Sample records for japonicus identified large

  1. Invasion Biology of Aedes japonicus japonicus (Diptera: Culicidae)

    PubMed Central

    Fonseca, Dina M.

    2014-01-01

    Aedes japonicus japonicus (Theobald) (Diptera: Culicidae) has recently expanded beyond its native range of Japan and Korea into large parts of North America and Central Europe. Population genetic studies begun immediately after the species was detected in North America revealed genetically distinct introductions that subsequently merged, likely contributing to the successful expansion. Interactions, particularly in the larval stage, with other known disease vectors give this invasive subspecies the potential to influence local disease dynamics. Its successful invasion likely does not involve superior direct competitive abilities, but it is associated with the use of diverse larval habitats and a cold tolerance that allows an expanded seasonal activity range in temperate climates. We predict a continued but slower expansion of Ae. j. japonicus in North America and a continued rapid expansion into other areas as this mosquito will eventually be considered a permanent resident of much of North America, Europe, Asia, and parts of Hawaii. PMID:24397520

  2. Genome-wide identification of nuclear receptor (NR) superfamily genes in the copepod Tigriopus japonicus.

    PubMed

    Hwang, Dae-Sik; Lee, Bo-Young; Kim, Hui-Su; Lee, Min Chul; Kyung, Do-Hyun; Om, Ae-Son; Rhee, Jae-Sung; Lee, Jae-Seong

    2014-11-18

    Nuclear receptors (NRs) are a large superfamily of proteins defined by a DNA-binding domain (DBD) and a ligand-binding domain (LBD). They function as transcriptional regulators to control expression of genes involved in development, homeostasis, and metabolism. The number of NRs differs from species to species, because of gene duplications and/or lineage-specific gene losses during metazoan evolution. Many NRs in arthropods interact with the ecdysteroid hormone and are involved in ecdysone-mediated signaling in arthropods. The nuclear receptor superfamily complement has been reported in several arthropods, including crustaceans, but not in copepods. We identified the entire NR repertoire of the copepod Tigriopus japonicus, which is an important marine model species for ecotoxicology and environmental genomics. Using whole genome and transcriptome sequences, we identified a total of 31 nuclear receptors in the genome of T. japonicus. Nomenclature of the nuclear receptors was determined based on the sequence similarities of the DNA-binding domain (DBD) and ligand-binding domain (LBD). The 7 subfamilies of NRs separate into five major clades (subfamilies NR1, NR2, NR3, NR4, and NR5/6). Although the repertoire of NR members in, T. japonicus was similar to that reported for other arthropods, there was an expansion of the NR1 subfamily in Tigriopus japonicus. The twelve unique nuclear receptors identified in T. japonicus are members of NR1L. This expansion may be a unique lineage-specific feature of crustaceans. Interestingly, E78 and HR83, which are present in other arthropods, were absent from the genomes of T. japonicus and two congeneric copepod species (T. japonicus and Tigriopus californicus), suggesting copepod lineage-specific gene loss. We identified all NR receptors present in the copepod, T. japonicus. Knowledge of the copepod nuclear receptor repertoire will contribute to a better understanding of copepod- and crustacean-specific NR evolution.

  3. Genetic Screening Identifies Cyanogenesis-Deficient Mutants of Lotus japonicus and Reveals Enzymatic Specificity in Hydroxynitrile Glucoside Metabolism[W][OA

    PubMed Central

    Takos, Adam; Lai, Daniela; Mikkelsen, Lisbeth; Abou Hachem, Maher; Shelton, Dale; Motawia, Mohammed Saddik; Olsen, Carl Erik; Wang, Trevor L.; Martin, Cathie; Rook, Fred

    2010-01-01

    Cyanogenesis, the release of hydrogen cyanide from damaged plant tissues, involves the enzymatic degradation of amino acid–derived cyanogenic glucosides (α-hydroxynitrile glucosides) by specific β-glucosidases. Release of cyanide functions as a defense mechanism against generalist herbivores. We developed a high-throughput screening method and used it to identify cyanogenesis deficient (cyd) mutants in the model legume Lotus japonicus. Mutants in both biosynthesis and catabolism of cyanogenic glucosides were isolated and classified following metabolic profiling of cyanogenic glucoside content. L. japonicus produces two cyanogenic glucosides: linamarin (derived from Val) and lotaustralin (derived from Ile). Their biosynthesis may involve the same set of enzymes for both amino acid precursors. However, in one class of mutants, accumulation of lotaustralin and linamarin was uncoupled. Catabolic mutants could be placed in two complementation groups, one of which, cyd2, encoded the β-glucosidase BGD2. Despite the identification of nine independent cyd2 alleles, no mutants involving the gene encoding a closely related β-glucosidase, BGD4, were identified. This indicated that BGD4 plays no role in cyanogenesis in L. japonicus in vivo. Biochemical analysis confirmed that BGD4 cannot hydrolyze linamarin or lotaustralin and in L. japonicus is specific for breakdown of related hydroxynitrile glucosides, such as rhodiocyanoside A. By contrast, BGD2 can hydrolyze both cyanogenic glucosides and rhodiocyanosides. Our genetic analysis demonstrated specificity in the catabolic pathways for hydroxynitrile glucosides and implied specificity in their biosynthetic pathways as well. In addition, it has provided important tools for elucidating and potentially modifying cyanogenesis pathways in plants. PMID:20453117

  4. RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis

    PubMed Central

    Rai, Amit; Yamazaki, Mami; Takahashi, Hiroki; Nakamura, Michimi; Kojoma, Mareshige; Suzuki, Hideyuki; Saito, Kazuki

    2016-01-01

    The Panax genus has been a source of natural medicine, benefitting human health over the ages, among which the Panax japonicus represents an important species. Our understanding of several key pathways and enzymes involved in the biosynthesis of ginsenosides, a pharmacologically active class of metabolites and a major chemical constituents of the rhizome extracts from the Panax species, are limited. Limited genomic information, and lack of studies on comparative transcriptomics across the Panax species have restricted our understanding of the biosynthetic mechanisms of these and many other important classes of phytochemicals. Herein, we describe Illumina based RNA sequencing analysis to characterize the transcriptome and expression profiles of genes expressed in the five tissues of P. japonicus, and its comparison with other Panax species. RNA sequencing and de novo transcriptome assembly for P. japonicus resulted in a total of 135,235 unigenes with 78,794 (58.24%) unigenes being annotated using NCBI-nr database. Transcriptome profiling, and gene ontology enrichment analysis for five tissues of P. japonicus showed that although overall processes were evenly conserved across all tissues. However, each tissue was characterized by several unique unigenes with the leaves showing the most unique unigenes among the tissues studied. A comparative analysis of the P. japonicus transcriptome assembly with publically available transcripts from other Panax species, namely, P. ginseng, P. notoginseng, and P. quinquefolius also displayed high sequence similarity across all Panax species, with P. japonicus showing highest similarity with P. ginseng. Annotation of P. japonicus transcriptome resulted in the identification of putative genes encoding all enzymes from the triterpene backbone biosynthetic pathways, and identified 24 and 48 unigenes annotated as cytochrome P450 (CYP) and glycosyltransferases (GT), respectively. These CYPs and GTs annotated unigenes were conserved across

  5. A new focus of Aedes japonicus japonicus (Theobald, 1901) (Diptera, Culicidae) distribution in Western Germany: rapid spread or a further introduction event?

    PubMed Central

    2012-01-01

    Background The Asian bush mosquito, Aedes japonicus japonicus, a potential vector of several viruses, was first detected in Germany in 2008 on the Swiss-German border. In the following years, this invasive species apparently succeeded in establishing populations in southern Germany and in spreading northwards. In 2011, its distribution area already covered large areas of the federal state of Baden-Wurttemberg, and its northernmost German collection point was reported to be close to Stuttgart. Several independent submissions to our laboratories of Ae. j. japonicus specimens in July 2012, originating from the same area in the federal state of North Rhine-Westphalia, western Germany, prompted us to carry out an immediate surveillance in this region in the expectation of finding a further distribution focus of Ae. j. japonicus in Germany. Methods After inspecting the places of residence of the collectors of the submitted mosquito specimens, all kinds of water containers in 123 cemeteries in surrounding towns and villages were checked for mosquito developmental stages. These were collected and kept to produce adults for morphological species identification. One specimen per collection site was identified genetically by COI sequence analysis. Results Aedes j. japonicus adults and immature stages were found in 36 towns/villages that were checked (29%) over an area of approximately 2,000 km2 in southern North Rhine-Westphalia and northern Rhineland Palatinate. The species could not be demonstrated further south when monitoring towards the northernmost previous collection sites in southern Germany. It therefore remains to be elucidated whether the species has entered western Germany from the south, from Belgium in the west where it has been demonstrated to occur locally since 2002, or through a new introduction. Conclusions Aedes j. japonicus is obviously much more widely distributed in Germany than previously thought. It appears to be well adapted, to have a strong

  6. First record of the Asian bush mosquito, Aedes japonicus japonicus, in Italy: invasion from an established Austrian population.

    PubMed

    Seidel, Bernhard; Montarsi, Fabrizio; Huemer, Hartwig P; Indra, Alexander; Capelli, Gioia; Allerberger, Franz; Nowotny, Norbert

    2016-05-16

    In 2011 we identified the Asian bush mosquito, Aedes japonicus japonicus (Theobald, 1901) (Diptera: Culicidae) for the first time in northern Slovenia and in the bordering Austrian federal state of Styria. Between May and July 2012 the distribution area of Ae. j. japonicus was already found to be extended westwards into Carinthia and eastwards towards Burgenland and bordering Hungary. In August 2012 the species was first detected in a western province of Hungary. In subsequent years, follow-up field studies demonstrated an active spread westwards throughout Carinthia, reaching the border to northern Italy. In July 2015 several aquatic-stage specimens of the species were discovered at three different sites in the Friuli Venezia Giulia region, north-eastern Italy. In September 2015, co-occurrence of Ae. j. japonicus and Aedes albopictus (Skuse, 1895) was observed in the same sample in that region. Ae. j. japonicus actively extended its geographic range from an established population in Carinthia (Austria) southwards to northern Italy by crossing Alpine ranges. Since Ae. albopictus and Aedes koreicus (Edwards, 1917) are already well established in northern Italy, it will be pivotal to monitor the consequences of a third invasive mosquito species trying to populate the same geographic region.

  7. Presence and Potential Distribution of Aedes albopictus and Aedes japonicus japonicus (Diptera: Culicidae) in Slovenia.

    PubMed

    Kalan, Katja; Ivovic, Vladimir; Glasnovic, Peter; Buzan, Elena

    2017-11-07

    In Slovenia, two invasive mosquito species are present, Aedes albopictus (Skuse, 1895) (Diptera: Culicidae) and Aedes japonicus (Theobald, 1901) (Diptera: Culicidae). In this study, we examined their actual distribution and suitable habitats for new colonizations. Data from survey of species presence in 2013 and 2015, bioclimatic variables and altitude were used for the construction of predictive maps. We produced various models in Maxent software and tested two bioclimatic variable sets, WorldClim and CHELSA. For the variable selection of A. albopictus modeling we used statistical and expert knowledge-based approach, whereas for A. j. japonicus we used only a statistically based approach. The best performing models for both species were chosen according to AIC score-based evaluation. In 2 yr of sampling, A. albopictus was largely confined to the western half of Slovenia, whereas A. j. japonicus spread significantly and can be considered as an established species in a large part of the country. Comparison of models with WorldClim and CHELSA variables for both species showed models with CHELSA variables as a better tool for prediction. Finally, we validated the models performance in predicting distribution of species according to collected field data. Our study confirms that both species are co-occurring and are sympatric in a large part of the country area. The tested models could be used for future prevention of invasive mosquitoes spreading in other countries with similar bioclimatic conditions. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. The complete chloroplast genome sequence of Euonymus japonicus (Celastraceae).

    PubMed

    Choi, Kyoung Su; Park, SeonJoo

    2016-09-01

    The complete chloroplast (cp) genome sequence of the Euonymus japonicus, the first sequenced of the genus Euonymus, was reported in this study. The total length was 157 637 bp, containing a pair of 26 678 bp inverted repeat region (IR), which were separated by small single copy (SSC) region and large single copy (LSC) region of 18 340 bp and 85 941 bp, respectively. This genome contains 107 unique genes, including 74 coding genes, four rRNA genes, and 29 tRNA genes. Seventeen genes contain intron of E. japonicus, of which three genes (clpP, ycf3, and rps12) include two introns. The maximum likelihood (ML) phylogenetic analysis revealed that E. japonicus was closely related to Manihot and Populus.

  9. Establishment of Ochlerotatus japonicus (Diptera: Culicidae) in Ontario, Canada.

    PubMed

    Thielman, Aynsley; Hunter, Fiona F

    2006-03-01

    Ochlerotatus (Finlaya) japonicus (Theobold) is newly established in Ontario, Canada. It was first discovered in 2001 during the province-wide West Nile virus mosquito surveillance program implemented by the Ontario Ministry of Health and Long Term Care. Although the numbers of adults trapped in CDC light traps were low in 2001 and 2002, they increased during the 2003 and 2004 surveillance seasons. Oc. japonicus larvae also have been collected in large numbers in the Niagara Peninsula in a variety of natural and artificial containers. The number of health units with records for Oc. japonicus has increased over the 4 yr of surveillance, illustrating the ability of this species to rapidly extend its range. As a potential arboviral bridge vector, its establishment in Ontario requires further study and should be considered a public health concern.

  10. [Studies on the chemical constituents from the flowers of Ophiopogon japonicus].

    PubMed

    Zhu, Yu-Hong; Zhao, Min; Ren, Lu; Tian, Di; Dou, Fang; Wang, Jun-Xian

    2011-05-01

    To study the chemical constituents from the flowers of Ophiopogon japonicus. Column chromatography and spectral analysis were used to isolate and identify the constituents. Eleven compounds were obtained and identified as beta-sitosterol (I), diosgenin (II), daucosterol (III), ophiopogonin C' (IV), dioscin (V), 7-dihy-droxy-6-methyl-3-(4'-hydroxybenzyl) chroman-4-one(VI), luteolin (VII), kaempferol-3-O-beta-D-glucopyranosides (VIII), kaempferol-3-O-(6"-tigloyl) -beta-D-glucopyranosides (IX), kaempferol-3-O-(6"-acetyl) -beta-D-glucopyranosides (X), glucose (XI). Eleven compounds are obtained from the flowers of O. japonicus for the first time. Compond VI is isolated as a simple substance compound of O. japonicus for the first time. Componds VII, VIII, IX and X are isolated from this genus for the first time.

  11. The WRKY Transcription Factor Genes in Lotus japonicus.

    PubMed

    Song, Hui; Wang, Pengfei; Nan, Zhibiao; Wang, Xingjun

    2014-01-01

    WRKY transcription factor genes play critical roles in plant growth and development, as well as stress responses. WRKY genes have been examined in various higher plants, but they have not been characterized in Lotus japonicus. The recent release of the L. japonicus whole genome sequence provides an opportunity for a genome wide analysis of WRKY genes in this species. In this study, we identified 61 WRKY genes in the L. japonicus genome. Based on the WRKY protein structure, L. japonicus WRKY (LjWRKY) genes can be classified into three groups (I-III). Investigations of gene copy number and gene clusters indicate that only one gene duplication event occurred on chromosome 4 and no clustered genes were detected on chromosomes 3 or 6. Researchers previously believed that group II and III WRKY domains were derived from the C-terminal WRKY domain of group I. Our results suggest that some WRKY genes in group II originated from the N-terminal domain of group I WRKY genes. Additional evidence to support this hypothesis was obtained by Medicago truncatula WRKY (MtWRKY) protein motif analysis. We found that LjWRKY and MtWRKY group III genes are under purifying selection, suggesting that WRKY genes will become increasingly structured and functionally conserved.

