Spatiotemporal catch distribution of age-0 Pacific bluefin tuna Thunnus orientalis caught by the Japanese troll fishery in relation to surface sea temperature and seasonal migration

This study used a delta-lognormal model to analyze monthly catches of age-0 Pacific bluefin tuna by the troll fishery. The model included fixed effects of month, area, and month–area interaction, and random effects of port, year and port–year interaction. The catch patterns by month and area predicted by the statistical model (standardized catch) revealed that main fishing grounds along the Tsushima Warm Current generally shifted from north to south as the season turned from autumn to winter. In contrast, the standardized catch along the Kuroshio Current did not show such clear spatiotemporal patterns. The standardized catch along the Tsushima Warm Current is significantly associated with average monthly sea surface temperatures in the fishing grounds and consistent with migration routes revealed by tagging experiments in previous studies. These associations indicate the spatiotemporal catch pattern in the Tsushima Warm Current region partly reflects seasonal migration. Knowledge of the possible associations among fish migration, environmental factors and spatiotemporal distribution of the catch will contribute to future management of this species.     

Impacts of the nonlinear relationship between abundance and its index in a tuned virtual population analysis

The abundance index used in a tuned virtual population analysis (VPA) is usually assumed to be proportional to actual abundance. However, the actual abundance and abundance index do not always have a linear relationship. Such nonlinearity can cause biases in abundance estimates as well as retrospective biases arising from systematic differences in abundance estimates when more data are successively added. Severe retrospective biases can damage the reliability of stock assessments. In this study, we use an approach to estimate an additional parameter that controls the nonlinearity in a tuned VPA. A performance test using simulated data revealed that the tuned VPA was able to accurately estimate the nonlinearity parameter and thus yielded less biased abundance estimates and smaller retrospective biases. We also found that estimating the nonlinearity parameters was effective even under other model misspecification scenarios, such as disregarding historical increases in catchability and time-varying natural mortality. Moreover, we applied this approach to some Japanese fish stocks and evaluated its validity. We found that estimating the nonlinearity parameters in the tuned VPA enhances the reliability of fisheries stock assessments.     

A resource selection model for analyzing pseudoreplicated data due to grouping behavior of animals

Quantifying resource selection is of primary interest in animal ecology. Many analyses of resource selection assume spatial and temporal independence of the sampling unit. Autocorrelation between observations, which is a general property of ecological variables, causes difficulties for most standard statistical procedures of resource selection because autocorrelated data violate the assumption of independence. To overcome this problem, we develop a mixed-effects model to estimate resource selection functions from data that are autocorrelated because of unobserved grouping behavior by animals. In the application of the expectation-maximization (EM) algorithm, the computation of the conditional expectation of the complete-data log-likelihood function does not have a closed-form solution requiring numerical integration. A Monte Carlo EM algorithm with Gibbs sampling can be used effectively in such situations to find exact maximum likelihood estimates. We propose a simple automated Monte Carlo EM algorithm with multiple sequences in which the Monte Carlo sample size is increased when the EM step is swamped by Monte Carlo errors.We demonstrate that the model can detect inherent autocorrelation and provide reasonable variance estimates when applied to nocturnal bird migration data. This approach could also be applied to ecological processes with various types of spatially and temporally autocorrelated data, circumventing serious problems caused by dangerous pseudoreplication.     

Association of the amino acid motifs of BoLA-DRB3 alleles with mastitis pathogens in Japanese Holstein cows

The association of the polymorphism of bovine leukocyte antigen ( BoLA-DRB3 ) genes, identified by the polymerase chain reaction sequence-based typing (PCR-SBT) method, with resistance and susceptibility to mastitis caused by Streptococci , coagulase-negative Staphylococci, Escherichia coli and Staphylococcus aureus was investigated. Blood samples for DNA extraction were collected from 170 Holstein cows (129 mastitis and 41 healthy cows) from 5 districts in Chiba prefecture, Japan. Susceptibility or resistance to the mastitis-causing pathogens was thought to vary by the presence of amino acid substitutions at the 9, 11, 13, and 30 positions. DRB3*0101 and DRB3*1501 had amino acid motifs of Glu⁹, Ser¹¹, Ser¹³, and Tyr³⁰, and they were considered to have susceptibility to all 4 mastitis pathogens. In contrast, DRB3*1101 and DRB3*1401 had amino acid motifs of Gln⁹, His¹¹, Gly¹³, and His³⁰ in these positions, and they also had Val⁸⁶, so these alleles were considered to have resistance to Streptococcal and coagulase-negative Staphylococcal mastitis. However, in the case of Escherichia coli mastitis, amino acid substitutions at the 9, 11, 13, and 30 positions had little effect, but rather substitutions at the 47, 67 positions of pocket 7, and at the 71, 74 positions of pocket 4, Tyr⁴⁷, Ile⁶⁷, Ala⁷¹, and Ala⁷⁴, were associated with resistance. This motif was present in DRB3*1201 .     

