Draft Genome Sequences of Two Genetic Variant Strains of Edwardsiella piscicida, JF1305 and RSB1309, Isolated from Olive Flounder (Paralichythys olivaceus) and Red Sea Bream (Pagrus major) Cultured in Japan, Respectively.

Edwardsiella piscicida is a new species discovered within the group of organisms traditionally classified as Edwardsiella tarda. We present draft genome sequences of two variant strains of E. piscicida, JF1305 and RSB1309. Differences in protein-coding sequence between these isolates are associated with virulence, disease, and defense, suggesting differences in pathogenicity.

Short-term prediction of dynamical behavior of flame front instability induced by radiative heat loss.

We apply nonlinear forecasting to the time series of the flame front instability induced by radiative heat loss to test for the short-term predictability and long-term unpredictability characteristic of deterministic chaos in flame front instability. Our results indicate that the flame front instability represents high-dimensional chaos generated via the period-doubling cascade process reported in our previous study [H. Gotoda, K. Michigami, K. Ikeda, and T. Miyano, Combust Theory Modell. 14, 479 (2010)], while its short-term behavior is predictable using a local nonlinear predictor based on the Sugihara-May method [H. Gotoda, H. Nikimoto, T. Miyano, and S. Tachibana, Chaos 20, 013124 (2011); G. Sugihara and R. M. May, Nature 344, 734 (1990)] as well as a generalized radial basis function network as a global nonlinear predictor. The feasibility of a new approach based on short-term prediction is also discussed in this work from the practical viewpoint of combustion systems.

Characterization of complexities in combustion instability in a lean premixed gas-turbine model combustor.

We characterize complexities in combustion instability in a lean premixed gas-turbine model combustor by nonlinear time series analysis to evaluate permutation entropy, fractal dimensions, and short-term predictability. The dynamic behavior in combustion instability near lean blowout exhibits a self-affine structure and is ascribed to fractional Brownian motion. It undergoes chaos by the onset of combustion oscillations with slow amplitude modulation. Our results indicate that nonlinear time series analysis is capable of characterizing complexities in combustion instability close to lean blowout.

Predation risk suppresses the positive feedback between size structure and cannibalism.

1. Cannibalism can play a prominent role in the structuring and dynamics of ecological communities. Previous studies have emphasized the importance of size structure and density of cannibalistic species in shaping short- and long-term cannibalism dynamics, but our understanding of how predators influence cannibalism dynamics is limited. This is despite widespread evidence that many prey species exhibit behavioural and morphological adaptations in response to predation risk. 2. This study examined how the presence and absence of predation risk from larval dragonflies Aeshna nigroflava affected cannibalism dynamics in its prey larval salamanders Hynobius retardatus. 3. We found that feedback dynamics between size structure and cannibalism depended on whether dragonfly predation risk was present. In the absence of dragonfly risk cues, a positive feedback between salamander size structure and cannibalism through time occurred because most of the replicates in this treatment contained at least one salamander larvae having an enlarged gape (i.e. cannibal). In contrast, this feedback and the emergence of cannibalism were rarely observed in the presence of the dragonfly risk cues. Once salamander size divergence occurred, experimental reversals of the presence or absence of dragonfly risk cues did not alter existing cannibalism dynamics as the experiment progressed. Thus, the effects of risk on the mechanisms driving cannibalism dynamics likely operated during the early developmental period of the salamander larvae. 4. The effects of dragonfly predation risk on behavioural aspects of cannibalistic interactions among hatchlings may prohibit the initiation of dynamics between size structure and cannibalism. Our predation trials clearly showed that encounter rates among hatchlings and biting and ingestion rates of prospective prey by prospective cannibals were significantly lower in the presence vs. absence of dragonfly predation risk even though the size asymmetry between cannibals and victims was similar in both risk treatments. These results suggest that dragonfly risk cues first suppress cannibalism among hatchlings and then prevent size variation from increasing through time. 5. We suggest that the positive feedback dynamics between size structure and cannibalism and their modification by predation risk may also operate in other systems to shape the population dynamics of cannibalistic prey species as well as overall community dynamics.

Presence of Merkel cell polyomavirus in Japanese cutaneous squamous cell carcinoma.