  12. The WRKY Transcription Factor Genes in Lotus japonicus

    PubMed Central

    Wang, Pengfei; Wang, Xingjun

    2014-01-01

    WRKY transcription factor genes play critical roles in plant growth and development, as well as stress responses. WRKY genes have been examined in various higher plants, but they have not been characterized in Lotus japonicus. The recent release of the L. japonicus whole genome sequence provides an opportunity for a genome wide analysis of WRKY genes in this species. In this study, we identified 61 WRKY genes in the L. japonicus genome. Based on the WRKY protein structure, L. japonicus WRKY (LjWRKY) genes can be classified into three groups (I–III). Investigations of gene copy number and gene clusters indicate that only one gene duplication event occurred on chromosome 4 and no clustered genes were detected on chromosomes 3 or 6. Researchers previously believed that group II and III WRKY domains were derived from the C-terminal WRKY domain of group I. Our results suggest that some WRKY genes in group II originated from the N-terminal domain of group I WRKY genes. Additional evidence to support this hypothesis was obtained by Medicago truncatula WRKY (MtWRKY) protein motif analysis. We found that LjWRKY and MtWRKY group III genes are under purifying selection, suggesting that WRKY genes will become increasingly structured and functionally conserved. PMID:24745006

  13. Density Dependence, Landscape, and Weather Impacts on Aquatic Aedes japonicus japonicus (Diptera: Culicidae) Abundance Along an Urban Altitudinal Gradient.

    PubMed

    Chaves, Luis Fernando; Moji, Kazuhiko

    2018-02-28

    The Asian Bush Mosquito, Aedes (Finlaya) japonicus japonicus (Theobald) is an important globally invasive mosquito species. In comparison with other major invasive mosquitoes, relatively little is known about Ae. j. japonicus population dynamics in the field. Here, we present results from a 54-biweek long study of Ae. j. japonicus abundance in ovitraps set across the altitudinal gradient of Mt. Konpira, Nagasaki, Japan. Spatially, we found that Ae. j. japonicus fourth instar larvae (Aj4il) were more abundant at the base and top of Mt. Konpira and in ovitraps with more platykurtic water temperature (WT) distributions. In contrast, we found that temporally Aj4il were more abundant when ovitrap WT was more leptokurtic with 2 weeks of lag, and with high relative humidity SD with 2 months of lag. We also found that Aj4il were unlikely present when ovitrap WT was below 12.41°C. Parameter estimates for the Ricker model suggested that Ae. j. japonicus population growth was under density-dependence regulation, with a stable population dynamics whose fluctuations were associated with changes in ovitrap WT kurtosis and demographic stochasticity. Our results suggest that Aj4il abundance is more sensitive to temperature changes in kurtosis than mean values, potentially limiting the predictive ability of Ae. j. japonicus niche models based on the increase of average temperatures with global warming, and suggesting this mosquito species has a relatively coarse-grained response to temperature changes.

  14. Seasonal parasitism and host specificity of Trissolcus japonicus in northern China.

    PubMed

    Zhang, Jinping; Zhang, Feng; Gariepy, Tara; Mason, Peter; Gillespie, Dave; Talamas, Elijah; Haye, Tim

    2017-01-01

    The brown marmorated stink bug, Halyomorpha halys (Stål), native to China, Japan, and Korea, has emerged as a harmful invasive pest of a variety of crops in North America and Europe. The Asian egg parasitoid Trissolcus japonicus has been identified as the most promising agent for classical biological control of invasive H. halys populations. A 4-year study evaluated the fundamental and ecological host ranges of T. japonicus as well as its phenology and impact on H. halys populations in fruit orchards in its native range in northern China. In laboratory no-choice tests, developmental suitability of eight non-target host species for T. japonicus was demonstrated by the successful production of progeny on the majority (>85%) of non-target host species tested. In field-collected, naturally laid egg masses, T. japonicus was the most abundant parasitoid associated with H. halys and Dolycoris baccarum , but was also sporadically found in Plautia crossota . Furthermore, it was regularly reared from sentinel egg masses of Menida violacea , Arma chinensis , and Carbula eoa . The only species that did not support development in the laboratory and field was Cappaea tibialis . Besides the benefit of having a high impact on H. halys populations in Northern China, the risk assessment conducted in the area of origin indicates that native Pentatomidae in North America and Europe could be negatively impacted by T. japonicus . Whether the benefits of T. japonicus outweigh the possible risks will have to be evaluated based on the outcome of additional host range studies in the two invaded regions.

  15. Influence of flow velocity on motor behavior of sea cucumber Apostichopus japonicus.

    PubMed

    Pan, Yang; Zhang, Libin; Lin, Chenggang; Sun, Jiamin; Kan, Rentao; Yang, Hongsheng

    2015-05-15

    The influence of flow velocity on the motor behavior of the sea cucumber, Apostichopus japonicus was investigated in the laboratory. Cameras were used to record sea cucumber movements and behavior analysis software was used to measure the distance traveled, time spent, upstream or downstream of the start position and the speed of movements. In general, the mean velocity of A. japonicus was below 0.7mms(-1). The maximum velocity recorded for all the sea cucumbers tested was for a large individual (89.25±17.11g), at a flow rate of 4.6±0.5cms(-1). Medium sized (19.68±5.53g) and large individuals moved significantly faster than small individuals (2.65±1.24g) at the same flow rate. A. japonicus moved significantly faster when there was a moderate current (4.6±0.5cms(-1) and 14.7±0.3cms(-1)), compared with the fast flow rate (29.3±3.7cms(-1)) and when there was no flow (0cms(-1)). Sea cucumbers did not show positive rheotaxis in general, but did move in a downstream direction at faster current speeds. Large, medium and small sized individuals moved downstream at the fastest current speed tested, 29.3±3.7cms(-1). When there was no water flow, sea cucumbers tended to move in an irregular pattern. The movement patterns show that the sea cucumber, A. japonicus can move across the direction of flow, and can move both upstream and downstream along the direction of flow. Copyright © 2015. Published by Elsevier Inc.

  16. Introduction and establishment of Aedes (Finlaya) Japonicus japonicus (Theobald) on the island of Hawaii: implications for arbovirus transmission.

    PubMed

    Larish, Linda Burnham; Savage, Harry M

    2005-09-01

    On November 24, 2003, 1 female adult specimen of Aedes (Finlaya) japonicus japonicus (Theobald) was collected in a New Jersey (NJ) light trap on the island of Hawaii. From June through October, 2004, female and male adults were collected by NJ light traps and gravid traps placed at multiple sites on the island of Hawaii. Larvae were collected in artificial containers and reared to adults for identification. Aedes (Fin.) j. japonicus is the 8th mosquito species to be introduced and established in the State of Hawaii. Currently, this species is known only from the island of Hawaii. Aedes (Fin.) j. japonicus is a competent laboratory vector for a number of arboviruses. Increased quarantine inspections, inspection and treatment of imported used tires and plants, disinsection of airline cargo holds, enhanced vector surveillance, and the development of sanitary corridors around airports and port facilities are necessary to reduce the introduction of vectors and pathogens.

  17. Proteomic investigation of the secretome of Cellvibrio japonicus during growth on chitin.

    PubMed

    Tuveng, Tina Rise; Arntzen, Magnus Øverlie; Bengtsson, Oskar; Gardner, Jeffrey G; Vaaje-Kolstad, Gustav; Eijsink, Vincent G H

    2016-07-01

    Studies of the secretomes of microbes grown on insoluble substrates are important for the discovery of novel proteins involved in biomass conversion. However, data in literature and this study indicate that secretome samples tend to be contaminated with cytoplasmic proteins. We have examined the secretome of the Gram-negative soil bacterium Cellvibrio japonicus using a simple plate-based culturing technique that yields samples with high fractions (60-75%) of proteins that are predicted to be secreted. By combining this approach with label-free quantification using the MaxLFQ algorithm, we have mapped and quantified proteins secreted by C. japonicus during growth on α- and β-chitin. Hierarchical clustering of the detected protein quantities revealed groups of up-regulated proteins that include all five putative C. japonicus chitinases as well as a chitin-specific lytic polysaccharide monooxygenase (CjLPMO10A). A small set of secreted proteins were co-regulated with known chitin-specific enzymes, including several with unknown catalytic functions. These proteins provide interesting targets for further studies aimed at unraveling the enzymatic machineries used by C. japonicus for recalcitrant polysaccharide degradation. Studies of chitin degradation indicated that C. japonicus indeed produces an efficient chitinolytic enzyme cocktail. All MS data have been deposited in the ProteomeXchange with the dataset identifier PXD002843 (http://proteomecentral.proteomexchange.org/dataset/PXD002843). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Identification and molecular characterization of nitric oxide synthase (NOS) gene in the intertidal copepod Tigriopus japonicus.

    PubMed

    Jeong, Chang-Bum; Kang, Hye-Min; Seo, Jung Soo; Park, Heum Gi; Rhee, Jae-Sung; Lee, Jae-Seong

    2016-02-10

    In copepods, no information has been reported on the structure or molecular characterization of the nitric oxide synthase (NOS) gene. In the intertidal copepod Tigriopus japonicus, we identified a NOS gene that is involved in immune responses of vertebrates and invertebrates. In silico analyses revealed that nitric oxide (NO) synthase domains, such as the oxygenase and reductase domains, are highly conserved in the T. japonicus NOS gene. The T. japonicus NOS gene was highly transcribed in the nauplii stages, implying that it plays a role in protecting the host during the early developmental stages. To examine the involvement of the T. japonicus NOS gene in the innate immune response, the copepods were exposed to lipopolysaccharide (LPS) and two Vibrio sp. After exposure to different concentrations of LPS and Vibrio sp., T. japonicus NOS transcription was significantly increased over time in a dose-dependent manner, and the NO/nitrite concentration increased as well. Taken together, our findings suggest that T. japonicus NOS transcription is induced in response to an immune challenge as part of the conserved innate immunity. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. The Effectiveness of Asian Bush Mosquito (Aedes japonicus japonicus) Control Actions in Colonised Peri-urban Areas in the Netherlands

    PubMed Central

    Ibañez-Justicia, A; Teekema, S; den Hartog, W; Jacobs, F; Dik, M; Stroo, A

    2018-01-01

    Abstract The Asian bush mosquito (Aedes japonicus japonicus (Theobald)) is an invasive mosquito species in Europe. In 2012, it was for the first time detected in the Netherlands, in the municipality of Lelystad. After further research, thousands of specimens were found in the surrounding peri-urban areas of the city. A targeted mosquito control campaign began in 2015 with the objective of reducing populations in locations with the highest concentrations of Ae. japonicus breeding sites: allotment garden complexes. Mosquito control consisted of source reduction combined with application of the larvicide Vectomax in breeding sites. At eight complexes, mosquito control effectiveness has been systematically measured by sampling larvae from breeding sites. Six measurements were performed between 2015 and 2016. Results show that the effectiveness of mosquito control actions was similar in all treated allotment gardens and resulted in a significant reduction in Ae. japonicus larval abundance. Rain barrels at the allotments represent the most frequent breeding site in Lelystad, but every water filled artificial container is a potential breeding site for the species. Ae. japonicus was not found in the samples taken in other allotment gardens in the province of Flevoland; however, the collection methodology used proven to be effective in detecting this species when it has newly colonized surrounding areas. Targeted mosquito control actions at the breeding sites are crucial for successful reduction of populations of an invasive mosquito species, and systematic measurements of the effectiveness, is in this case, the base to understand the dynamics of Ae. japonicus populations after mosquito control. PMID:29452383

  20. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gardner, Jeffrey G.

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. Furthermore, this review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkablemore » ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.« less

  1. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    DOE PAGES

    Gardner, Jeffrey G.

    2016-06-04

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. Furthermore, this review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkablemore » ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.« less

  2. Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis.

    PubMed

    Asamizu, Erika; Nakamura, Yasukazu; Sato, Shusei; Tabata, Satoshi

    2004-02-01

    To perform a comprehensive analysis of genes expressed in a model legume, Lotus japonicus, a total of 74472 3'-end expressed sequence tags (EST) were generated from cDNA libraries produced from six different organs. Clustering of sequences was performed with an identity criterion of 95% for 50 bases, and a total of 20457 non-redundant sequences, 8503 contigs and 11954 singletons were generated. EST sequence coverage was analyzed by using the annotated L. japonicus genomic sequence and 1093 of the 1889 predicted protein-encoding genes (57.9%) were hit by the EST sequence(s). Gene content was compared to several plant species. Among the 8503 contigs, 471 were identified as sequences conserved only in leguminous species and these included several disease resistance-related genes. This suggested that in legumes, these genes may have evolved specifically to resist pathogen attack. The rate of gene sequence divergence was assessed by comparing similarity level and functional category based on the Gene Ontology (GO) annotation of Arabidopsis genes. This revealed that genes encoding ribosomal proteins, as well as those related to translation, photosynthesis, and cellular structure were more abundantly represented in the highly conserved class, and that genes encoding transcription factors and receptor protein kinases were abundantly represented in the less conserved class. To make the sequence information and the cDNA clones available to the research community, a Web database with useful services was created at http://www.kazusa.or.jp/en/plant/lotus/EST/.

  3. Evaluation of raw nepodin extraction from Rumex japonicus and R. obtusifolius and their DNA polymorphisms.

    PubMed

    Minami, Motoyasu; Mori, Takako; Yonezawa, Takayuki; Saito, Yukiko; Teruya, Toshiaki; Woo, Je-Tae

    2018-01-01

    Nepodin, found in the roots of Rumex japonicus Houtt. (Polygonaceae), inhibits osteoclast differentiation and has an antidiabetic effect. We propose nepodin as an ingredient of new functional foods or as a drug candidate for reducing the risk of reduced locomotion resulting from diseases such as osteoporosis. Although there are no previous reports of R. obtusifolius L., which is found throughout Japan, having roots containing nepodin, we found nepodin in the roots of this species. Therefore, R. obtusifolius as well as R. japonicus was considered a candidate raw material for nepodin extraction. We also discuss the suitability of R. japonicus and R. obtusifolius as sources of raw nepodin for cultivation on the Ryukyu Islands. In this study, all specimens on the Ryukyu Islands were identified as R. japonicus. Conversely, all specimens on mainland Japan were R. obtusifolius. The DNA sequence of the chloroplast trnL-trnF intergenic spacer region and partial nuclear internal transcribed spacer was consistent with the identification of R. japonicus and R. obtusifolius by morphological characteristics of the perianth segments. Therefore, to avoid erroneous identification and misuse of the plant species used for extraction of raw materials, it is preferable to develop DNA markers for these two regions. The content of nepodin varied from undetectable to 0.34% of the fresh weight (%FW) in R. japonicus and from undetectable to 0.21%FW in R. obtusifolius. From a pharmacological perspective, as plants that might be suitable as raw materials for nepodin extraction, it became clear that both R. japonicus and R. obtusifolius can be used with the same expected extraction efficiency. Based on our findings, R. obtusifolius could not be confirmed as inhabiting the Ryukyu Islands. For this reason, to conserve the endemic genetic characteristics of the Ryukyu Islands and to prevent genetic pollution by R. obtusifolius, only R. japonicus should be cultivated on the Ryukyu Islands.

  4. Out of the bush: the Asian bush mosquito Aedes japonicus japonicus (Theobald, 1901) (Diptera, Culicidae) becomes invasive.

    PubMed

    Kampen, Helge; Werner, Doreen

    2014-02-04

    The Asian bush or rock pool mosquito Aedes japonicus japonicus is one of the most expansive culicid species of the world. Being native to East Asia, this species was detected out of its original distribution range for the first time in the early 1990s in New Zealand where it could not establish, though. In 1998, established populations were reported from the eastern US, most likely as a result of introductions several years earlier. After a massive spread the mosquito is now widely distributed in eastern North America including Canada and two US states on the western coast. In the year 2000, it was demonstrated for the first time in Europe, continental France, but could be eliminated. A population that had appeared in Belgium in 2002 was not controlled until 2012 as it did not propagate. In 2008, immature developmental stages were discovered in a large area in northern Switzerland and bordering parts of Germany. Subsequent studies in Germany showed a wide distribution and several populations of the mosquito in various federal states. Also in 2011, the species was found in southeastern Austria (Styria) and neighbouring Slovenia. In 2013, a population was detected in the Central Netherlands, specimens were collected in southern Alsace, France, and the complete northeastern part of Slovenia was found colonized, with specimens also present across borders in adjacent Croatia. Apparently, at the end of 2013 a total of six populations occurred in Europe although it is not clear whether all of them are completely isolated. Similarly, it is not known whether these populations go back to the same number of introductions. While entry ports and long-distance continental migration routes are also obscure, it is likely that the international used tyre trade is the most important mode of intercontinental transportation of the mosquito. Aedes j. japonicus does not only display an aggressive biting behaviour but is suspected to be a vector of various disease agents and to displace

  5. Spread of Aedes japonicus japonicus (Theobald, 1901) in Austria, 2011-2015, and first records of the subspecies for Hungary, 2012, and the principality of Liechtenstein, 2015.

