Tokyo University of Marine Science and Technology

Abstract A new version of the atmosphere–ocean general circulation model cooperatively produced by the Japanese research community, known as the Model for Interdisciplinary Research on Climate (MIROC), has recently been developed. A century-long control experiment was performed using the new version (MIROC5) with the standard resolution of the T85 atmosphere and 1° ocean models. The climatological mean state and variability are then compared with observations and those in a previous version (MIROC3.2) with two different resolutions (medres, hires), coarser and finer than the resolution of MIROC5. A few aspects of the mean fields in MIROC5 are similar to or slightly worse than MIROC3.2, but otherwise the climatological features are considerably better. In particular, improvements are found in precipitation, zonal mean atmospheric fields, equatorial ocean subsurface fields, and the simulation of El Niño–Southern Oscillation. The difference between MIROC5 and the previous model is larger than that between the two MIROC3.2 versions, indicating a greater effect of updating parameterization schemes on the model climate than increasing the model resolution. The mean cloud property obtained from the sophisticated prognostic schemes in MIROC5 shows good agreement with satellite measurements. MIROC5 reveals an equilibrium climate sensitivity of 2.6 K, which is lower than that in MIROC3.2 by 1 K. This is probably due to the negative feedback of low clouds to the increasing concentration of CO2, which is opposite to that in MIROC3.2.

Abstract Cellulose is the most abundant polysaccharide on Earth. It can be obtained from a vast number of sources, e.g. cell walls of wood and plants, some species of bacteria, and algae, as well as tunicates, which are the only known cellulose-containing animals. This inherent abundance naturally paves the way for discovering new applications for this versatile material. This review provides an extensive survey on cellulose and its derivatives, their structural and biochemical properties, with an overview of applications in tissue engineering, wound dressing, and drug delivery systems. Based on the available means of selecting the physical features, dimensions, and shapes, cellulose exists in the morphological forms of fiber, microfibril/nanofibril, and micro/nanocrystalline cellulose. These different cellulosic particle types arise due to the inherent diversity among the source of organic materials or due to the specific conditions of biosynthesis and processing that determine the consequent geometry and dimension of cellulosic particles. These different cellulosic particles, as building blocks, produce materials of different microstructures and properties, which are needed for numerous biomedical applications. Despite having great potential for applications in various fields, the extensive use of cellulose has been mainly limited to industrial use, with less early interest towards the biomedical field. Therefore, this review highlights recent developments in the preparation methods of cellulose and its derivatives that create novel properties benefiting appropriate biomedical applications.

Abstract. The sixth version of the Model for Interdisciplinary Research on Climate (MIROC), called MIROC6, was cooperatively developed by a Japanese modeling community. In the present paper, simulated mean climate, internal climate variability, and climate sensitivity in MIROC6 are evaluated and briefly summarized in comparison with the previous version of our climate model (MIROC5) and observations. The results show that the overall reproducibility of mean climate and internal climate variability in MIROC6 is better than that in MIROC5. The tropical climate systems (e.g., summertime precipitation in the western Pacific and the eastward-propagating Madden–Julian oscillation) and the midlatitude atmospheric circulation (e.g., the westerlies, the polar night jet, and troposphere–stratosphere interactions) are significantly improved in MIROC6. These improvements can be attributed to the newly implemented parameterization for shallow convective processes and to the inclusion of the stratosphere. While there are significant differences in climates and variabilities between the two models, the effective climate sensitivity of 2.6 K remains the same because the differences in radiative forcing and climate feedback tend to offset each other. With an aim towards contributing to the sixth phase of the Coupled Model Intercomparison Project, designated simulations tackling a wide range of climate science issues, as well as seasonal to decadal climate predictions and future climate projections, are currently ongoing using MIROC6.

Continuous observations of aerosols in China and Japan were made by polarization lidars during March to May 2001, corresponding with the Asian Pacific Regional Aerosol Characterization Experiment (ACE‐Asia) field campaign period. Lidars in Beijing, Nagasaki, and Tsukuba were continuously operated regardless of weather conditions. Scatterers in the atmosphere were categorized for all vertical profiles, and occurrence frequencies of dust, spherical aerosols, and clouds up to 6 km were calculated. The frequency of dust was highest in Beijing for the whole height range. There was a peak of dust occurrence near the ground in Nagasaki. Dust was frequently detected in the free troposphere in Tsukuba. The contributions of dust and spherical aerosols to the total backscattering coefficient were estimated from the depolarization ratio with the assumption of the external mixture of both kinds of aerosols. Vertical profiles of backscattering by dust and by spherical aerosols represented the different characteristics of these aerosols. The monthly averaged backscattering coefficients by dust near the surface were 0.003/km/sr in Beijing, 0.001–0.002/km/sr in Nagasaki, and 0.0006/km/sr in Tsukuba. The backscattering coefficients by spherical aerosols near the surface were 0.002–0.004/km/sr at all three observatories. We compared the derived backscattering coefficients with aerosol mass concentrations calculated by a numerical model, Chemical Weather Forecasting System (CFORS). CFORS reproduced well the vertical structures of the tall dust events and the enhancements of spherical aerosols throughout the observation period. A specific dust event on 16–19 May 2001 was analyzed by using five lidars in Japan, and its fine structure is described.

