First capture of post-spawning female of the Japanese eel Anguilla japonica at the southern West Mariana Ridge

Two adult male freshwater eels, Anguilla japonica, were captured in June 2008 in the West Mariana Ridge (13°N, 142°E) in the North Pacific, but collections of females have yet to be reported. In September 2008, we successfully caught two adult female A. japonica, 55.5 and 66.2 cm in total length, in the adjacent but northern area (14°N, 143°E). Six newly hatched eel larvae (pre-leptocephali) were also collected by subsequent plankton sampling conducted near the female catch area. Female adults appeared to be in the post-spawning state, probably a considerable time after spawning, since a small number of remarkably regressed oocytes (50–250 μm in diameter) were observed in the ovaries. Capture of post-spawning female eels and newly hatched larvae near the Suruga Seamount (14°N) together with the previous collection of mature males in the southern area (13°N) corroborates that the area along the West Mariana Ridge is the spawning area of this species, but suggests that the eel spawning may occur over a wider area than previously expected.     

Characterization of an Unknown Region Linked to the Glycoside Hydrolase Family 17 β-1,3-Glucanase of Vibrio vulnificus Reveals a Novel Glucan-Binding Domain

The glycoside hydrolase family 17 β-1,3-glucanase of Vibrio vulnificus (VvGH17) has two unknown regions in the N- and C-termini. Here, we characterized these domains by preparing mutant enzymes. VvGH17 demonstrated hydrolytic activity of β-(1→3)-glucan, mainly producing laminaribiose, but not of β-(1→3)/β-(1→4)-glucan. The C-terminal-truncated mutants (ΔC466 and ΔC441) showed decreased activity, approximately one-third of that of the WT, and ΔC415 lost almost all activity. An analysis using affinity gel containing laminarin or barley β-glucan revealed a shift in the mobility of the ΔC466, ΔC441, and ΔC415 mutants compared to the WT. Tryptophan residues showed a strong affinity for carbohydrates. Three of four point-mutations of the tryptophan in the C-terminus (W472A, W499A, and W542A) showed a reduction in binding ability to laminarin and barley β-glucan. The C-terminus was predicted to have a β-sandwich structure, and three tryptophan residues (Trp472, Trp499, and Trp542) constituted a putative substrate-binding cave. Linker and substrate-binding functions were assigned to the C-terminus. The N-terminal-truncated mutants also showed decreased activity. The WT formed a trimer, while the N-terminal truncations formed monomers, indicating that the N-terminus contributed to the multimeric form of VvGH17. The results of this study are useful for understanding the structure and the function of GH17 β-1,3-glucanases.     

Development of thyroid gland and changes in thyroid hormone levels in Leptocephali of Japanese Eel (Anguilla japonica)

Development of the thyroid gland of the Japanese eel (Anguilla japonica) was studied with the use of tank-reared fish. A single thyroid follicle was first found in larvae at 29 days post hatching (dph), total length (TL) 12 mm. Until reaching 25 mm in TL (100 dph), leptocephali had one or two follicles per individual. The inner colloid of the follicles was weakly immuno-positive against the anti-thyroxine (T₄) antibody. The number of thyroid follicles and the immunoreactivity later increased as the larvae grew. Thyroid hormones (TH) T₄ and triiodothyronine (T₃) were not detected in premetamorphic larvae by radioimmunoassays, but became detectable during metamorphosis. The maximum level of T₄ was seen in fish at the end of metamorphosis and in just-metamorphosed juveniles, whereas T₃ reached the highest level during metamorphosis and declined toward the end of metamorphosis. The results indicated that the thyroid gland first became active during metamorphosis in the development of eel.     

Relationship between prey utilization and growth variation in hatchery‐reared Pacific bluefin tuna,Thunnus orientalis (Temminck et Schlegel), larvae estimated using nitrogen stable isotope analysis

In mass culture of Pacific bluefin tuna Thunnus orientalis, a marked growth variation is observed after they start feeding at 6–7 mm in body length (BL) on yolk‐sac larvae of other species, and the growth variation in tuna larvae is a factor leading to the prevalence of cannibalism. To examine the relationship between prey utilization and growth variation, nitrogen stable isotope ratios (δ¹⁵N) of individual larvae were analysed. A prey switch experiment was conducted under two different feeding regimes: a group fed rotifers (rotifer fed group), and a group fed yolk‐sac larvae of spangled emperor, Lethrinus nebulosus (fish fed group) from 15 days after hatching (6.87 mm BL). The fish fed group showed significantly higher growth than the rotifer fed group. Changes in the δ¹⁵N of the fish fed group were expressed as an exponential model and showed different patterns from those of the rotifer fed group. The δ¹⁵N of fast‐growing tuna larvae collected in an actual mass culture tank after the feeding of yolk‐sac larvae was significantly higher than those of the slow‐growing larvae, indicating that slow glowing larvae depended largely on rotifers rather than the yolk‐sac larvae.     