    PubMed

    Seidel, Bernhard; Nowotny, Norbert; Bakonyi, Tamás; Allerberger, Franz; Schaffner, Francis

    2016-06-24

    The Asian bush mosquito, Aedes (Hulecoeteomyia) japonicus japonicus (Theobald, 1901) (Diptera: Culicidae), was first identified in Austria in August 2011 in the federal state of Styria at the border to Slovenia. Between 2011 and 2015 the spread of Ae. j. japonicus was monitored in southern, eastern and western Austrian provinces as well as in neighbouring countries by checking natural and man-made container habitats for the aquatic stages. The search concentrated around the most recent occurrence of Ae. j. japonicus and extended up to several kilometres until the subspecies could not be found anymore. Between May and July 2012 the distribution area of Ae. j. japonicus was found to be extended westwards into Carinthia, and eastwards towards the federal state of Burgenland. In August 2012, the subspecies was found in Hungary, representing the first record of an invasive mosquito species in this country. In 2013 its expansion was confirmed at several sites in Austria. Additionally, between April and July 2015, the subspecies was detected in all districts of the westernmost Austrian state Vorarlberg reaching the alpine Montafon valley at the end of October 2015, at all three examined sites in southern Bavaria bordering Vorarlberg, and in the adjacent Principality of Liechtenstein, for which it also represents the first record of an invasive mosquito species. One remarkable finding of the subspecies was located close to the city of Kufstein in the lower Inn valley of the Tyrol in September 2015, which is an isolated occurrence without spatial connection to any known established population. Our findings demonstrate the ongoing spread of Ae. j. japonicus towards all directions within Austria and beyond. Together with the absence of supposed natural barriers, e.g. high mountain chains, at the borders of the current subspecies' distribution area in south-eastern Austria, these findings suggest a further spread to the Austrian capital Vienna and the Hungarian tourist region

  6. Larval mosquito habitat utilization and community dynamics of Aedes albopictus and Aedes japonicus (Diptera: Culicidae).

    PubMed

    Bartlett-Healy, Kristen; Unlu, Isik; Obenauer, Peter; Hughes, Tony; Healy, Sean; Crepeau, Taryn; Farajollahi, Ary; Kesavaraju, Banu; Fonseca, Dina; Schoeler, George; Gaugler, Randy; Strickman, Daniel

    2012-07-01

    Aedes albopictus (Skuse) and Ae. japonicus (Theobald) are important container-inhabiting mosquitoes that transmit disease agents, outcompete native species, and continue to expand their range in the United States. Both species deposit eggs in natural and artificial containers and thrive in peridomestic environments. The goal of our study was to examine the types and characteristics of containers that are most productive for these species in the northeastern United States. In total, 306 containers were sampled in urban, suburban, and rural areas of New Jersey. Multiple biotic and abiotic factors were recorded in an attempt to identify variables associated with the productivity of each species. Based on pupal abundance and density of container types, results showed that tires, trash cans, and planter dishes were the most important containers for Ae. albopictus, while planter dishes were the most important containers for Ae. japonicus. Container color (black and gray), material (rubber), and type (tires) were correlated with species presence for Ae. albopictus and Ae. japonicus. These factors may play a role in the selection of oviposition sites by female mosquitoes or in the survival of their progeny. Differences in species composition and abundance were detected between areas classified as urban, suburban, and rural. In urban and suburban areas, Ae. albopictus was more abundant in container habitats than Ae. japonicus; however, Ae. japonicus was more abundant in rural areas, and when water temperatures were below 14 degrees C. Our results suggest many variables can influence the presence of Ae. albopictus and Ae. japonicus in container habitats in northeastern United States.

  7. Taxonomic review of Argentine mackerel Scomber japonicus (Houttuyn, 1782) by phylogenetic analysis

    PubMed Central

    Trucco, María Inés; Buratti, Claudio César

    2017-01-01

    Taxonomically, Argentine mackerels were first considered as Scomber japonicus marplatensis and later as Scomber japonicus Houttuyn 1782, although, in the last years, different studies have suggested that South Atlantic mackerel species belongs to Scomber colias Gmelin 1789. These latter results, incorporated in the main fish databases (FishBase and Catalog of Fishes), promoted a phylogenetic study using cytochrome c oxidase I (COI) gene sequences taken from the Barcode of Life (FISH-BOL) database. Thus, 76 sequences of S. japonicus, S. colias, S. australasicus and S. scombrus from different regions were used; including 3 from Sarda sarda as outgroup. Among S. japonicus selected sequences are those corresponding to the Argentine mackerels collected in 2007. Phylogenetic trees were obtained by neighbor joining and maximum likelihood methods and a network of haplotypes was reconstructed to analyze the relationship between species. The results showed the clear differentiation of S. australasicus, S. scombrus and S. japonicus from the Pacific while S. japonicus from Argentina was included in the S. colias group, with genetic differences corresponding to conspecific populations (0.1%). Four of the five Argentine specimens shared the same haplotype with S. colias, and none were shared with S. japonicus from the Pacific. These results suggest that the current specific name of Argentine mackerel S. japonicus should be changed to S. colias, in agreement with several genetic studies carried out with species of the genus Scomber. PMID:29071283

  8. Experimental transmission of St. Louis encephalitis virus by Ochlerotatus j. japonicus.

    PubMed

    Sardelis, Michael R; Turell, Michael J; Andre, Richard G

    2003-06-01

    Ochlerotatus japonicus japonicus a newly discovered nonindigenous mosquito species in North America, and a colonized strain of Culex pipiens were compared for their vector competence for St. Louis encephalitis virus (SLE). Infection rates in Oc. j. japonicus were 0-33% after feeding on chickens with viremias between 10(4.1) and 10(4.7) plaque-forming units (PFU)/ml of blood. In comparison, infection rates were 12-94% for Cx. pipiens that fed on the same chickens. When fed on chickens with viremias between 10(5.3) and 10(5.6) PFU/ml of blood, infection rates for Oc. j. japonicus and Cx. pipiens were similar, 96% and 100%, respectively. After 12-14 days of extrinsic incubation at 26 degrees C, all 34 infected Oc. j. japonicus had a disseminated infection. In contrast, only 23 (43%) of 54 infected Cx. pipiens had a disseminated infection after feeding on the same chickens. If they developed a disseminated infection, both species efficiently transmitted (> or = 87%) SLE. Estimated transmission rates at viral doses sufficient to infect both of the tested species were 29-84% for Oc. j. japonicus and 30-50% for Cx. pipiens. Because of its continued geographic expansion, field and laboratory evidence incriminating it as a vector of the closely related West Nile virus, and its ability to transmit SLE in the laboratory, Oc. j. japonicus should be considered as a potential enzootic or epizootic vector of SLE.

  9. Aedes albopictus and Aedes japonicus - two invasive mosquito species with different temperature niches in Europe.

    PubMed

    Cunze, Sarah; Koch, Lisa K; Kochmann, Judith; Klimpel, Sven

    2016-11-04

    Aedes albopictus and Ae. japonicus are two of the most widespread invasive mosquito species that have recently become established in western Europe. Both species are associated with the transmission of a number of serious diseases and are projected to continue their spread in Europe. In the present study, we modelled the habitat suitability for both species under current and future climatic conditions by means of an Ensemble forecasting approach. We additionally compared the modelled MAXENT niches of Ae. albopictus and Ae. japonicus regarding temperature and precipitation requirements. Both species were modelled to find suitable habitat conditions in distinct areas within Europe: Ae. albopictus within the Mediterranean regions in southern Europe, Ae. japonicus within the more temperate regions of central Europe. Only in few regions, suitable habitat conditions were projected to overlap for both species. Whereas Ae. albopictus is projected to be generally promoted by climate change in Europe, the area modelled to be climatically suitable for Ae. japonicus is projected to decrease under climate change. This projection of range reduction under climate change relies on the assumption that Ae. japonicus is not able to adapt to warmer climatic conditions. The modelled MAXENT temperature niches of Ae. japonicus were found to be narrower with an optimum at lower temperatures compared to the niches of Ae. albopictus. Species distribution models identifying areas with high habitat suitability can help improving monitoring programmes for invasive species currently in place. However, as mosquito species are known to be able to adapt to new environmental conditions within the invasion range quickly, niche evolution of invasive mosquito species should be closely followed upon in future studies.

  10. Transcriptome Response Mediated by Cold Stress in Lotus japonicus.

    PubMed

    Calzadilla, Pablo I; Maiale, Santiago J; Ruiz, Oscar A; Escaray, Francisco J

    2016-01-01

    Members of the Lotus genus are important as agricultural forage sources under marginal environmental conditions given their high nutritional value and tolerance of various abiotic stresses. However, their dry matter production is drastically reduced in cooler seasons, while their response to such conditions is not well studied. This paper analyzes cold acclimation of the genus by studying Lotus japonicus over a stress period of 24 h. High-throughput RNA sequencing was used to identify and classify 1077 differentially expressed genes, of which 713 were up-regulated and 364 were down-regulated. Up-regulated genes were principally related to lipid, cell wall, phenylpropanoid, sugar, and proline regulation, while down-regulated genes affected the photosynthetic process and chloroplast development. Together, a total of 41 cold-inducible transcription factors were identified, including members of the AP2/ERF, NAC, MYB, and WRKY families; two of them were described as putative novel transcription factors. Finally, DREB1/CBFs were described with respect to their cold stress expression profiles. This is the first transcriptome profiling of the model legume L. japonicus under cold stress. Data obtained may be useful in identifying candidate genes for breeding modified species of forage legumes that more readily acclimate to low temperatures.

  11. Newly discovered population of Aedes japonicus japonicus (Diptera: Culicidae) in Upper Bavaria, Germany, and Salzburg, Austria, is closely related to the Austrian/Slovenian bush mosquito population.

    PubMed

    Zielke, Dorothee E; Walther, Doreen; Kampen, Helge

    2016-03-21

    The German mosquito surveillance instrument 'Mueckenatlas' requests the general public to collect and submit mosquito specimens. Among these, increasing numbers of individuals of invasive species have been registered. Specimens of the Asian bush mosquito Aedes japonicus japonicus submitted from German Upper Bavaria, where this species had not previously been recorded, triggered regional monitoring in mid-2015. The search for Ae. j. japonicus breeding sites and developmental stages concentrated on cemeteries in the municipality of origin of the submitted specimens and, subsequently, in the whole region. A virtual grid consisting of 10 × 10 km(2) cells in which up to three cemeteries were checked, was laid over the region. A cell was considered positive as soon as Ae. j. japonicus larvae were detected, and regarded negative when no larvae could be found in any of the cemeteries inspected. All cells surrounding a positive cell were screened accordingly. A subset of collected Aedes j. japonicus specimens was subjected to microsatellite and nad4 sequence analyses, and obtained data were compared to individuals from previously discovered European populations. Based on the grid cells, an area of approximately 900 km(2) was populated by Ae. j. japonicus in Upper Bavaria and neighbouring Austria. Genetic analyses of microsatellites and nad4 gene sequences generated one genotype out of two previously described for Europe and three haplotypes, one of which had previously been found in Europe only in Ae. j. japonicus samples from a population in East Austria and Slovenia. The genetic analysis suggests the new population is closely related to the Austrian/Slovenian population. As Ae. j. japonicus is well adapted to temperate climates, it has a strong tendency to expand and to colonise new territories in Central Europe, which is facilitated by human-mediated, passive transportation. The new population in Upper Bavaria/Austria is the seventh separate population described in

  12. Evaluation of body weight of sea cucumber Apostichopus japonicus by computer vision

    NASA Astrophysics Data System (ADS)

    Liu, Hui; Xu, Qiang; Liu, Shilin; Zhang, Libin; Yang, Hongsheng

    2015-01-01

    A postichopus japonicus (Holothuroidea, Echinodermata) is an ecological and economic species in East Asia. Conventional biometric monitoring method includes diving for samples and weighing above water, with highly variable in weight measurement due to variation in the quantity of water in the respiratory tree and intestinal content of this species. Recently, video survey method has been applied widely in biometric detection on underwater benthos. However, because of the high flexibility of A. japonicus body, video survey method of monitoring is less used in sea cucumber. In this study, we designed a model to evaluate the wet weight of A. japonicus, using machine vision technology combined with a support vector machine (SVM) that can be used in field surveys on the A. japonicus population. Continuous dorsal images of free-moving A. japonicus individuals in seawater were captured, which also allows for the development of images of the core body edge as well as thorn segmentation. Parameters that include body length, body breadth, perimeter and area, were extracted from the core body edge images and used in SVM regression, to predict the weight of A. japonicus and for comparison with a power model. Results indicate that the use of SVM for predicting the weight of 33 A. japonicus individuals is accurate ( R 2=0.99) and compatible with the power model ( R 2 =0.96). The image-based analysis and size-weight regression models in this study may be useful in body weight evaluation of A. japonicus in lab and field study.

  13. Habitat suitability index model of the sea cucumber Apostichopus japonicus (Selenka): A case study of Shandong Peninsula, China.

    PubMed

    Zhang, Zhipeng; Zhou, Jian; Song, Jingjing; Wang, Qixiang; Liu, Hongjun; Tang, Xuexi

    2017-09-15

    A habitat suitability index (HSI) model for the sea cucumber Apostichopus japonicus (Selenka) was established in the present study. Based on geographic information systems, the HSI model was used to identify potential sites around the Shandong Peninsula suitable for restoration of immature (<25g) and mature (>25g) A. japonicus. Six habitat factors were used as input variables for the HSI model: sediment classification, water temperature, salinity, water depth, pH and dissolved oxygen. The weighting of each habitat factor was defined through the Delphi method. Sediment classification was the most important condition affecting the HSI of A. japonicus in the different study areas, while water temperature was the most important condition in different seasons. The HSI of Western Laizhou Bay was relatively low, meaning the site was not suitable for aquaculture-based restoration of A. japonicus. In contrast, Xiaoheishan Island, Rongcheng Bay and Qingdao were preferable sites, suitable as habitats for restoration efforts. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Genome Structure of the Legume, Lotus japonicus

    PubMed Central

    Sato, Shusei; Nakamura, Yasukazu; Kaneko, Takakazu; Asamizu, Erika; Kato, Tomohiko; Nakao, Mitsuteru; Sasamoto, Shigemi; Watanabe, Akiko; Ono, Akiko; Kawashima, Kumiko; Fujishiro, Tsunakazu; Katoh, Midori; Kohara, Mitsuyo; Kishida, Yoshie; Minami, Chiharu; Nakayama, Shinobu; Nakazaki, Naomi; Shimizu, Yoshimi; Shinpo, Sayaka; Takahashi, Chika; Wada, Tsuyuko; Yamada, Manabu; Ohmido, Nobuko; Hayashi, Makoto; Fukui, Kiichi; Baba, Tomoya; Nakamichi, Tomoko; Mori, Hirotada; Tabata, Satoshi

    2008-01-01

    The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10 951 complete and 19 848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes. PMID:18511435

  15. QTL analysis of ferric reductase activity in the model legume lotus japonicus

    USDA-ARS?s Scientific Manuscript database

    Physiological and molecular studies have demonstrated that iron accumulation from the soil into Strategy I plants can be limited by ferric reductase activity. An initial study of Lotus japonicus ecotypes Miyakojima MG-20 and Gifu B-129 identified significant leaf chlorosis and ferric reductase activ...

  16. Changes in collagenous tissue microstructures and distributions of cathepsin L in body wall of autolytic sea cucumber (Stichopus japonicus).

    PubMed

    Liu, Yu-Xin; Zhou, Da-Yong; Ma, Dong-Dong; Liu, Yan-Fei; Li, Dong-Mei; Dong, Xiu-Ping; Tan, Ming-Qian; Du, Ming; Zhu, Bei-Wei

    2016-12-01

    The autolysis of sea cucumber (Stichopus japonicus) was induced by ultraviolet (UV) irradiation, and the changes of microstructures of collagenous tissues and distributions of cathepsin L were investigated using histological and histochemical techniques. Intact collagen fibers in fresh S. japonicus dermis were disaggregated into collagen fibrils after UV stimuli. Cathepsin L was identified inside the surface of vacuoles in the fresh S. japonicus dermis cells. After the UV stimuli, the membranes of vacuoles and cells were fused together, and cathepsin L was released from cells and diffused into tissues. The density of cathepsin L was positively correlated with the speed and degree of autolysis in different layers of body wall. Our results revealed that lysosomal cathepsin L was released from cells in response to UV stimuli, which contacts and degrades the extracellular substrates such as collagen fibers, and thus participates in the autolysis of S. japonicus. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants.