A pronounced, widespread and persistent regime shift among marine ecosystems is observable on temperate rocky reefs as a result of sea urchin overgrazing. Here, we empirically define regime-shift dynamics for this grazing system which transitions between productive macroalgal beds and impoverished urchin barrens. Catastrophic in nature, urchin overgrazing in a well-studied Australian system demonstrates a discontinuous regime shift, which is of particular management concern as recovery of desirable macroalgal beds requires reducing grazers to well below the initial threshold of overgrazing. Generality of this regime-shift dynamic is explored across 13 rocky reef systems (spanning 11 different regions from both hemispheres) by compiling available survey data (totalling 10 901 quadrats surveyed in situ ) plus experimental regime-shift responses (observed during a total of 57 in situ manipulations). The emergent and globally coherent pattern shows urchin grazing to cause a discontinuous ‘catastrophic’ regime shift, with hysteresis effect of approximately one order of magnitude in urchin biomass between critical thresholds of overgrazing and recovery. Different life-history traits appear to create asymmetry in the pace of overgrazing versus recovery. Once shifted, strong feedback mechanisms provide resilience for each alternative state thus defining the catastrophic nature of this regime shift. Importantly, human-derived stressors can act to erode resilience of desirable macroalgal beds while strengthening resilience of urchin barrens, thus exacerbating the risk, spatial extent and irreversibility of an unwanted regime shift for marine ecosystems.

Gonadal sex determination in vertebrates generally follows a sequence of genetically programmed events. In what is seemingly becoming a pattern, all confirmed or current candidate "master" sex-determining genes reported in this group, e.g., SRY in eutherian mammals, DMY/dmrt1bY in medaka, DM-W in the African clawed frog, and DMRT1 in chicken encode transcription factors. In contrast, here we show that a male-specific, duplicated copy of the anti-Müllerian hormone (amh) is implicated in testicular development of the teleost fish Patagonian pejerrey (Odontesthes hatcheri). The gene, termed amhy because it is found in a single metacentric/submetacentric chromosome of XY individuals, is expressed much earlier than the autosomal amh (6 d after fertilization vs. 12 wk after fertilization) and is localized to presumptive Sertoli cells of XY males during testicular differentiation. Moreover, amhy knockdown in XY embryos resulted in the up-regulation of foxl2 and cyp19a1a mRNAs and the development of ovaries. These results are evidence of a functional amh duplication in vertebrates and suggest that amhy may be the master sex-determining gene in this species. If confirmed, this would be a unique instance of a hormone-related gene, a member of the TGF-β superfamily, in such a role.

Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.

The Argo Program has been implemented and sustained for almost two decades, as a global array of about 4000 profiling floats. Argo provides continuous observations of ocean temperature and salinity versus pressure, from the sea surface to 2000 dbar. The successful installation of the Argo array and its innovative data management system arose opportunistically from the combination of great scientific need and technological innovation. Through the data system, Argo provides fundamental physical observations with broad societally-valuable applications, built on the cost-efficient and robust technologies of autonomous profiling floats. Following recent advances in platform and sensor technologies, even greater opportunity exists now than 20 years ago to (i) improve Argo’s global coverage and value beyond the original design, (ii) extend Argo to span the full ocean depth, (iii) add biogeochemical sensors for improved understanding of oceanic cycles of carbon, nutrients, and ecosystems, and (iv) consider experimental sensors that might be included in the future, for example to document the spatial and temporal patterns of ocean mixing. For Core Argo and each of these enhancements, the past, present, and future progression along a path from experimental deployments to regional pilot arrays to global implementation is described. The objective is to create a fully global, top-to-bottom, dynamically complete, and multidisciplinary Argo Program that will integrate seamlessly with satellite and with other in situ elements of the Global Ocean Observing System (Legler et al., 2015). The integrated system will deliver operational reanalysis and forecasting capability, and assessment of the state and variability of the climate system with respect to physical, biogeochemical, and ecosystems parameters. It will enable basic research of unprecedented breadth and magnitude, and a wealth of ocean-education and outreach opportunities.

