challenge for open science. This data paper describes online published photo images, 3D/CT and mtDNA data and SEM/EDS analyses of the shell of freshwater mussels that inhabit the Kyushu and Ryukyu Islands, Japan. Our data will provide basic information regarding freshwater biology and be of public interest as open science. NEW INFORMATION: Photo images, 3D/CT data, mtDNA data, SEM images and EDS elemental analysis of freshwater mussels that inhabit the Kyushu and Ryukyu Islands (61 individuals, nine species/subspecies) were published online in a local database (http://ffish.asia/Unionidae3D), GBIF (http://ipt.pensoft.net/resource?r=unionidae3d) and DDBJ/EMBL/Genbank (LC431810-LC431840).

A model for germ cell development in a fully segmented worm.

INTRODUCTION: Polychaetes are segmented marine worms with body segments separated by a complete or incomplete septum. In most polychaetes the whole body cavity is filled with gametes during the breeding season. Platynereis dumerilii (Pl. dumerilii), which has an incomplete septum was shown to develop a single gonadal structure for gamete production located in the neck region. However, in Perinereis nuntia (Pe. nuntia), which has a complete septum separating each segment, the developmental feature of gametes remains unknown. To clarify this, the marker gene vasa was used to trace the development of germ cells throughout the life stages of Pe. nuntia. RESULTS: In three-segmented juveniles, Pn-vasa was expressed in the parapodia and in the two cells localized in the pygidium. During the addition of a new segment, Pn-vasa positive cells in the pygidium increased from two to four and two new Pn-vasa positive cells were found in the newly-generated segment. In adults, Pn-vasa was expressed in a large cell cluster at the distal end of the parapodia, in smaller cell clusters (which had an elongated form in the trunk area of the parapodia), and in oocytes in the coelomic cavity. This may suggest that germ cells settle in the parapodia and later translocate into the coelomic cavity to develop into oocytes. CONCLUSION: Our observations will help in understanding the mechanism of germ cell development in all body segments of Pe. nuntia. We hypothesize that primordial germ cells are supplied from the pygidium to every newly-generating segment which later settle in the parapodium. This will explain how polychaetes can generate gametes in each body segment, even those that are independently separated with a complete septum.

Cleavage pattern and development of isolated D blastomeres in bivalves.

Although bivalves develop through spiral cleavage patterns, similar to other lophotrochozoans, the cleavage pattern of D lineage blastomeres is unique, since 2d shows four rounds of stereotypic unequal cleavage before bilateral cleavage of the largest derivative of 2d: 2d(1121) . This unique modification of spiral cleavage is directly associated with the characteristic morphology of bivalves, namely, bilaterally separated shell plates, because the bilateral shell plates are thought to be derived from the bilateral derivatives of 2d(1121) . In this report, to determine whether the unique cleavage pattern of bivalves is regulated depending on the interaction with other cells or by cell autonomous mechanisms, we performed cell isolation experiments and observed subsequent cleavage patterns of isolated blastomeres. When focusing on the largest derivatives of D blastomeres, 8% of isolated D blastomeres followed the cleavage pattern of normal development up to bilateral cleavage. Importantly, the remainder of the partial embryos ended cleavage before that stage, and none of the isolated blastomeres showed abnormal cleavage patterns. We also examined the development of isolated blastomeres and found that isolated D blastomeres could develop shell plates, whereas larvae developed from AB blastomeres never had shell plates. Based on these observations, we concluded that D blastomeres control their unique cleavage pattern through intrinsic mechanisms and develop shell glands autonomously without any cell-cell interaction with other lineages.

Developmental role of dpp in the gastropod shell plate and co-option of the dpp signaling pathway in the evolution of the operculum.