Kisspeptin as a master player in the central control of reproduction in mammals: An overview of kisspeptin research in domestic animals

The hypothalamo‐pituitary‐gonadal (HPG) axis is the regulatory system for reproduction in mammals. Because secretion of gonadotropin‐releasing hormone (GnRH) into the portal vessels is the final step at which the brain controls gonadal activities, the GnRH neuronal system had been thought to be central to the HPG axis. A newly discovered neural peptide, kisspeptin, has opened a new era in reproductive neuroendocrinology. As shown in a variety of mammals, kisspeptin is a potent endogenous secretagogue of GnRH, and the kisspeptin neuronal system governs both the pulsatile GnRH secretion that drives folliculogenesis, spermatogenesis and steroidogenesis, and the GnRH surge that triggers ovulation in females. The kisspeptin neuronal system is therefore considered a master player in the central control of mammalian reproduction, and kisspeptin and related substances could therefore be valuable for the development of novel strategies for the management of fertility in farm animals. To this end, the present review aimed to summarize the current research on kisspeptin signaling with a focus on domestic animals such as sheep, goats, cattle, pigs and horses.     

Abundance of sulphate-reducing bacteria in fish farm sediments along the coast of Japan and South Korea

The abundance of sulphate-reducing bacteria (SRB) was investigated in the coastal marine sediments along the coast of Japan and South Korea. Sediment samples were collected from fish and shellfish farms between 2006 and 2008. As non-fish farming reference sites, sediments were also collected from highly eutrophic bays, a highly sulphidogenic saline lake, and the deep sea. A quantitative real-time PCR analysis that targeted the gene coding for a portion of the α-subunit of dissimilatory sulphite reductase (dsrA) was performed to assess the abundance of the SRB in the sediments. Between 2.8 × 10⁷ and 2.5 × 10⁹ copies of the dsrA gene per gram dry sediment were detected. There was no relationship between dsrA gene copy number and total bacterial count in the sediments, whereas organic matter contents (particulate organic carbon and nitrogen, ignition loss and chemical oxygen demand) and acid-volatile sulphide contents were significantly correlated with the dsrA copy number. The data presented demonstrate that organic enrichment of sediment may influence the abundance of SRB communities in coastal marine sediments and that the cell density of SRB may be used as a biological indicator for assessing pollution levels in sediments of marine fish farms.     

Photic induction of mPer1 and mPer2 in cry-deficient mice lacking a biological clock

Mice lacking mCry1 and mCry2 are behaviorally arrhythmic. As shown here, cyclic expression of the clock genes mPer1 and mPer2 (mammalian Period genes 1 and 2) in the suprachiasmatic nucleus and peripheral tissues is abolished and mPer1 and mPer2 mRNA levels are constitutively high. These findings indicate that the biological clock is eliminated in the absence of both mCRY1 and mCRY2 (mammalian cryptochromes 1 and 2) and support the idea that mammalian CRY proteins act in the negative limb of the circadian feedback loop. The mCry double-mutant mice retain the ability to have mPer1 and mPer2 expression induced by a brief light stimulus known to phase-shift the biological clock in wild-type animals. Thus, mCRY1 and mCRY2 are dispensable for light-induced phase shifting of the biological clock.     

Differences among six Salmonella serovars in abilities to colonize reproductive organs and to contaminate eggs in laying hens

The abilities of Salmonella serovars to colonize the reproductive organs of chickens and to contaminate eggs were compared. Mature laying hens were inoculated intravenously with 10(5) colony-forming units of Salmonella enteritidis, Salmonella typhimurium, Salmonella infantis, Salmonella hadar, Salmonella heidelberg, or Salmonella montevideo to cause the systemic infection. Salmonella enteritidis was recovered from three yolks of the laid eggs (7.0%), suggesting egg contamination from the transovarian transmission of S. enteritidis. The liver, spleen, and cecum were colonized by each serovar similarly at 4 or 7 days postinoculation (PI), whereas the ovary and preovulatory follicles were colonized by S. enteritidis with significantly (P < 0.05) higher levels than by the other serovars at 4 and 7 days PI. Salmonella enteritidis was recovered from the cloaca and vagina at 2, 4, and 7 days PI and from the other portions of the oviduct at 4 and 7 days PI. In addition, S. enteritidis had been persistent in the peripheral blood for 7 days PI. These results suggest that S. enteritidis is the predominant serovar to colonize the reproductive organs of mature laying hens among six serovars used in this study, reflecting the field situatibn in which the predominant outbreaks of human salmonellosis were caused by S. enteritidis-contaminated eggs recently. The ability of S. enteritidis to colonize the reproductive organs may be one of the reasons that egg contamination with S. enteritidis has increased.     

Natural acidification of lakes and rivers in Japan: The ecosystem of Lake Usoriko (ph 3.4–3.8)

Most of the acid lakes and rivers in Japan have been influenced by acid waters of volcanic origin. Acidophilic and acidotolerant organisms are observed in these natural acid lakes and rivers, each of which has its own ecosystem and history. Lake Usoriko (pH 3.4–3.8) is a lake which.has been acidified by strongly acid water containing sulfuric acid and hydrochloric acid. The ecosystem of Lake Usoriko consists of aquatic vascular plants, aquatic bryophytes (Drepanocladus fluitans, etc.), algae, fish (Tribolodon hakonensis), insects, Zooplankton, fungi and bacteria. The paleosediment distributed along Lake Usoriko's northern shore is partly silicified and it contains fossils of a moss (Drepanocladus fluitans) and diatoms such as Pinnularia braunii var. amphicephala which are also distributed in the present lake. ¹⁴C dating of the specimens in the paleosediment, shoots of D. fluitans and the wood and cones of Picea glehnii gave values in the range 11500–34000y B.P. This record shows how long Lake Usoriko has been an acid lake.