Abstract The Arctic Ocean is a fundamental node in the global hydrological cycle and the ocean's thermohaline circulation. We here assess the system's key functions and processes: (1) the delivery of fresh and low‐salinity waters to the Arctic Ocean by river inflow, net precipitation, distillation during the freeze/thaw cycle, and Pacific Ocean inflows; (2) the disposition (e.g., sources, pathways, and storage) of freshwater components within the Arctic Ocean; and (3) the release and export of freshwater components into the bordering convective domains of the North Atlantic. We then examine physical, chemical, or biological processes which are influenced or constrained by the local quantities and geochemical qualities of freshwater; these include stratification and vertical mixing, ocean heat flux, nutrient supply, primary production, ocean acidification, and biogeochemical cycling. Internal to the Arctic the joint effects of sea ice decline and hydrological cycle intensification have strengthened coupling between the ocean and the atmosphere (e.g., wind and ice drift stresses, solar radiation, and heat and moisture exchange), the bordering drainage basins (e.g., river discharge, sediment transport, and erosion), and terrestrial ecosystems (e.g., Arctic greening, dissolved and particulate carbon loading, and altered phenology of biotic components). External to the Arctic freshwater export acts as both a constraint to and a necessary ingredient for deep convection in the bordering subarctic gyres and thus affects the global thermohaline circulation. Geochemical fingerprints attained within the Arctic Ocean are likewise exported into the neighboring subarctic systems and beyond. Finally, we discuss observed and modeled functions and changes in this system on seasonal, annual, and decadal time scales and discuss mechanisms that link the marine system to atmospheric, terrestrial, and cryospheric systems.

Laboratory-based studies have suggested that marine organisms can be harmed by ingesting microplastics. However, unless the current and future microplastic abundance in the ocean environment is quantified, these experimental studies could be criticized for using an unrealistic density or sparsity of microplastics. Here we show the secular variations of pelagic microplastic abundance in the Pacific Ocean from 1957 to 2066, based on a combination of numerical modeling and transoceanic surveys conducted meridionally from Antarctica to Japan. Marine plastic pollution is an ongoing concern especially in the North Pacific, and pelagic microplastics are regarded as non-conservative matter due to the removal processes that operate in the upper ocean. The results of our numerical model incorporating removal processes on a 3-year timescale suggested that the weight concentrations of pelagic microplastics around the subtropical convergence zone would increase approximately twofold (fourfold) by 2030 (2060) from the present condition.

Balanced fishing across a range of species, stocks, and sizes could mitigate adverse effects and address food security better than increased selectivity.

We constructed a genetic linkage map for a tetraploid derivative species, the rainbow trout (Oncorhynchus mykiss), using 191 microsatellite, 3 RAPD, 7 ESMP, and 7 allozyme markers in three backcross families. The linkage map consists of 29 linkage groups with potential arm displacements in the female map due to male-specific pseudolinkage arrangements. Synteny of duplicated microsatellite markers was used to identify and confirm some previously reported pseudolinkage arrangements based upon allozyme markers. Fifteen centromeric regions (20 chromosome arms) were identified with a half-tetrad analysis using gynogenetic diploids. Female map length is approximately 10 M, but this is a large underestimate as many genotyped segments remain unassigned at a LOD threshold of 3.0. Extreme differences in female:male map distances were observed (ratio F:M, 3.25:1). Females had much lower recombination rates (0.14:1) in telomeric regions than males, while recombination rates were much higher in females within regions proximal to the centromere (F:M, 10:1). Quadrivalent formations that appear almost exclusively in males are postulated to account for the observed differences.

Superconducting technology applications in electric machines have long been pursued due to their significant advantages of higher efficiency and power density over conventional technology. However, in spite of many successful technology demonstrations, commercial adoption has been slow, presumably because the threshold for value versus cost and technology risk has not yet been crossed. One likely path for disruptive superconducting technology in commercial products could be in applications where its advantages become key enablers for systems which are not practical with conventional technology. To help systems engineers assess the viability of such future solutions, we present a technology roadmap for superconducting machines. The timeline considered was ten years to attain a Technology Readiness Level of 6+, with systems demonstrated in a relevant environment. Future projections, by definition, are based on the judgment of specialists, and can be subjective. Attempts have been made to obtain input from a broad set of organizations for an inclusive opinion. This document was generated through a series of teleconferences and in-person meetings, including meetings at the 2015 IEEE PES General meeting in Denver, CO, the 2015 ECCE in Montreal, Canada, and a final workshop in April 2016 at the University of Illinois, Urbana-Champaign that brought together a broad group of technical experts spanning the industry, government and academia.