The operculum is a novel structure in gastropod molluscs. Because the operculum shows notable similarities to the shell plate, we asked whether there were an evolutionary link between these two secretory organs. We found that some of the genes involved in shell-field development are expressed in the operculum, such as dpp and grainyhead, whereas engrailed and Hox1 are not. Specific knockdown of dpp by injection of double-stranded RNA (dsRNA) resulted in malformation of the shell plate. The shell plate was smaller due to failure of activation of cell proliferation in the shell-field margin. The expressions of grainyhead and chitin synthase 1 in the shell field margin were suppressed by dpp-dsRNA. However, matrix secretion was not completely abolished, and the expressions of ferritin, engrailed or Hox1 were not affected by dpp-dsRNA, indicating that dpp is partly involved in the developmental pathway for shell matrix secretion. We also present evidence that dpp performs a key role in operculum development. Indeed, dpp-dsRNA impaired matrix secretion in the operculum as well as expression of grainyhead. Based on these observations that dpp is important for development of both the shell plate and operculum, we conclude that co-option of dpp to the posterior part of the foot contributed to the innovation of the operculum in gastropods.

Evidence that gastropod torsion is driven by asymmetric cell proliferation activated by TGF-beta signalling.

Gastropods are characterized by their asymmetric bodyplan, which develops through a unique ontogenetic process called 'torsion'. Despite several intensive studies, the driving force of torsion remains to be determined. Although torsion was traditionally believed to be driven by contraction of the retractor muscle connecting the foot and the shell, some recent reports cast doubt on that idea. Here, we report that torsion is accompanied by left-right asymmetric cell proliferation in the mantle epithelium in the limpet Nipponacmea fuscoviridis. Furthermore, we found that pharmacological inhibition of the transforming growth factor-ß (TGF-ß) signalling pathway, including that of Nodal, blocked torsion. We confirmed that the blocking was brought about through failure of the activation of cell proliferation in the right-hand side of the mantle epithelium, while the retractor muscle apparently developed normally. These results suggest that limpet torsion is driven by left-right asymmetric cell proliferation in the mantle epithelium, induced by the TGF-ß pathway.

Early development and cleavage pattern of the Japanese purple mussel, Septifer virgatus.

Despite easy access to bivalves, few studies have examined the development of these animals, at least in part because most bivalve eggs are very small. In addition, annotating cells of the early bivalve embryo is difficult because few landmarks are present. We conducted detailed cell annotations of the Japanese purple mussel, Septifer virgatus, during early embryogenesis because of its relatively large eggs (ca. 130 microm in diameter). Septifer virgatus underwent the unique cell division profile reported for four other bivalve species, suggesting that the cleavage pattern itself is important for bivalve morphogenesis. The shell field invagination was led by 2d (X) lineage cells, supporting the hypothesis that lineage cells differentiate into cells excreting the shell matrix. The large egg size enabled us to trace cell movements in the early gastrulation phase, during which the invagination of the archenteron was initiated by 4d (M) lineage cells. These observations will serve as a basis for future analyses of S. virgatus embryogenesis and will contribute to understanding the evolution of the molluscan body plan, which is achieved by modification of early embryogenesis.

Molecular cloning of cDNA encoding APC11, a catalytic component of anaphase-promoting-complex (APC/C), from goldfish (Carassius auratus), and establishment of in vitro ubiquitinating system.

Destruction of cyclin B is required for exit from mitosis and meiosis. A cyclin-degrading system, including anaphase-promoting-complex/cyclosome (APC/C), has been shown to be responsible for cyclin B destruction. Here we present the cloning, sequencing, and expression analysis of goldfish (Carassius auratus) APC11, which encodes the catalytic component of APC/C from goldfish ovary. The cloned cDNA is 348 bp long and encodes 88 amino acids. The deduced amino acid sequence is highly homologous to APC11 from other species. The expression of mRNA for APC11 was ubiquitous among tissues, as opposed to that of mRNA for E2-C, which occurred at a very high level in the ovary. Recombinant goldfish APC11 possesses ubiquitinating activity against cyclin B. We established an in vitro ubiquitinating system of proteins composed of purified recombinant E1, E2-C, and APC11 from goldfish. The reconstructed system for these ubiquitinating enzymes makes it feasible to elucidate the molecular mechanism of cyclin B degradation.