    PubMed

    Jo, Jihoon; Oh, Jooseong; Lee, Hyun-Gwan; Hong, Hyun-Hee; Lee, Sung-Gwon; Cheon, Seongmin; Kern, Elizabeth M A; Jin, Soyeong; Cho, Sung-Jin; Park, Joong-Ki; Park, Chungoo

    2017-01-01

    The Japanese sea cucumber (Apostichopus japonicus Selenka 1867) is an economically important species as a source of seafood and ingredient in traditional medicine. It is mainly found off the coasts of northeast Asia. Recently, substantial exploitation and widespread biotic diseases in A. japonicus have generated increasing conservation concern. However, the genomic knowledge base and resources available for researchers to use in managing this natural resource and to establish genetically based breeding systems for sea cucumber aquaculture are still in a nascent stage. A total of 312 Gb of raw sequences were generated using the Illumina HiSeq 2000 platform and assembled to a final size of 0.66 Gb, which is about 80.5% of the estimated genome size (0.82 Gb). We observed nucleotide-level heterozygosity within the assembled genome to be 0.986%. The resulting draft genome assembly comprising 132 607 scaffolds with an N50 value of 10.5 kb contains a total of 21 771 predicted protein-coding genes. We identified 6.6-14.5 million heterozygous single nucleotide polymorphisms in the assembled genome of the three natural color variants (green, red, and black), resulting in an estimated nucleotide diversity of 0.00146. We report the first draft genome of A. japonicus and provide a general overview of the genetic variation in the three major color variants of A. japonicus. These data will help provide a comprehensive view of the genetic, physiological, and evolutionary relationships among color variants in A. japonicus, and will be invaluable resources for sea cucumber genomic research. © The Author 2017. Published by Oxford University Press.

  18. Differential gene expression in the intestine of sea cucumber (Apostichopus japonicus) under low and high salinity conditions.

    PubMed

    Zhang, Libin; Feng, Qiming; Sun, Lina; Ding, Kui; Huo, Da; Fang, Yan; Zhang, Tao; Yang, Hongsheng

    2018-03-01

    Sea cucumber, Apostichopus japonicus is an important species for aquaculture, and its behavior and physiology can change in response to changing salinity conditions. For this reason, it is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity. In this study, RNA-Seq provided a general overview of the gene expression profiles in the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environments. Screening for differentially expressed genes (DEGs) using the NOISeq method identified 109, 100, and 89 DEGs based on a fold change of ≥2 and divergence probability ≥0.8 according to the comparisons of SD20 vs. SD30, SD20 vs.SD40, and SD30 vs. SD40, respectively. Gene ontology analysis showed that the terms "metabolic process" and "catalytic activity" comprised the most enriched DEGs. These fell into the categories of "biological process" and "molecular function". While "cell" and "cell part" had the most enriched DEGs in the category of "cellular component". With these DEGs mapping to 2119, 159, and 160 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Of these 51, 2, and 57 pathways were significantly enriched, respectively. The osmosis-specific DEGs identified in this study of A. japonicus will be important targets for further studies to understand the biochemical mechanisms involved with the adaption of sea cucumbers to changes in salinity. Copyright © 2017. Published by Elsevier Inc.

  19. [Principal component analysis and cluster analysis of inorganic elements in sea cucumber Apostichopus japonicus].

    PubMed

    Liu, Xiao-Fang; Xue, Chang-Hu; Wang, Yu-Ming; Li, Zhao-Jie; Xue, Yong; Xu, Jie

    2011-11-01

    The present study is to investigate the feasibility of multi-elements analysis in determination of the geographical origin of sea cucumber Apostichopus japonicus, and to make choice of the effective tracers in sea cucumber Apostichopus japonicus geographical origin assessment. The content of the elements such as Al, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd, Hg and Pb in sea cucumber Apostichopus japonicus samples from seven places of geographical origin were determined by means of ICP-MS. The results were used for the development of elements database. Cluster analysis(CA) and principal component analysis (PCA) were applied to differentiate the sea cucumber Apostichopus japonicus geographical origin. Three principal components which accounted for over 89% of the total variance were extracted from the standardized data. The results of Q-type cluster analysis showed that the 26 samples could be clustered reasonably into five groups, the classification results were significantly associated with the marine distribution of the sea cucumber Apostichopus japonicus samples. The CA and PCA were the effective methods for elements analysis of sea cucumber Apostichopus japonicus samples. The content of the mineral elements in sea cucumber Apostichopus japonicus samples was good chemical descriptors for differentiating their geographical origins.

  20. Seasonal parasitism and host specificity of Trissolcus japonicus in northern China

    USDA-ARS?s Scientific Manuscript database

    The Asian egg parasitoid Trissolcus japonicus is considered the most promising species for classical biological control of Halyomorpha halys. We investigated the fundamental and ecological host range of T. japonicus in northern China to define its host specificity, and we determined that T. japonicu...

  1. Identification of the centromere-specific histone H3 variant in Lotus japonicus.

    PubMed

    Tek, Ahmet L; Kashihara, Kazunari; Murata, Minoru; Nagaki, Kiyotaka

    2014-03-15

    The centromere is a structurally and functionally specialized region present on every eukaryotic chromosome. Lotus japonicus is a model legume species for which there is very limited information on the centromere structure. Here we cloned and characterized the L. japonicus homolog of the centromere-specific histone H3 gene (LjCenH3) encoding a 159-amino acid protein. Using an Agrobacterium-based transformation system, LjCenH3 tagged with a green fluorescent protein was transferred into L. japonicus cells. The centromeric position of LjCENH3 protein was revealed on L. japonicus metaphase chromosomes by an immunofluorescence assay. The identification of LjCenH3 as a critical centromere landmark could pave the way for a better understanding of centromere structure in this model and other agriculturally important legume species. Published by Elsevier B.V.

  2. Feeding behavior and digestive physiology in sea cucumber Apostichopus japonicus.

    PubMed

    Sun, Jiamin; Zhang, Libin; Pan, Yang; Lin, Chenggang; Wang, Fang; Kan, Rentao; Yang, Hongsheng

    2015-02-01

    The feeding behavior and digestive physiology of the sea cucumber, Apostichopus japonicus are not well understood. A better understanding may provide useful information for the development of the aquaculture of this species. In this article the tentacle locomotion, feeding rhythms, ingestion rate (IR), feces production rate (FPR) and digestive enzyme activities were studied in three size groups (small, medium and large) of sea cucumber under a 12h light/12h dark cycle. Frame-by-frame video analysis revealed that all size groups had similar feeding strategies using a grasping motion to pick up sediment particles. The tentacle insertion rates of the large size group were significantly faster than those of the small and medium-sized groups (P<0.05). Feeding activities investigated by charge coupled device cameras with infrared systems indicated that all size groups of sea cucumber were nocturnal and their feeding peaks occurred at 02:00-04:00. The medium and large-sized groups also had a second feeding peak during the day. Both IR and FPR in all groups were significantly higher at night than those during the daytime (P<0.05). Additionally, the peak activities of digestive enzymes were 2-4h earlier than the peak of feeding. Taken together, these results demonstrated that the light/dark cycle was a powerful environment factor that influenced biological rhythms of A. japonicus, which had the ability to optimize the digestive processes for a forthcoming ingestion. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Involvement of three putative glucosyltransferases from the UGT72 family in flavonol glucoside/rhamnoside biosynthesis in Lotus japonicus seeds

    PubMed Central

    Yin, Qinggang; Shen, Guoan; Chang, Zhenzhan; Tang, Yuhong; Gao, Hongwen

    2017-01-01

    Abstract Flavonols are one of the largest groups of flavonoids that confer benefits for the health of plants and animals. Flavonol glycosides are the predominant flavonoids present in the model legume Lotus japonicus. The molecular mechanisms underlying the biosynthesis of flavonol glycosides as yet remain unknown in L. japonicus. In the present study, we identified a total of 188 UDP-glycosyltransferases (UGTs) in L. japonicus by genome-wide searching. Notably, 12 UGTs from the UGT72 family were distributed widely among L. japonicus chromosomes, expressed in all tissues, and showed different docking scores in an in silico bioinformatics docking analysis. Further enzymatic assays showed that five recombinant UGTs (UGT72AD1, UGT72AF1, UGT72AH1, UGT72V3, and UGT72Z2) exhibit activity toward flavonol, flavone, and isoflavone aglycones. In particular, UGT72AD1, UGT72AH1, and UGT72Z2 are flavonol-specific UGTs with different kinetic properties. In addition, the overexpression of UGT72AD1 and UGT72Z2 led to increased accumulation of flavonol rhamnosides in L. japonicus and Arabidopsis thaliana. Moreover, the increase of kaempferol 3-O-rhamnoside-7-O-rhamnoside in transgenic A. thaliana inhibited root growth as compared with the wild-type control. These results highlight the significance of the UGT72 family in flavonol glycosylation and the role of flavonol rhamnosides in plant growth. PMID:28204516

  4. Occurrence and Spread of the Invasive Asian Bush Mosquito Aedes japonicus japonicus (Diptera: Culicidae) in West and North Germany since Detection in 2012 and 2013, Respectively.

    PubMed

    Kampen, Helge; Kuhlisch, Cornelius; Fröhlich, Andreas; Scheuch, Dorothee E; Walther, Doreen

    2016-01-01

    The invasive Asian bush mosquito Aedes japonicus japonicus was first recognised as established in Germany in 2008. In addition to the first known and quickly expanding population in the southwestern part of the country, three separate populations were discovered in West, North and southeastern Germany in 2012, 2013 and 2015, respectively, by means of the 'Mueckenatlas', a German instrument of passive mosquito surveillance. Since the first findings of mosquito specimens in West and North Germany, these regions were checked annually for continuing colonisation and spread of the species. Both affected areas were covered by a virtual 10x10km2 grid pattern in the cells of which cemeteries were screened for immature stages of the mosquito. The cells were considered populated as soon as larvae or pupae were detected, whereas they were classified as negative when no mosquito stages were found in the cemeteries of at least three different towns or villages. Presence was also recorded when Ae. j. japonicus adults were submitted to the 'Mueckenatlas' from the respective cell or when there was evidence of local occurrence in localities other than cemeteries. Based on this approach, a significant expansion of the populated area was documented in West Germany since the first detection of Ae. j. japonicus in 2012 (increase in positive grid cells by more than 400%), while the North German population appears not to be expanding so far (reduction of positive grid cells by ca. 30% since 2013). As Ae. j. japonicus finds suitable climatic and ecological conditions in Germany, the differential expansion of the two populations might be attributed to the West German population being older and thus more firmly established than the closely related but younger North German population that might still be in its founder phase. However, geographic spread of all German populations in the future is anticipated. Continuous surveillance is recommended, as Ae. j. japonicus is a competent vector of

  5. Construction of a Lotus japonicus late nodulin expressed sequence tag library and identification of novel nodule-specific genes.

    PubMed Central

    Szczyglowski, K; Hamburger, D; Kapranov, P; de Bruijn, F J

    1997-01-01

    A range of novel expressed sequence tags (ESTs) associated with late developmental events during nodule organogenesis in the legume Lotus japonicus were identified using mRNA differential display; 110 differentially displayed polymerase chain reaction products were cloned and analyzed. Of 88 unique cDNAs obtained, 22 shared significant homology to DNA/protein sequences in the respective databases. This group comprises, among others, a nodule-specific homolog of protein phosphatase 2C, a peptide transporter protein, and a nodule-specific form of cytochrome P450. RNA gel-blot analysis of 16 differentially displayed ESTs confirmed their nodule-specific expression pattern. The kinetics of mRNA accumulation of the majority of the ESTs analyzed were found to resemble the expression pattern observed for the L. japonicus leghemoglobin gene. These results indicate that the newly isolated molecular markers correspond to genes induced during late developmental stages of L. japonicus nodule organogenesis and provide important, novel tools for the study of nodulation. PMID:9276951

  6. Interspecific Larval Competition Between Aedes albopictus and Aedes japonicus (Diptera: Culicidae) in Northern Virginia

    PubMed Central

    Armistead, J. S.; Arias, J. R.; Nishimura, N.; Lounibos, L. P.

    2008-01-01

    Aedes albopictus (Skuse) and Aedes japonicus (Theobald) are two of the most recent and widespread invasive mosquito species to have become established in the United States. The two species co-occur in water-filled artificial containers, where crowding and limiting resources are likely to promote inter- or intraspecific larval competition. The performance of northern Virginia populations of Ae. japonicus and Ae. albopictus competing as larvae under field conditions was evaluated. Per capita rates of population increase for each species were estimated, and the effects of species composition and larval density were determined. In water-containing cups provided with oak leaves, Ae. albopictus larvae exhibited a competitive advantage over Ae. japonicus as a consequence of higher survivorship, shorter developmental time, and a significantly higher estimated population growth rate under conditions of interspecific competition. Intraspecific competition constrained population performance of Ae. albopictus significantly more than competition with Ae. japonicus. In the context of the Lotka-Volterra model of competition, these findings suggest competitive exclusion of Ae. japonicus in those habitats where this species co-occurs with Ae. albopictus. PMID:18714861

  7. Interspecific larval competition between Aedes albopictus and Aedes japonicus (Diptera: Culicidae) in northern Virginia.

    PubMed

    Armistead, J S; Arias, J R; Nishimura, N; Lounibos, L P

    2008-07-01

    Aedes albopictus (Skuse) and Aedes japonicus (Theobald) are two of the most recent and widespread invasive mosquito species to have become established in the United States. The two species co-occur in water-filled artificial containers, where crowding and limiting resources are likely to promote inter- or intraspecific larval competition. The performance of northern Virginia populations of Ae. japonicus and Ae. albopictus competing as larvae under field conditions was evaluated. Per capita rates of population increase for each species were estimated, and the effects of species composition and larval density were determined. In water-containing cups provided with oak leaves, Ae. albopictus larvae exhibited a competitive advantage over Ae. japonicus as a consequence of higher survivorship, shorter developmental time, and a significantly higher estimated population growth rate under conditions of interspecific competition. Intraspecific competition constrained population performance of Ae. albopictus significantly more than competition with Ae. japonicus. In the context of the Lotka-Volterra model of competition, these findings suggest competitive exclusion of Ae. japonicus in those habitats where this species co-occurs with Ae. albopictus.

  8. SJL-1, a C-type lectin, acts as a surface defense molecule in Japanese sea cucumber, Apostichopus japonicus.

    PubMed

    Ono, Keisuke; Suzuki, Takuya Alan; Toyoshima, Youichi; Suzuki, Tomoya; Tsutsui, Shigeyuki; Odaka, Tomoyuki; Miyadai, Toshiaki; Nakamura, Osamu

    2018-05-01

    The surface defense molecules of aquatic invertebrates against infectious microorganisms have remained largely unexplored. In the present study, hemagglutinins were isolated from an extract of body surface layer of Japanese sea cucumber, Apostichopus japonicus, by affinity chromatography with fixed rabbit erythrocyte membranes. The N-terminal sequence of a 15-kDa agglutinin was almost identical with that of SJL-1, a C-type lectin formerly identified in this species. Because cDNA sequence and tissue distribution of SJL-1 have not been reported, we performed cDNA sequencing, gene expression analysis, and western blotting and immunohistochemical evaluation with anti-recombinant SJL-1 (rSJL-1) antibodies. The hemagglutinin gene was transcribed mainly in the integument, tentacles, and respiratory tree. Western blotting revealed that SJL-I is present in a body surface rinse, indicating that SJL-1 is secreted onto the body surface. SJL-1-positive cells scattered beneath the outermost layer of the integument were detected by immunohistochemistry. Furthermore, rSJL-1 agglutinated Gram-positive and Gram-negative bacteria, and yeast. These results indicate that SJL-1 acts as a surface defense molecule in A. japonicus. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes

    PubMed Central

    Cannon, Steven B.; Sterck, Lieven; Rombauts, Stephane; Sato, Shusei; Cheung, Foo; Gouzy, Jérôme; Wang, Xiaohong; Mudge, Joann; Vasdewani, Jayprakash; Schiex, Thomas; Spannagl, Manuel; Monaghan, Erin; Nicholson, Christine; Humphray, Sean J.; Schoof, Heiko; Mayer, Klaus F. X.; Rogers, Jane; Quétier, Francis; Oldroyd, Giles E.; Debellé, Frédéric; Cook, Douglas R.; Retzel, Ernest F.; Roe, Bruce A.; Town, Christopher D.; Tabata, Satoshi; Van de Peer, Yves; Young, Nevin D.