BACKGROUND: Merkel cell polyomavirus (MCPyV) was first identified in Merkel cell carcinoma (MCC) as a new tumor virus. Studies have also reported differing frequencies of MCPyV detection in other skin cancers in western countries. OBJECTIVES: Little is known about geographical differences of MCPyV prevalence in non-MCC tumors. We examined the existence of MCPyV in non-MCC skin cancers including squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) in Japanese patients. STUDY DESIGN: Paraffin-embedded tissues of cutaneous SCC (n=30) and BCC (n=10) from Japanese patients were tested for the presence of MCPyV by polymerase chain reaction (PCR) with primer sets directed against the genes encoding large-T antigen 3 (LT3) and viral protein 1 (VP1). This was followed by DNA fragment sequencing and immunohistochemistry. RESULTS: PCR analysis targeting the LT3 gene showed that the viral sequences were found in 4 of 30 (13%) SCC cases. Nested PCR detected the VP1 region in four cases. Sequencing analysis of these PCR-amplified fragments showed a close homology to the previously published MCPyV sequences. Immunohistochemistry with the monoclonal antibody to MCPyV LT-antigen showed positive staining in 2 of 4 LT3 PCR-positive cases. On the other hand, our BCC samples were all negative for MCPyV. CONCLUSION: This study suggested that Japanese cutaneous SCC is infrequently associated with MCPyV. Further worldwide epidemiological surveys are warranted to determine the possible association of MCPyV with pathogenesis of non-MCC skin cancers.

Protection of red sea bream Pagrus major against red sea bream iridovirus infection by vaccination with a recombinant viral protein.

Megalocytivirus infections cause serious mass mortality in marine fish in East and Southeast Asian countries. In this study the immunogenicity of crude subunit vaccines against infection by the Megalocytivirus RSIV was investigated. Three capsid proteins, 18R, 351R and a major capsid protein, were selected for use as crude subunit vaccines. High homology among Megalocytivirus types was found in the initial sequence examined, the 351R region. Red sea bream (Pagrus major) juveniles were vaccinated by intraperitoneal injection of recombinant formalin-killed Escherichia coli cells expressing these three capsid proteins. After challenge infection with RSIV, fish vaccinated with the 351R-recombinant bacteria showed significantly greater survival than those vaccinated with control bacteria. The 351R protein was co-expressed with GAPDH from the bacterium Edwardsiella tarda in E. coli; this also protected against viral challenge. A remarkable accumulation of RSIV was observed in the blood of vaccinated fish, with less accumulation in the gills and spleen tissues. Thus, the 351R-GAPDH fusion protein is a potential vaccine against Megalocytivirus infection in red sea bream.

Phenotypic diversity of infectious red sea bream iridovirus isolates from cultured fish in Japan.

Megalocytivirus is causing economically serious mass mortality by infecting fish in and around the Pacific region of Asia. The recent emergence of many new iridoviruses has drawn attention to the marked taxonomic variation within this virus family. Most studies of these viruses have not included extensive study of these emergent species. We explored the emergence of red sea bream iridovirus (RSIV) on a fish farm in Japan, and we specifically endeavored to quantify genetic and phenotypic differences between RSIV isolates using in vitro and in vivo methods. The three isolates had identical major capsid protein sequences, and they were closely related to Korean RSIV isolates. In vitro studies revealed that the isolates differed in replication rate, which was determined by real-time quantitative PCR of viral genomes in infected cells and cell culture supernatant, and in cell viability, estimated by the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay for infected cells. In vivo studies showed that the isolates exhibit different virulence characteristics: infected red sea bream showed either acute death or subacute death according to infection with different isolates. Significant differences were seen in the antigenicity of isolates by a formalin-inactivated vaccine test. These results revealed that variant characteristics exist in the same phylogenetic location in emergent iridoviruses. We suggest that this strain variation would expand the host range in iridoviral epidemics.

Characterization of a new fibroblast cell line from a tail fin of red sea bream, Pagrus major, and phylogenetic relationships of a recent RSIV isolate in Japan.

Red sea bream iridovirus (RSIV) is a causative agent of red sea bream iridoviral disease (RSIVD) in marine fish species in Japan. Fibroblast cells were developed from a tail fin of red sea bream, Pagrus major, and then underwent single cell cloning. The successful cloned cells were named CRF-1 cells. Most CRF-1 cells had a normal diploid karyotype with 2n=48 by chromosomal analysis. RSIV-infected CRF-1 cells showed typical morphological changes that were associated with apoptosis by EGFP-annexin V staining. The serial viral passages were successful in CRF-1 cells but failed in BF-2 cells as judged by MTT assay. The expression of three genes obviously decreased in BF-2 cells compared with CRF-1 cells and finally was below detectable level. Because the expression of 591R gene showed the fastest decrease among three transcripts, the suppression of IE transcript may be responsible for the restricted replication in BF-2 cells. MCP and ATPase phylogenetic trees showed that RSIV strain U-1 belongs to a distinct group from RSIV strain ehime-1. Therefore, possibly recent epizootics of RSIVD in Japan do not originate directly from RSIV strain ehime-1. Taken together, this study confirmed that RSIV strain U-1 is more closely related to Korean RSIV isolates.