To investigate concentrations of pelagic micro- (<5mm in size) and mesoplastics (>5mm) in the East Asian seas around Japan, field surveys using two vessels were conducted concurrently in summer 2014. The total particle count (pieces km(-2)) was computed based on observed concentrations (pieces m(-3)) of small plastic fragments (both micro- and mesoplastics) collected using neuston nets. The total particle count of microplastics within the study area was 1,720,000 pieces km(-2), 16 times greater than in the North Pacific and 27 times greater than in the world oceans. The proportion of mesoplastics increased upstream of the northeastward ocean currents, such that the small plastic fragments collected in the present surveys were considered to have originated in the Yellow Sea and East China Sea southwest of the study area.

Abstract Marine finfish require n‐3 HUFA such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) as essential fatty acids (EFA) for their normal growth. But it remained unclear as to which of the n‐3 HUFA, either EPA or DHA, was important. Unlike the freshwater species, the EFA efficiency of EPA and DHA may vary in marine fish. The developing eggs rapidly utilize DHA either for energy or for production of physiologically important substances like prostaglandin. This report reveals that in marine larval fish DHA is superior to EPA as EFA. In the case of red seabream, feeding rotifers incorporating EPA and DHA or an n‐3 HUFA mixture prevented many of the ill‐effects observed when the rotifers were low in n‐3 HUFA. Apart from the best growth and survival in an activity test for the larvae fed on DHA‐rotifer, the incidence of hydrops seemed to be totally prevented dietetically by DHA. Similar results were obtained in larval yellowtail, striped jack, striped knifejaw and flounder. There seems to exist a functional difference between EPA and DHA.

In the past two decades, the Argo Program has collected, processed and distributed over two million vertical profiles of temperature and salinity from the upper two kilometers of the global ocean. A similar number of subsurface velocity observations near 1000 dbar have also been collected. This paper recounts the history of the global Argo Program, from its aspiration arising out of the World Ocean Circulation Experiment, to the development and implementation of its instrumentation and telecommunication systems, and the various technical problems encountered. We describe the Argo data system and its quality control procedures, and the gradual changes in the vertical resolution and spatial coverage of Argo data from 1999 to 2019. The accuracies of the float data have been assessed by comparison with high-quality shipboard measurements, and are concluded to be 0.002°C for temperature, 2.4 dbar for pressure, and 0.01 PSS-78 for salinity, after delayed-mode adjustments. Finally, the challenges faced by the vision of an expanding Argo Program beyond 2020 are discussed.

A field survey to collect microplastics with sizes < 5 mm was conducted in the Southern Ocean in 2016. We performed five net-tows and collected 44 pieces of plastic. Total particle counts of the entire water column, which is free of vertical mixing, were computed using the surface concentration (particle count per unit seawater volume) of microplastics, wind speed, and significant wave height during the observation period. Total particle counts at two stations near Antarctica were estimated to be in the order of 100,000 pieces km− 2.

Recent record lows of Arctic summer sea ice extent are found to be triggered by the Arctic atmospheric Dipole Anomaly (DA) pattern. This local, second–leading mode of sea–level pressure (SLP) anomaly in the Arctic produced a strong meridional wind anomaly that drove more sea ice out of the Arctic Ocean from the western to the eastern Arctic into the northern Atlantic during the summers of 1995, 1999, 2002, 2005, and 2007. In the 2007 summer, the DA also enhanced anomalous oceanic heat flux into the Arctic Ocean via Bering Strait, which accelerated bottom and lateral melting of sea ice and amplified the ice–albedo feedback. A coupled ice–ocean model was used to confirm the historical record lows of summer sea ice extent.

Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.

Abstract Analysis of modern and historical observations demonstrates that the temperature of the intermediate-depth (150–900 m) Atlantic water (AW) of the Arctic Ocean has increased in recent decades. The AW warming has been uneven in time; a local ∼1°C maximum was observed in the mid-1990s, followed by an intervening minimum and an additional warming that culminated in 2007 with temperatures higher than in the 1990s by 0.24°C. Relative to climatology from all data prior to 1999, the most extreme 2007 temperature anomalies of up to 1°C and higher were observed in the Eurasian and Makarov Basins. The AW warming was associated with a substantial (up to 75–90 m) shoaling of the upper AW boundary in the central Arctic Ocean and weakening of the Eurasian Basin upper-ocean stratification. Taken together, these observations suggest that the changes in the Eurasian Basin facilitated greater upward transfer of AW heat to the ocean surface layer. Available limited observations and results from a 1D ocean column model support this surmised upward spread of AW heat through the Eurasian Basin halocline. Experiments with a 3D coupled ice–ocean model in turn suggest a loss of 28–35 cm of ice thickness after ∼50 yr in response to the 0.5 W m−2 increase in AW ocean heat flux suggested by the 1D model. This amount of thinning is comparable to the 29 cm of ice thickness loss due to local atmospheric thermodynamic forcing estimated from observations of fast-ice thickness decline. The implication is that AW warming helped precondition the polar ice cap for the extreme ice loss observed in recent years.