    2006-01-01

    Genome sequencing of the model legumes, Medicago truncatula and Lotus japonicus, provides an opportunity for large-scale sequence-based comparison of two genomes in the same plant family. Here we report synteny comparisons between these species, including details about chromosome relationships, large-scale synteny blocks, microsynteny within blocks, and genome regions lacking clear correspondence. The Lotus and Medicago genomes share a minimum of 10 large-scale synteny blocks, each with substantial collinearity and frequently extending the length of whole chromosome arms. The proportion of genes syntenic and collinear within each synteny block is relatively homogeneous. Medicago–Lotus comparisons also indicate similar and largely homogeneous gene densities, although gene-containing regions in Mt occupy 20–30% more space than Lj counterparts, primarily because of larger numbers of Mt retrotransposons. Because the interpretation of genome comparisons is complicated by large-scale genome duplications, we describe synteny, synonymous substitutions and phylogenetic analyses to identify and date a probable whole-genome duplication event. There is no direct evidence for any recent large-scale genome duplication in either Medicago or Lotus but instead a duplication predating speciation. Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar). PMID:17003129

  10. Ontogenetic dietary shift in the larvae of Cybister japonicus (Coleoptera: Dytiscidae) in Japanese rice fields.

    PubMed

    Ohba, Shin-Ya

    2009-06-01

    A number of fragmentary reports suggest that the endangered diving beetle Cybister japonicus larvae feed on tadpoles, fish, and aquatic insects. However, no quantitative study on the feeding habits of C. japonicus larvae has been reported. In this study, field observations and rearing experiments were carried out to show the feeding ecology of C. japonicus larvae. Unlike previous commentaries, the first- and second-instar larvae of C. japonicus preyed on insects, mainly Odonata nymphs and Notonecta triguttata, irrespective of prey availability, but did not eat vertebrates such as tadpoles and fish in the field. On the contrary, the third-instar larvae fed on both insects and vertebrates. Rearing experiments showed that the number of Odonata nymphs consumed was significantly more than the number of tadpoles consumed by the first and second instars but third-instar larvae ate both the Odonata nymphs and tadpoles in the tadpole-Odonata nymph mixture experiment. The total body lengths of C. japonicus new adults in the Odonata nymph and tadpole-Odonata nymph mixture treatments were statistically equal. These results suggested that the first- and second-instar larvae of C. japonicus prey mainly on insects and do not eat vertebrate animals (insectivore), whereas the third-instar larvae fed on both insects and vertebrates (generalist).

  11. Transcriptome analysis of tube foot and large scale marker discovery in sea cucumber, Apostichopus japonicus.

    PubMed

    Zhou, Xiaoxu; Wang, Hongdi; Cui, Jun; Qiu, Xuemei; Chang, Yaqing; Wang, Xiuli

    2016-12-01

    Tube foot as one of the ambulacral appendages types in Aspidochirote holothurioids, is known for their functions in locomotion, feeding, chemoreception, light sensitivity and respiration. In this study, we explored the characteristic of transcriptome in the tube foot of sea cucumber (Apostichopus japonicus). Our results showed that among 390 unigenes which specifically expressed in the tube foot, 190 of them were annotated. Based on the assembly transcriptome, we found 219,860 SNPs from 34,749 unigenes, 97,683, 53,624, 27,767 and 40,786 were located in CDSs, 5'-UTRs, 3'-UTRs and non-CDS separately. Furthermore, 12,114 SSRs were detected from 7394 unigenes. Target genes of four specifically expressed miRNAs (miR-29a, miR-29b, miR-278-3p and miR-2005) in tube foot were also predicted based on the transcriptome, which contain immune-related factors (MBL, VLRA, AjC3, MyD88, CFB), skin pigmentation (MITF), candidate regeneration factor (TRP) and holothurians autolysis-related factor (CL). These results develop a relatively large number of molecular markers and transcriptome resources, and will provide a foundation for further analyses on the function and molecular mechanisms underlying A. japonicas tube foot. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Lotus japonicus flowers are defended by a cyanogenic β-glucosidase with highly restricted expression to essential reproductive organs.

    PubMed

    Lai, Daniela; Pičmanová, Martina; Abou Hachem, Maher; Motawia, Mohammed Saddik; Olsen, Carl Erik; Møller, Birger Lindberg; Rook, Fred; Takos, Adam M

    2015-09-01

    Flowers and leaves of Lotus japonicus contain α-, β-, and γ-hydroxynitrile glucoside (HNG) defense compounds, which are bioactivated by β-glucosidase enzymes (BGDs). The α-HNGs are referred to as cyanogenic glucosides because their hydrolysis upon tissue disruption leads to release of toxic hydrogen cyanide gas, which can deter herbivore feeding. BGD2 and BGD4 are HNG metabolizing BGD enzymes expressed in leaves. Only BGD2 is able to hydrolyse the α-HNGs. Loss of function mutants of BGD2 are acyanogenic in leaves but fully retain cyanogenesis in flowers pointing to the existence of an alternative cyanogenic BGD in flowers. This enzyme, named BGD3, is identified and characterized in this study. Whereas all floral tissues contain α-HNGs, only those tissues in which BGD3 is expressed, the keel and the enclosed reproductive organs, are cyanogenic. Biochemical analysis, active site architecture molecular modelling, and the observation that L. japonicus accessions lacking cyanogenic flowers contain a non-functional BGD3 gene, all support the key role of BGD3 in floral cyanogenesis. The nectar of L. japonicus flowers was also found to contain HNGs and additionally their diglycosides. The observed specialisation in HNG based defence in L. japonicus flowers is discussed in the context of balancing the attraction of pollinators with the protection of reproductive structures against herbivores.

  13. Biosynthesis and hyper production of pullulan by a newly isolated strain of Aspergillus japonicus-VIT-SB1.

    PubMed

    Mishra, Bishwambhar; Suneetha, V

    2014-07-01

    The main focus of this study was to screen and characterize novel microbial strains isolated from culinary leaf samples, capable of producing high concentrations of pullulan. Hundred isolates were screened from the phylloplane of different plants. The results revealed that eight strains had the capability to produce exopolysaccharide (EPS) and only one potential strain (designated as VIT-SB1) could produce the significant amount of EPS (3.9 ± 0.02%) on the 6th day of the fermentation without optimisation. The EPS synthesized by VIT-SB1 strain was confirmed to be pullulan on the basis of the results of FT-IR, HPLC and the enzymatic (Pullulanase) analysis. More than 91% hydrolysis of pullulan by pullulanase enzyme also indicated the presence of α (1 → 6) glycosidic linkages of α (1 → 4) linked maltotriose units. This VIT-SB1 strain was identified as Aspergillus japonicus based on the nucleotide sequence of the D1/D2 domain of Large-Subunit rRNA gene. The sequence was submitted to the GenBank Nucleotide sequence database with Accession No: KC128815. This study has confirmed that pullulan production capacity of this novel strain and Aureobasidium pullulans are comparable. Hence Aspergillus japonicus-VIT-SB1 strain can be commercially exploited as a potential pullulan producing strain.

  14. Accumulation and developmental toxicity of hexabromocyclododecanes (HBCDs) on the marine copepod Tigriopus japonicus.

    PubMed

    Shi, Dalin; Lv, Dongmei; Liu, Wanxin; Shen, Rong; Li, Dongmei; Hong, Haizheng

    2017-01-01

    The brominated flame retardants hexabromocyclododecanes (HBCDs) are ubiquitous environmental contaminants, widely distributed in aquatic systems including the marine environment and marine organisms. HBCDs are toxic to the development of both freshwater and marine fish. However, the impacts of HBCDs on marine invertebrates are not well known. In this study, the marine copepod, Tigriopus japonicus, was used to assess the bioaccumulation and developmental toxicity of technical HBCD (tHBCD) through water-borne exposure. The uptake rate constant of tHBCD by T. japonicus was high, which resulted in high bioaccumulation potential. The bioconcentration factors of tHBCD were 8.73 × 10 4 and 6.34 × 10 4  L kg -1 in T. japonicus, calculated using the kinetic and steady-state methods, respectively. Exposure of T. japonicus nauplii to tHBCD caused significant growth delay. The lowest-observable-effect-concentrations of tHBCD induced developmental delay were 30 and 8 μg L -1 for the F0 and F1 generations, respectively, which suggested that the F1 generation was more sensitive to tHBCD than the F0 generation and warranted multiple-generation toxicity tests for future studies. Furthermore, exposure of the adult copepods to tHBCD induced the transcription of oxidative stress response genes and apoptotic genes, e.g., SOD,CAT, GST, OGG1, P53 and Caspase-3. It was therefore speculated that tHBCD exposure induced the generation of reactive oxygen species in T. japonicus, which activated the oxidative stress defense genes and meanwhile resulted in oxidative DNA damage. The damaged DNA activated the transcription of p53 and triggered the caspase-mediated apoptosis pathway, which may be the reason for the tHBCD induced developmental delay in T. japonicus nauplii. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Systems analysis in Cellvibrio japonicus resolves predicted redundancy of β-glucosidases and determines essential physiological functions: Functional analysis of C. japonicus β-glucosidases

    DOE PAGES

    Nelson, Cassandra E.; Rogowski, Artur; Morland, Carl; ...

    2017-02-28

    Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes, many of which have been categorized as functionally redundant. Here we present data that suggests that carbohydrate active enzymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell. Our comprehensive study to understand cellodextrin utilization in the soil saprophyte Cellvibrio japonicus found that only one of four predicted β-glucosidases is required in amore » physiological context. Gene deletion analysis indicated that only the cel3B gene product is essential for efficient cellodextrin utilization in C. japonicus and is constitutively expressed at high levels. Interestingly, expression of individual β-glucosidases in Escherichia coli K-12 enabled this non-cellulolytic bacterium to be fully capable of using cellobiose as a sole carbon source. Furthermore, enzyme kinetic studies indicated that the Cel3A enzyme is significantly more active than the Cel3B enzyme on the oligosaccharides but not disaccharides. Finally, our approach for parsing related carbohydrate active enzymes to determine actual physiological roles in the cell can be applied to other polysaccharide-degradation systems.« less

  16. The Hair Growth-Promoting Effect of Rumex japonicus Houtt. Extract

    PubMed Central

    Lee, Hyunkyoung; Kim, Na-Hyun; Yang, Hyeryeon; Bae, Seong Kyeong; Heo, Yunwi; Choudhary, Indu; Kwon, Young Chul; Byun, Jae Kuk; Yim, Hyeong Jun; Noh, Byung Seung; Heo, Jeong-Doo; Kim, Euikyung

    2016-01-01

    Rumex japonicus Houtt. is traditionally used as a medicinal plant to treat patients suffering from skin disease in Korea. However, the beneficial effect of Rumex japonicus Houtt. on hair growth has not been thoroughly examined. Therefore, the present study aims to investigate the hair growth-promoting effect of Rumex japonicus (RJ) Houtt. root extract using human dermal papilla cells (DPCs), HaCaT cells, and C57BL/6 mice model. RJ induced antiapoptotic and proliferative effects on DPCs and HaCaT cells by increasing Bcl-2/Bax ratio and activating cellular proliferation-related proteins, ERK and Akt. RJ also increased β-catenin via the inhibition of GSK-3β. In C57BL/6 mice model, RJ promoted the anagen induction and maintained its period. Immunohistochemistry analysis demonstrated that RJ upregulated Ki-67 and β-catenin expressions, suggesting that the hair growth effect of RJ may be mediated through the reinforcement of hair cell proliferation. These results provided important insights for the possible mechanism of action of RJ and its potential as therapeutic agent to promote hair growth. PMID:27974900

  17. Individual variation in growth in sea cucumber Apostichopus japonicus (Selenck) housed individually

    NASA Astrophysics Data System (ADS)

    Liang, Miao; Dong, Shuanglin; Gao, Qinfeng; Wang, Fang; Tian, Xiangli

    2010-09-01

    The exceptionally large individual growth variation has been previously recognized in several sea cucumber cohorts. However, there is a lack of information regarding the mechanism of such individual differences. In this study, the sea cucumber Apostichopus japonicus (Selenka) was reared individually in order to eliminate possible effects of social interaction, stocking density, etc. The results showed that there were substantial differences in growth among the sea cucumber individuals during the 100-day experiment. The special growth rate of the sea cucumber individuals differed by up to three folds (from 0.40% to 1.01%), and the coefficient of variation in body weight increased from 12.04% to 40.51%. The final wet body weight, food intake and food conversion efficiency for each sea cucumber were generally positively correlated with their initial wet body weight ( P<0.05). Energy budget of the animals showed that the food energy spent on respiration was much greater (about four folds) but energy deposited for growth was much less for (initially) smaller than for larger A. japonicus. The present result implies that there are obvious genetic differences among the sea cucumber individuals, largely accounting for the individual growth variation of the cohort sea cucumber. These results will provide some basic data for promoting selective breeding and farming of the sea cucumber.

  18. The application of compound-specific isotope analysis of fatty acids for traceability of sea cucumber (Apostichopus japonicus) in the coastal areas of China.

    PubMed

    Liu, Yu; Zhang, Xufeng; Li, Ying; Wang, Haixia

    2017-11-01

    Geographical origin traceability is an important issue for controlling the quality of seafood and safeguarding the interest of consumers. In the present study, a new method of compound-specific isotope analysis (CSIA) of fatty acids was established to evaluate its applicability in establishing the origin traceability of Apostichopus japonicus in the coastal areas of China. Moreover, principal component analysis (PCA) and discriminant analysis (DA) were applied to distinguish between the origins of A. japonicus. The results show that the stable carbon isotope compositions of fatty acids of A. japonicus significantly differ in terms of both season and origin. They also indicate that the stable carbon isotope composition of fatty acids could effectively discriminate between the origins of A. japonicus, except for between Changhai Island and Zhangzi Island in the spring of 2016 because of geographical proximity or the similarity of food sources. The fatty acids that have the highest contribution to identifying the geographical origins of A. japonicus are C22:6n-3, C16:1n-7, C20:5n-3, C18:0 and C23:1n-9, when considering the fatty acid contents, the stable carbon isotope composition of fatty acids and the results of the PCA and DA. We conclude that CSIA of fatty acids, combined with multivariate statistical analysis such as PCA and DA, may be an effective tool for establishing the traceability of A. japonicus in the coastal areas of China. The relevant conclusions of the present study provide a new method for determining the traceability of seafood or other food products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  19. The host preference and impact of Argulus japonicus ectoparasite on cyprinids in Central Java, Indonesia

    NASA Astrophysics Data System (ADS)

    Kismiyati; Wulansari, P. D.; Dewi, N. N.

    2018-04-01

    The most widely cultivated freshwater fish are from Familia Cyprinidae, among others goldfish (Carassius auratus), koi (Cyprinus carpio) and comet goldfish (Carassius auratus auratus). One of the constraints of freshwater fish cultivation is ectoparasite infestation Argulus japonicus. Financial losses have been experienced by some farmers, caused by these ectoparasitic infestaions. This study was aimed to determine the impact of ectoparasite Argulus japonicus infestation on host (freshwater ornamental fish from Familia Cyprinidae), in order to find a preventive solution to treatment on the host. The results showed that prevalence of infested fish by Argulus japonicus were 57 % goldfish, 31 % comet fish and 65 % koi. Changes of histopathology on host were congestion, baoning degeneration, epithelium erosion and inflammatory cell infiltration. The image of infected leukocytes infested by Argulus japonicus were 8.5 % of lymphocytes, 4.7 % neurophils, 3.9 % monocytes, 1.45 % eosinophils and 0,17% basophils.