Reducing sea turtle by-catch in pelagic longline fisheries

Reducing by‐catch of sea turtles in pelagic longline fisheries, in concert with activities to reduce other anthropogenic sources of mortality, may contribute to the recovery of marine turtle populations. Here, we review research on strategies to reduce sea turtle by‐catch. Due to the state of management regimes in most longline fisheries, strategies to reduce turtle interactions must not only be effective but also must be commercially viable. Because most research has been initiated only recently, many results are not yet peer‐reviewed, published or readily accessible. Moreover, most experiments have small sample sizes and have been conducted over only a few seasons in a small number of fisheries; many study designs preclude drawing conclusions about the independent effect of single factors on turtle by‐catch and target catch rates; and few studies consider effects on other by‐catch species. In the US North Atlantic longline swordfish fishery, 4.9‐cm wide circle hooks with fish bait significantly reduced sea turtle by‐catch rates and the proportion of hard‐shell turtles that swallowed hooks vs. being hooked in the mouth compared to 4.0‐cm wide J hooks with squid bait without compromising commercial viability for some target species. But these large circle hooks might not be effective or economically viable in other longline fisheries. The effectiveness and commercial viability of a turtle avoidance strategy may be fishery‐specific, depending on the size and species of turtles and target fish and other differences between fleets. Testing of turtle avoidance methods in individual fleets may therefore be necessary. It is a priority to conduct trials in longline fleets that set gear shallow, those overlapping the most threatened turtle populations and fleets overlapping high densities of turtles such as those fishing near breeding colonies. In addition to trials using large 4.9‐cm wide circle hooks in place of smaller J and Japan tuna hooks, other fishing strategies are under assessment. These include: (i) using small circle hooks (≤ 4.6‐cm narrowest width) in place of smaller J and Japan tuna hooks; (ii) setting gear below turtle‐abundant depths; (iii) single hooking fish bait vs. multiple hook threading; (iv) reducing gear soak time and retrieval during daytime; and (v) avoiding by‐catch hotspots through fleet communication programmes and area and seasonal closures.     

Effects of Observed Incubation Behavior on Egg Production in Laying Hens of a Commercial Chicken Breed and Detection of Single-Nucleotide Polymorphisms Associated with the Incubation Behavior

Upon contact with laid eggs, avians initiate incubation behavior and stop laying additional eggs. This phenomenon suggests that the productivity of laying hens in free-range facilities may decrease because of frequent contact with laid eggs. Here, we examined whether hens of a commercial breed exhibit incubation behavior in a free-range facility and whether egg productivity subsequently decreases. One-hour observations were performed twice weekly for 3 weeks, during which 9 of 129 hens (7.0%) exhibited incubation behavior (i.e., sitting on eggs) in the free-range facility and were defined as incubating hens. During 4 d of continuous behavioral observation, incubating and non-incubating hens laid the same number of eggs statistically (4.6 and 3.6, on average, respectively); however, incubating hens spent significantly more time on average incubating the eggs (2071.9 min) than did the non-incubating hens (20.9 min; P<0.05), indicating a clear behavioral difference. Subsequently, the incubation behavior and egg productivity of incubating hens and a Silkie Fowl breed hen, which is known to exhibit typical incubation behavior and cessation of laying, were continuously compared for 27 d. The average minutes spent incubating eggs during the observation period increased in both the incubating hens and Silkie Fowl hen and the total time was almost the same (18,088.5 and 23,092 min, respectively). However, the Silkie Fowl hen stopped laying on day 17 after laying 17 eggs, whereas the incubating hens continued laying throughout the observation period. Incubating hens laid an average of 24.5 eggs, indicating that some hens (at least those of the commercial breed used in our study) can continue laying while exhibiting incubation behavior. A single-nucleotide polymorphism associated with incubation behavior was detected on chromosome 4 through genome-wide association analysis.     

Screening of bacterial DNA in bile sampled from healthy dogs and dogs suffering from liver- or gallbladder-associated disease

Although the biliary system is generally aseptic, gallbladder microbiota has been reported in humans and some animals apart from dogs. We screened and analyzed the bacterial deoxyribonucleic acid in canine gallbladders using bile sampled from 7 healthy dogs and 52 dogs with liver- or gallbladder-associated disease. PCR screening detected bacteria in 17.3% of diseased dogs (9/52) and none in healthy dogs. Microbiota analysis of PCR-positive samples showed that the microbial diversity differed between liver- and gallbladder-associated disease groups. Thus, a specific bacterial community appears to occur at a certain frequency in the bile of diseased dogs.     

Chemical Characteristics of Fog Water at Mt. Tateyama, Near the Coast of the Japan Sea in Central Japan

Measurements of the chemical composition of fog water at Murododaira (altitude, 2,450 m), on the western slope of Mt. Tateyama near the coast of the Japan Sea, were performed each autumn from 2004 through 2007. Strong acidic fogs (pH?<?4) containing high concentrations of nssSO ₄ ^2? were frequently observed in the autumn of 2005, when the air mass at Mt. Tateyama originated mainly from the polluted regions of Asia. The ratio of NO ₃ ^? /nssSO ₄ ^2? in fog water was relatively high in 2004 and 2007. High concentrations of nssCa²⁺ derived from dust particles were detected in 2006. Background Kosa particles might have been predominant in the free troposphere and could have neutralized acidic fogs in the autumn of 2006. High concentrations of sea-salt components were also observed in October 2005. The sea-salt particles might have been transported from the Pacific Ocean by a strong typhoon, and significant Mg²⁺ loss was observed. Peroxides higher than 100 μM, which are seriously harmful to vegetation were sometimes detected.     

Chromosome-level de novo genome assemblies of over 100 plant species

Genome sequence analysis in higher plants began with the whole-genome sequencing of Arabidopsis thaliana. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 400 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level de novo genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 89.1%, the average coverage of chromosome-level pseudomolecules was 73.3%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.