  20. Particulate matter and heavy metal deposition on the leaves of Euonymus japonicus during the East Asian monsoon in Beijing, China

    PubMed Central

    Hong, Xiuling; Sun, Liwei

    2017-01-01

    Plants can be effectively used as bio-monitors of environmental pollution. However, how the particulate matter (PM) and heavy metal retention ability of plants changes in different areas with human disturbance along with monsoon has not yet been investigated in urban ecosystems. In this study, we measured the amount of PM and heavy metals such as Ni, Cr, Cu, Pb, and Zn accumulated by the leaves of Euonymus japonicus during the East Asian monsoon from different functional units in Beijing, China. A rinse-and-weigh method developed in our laboratory was used to determine the mass of the PM, and electro-thermal atomic absorption spectrometry was used for heavy metal analysis. We found that the types of functional units had little influence, whereas the monsoon had a significant effect on the deposition of PM: northwest areas during the monsoon had the lowest effect (with 0.005, 0.453, 0.643, and 1.569 g/m2 fine, coarse, large, and total PM, respectively), and the southeast areas during the monsoon had the highest effect (0.015, 2.687, 1.941, and 4.228 g/m2 for fine, coarse, large, and total PM, respectively). Notable, we found considerable variations in heavy metal accumulation across the functional units analyzed, that is, the accumulation level was higher in communities than in parks (P < 0.0001 for all heavy metals). Moreover, a positive relationship was found between PM retention and heavy metal accumulation by the leaves of E. japonicus. Taken together, our results suggested that the PM and heavy metal retention ability of E. japonicus was sensitive to human disturbance and monsoon in Beijing. Since E. japonicus is a widely distributed tree and has the ability of to purify the atmosphere, it is an ideal plant for mitigating urban environmental pollution. PMID:28662081

  1. Identification and expression characterization of WntA during intestinal regeneration in the sea cucumber Apostichopus japonicus.

    PubMed

    Li, Xiaoni; Sun, Lina; Yang, Hongsheng; Zhang, Libin; Miao, Ting; Xing, Lili; Huo, Da

    2017-08-01

    Wnt genes encode secreted glycoproteins that act as signaling molecules; these molecules direct cell proliferation, migration, differentiation and survival during animal development, maintenance of homeostasis and regeneration. At present, although the regeneration mechanism in Apostichopus japonicus has been studied, there is a little research on the Wnt signaling pathway in A. japonicus. To understand the potential role of the Wnt signaling pathway in A. japonicus, we cloned and sequenced the WntA gene in A. japonicus. Protein localization analysis showed that WntA protein was ubiquitously expressed in epidermal cells, the muscle and submucosa of the intestinal tissue. After stimulation and evisceration, the dynamic changes in expression of the WntA gene and protein showed that WntA was constitutively expressed during different stages of intestine regeneration in A. japonicus, with higher levels during the early wound healing stage and late lumen formation in the residual and nascent intestinal tissues, indicating its response to intestinal regeneration. Simultaneously, cell proliferation and apoptosis analysis showed that the patterns of cell proliferation were similar to the patterns of WntA protein expression during different intestinal regeneration stages in this organism. Taken together, these results suggested that WntA might participate in intestinal regeneration and may be connected with cell proliferation, apoptosis in different intestinal layers. This research could establish a basis for further examination of WntA functions in A. japonicus and Wnt genes in other echinoderms. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Apoptosis induction is involved in UVA-induced autolysis in sea cucumber Stichopus japonicus.

    PubMed

    Qi, Hang; Fu, Hui; Dong, Xiufang; Feng, Dingding; Li, Nan; Wen, Chengrong; Nakamura, Yoshimasa; Zhu, Beiwei

    2016-05-01

    Autolysis easily happens to sea cucumber (Stichopus japonicus, S. japonicus) for external stimulus like UV exposure causing heavy economic losses. Therefore, it is meaningful to reveal the mechanism of S. japonicas autolysis. In the present study, to examine the involvement of apoptosis induction in UVA-induced autolysis of S. japonicas, we investigated the biochemical events including the DNA fragmentation, caspase-3 activation, mitogen-activated protein kinases (MAPKs) phosphorylation and free radical formation. Substantial morphological changes such as intestine vomiting and dermatolysis were observed in S. japonicus during the incubation after 1-h UVA irradiation (10W/m(2)). The degradation of the structural proteins and enhancement of cathepsin L activity were also detected, suggesting the profound impact of proteolysis caused by the UVA irradiation even for 1h. Furthermore, the DNA fragmentation and specific activity of caspase-3 was increased up to 12h after UVA irradiation. The levels of phosphorylated p38 mitogen activated protein kinase (MAPK) and phosphorylated c-Jun.-N-terminal kinase (JNK) were significantly increased by the UVA irradiation for 1h. An electron spin resonance (ESR) analysis revealed that UVA enhanced the free radical formation in S. japonicas, even through we could not identify the attributed species. These results suggest that UVA-induced autolysis in S. japonicas at least partially involves the oxidative stress-sensitive apoptosis induction pathway. These data present a novel insight into the mechanisms of sea cucumber autolysis induced by external stress. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Lotus Base: An integrated information portal for the model legume Lotus japonicus

    PubMed Central

    Mun, Terry; Bachmann, Asger; Gupta, Vikas; Stougaard, Jens; Andersen, Stig U.

    2016-01-01

    Lotus japonicus is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various Lotus studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of Lotus genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present Lotus Base, which opens to the research community a large, established LORE1 insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from Lotus, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the L. japonicus gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks. Lotus Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated Lotus data. Lotus Base is freely accessible at: https://lotus.au.dk. PMID:28008948

  4. Community Ecology of Container Mosquitoes (Diptera: Culicidae) in Virginia Following Invasion by Aedes japonicus

    PubMed Central

    ARMISTEAD, JENNIFER S.; NISHIMURA, NAOYA; ARIAS, JORGE R.; LOUNIBOS, L. PHILIP

    2012-01-01

    The success of an invasive species in a new region depends on its interactions with ecologically similar resident species. Invasions by disease vector mosquitoes are important as they may have ecological and epidemiological consequences. Potential interactions of a recent invasive mosquito, Aedes japonicus Theobald, with resident species in Virginia were evaluated by sampling larvae from containers and trapping adults. Distinct species compositions were observed for artificial containers and rock pools, with Ae. albopictus most abundant in the former and Ae. japonicus in the latter. However, these two species were found to co-occur in 21.2% of containers sampled. Among the six mosquito species most common in containers from May through September, 2006, only interspecific associations of Ae.japonicus with Aedesalbopictus(Skuse) and Aedestriseriatus(Say) were significant, and both were negative. In addition to differences in habitat preference, mean crowding estimates suggest that interspecific repulsion may contribute to the significant negative associations observed between these species. High relative abundances of late instars and pupae of Ae. japonicus seem to provide this species with a mechanism of evading competition with Ae. albopictus, facilitating their coexistence in artificial containers. Although annual fluctuations were observed, trends in adult populations over a 6-yr period provide no evidence of declines. In summary, this survey of diverse container types and all life stages provided only limited evidence for competitive displacements or reductions of resident container species by Ae. japonicus, as observed elsewhere in its invasive range. PMID:23270159

  5. Change of digestive physiology in sea cucumber Apostichopus japonicus (Selenka) induced by corn kernels meal and soybean meal in diets

    NASA Astrophysics Data System (ADS)

    Yu, Haibo; Gao, Qinfeng; Dong, Shuanglin; Hou, Yiran; Wen, Bin

    2016-08-01

    The present study was conducted to determine the change of digestive physiology in sea cucumber Apostichopus japonicus (Selenka) induced by corn kernels meal and soybean meal in diets. Four experimental diets were tested, in which Sargassum thunbergii was proportionally replaced by the mixture of corn kernels meal and soybean meal. The growth performance, body composition and intestinal digestive enzyme activities in A. japonicus fed these 4 diets were examined. Results showed that the sea cucumber exhibited the maximum growth rate when 20% of S. thunbergii in the diet was replaced by corn kernels meal and soybean meal, while 40% of S. thunbergii in the diet can be replaced by the mixture of corn kernels meal and soybean meal without adversely affecting growth performance of A. japonicus. The activities of intestinal trypsin and amylase in A. japonicus can be significantly altered by corn kernels meal and soybean meal in diets. Trypsin activity in the intestine of A. japonicus significantly increased in the treatment groups compared to the control, suggesting that the supplement of corn kernels meal and soybean meal in the diets might increase the intestinal trypsin activity of A. japonicus. However, amylase activity in the intestine of A. japonicus remarkably decreased with the increasing replacement level of S. thunbergii by the mixture of corn kernels meal and soybean meal, suggesting that supplement of corn kernels meal and soybean meal in the diets might decrease the intestinal amylase activity of A. japonicus.

  6. Novel SINEs families in Medicago truncatula and Lotus japonicus: bioinformatic analysis.

    PubMed

    Gadzalski, Marek; Sakowicz, Tomasz

    2011-07-01

    Although short interspersed elements (SINEs) were discovered nearly 30 years ago, the studies of these genomic repeats were mostly limited to animal genomes. Very little is known about SINEs in legumes--one of the most important plant families. Here we report identification, genomic distribution and molecular features of six novel SINE elements in Lotus japonicus (named LJ_SINE-1, -2, -3) and Medicago truncatula (MT_SINE-1, -2, -3), model species of legume. They possess all the structural features commonly found in short interspersed elements including RNA polymerase III promoter, polyA tail and flanking repeats. SINEs described here are present in low to moderate copy numbers from 150 to 3000. Bioinformatic analyses were used to searched public databases, we have shown that three of new SINE elements from M. truncatula seem to be characteristic of Medicago and Trifolium genera. Two SINE families have been found in L. japonicus and one is present in both M. truncatula and L. japonicus. In addition, we are discussing potential activities of the described elements. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Trissolcus japonicus (Ashmead) emerges in North America

    USDA-ARS?s Scientific Manuscript database

    Trissolcus japonicus (Ashmead) is an Asian egg parasitoid of the brown marmorated stink bug, Halyomorpha halys (Stål). It has been under study in U.S. quarantine facilities since 2007 to evaluate its efficacy as a candidate classical biological control agent and its host specificity with regard to t...

  8. Comparative transcriptome analysis of three color variants of the sea cucumber Apostichopus japonicus.

    PubMed

    Jo, Jihoon; Park, Jongsun; Lee, Hyun-Gwan; Kern, Elizabeth M A; Cheon, Seongmin; Jin, Soyeong; Park, Joong-Ki; Cho, Sung-Jin; Park, Chungoo

    2016-08-01

    The sea cucumber Apostichopus japonicus Selenka 1867 represents an important resource in biomedical research, traditional medicine, and the seafood industry. Much of the commercial value of A. japonicus is determined by dorsal/ventral color variation (red, green, and black), yet the taxonomic relationships between these color variants are not clearly understood. We performed the first comparative analysis of de novo assembled transcriptome data from three color variants of A. japonicus. Using the Illumina platform, we sequenced nearly 177,596,774 clean reads representing a total of 18.2Gbp of sea cucumber transcriptome. A comparison of over 0.3 million transcript scaffolds against the Uniprot/Swiss-Prot database yielded 8513, 8602, and 8588 positive matches for green, red, and black body color transcriptomes, respectively. Using the Panther gene classification system, we assessed an extensive and diverse set of expressed genes in three color variants and found that (1) among the three color variants of A. japonicus, genes associated with RNA binding protein, oxidoreductase, nucleic acid binding, transferase, and KRAB box transcription factor were most commonly expressed; and (2) the main protein functional classes are differently regulated in all three color variants (extracellular matrix protein and phosphatase for green color, transporter and potassium channel for red color, and G-protein modulator and enzyme modulator for black color). This work will assist in the discovery and annotation of novel genes that play significant morphological and physiological roles in color variants of A. japonicus, and these sequence data will provide a useful set of resources for the rapidly growing sea cucumber aquaculture industry. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Proteomic analysis reveals the important roles of alpha-5-collagen and ATP5β during skin ulceration syndrome progression of sea cucumber Apostichopus japonicus.

    PubMed

    Zhao, Zelong; Jiang, Jingwei; Pan, Yongjia; Sun, Hongjuan; Guan, Xiaoyan; Gao, Shan; Chen, Zhong; Dong, Ying; Zhou, Zunchun

    2018-03-20

    Apostichopus japonicus is one of the most important aquaculture species in China. Skin ulceration syndrome (SUS) of sea cucumber is a common and serious disease affected the development of A. japonicus culture industry. To better understand the response mechanisms of A. japonicus during SUS progression, the protein variations in the body wall of A. japonicus at different stages of SUS were investigated by a comparative proteomic approach based on isobaric tags for relative and absolute quantification. A total of 1449 proteins were identified from the samples at different SUS stages. Among these proteins, 145 proteins were differentially expressed in the SUS-related samples compared to those of healthy A. japonicus. These differentially expressed proteins involved a wide range of functions. Among these differentially expressed proteins, only two proteins, alpha-5-collagen and an unknown function protein, were differentially expressed during the whole progression of SUS compared with healthy A. japonicus. In addition, ATP synthase subunit beta (ATP5β) interacted with a variety of proteins with different functions during the SUS progression. These results implied that alpha-5-collagen and ATP5β could play important roles during the SUS progression of A. japonicus. Our study provided a new sight to understand the molecular responses of sea cucumber during the SUS progression and accumulated data for the prevention of SUS in sea cucumber aquaculture. The current study aimed to reveal how the body wall of Apostichopus japonicus response to skin ulceration syndrome (SUS). To the best of our knowledge, this is the first proteomic study analyzing the differences in protein profile of sea cucumber during the whole SUS progression. By analyzing the expression differences of the proteome via isobaric labeling-based quantitative proteomic, we identified some proteins which may play important roles during the SUS progression. According to the enrichment analyses of these

  10. Phylogeography of the sandy beach amphipod Haustorioides japonicus along the Sea of Japan: Paleogeographical signatures of cryptic regional divergences

    NASA Astrophysics Data System (ADS)

    Takada, Yoshitake; Sakuma, Kay; Fujii, Tetsuo; Kojima, Shigeaki

    2018-01-01

    Recent findings of genetic breaks within apparently continuous marine populations challenge the traditional vicariance paradigm in population genetics. Such "invisible" boundaries are sometimes associated with potential geographic barriers that have forced divergence of an ancestral population, habitat discontinuities, biogeographic disjunctions due to environmental gradients, or a combination of these factors. To explore the factors that influence the genetic population structure of apparently continuous populations along the Sea of Japan, the sandy beach amphipod Haustorioides japonicus was examined. We sampled a total of 300 individuals of H. japonicus from the coast of Japan, and obtained partial sequences of the mitochondrial COI gene. The sequences from 19 local populations were clustered into five groups (Northwestern Pacific, Northern, Central, Southern Sea of Japan, and East China Sea) based on a spatial genetic mixture analysis and a minimum-spanning network. AMOVA and pairwise Fst tests further supported the significant divergence of the five groups. Phylogenetic analysis revealed the relationship among the haplotypes of H. japonicus and outgroups, which inferred the northward range expansion of the species. A relaxed molecular-clock Bayesian analysis inferred the early-to middle-Pleistocene divergence of the populations. Among the five clusters, the Central Sea of Japan showed the highest values for genetic diversity indices indicating the existence of a relatively stable and large population there. The hypothesis is also supported by Bayesian Skyline Plots that showed sudden population expansion for all the clusters except for Central Sea of Japan. The present study shows genetic boundaries between the Sea of Japan and the neighboring seas, probably due to geographic isolation during the Pleistocene glacial periods. We further found divergence between the populations along the apparently continuous coast of the Sea of Japan. Historical changes in the

  11. Development of Dirofilaria immitis and Dirofilaria repens in Aedes japonicus and Aedes geniculatus.

    PubMed

    Silaghi, Cornelia; Beck, Relja; Capelli, Gioia; Montarsi, Fabrizio; Mathis, Alexander

    2017-02-20

    The mosquito-borne filarial nematodes Dirofilaria immitis and Dirofilaria repens primarily affect dogs but also cats, causing heartworm disease or subcutaneous dirofilariosis, respectively, and both may also cause zoonotic diseases in humans. Several mosquito species have been reported as competent vectors for these nematodes, but no data are available for the invasive mosquito species Aedes japonicus (Theobald, 1901). The objective of this study was to describe the development of both D. immitis and D. repens under standardised experimental laboratory conditions in mosquitoes. For this purpose, both a laboratory strain and field-collected individuals of the invasive mosquito species Ae. japonicus and, for comparative purposes, a laboratory strain of Aedes geniculatus, a rare indigenous species sharing habitats with Ae. japonicus, and of the tropical species Aedes aegypti were used. Anticoagulated microfilariaemic blood was fed at a density of 3000 mf/ml to mosquitoes with a hemotek system. Blood-fed mosquitoes were incubated at 27 °C and 85% relative humidity, and specimens were dissected under the microscope at pre-set time points to observe developmental stages of both Dirofilaria species. Additionally, real-time PCRs were carried out in some microscopically negative samples to determine the infection rates. In field-collected Ae. japonicus infectious L3 larvae of both D. immitis and D. repens developed, rendering this mosquito species an efficient vector for both filarial species. Additionally, Ae. geniculatus was shown to be an equally efficient vector for both filarial species. Aedes japonicus mosquitoes from a laboratory colony were refractory to D. immitis but susceptible to D. repens, whereas Ae. aegypti was refractory to both filarial species. To our knowledge, Aedes japonicus was for the first time shown to be an efficient vector for both D. immitis and D. repens, indicating that this invasive and locally highly abundant species may contribute to a

  12. Analysis of fatty acid composition of sea cucumber Apostichopus japonicus using multivariate statistics

    NASA Astrophysics Data System (ADS)

    Xu, Qinzeng; Gao, Fei; Xu, Qiang; Yang, Hongsheng

    2014-11-01

    Fatty acids (FAs) provide energy and also can be used to trace trophic relationships among organisms. Sea cucumber Apostichopus japonicus goes into a state of aestivation during warm summer months. We examined fatty acid profiles in aestivated and non-aestivated A. japonicus using multivariate analyses (PERMANOVA, MDS, ANOSIM, and SIMPER). The results indicate that the fatty acid profiles of aestivated and non-aestivated sea cucumbers differed significantly. The FAs that were produced by bacteria and brown kelp contributed the most to the differences in the fatty acid composition of aestivated and nonaestivated sea cucumbers. Aestivated sea cucumbers may synthesize FAs from heterotrophic bacteria during early aestivation, and long chain FAs such as eicosapentaenoic (EPA) and docosahexaenoic acid (DHA) that produced from intestinal degradation, are digested during deep aestivation. Specific changes in the fatty acid composition of A. japonicus during aestivation needs more detailed study in the future.

  13. Sustainability evaluation of different systems for sea cucumber ( Apostichopus japonicus) farming based on emergy theory

    NASA Astrophysics Data System (ADS)

    Wang, Guodong; Dong, Shuanglin; Tian, Xiangli; Gao, Qinfeng; Wang, Fang

    2015-06-01

    Emergy analysis is effective for analyzing ecological economic systems. However, the accuracy of the approach is affected by the diversity of economic level, meteorological and hydrological parameters in different regions. The present study evaluated the economic benefits, environmental impact, and sustainability of indoor, semi-intensive and extensive farming systems of sea cucumber ( Apostichopus japonicus) in the same region. The results showed that A. japonicus indoor farming system was high in input and output (yield) whereas pond extensive farming system was low in input and output. The output/input ratio of indoor farming system was lower than that of pond extensive farming system, and the output/input ratio of semi-intensive farming system fell in between them. The environmental loading ratio of A. japonicus extensive farming system was lower than that of indoor farming system. In addition, the emergy yield and emergy exchange ratios, and emergy sustainability and emergy indexes for sustainable development were higher in extensive farming system than those in indoor farming system. These results indicated that the current extensive farming system exerted fewer negative influences on the environment, made more efficient use of available resources, and met more sustainable development requirements than the indoor farming system. A. japonicus farming systems showed more emergy benefits than fish farming systems. The pond farming systems of A. japonicus exploited more free local environmental resources for production, caused less potential pressure on the local environment, and achieved higher sustainability than indoor farming system.

  14. Identification and pathogenicity of Vibrio ponticus affecting cultured Japanese sea bass, Lateolabrax japonicus (Cuvier in Cuvier and Valenciennes).

    PubMed

    Xie, Z Y; Hu, C Q; Zhang, L P; Chen, C; Ren, C H; Shen, Q

    2007-07-01

    To rapidly determine the causative agent of mass death in Lateolabrax japonicus in Zhelin Bay of Guangdong Province in China in April 2004. Thirty-six strains, numbered sequentially from RP01 to RP36, were isolated from six diseased fish. All of the strains were identified as being of the same vibrio species according to the results of universal primer PCR combined with DGGE (UPPCR-DGGE). RP30 was one of these strains that was randomly selected and analysed by using a morphological, physiological and biochemical plate, Biolog GN2 Microplate System and API 20E system. Furthermore, RP30' 16S rDNA was sequenced and aligned in Genbank. Its virulence to Lateolabrax japonicus (Cuvier in Cuvier and Valenciennes) was also tested. RP30 is most closely related to four Vibrio ponticus strains (99.3% similarity). LD50s were 2.5 (x103 CFU per fish for intraperitoneal inoculation (IP) and 3.2 (x103 CFU per fish for intramuscular inoculation (IM), respectively. The investigated pathogenic agent of Lateolabrax japonicus (Cuvier in Cuvier and Valenciennes) was V. ponticus. UPPCR-DGGE is very helpful in epidemiologic investigation. Interestingly, this is the first report that V. ponticus infects cultured marine fish. DGGE was likewise first introduced to epidemiologic investigation of fish disease.

  15. Comparison of intestinal microbiota and activities of digestive and immune-related enzymes of sea cucumber Apostichopus japonicus in two habitats

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Zhang, Xiumei; Chen, Muyan; Li, Wentao; Zhang, Peidong

    2017-09-01

    Sea cucumber Apostichopus japonicus stock enhancement by releasing hatchery-produced seeds is a management tool used to recover its population under natural environmental conditions. To assess the suitability of releasing sites, we examined the microbiota of the gut contents of A. japonicus from two populations (one in sandy-muddy seagrass beds and one in rocky intertidal reefs) and the microbiota in their surrounding sediments. The activities of digestive and immune-related enzymes in the A. japonicus were also examined. The results indicated that higher bacterial richness and Shannon diversity index were observed in all the seagrass-bed samples. There were significant differences in intestinal and sediment microorganisms between the two habitats, with a 2.87 times higher abundance of Firmicutes in the seagrass bed sediments than that in the reefs. Meanwhile, Bacteroidetes and Actinobacteria were significantly higher abundant in the gut content of A. japonicus from seagrass bed than those from the reefs. In addition, the seagrass-bed samples exhibited a relatively higher abundance of potential probiotics. Principal coordinates analysis and heatmap showed the bacterial communities were classified into two groups corresponding to the two habitat types. Moreover, compared to A. japonicus obtained from rocky intertidal habitat, those obtained from the seagrass bed showed higher lysozyme, superoxide dismutase and protease activities. Our results suggest that bacterial communities present in seagrass beds might enhance the digestive function and immunity of A. japonicus. Therefore, compared with the rocky intertidal reef, seagrass bed seems to be more beneficial for the survival of A. japonicus.

  16. Succession and seasonal variation in epilithic biofilms on artificial reefs in culture waters of the sea cucumber Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Liu, Liming; Du, Rongbin; Zhang, Xiaoling; Dong, Shuanglin; Sun, Shichun

    2017-01-01

    Periphytic biofilms in aquaculture waters are thought to improve water quality, provide an additional food source, and improve the survival and growth of some reared animals. In the Asia- Pacific region, particularly in China, artificial reefs are commonly used in the commercial farming of sea cucumbers. However, few studies have examined the epilithic biofilms on the artificial reefs. To gain a better understanding of the succession of epilithic biofilms and their ecological processes in sea cucumber culture waters, two experiments were conducted in culture waters of the sea cucumber Apostichopus japonicus in Rongcheng, China, using artificial test panels. On the test panels of succession experiment, more than 67 species were identified in the biofilms. On the test panels of seasonal variation experiment, more than 46 species were recorded in the biofilms. In both experiments, communities of epilithic biofilms were dominated by diatoms, green algae and the annelid Spirorbis sp. In the initial colonization, the dominant diatoms were Cocconeis sp., Amphora spp. and Nitzschia closterium in June, which were succeeded by species of Navicula, Cocconeis and Nitzschia (July to September), and then by Licmophora abbreviata, Nitzschia closterium and Synedra spp. in the following months. A diatom bloom in the autumn and filamentous green algae burst in the summer were also observed. Ecological indices well annotated the succession and seasonal changes in epilithic communities. Multidimensional scaling (MDS) analysis found significant differences in diatom community composition among months and seasons. Fast growth of biofilms was observed in the summer and autumn, whereas the biomass of summer biofilms was largely made up of filamentous green algae. Present results show that the components of epilithic biofilms are mostly optimal foods of A. japonicus, suggesting that biofilms on artificial reefs may contribute important nutritional sources for sea cucumbers during their

  17. Comparative expression analysis of immune-related factors in the sea cucumber Apostichopus japonicus.

    PubMed

    Jiang, Jingwei; Zhou, Zunchun; Dong, Ying; Zhao, Zelong; Sun, Hongjuan; Wang, Bai; Jiang, Bei; Chen, Zhong; Gao, Shan

    2018-01-01

    In order to preliminarily explore the joint involvement of different immune-related factors during the same immune process in Apostichopus japonicus, the transcriptional expression of Cu/Zn superoxide dismutase (Cu/Zn-SOD), catalase (CAT), c-type lysozyme (c-LYZ), i-type lysozyme (i-LYZ), cathepsin D, melanotransferrin (MTF), Toll, c-type lectin (c-LCT) and complement 3 (C3) during the development from fertilized eggs to juveniles and after challenging the juveniles with Vibrio splendidus, Pseudoalteromonas nigrifaciens, Shewanella baltica and Bacillus cereus, respectively, was measured using the method of quantitative real-time PCR (qRT-PCR), and then the correlations among different immune-related factors were analyzed. The results showed that the selected immune-related factors were expressed at all of the determined developmental stages and significantly up-regulated at doliolaria stage, suggesting the selected factors are indispensable immune components and the immune system might be broadly activated at doliolaria stage in A. japonicus. After challenged with four pathogenic bacteria, Cu/Zn-SOD, CAT, i-LYZ, cathepsin D, MTF, Toll, C3 were all significantly down-regulated at 4 h, indicating that some components of A. japonicus immune system might be inhibited at the beginning of pathogenic bacteria invasion. The immune-responsive analysis also showed that the significant regulation in Toll after challenged with four tested bacteria, that in MTF after challenged with S. baltica and that in C3 after challenged with P. nigrifaciens were all minus, suggesting Toll, MTF and C3 are probably the primary targets of pathogenic bacteria attack. Furthermore, the correlation analysis indicated that, all of the selected immune-related factors except cathepsin D might be in the same immune regulatory network during A. japonicus development, while all of the selected immune-related factors except c-LYZ might be in the same responsive regulatory network after challenged with

  18. Contributions of temporal segregation, oviposition choice, and non-additive effects of competitors to invasion success of Aedes japonicus (Diptera: Culicidae) in North America

    PubMed Central

    Murrell, Ebony G.; Noden, Bruce H.; Juliano, Steven A.

    2015-01-01

    The mosquito Aedes japonicus (Diptera: Culicidae) has spread rapidly through North America since its introduction in the 1990s. The mechanisms underlying its establishment in container communities occupied by competitors Aedes triseriatus and Aedes albopictus are unclear. Possibilities include (A) temporal separation of A. japonicus from other Aedes, (B) oviposition avoidance by A. japonicus of sites containing heterospecific Aedes larvae, and (C) non-additive competitive effects in assemblages of multiple Aedes. Containers sampled throughout the summer in an oak-hickory forest near Eureka, MO showed peak abundance for A. japonicus occurring significantly earlier in the season than either of the other Aedes species. Despite this, A. japonicus co-occurred with one other Aedes species in 53 % of samples when present, and co-occurred with both other Aedes in 18 % of samples. In a field oviposition experiment, A. japonicus laid significantly more eggs in forest edge containers than in forest interior containers, but did not avoid containers with low or high densities of larvae of A. triseriatus, A. albopictus, or both, compared to containers without larvae. Interspecific competitive effects (measured as decrease in the index of performance, λ′) of A. triseriatus or A. albopictus alone on A. japonicus larvae were not evident at the densities used, but the effect of both Aedes combined was significantly negative and super-additive of effects of individual interspecific competitors. Thus, neither oviposition avoidance of competitors nor non-additive competitive effects contribute to the invasion success of A. japonicus in North America. Distinct seasonal phenology may reduce competitive interactions with resident Aedes. PMID:26101466

  19. Seasonal changes in food uptake by the sea cucumber Apostichopus japonicus in a farm pond: Evidence from C and N stable isotopes

    NASA Astrophysics Data System (ADS)

    Sun, Zhenlong; Gao, Qinfeng; Dong, Shuanglin; Shin, Paul K. S.; Wang, Fang

    2013-03-01

    This study investigated the seasonal changes in carbon (C) and nitrogen (N) stable isotope values of several typical food sources of Apostichopus japonicus in a farm pond, including particulate organic matter (POM), macroalgae, benthic microalgae and animals such as nematode and copepod. The stable isotope technique was used to quantify relative contributions of various sources to the food uptake by A. japonicus. The results showed that significant changes occurred in the C and N stable isotope values of sea cucumber food sources due to the seasonality of micro- or macroalgae prosperity and the fluctuation of environmental conditions. The sea cucumber A. japonicus exhibited corresponding alterations in feeding strategy in response to the changes in food conditions. Calculation with a stable isotope mixing model showed that macroalgae was the principal food source for A. japonicus throughout the 1-yr investigation, with the relative contribution averaging 28.1%-63.2%. The relative contributions of other food sources such as copepod and nematode, POM, benthic microalgae to the total food uptake by sea cucumber averaged 22.6%-39.1%, 6.3% -22.2%, 2.8%-6.5%, and 2.8%-4.2%, respectively. Together these results indicated that the seasonal changes in food sources led to the obvious temporal differences in the relative contribution of various food sources utilized by A. japonicus. Such findings provide the basic scientific information for improving the aquaculture techniques of A. japonicus, particularly for optimizing the food environment of A. japonicus culture in farm ponds.

  20. Identification of the geographical origins of sea cucumber (Apostichopus japonicus) in northern China by using stable isotope ratios and fatty acid profiles.

    PubMed

    Zhang, Xufeng; Liu, Yu; Li, Ying; Zhao, Xinda

    2017-03-01

    Geographic traceability is an important issue for food quality and safety control of seafood. In this study,δ 13 C and δ 15 N values, as well as fatty acid (FA) content of 133 samples of A. japonicus from seven sampling points in northern China Sea were determined to evaluate their applicability in the origin traceability of A. japonicus. Principal component analysis (PCA) and discriminant analysis (DA) were applied to different data sets in order to evaluate their performance in terms of classification or predictive ability. δ 13 C and δ 15 N values could effectively discriminate between different origins of A. japonicus. Significant differences in the FA compositions showed the effectiveness of FA composition as a tool for distinguishing between different origins of A. japonicus. The two technologies, combined with multivariate statistical analysis, can be promising methods to discriminate A. japonicus from different geographical areas. Copyright © 2016. Published by Elsevier Ltd.

  1. Weighted gene co-expression network analysis reveals potential genes involved in early metamorphosis process in sea cucumber Apostichopus japonicus.

    PubMed

    Li, Yongxin; Kikuchi, Mani; Li, Xueyan; Gao, Qionghua; Xiong, Zijun; Ren, Yandong; Zhao, Ruoping; Mao, Bingyu; Kondo, Mariko; Irie, Naoki; Wang, Wen

    2018-01-01

    Sea cucumbers, one main class of Echinoderms, have a very fast and drastic metamorphosis process during their development. However, the molecular basis under this process remains largely unknown. Here we systematically examined the gene expression profiles of Japanese common sea cucumber (Apostichopus japonicus) for the first time by RNA sequencing across 16 developmental time points from fertilized egg to juvenile stage. Based on the weighted gene co-expression network analysis (WGCNA), we identified 21 modules. Among them, MEdarkmagenta was highly expressed and correlated with the early metamorphosis process from late auricularia to doliolaria larva. Furthermore, gene enrichment and differentially expressed gene analysis identified several genes in the module that may play key roles in the metamorphosis process. Our results not only provide a molecular basis for experimentally studying the development and morphological complexity of sea cucumber, but also lay a foundation for improving its emergence rate. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Comprehensive functional characterization of the Glycoside Hydrolase Family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nelson, Cassandra E.; Attia, Mohamed A.; Rogowski, Artur

    Here, lignocellulose degradation is central to the carbon cycle and renewable biotechnologies. The xyloglucan (XyG), β(1!3)/β(1!4) mixed-linkage glucan (MLG), and β(1!3) glucan components of lignocellulose represent significant carbohydrate energy sources for saprophytic microorganisms. The bacterium Cellvibrio japonicus has a robust capacity for plant polysaccharide degradation, due to a genome encoding a large contingent of Carbohydrate-Active Enzymes (CAZymes), many of whose specific functions remain unknown. Using a comprehensive genetic and biochemical approach we have delineated the physiological roles of the four C. japonicus Glycoside Hydrolase Family 3 (GH3) members on diverse β-glucans. Despite high protein sequence similarity and partially overlapping activitymore » profiles on disaccharides, these β-glucosidases are not functionally equivalent. Bgl3A has a major role in MLG and sophorose utilization, and supports β(1!3) glucan utilization, while Bgl3B underpins cellulose utilization and supports MLG utilization. Bgl3C drives β(1!3) glucan utilization. Finally, Bgl3D is the crucial β-glucosidase for XyG utilization. This study not only sheds the light on the metabolic machinery of C. japonicus, but also expands the repertoire of characterized CAZymes for future deployment in biotechnological applications. In particular, the precise functional analysis provided here serves as a reference for informed bioinformatics on the genomes of other Cellvibrio and related species.« less

  3. Comprehensive functional characterization of the Glycoside Hydrolase Family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification

    DOE PAGES

    Nelson, Cassandra E.; Attia, Mohamed A.; Rogowski, Artur; ...

    2017-10-20

    Here, lignocellulose degradation is central to the carbon cycle and renewable biotechnologies. The xyloglucan (XyG), β(1!3)/β(1!4) mixed-linkage glucan (MLG), and β(1!3) glucan components of lignocellulose represent significant carbohydrate energy sources for saprophytic microorganisms. The bacterium Cellvibrio japonicus has a robust capacity for plant polysaccharide degradation, due to a genome encoding a large contingent of Carbohydrate-Active Enzymes (CAZymes), many of whose specific functions remain unknown. Using a comprehensive genetic and biochemical approach we have delineated the physiological roles of the four C. japonicus Glycoside Hydrolase Family 3 (GH3) members on diverse β-glucans. Despite high protein sequence similarity and partially overlapping activitymore » profiles on disaccharides, these β-glucosidases are not functionally equivalent. Bgl3A has a major role in MLG and sophorose utilization, and supports β(1!3) glucan utilization, while Bgl3B underpins cellulose utilization and supports MLG utilization. Bgl3C drives β(1!3) glucan utilization. Finally, Bgl3D is the crucial β-glucosidase for XyG utilization. This study not only sheds the light on the metabolic machinery of C. japonicus, but also expands the repertoire of characterized CAZymes for future deployment in biotechnological applications. In particular, the precise functional analysis provided here serves as a reference for informed bioinformatics on the genomes of other Cellvibrio and related species.« less

  4. Effects of elevated pCO2 on reproductive properties of the benthic copepod Tigriopus japonicus and gastropod Babylonia japonica.

    PubMed

    Kita, Jun; Kikkawa, Takashi; Asai, Takamasa; Ishimatsu, Atsushi

    2013-08-30

    We investigated the effects of elevated pCO2 in seawater both on the acute mortality and the reproductive properties of the benthic copepod Tigriopus japonicus and gastropod Babylonia japonica with the purpose of accumulating basic data for assessing potential environmental impacts of sub-sea geological storage of anthropogenic CO2 in Japan. Acute tests showed that nauplii of T. japonicus have a high tolerance to elevated pCO2 environments. Full life cycle tests on T. japonicus indicated NOEC=5800μatm and LOEC=37,000μatm. Adult B. japonica showed remarkable resistance to elevated pCO2 in the acute tests. Embryonic development of B. japonica showed a NOEC=1500μatm and LOEC=5400μatm. T. japonicus showed high resistance to elevated pCO2 throughout the life cycle and B. japonica are rather sensitive during the veliger stage when they started to form their shells. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Parasitism of Argulus japonicus in cultured and wild fish of Guangdong, China with new record of three hosts.

    PubMed

    Alsarakibi, Muhamd; Wadeh, Hicham; Li, Guoqing

    2014-02-01

    This study aimed to demonstrate the ability of Argulus japonicus to infect a wide range of freshwater fishes, as well as to understand the effects of fish origin and host body size on the incidence of A. japonicus. Samples of cultured and wild fish were collected randomly from July 2010 to March 2013, using angling, long-lining, gill-netting, and trapping from rivers and fish farms in Guangdong province, South China. Eight fish species were found to be heavily infected including the common carp, the goldfish, the black carp, the silver carp, the brown trout, the rainbow trout, the mandarin fish, and the perch. Furthermore, the black carp, the brown trout, and the mandarin fish were recorded as new hosts for the first time. During the present study, a total of 2,271 fishes were examined, out of which 712 fishes were found to be infected by a total of 1,443 A. japonicus. Abundance and intensity of A. japonicus infection were significantly influenced by origin of fishes (cultured and wild) and total length (class I, <250 mm; class II, 250-350 mm; and class III, >350 mm) of fish species, whereas varied impacts on prevalence of infection were observed. The correlation between total length of fishes and prevalence of A. japonicus infection was variable, where no significant correlation was observed in the black carp, the silver carp, the mandarin fish, and the perch. In spite of the weak negative correlation between body size of the silver carp and prevalence of infection, A. japonicus was the most abundant and intensive in the silver carp. Thus, aquaculturists should pay particular attention to the control of these fish lice due to its host biodiversity.

  6. DNA Barcoding of genus Hexacentrus in China reveals cryptic diversity within Hexacentrus japonicus (Orthoptera, Tettigoniidae).

    PubMed

    Guo, Hui-Fang; Guan, Bei; Shi, Fu-Ming; Zhou, Zhi-Jun

    2016-01-01

    DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Hence, a study was undertaken to establish DNA barcodes for all morphologically determined Hexacentrus species in China collections. In total, 83 specimens of five Hexacentrus species were barcoded using standard mitochondrial cytochrome c oxidase subunit I (COI) gene. Except for Hexacentrus japonicus, barcode gaps were present in the remaining Hexacentrus species. Taxon ID tree generated seven BOLD's barcode index numbers (BINs), four of which were in agreement with the morphological species. For Hexacentrus japonicus, the maximum intraspecific divergence (4.43%) produced a minimal overlap (0.64%), and 19 specimens were divided into three different BINs. There may be cryptic species within the current Hexacentrus japonicus. This study adds to a growing body of DNA barcodes that have become available for katydids, and shows that a DNA barcoding approach enables the identification of known Hexacentrus species with a very high resolution.

  7. DNA Barcoding of genus Hexacentrus in China reveals cryptic diversity within Hexacentrus japonicus (Orthoptera, Tettigoniidae)

    PubMed Central

    Guo, Hui-Fang; Guan, Bei; Shi, Fu-Ming; Zhou, Zhi-Jun

    2016-01-01

    Abstract DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Hence, a study was undertaken to establish DNA barcodes for all morphologically determined Hexacentrus species in China collections. In total, 83 specimens of five Hexacentrus species were barcoded using standard mitochondrial cytochrome c oxidase subunit I (COI) gene. Except for Hexacentrus japonicus, barcode gaps were present in the remaining Hexacentrus species. Taxon ID tree generated seven BOLD’s barcode index numbers (BINs), four of which were in agreement with the morphological species. For Hexacentrus japonicus, the maximum intraspecific divergence (4.43%) produced a minimal overlap (0.64%), and 19 specimens were divided into three different BINs. There may be cryptic species within the current Hexacentrus japonicus. This study adds to a growing body of DNA barcodes that have become available for katydids, and shows that a DNA barcoding approach enables the identification of known Hexacentrus species with a very high resolution. PMID:27408576

  8. Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration

    PubMed Central

    Liu, Yan; Zhou, Qian; Wang, Yongjun; Luo, Longhai; Yang, Jian; Yang, Linfeng; Liu, Mei; Li, Yingrui; Qian, Tianmei; Zheng, Yuan; Li, Meiyuan; Li, Jiang; Gu, Yun; Han, Zujing; Xu, Man; Wang, Yingjie; Zhu, Changlai; Yu, Bin; Yang, Yumin; Ding, Fei; Jiang, Jianping; Yang, Huanming; Gu, Xiaosong

    2015-01-01

    Reptiles are the most morphologically and physiologically diverse tetrapods, and have undergone 300 million years of adaptive evolution. Within the reptilian tetrapods, geckos possess several interesting features, including the ability to regenerate autotomized tails and to climb on smooth surfaces. Here we sequence the genome of Gekko japonicus (Schlegel's Japanese Gecko) and investigate genetic elements related to its physiology. We obtain a draft G. japonicus genome sequence of 2.55 Gb and annotated 22,487 genes. Comparative genomic analysis reveals specific gene family expansions or reductions that are associated with the formation of adhesive setae, nocturnal vision and tail regeneration, as well as the diversification of olfactory sensation. The obtained genomic data provide robust genetic evidence of adaptive evolution in reptiles. PMID:26598231

  9. Influence of salinity on the early development and biochemical dynamics of a marine fish, Inimicus japonicus

    NASA Astrophysics Data System (ADS)

    Gong, Xu; Huang, Xuxiong; Wen, Wen

    2018-03-01

    Fertilised eggs of the devil stringer ( Inimicus japonicus) were incubated at different salinity levels (21, 25, 29, 33, and 37), and then the hatching performances, morphological parameters, and biochemical composition (protein, lipid and carbohydrate) of the larvae were assayed to determine the influence of salinity on the early development of I. japonicus. The tested salinity levels did not affect the times of hatching or mouth opening for yolk-sac larvae. However, the salinity significantly influenced the hatching and survival rates of open-mouthed larvae, as well as the morphology of yolk-sac larvae. The data indicated that 30.5 to 37.3 and 24.4 to 29.8 were suitable salinity ranges for the survival of embryos and larvae of I. japonicus, respectively. Larvae incubated at a salinity level of 29 had the greatest full lengths, and decreasing yolk volume was positively correlated with the environmental salinity. With increasing salinity, the individual dry weights of newly hatched larvae or open-mouthed larvae decreased significantly. Newly hatched larvae incubated at a salinity level of 29 had the greatest metabolic substrate contents and gross energy levels, while the openmouthed larvae's greatest values occurred at a salinity level of 25. Larvae incubated in the salinity range of 33 to 37 had the lowest nutritional reserves and energy values. Thus, the I. japonicus yolk-sac larvae acclimated more readily to the lower salinity level than the embryos, and higher salinity levels negatively influenced larval growth and development. In conclusion, the environmental salinity level should be maintained at 29-33 during embryogenesis and at 25-29 during early larval development for this species. Our results can be used to provide optimum aquaculture conditions for the early larval development of I. japonicus.

  10. Influence of salinity on the early development and biochemical dynamics of a marine fish, Inimicus japonicus

    NASA Astrophysics Data System (ADS)

    Gong, Xu; Huang, Xuxiong; Wen, Wen

    2017-05-01

    Fertilised eggs of the devil stringer (Inimicus japonicus) were incubated at different salinity levels (21, 25, 29, 33, and 37), and then the hatching performances, morphological parameters, and biochemical composition (protein, lipid and carbohydrate) of the larvae were assayed to determine the influence of salinity on the early development of I. japonicus. The tested salinity levels did not affect the times of hatching or mouth opening for yolk-sac larvae. However, the salinity significantly influenced the hatching and survival rates of open-mouthed larvae, as well as the morphology of yolk-sac larvae. The data indicated that 30.5 to 37.3 and 24.4 to 29.8 were suitable salinity ranges for the survival of embryos and larvae of I. japonicus, respectively. Larvae incubated at a salinity level of 29 had the greatest full lengths, and decreasing yolk volume was positively correlated with the environmental salinity. With increasing salinity, the individual dry weights of newly hatched larvae or open-mouthed larvae decreased significantly. Newly hatched larvae incubated at a salinity level of 29 had the greatest metabolic substrate contents and gross energy levels, while the openmouthed larvae's greatest values occurred at a salinity level of 25. Larvae incubated in the salinity range of 33 to 37 had the lowest nutritional reserves and energy values. Thus, the I. japonicus yolk-sac larvae acclimated more readily to the lower salinity level than the embryos, and higher salinity levels negatively influenced larval growth and development. In conclusion, the environmental salinity level should be maintained at 29-33 during embryogenesis and at 25-29 during early larval development for this species. Our results can be used to provide optimum aquaculture conditions for the early larval development of I. japonicus.

  11. Proteolysis of noncollagenous proteins in sea cucumber, Stichopus japonicus, body wall: characterisation and the effects of cysteine protease inhibitors.

    PubMed

    Wu, Hai-Tao; Li, Dong-Mei; Zhu, Bei-Wei; Sun, Jin-Jian; Zheng, Jie; Wang, Feng-Lin; Konno, Kunihiko; Jiang, Xi

    2013-11-15

    Proteolysis of noncollagenous proteins in sea cucumber, Stichopus Japonicus, body wall (sjBW) was investigated. The proteins removed from sjBW by SDS and urea extraction were mainly noncollagenous proteins with molecular weights about 200kDa (Band I) and 44kDa (Band II), respectively. Band I and Band II were identified as major yolk protein (MYP) and actin, respectively, from holothurian species by liquid chromatography-mass spectrometry (LC-MS/MS) with significant scores. Based on TCA-soluble oligopeptide assay, the optimum proteolysis condition of noncollagenous proteins was at 46.3°C and pH 6.1, by response surface methodology. The proteolysis of MYP, and actin, was partially inhibited by cysteine protease inhibitors, including Trans-epoxysuccinyl-l-leucyl-amido (4-guanidino) butane (E-64), iodoacetic acid, antipain and whey protein concentrate. These results suggest that cysteine proteases are partially involved in the proteolysis of noncollagenous proteins in body wall of sea cucumber, S. japonicus. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Crude oil exposure results in oxidative stress-mediated dysfunctional development and reproduction in the copepod Tigriopus japonicus and modulates expression of cytochrome P450 (CYP) genes.

    PubMed

    Han, Jeonghoon; Won, Eun-Ji; Hwang, Dae-Sik; Shin, Kyung-Hoon; Lee, Yong Sung; Leung, Kenneth Mei-Yee; Lee, Su-Jae; Lee, Jae-Seong

    2014-07-01

    In this study, we investigated the effects of the water-accommodated fraction (WAF) of crude oil on the development and reproduction of the intertidal copepod Tigriopus japonicus through life-cycle experiments. Furthermore, we investigated the mechanisms underlying the toxic effects of WAF on this benthic organism by studying expression patterns of cytochrome P450 (CYP) genes. Development of T. japonicus was delayed and molting was interrupted in response to WAF exposure. Hatching rate was also significantly reduced in response to WAF exposure. Activities of antioxidant enzymes such as glutathione S-transferase (GST), glutathione reductase (GR), and catalase (CAT) were increased by WAF exposure in a concentration-dependent manner. These results indicated that WAF exposure resulted in oxidative stress, which in turn was associated with dysfunctional development and reproduction. To evaluate the involvement of cytochrome P450 (CYP) genes, we cloned the entire repertoire of CYP genes in T. japonicus (n=52) and found that the CYP genes belonged to five different clans (i.e., Clans 2, 3, 4, mitochondrial, and 20). We then examined expression patterns of these 52 CYP genes in response to WAF exposure. Three TJ-CYP genes (CYP3024A2, CYP3024A3, and CYP3027C2) belonging to CYP clan 3 were significantly induced by WAF exposure in a time- and concentration-dependent manner. We identified aryl hydrocarbon responsive elements (AhRE), xenobiotic responsive elements (XREs), and metal response elements (MRE) in the promoter regions of these three CYP genes, suggesting that these genes are involved in detoxification of toxicants. Overall, our results indicate that WAF can trigger oxidative stress and thus induce dysfunctional development and reproduction in the copepod T. japonicus. Furthermore, we identified three TJ-CYP genes that represent potential biomarkers of oil pollution. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification.

    PubMed

    Nelson, Cassandra E; Attia, Mohamed A; Rogowski, Artur; Morland, Carl; Brumer, Harry; Gardner, Jeffrey G

    2017-12-01

    Lignocellulose degradation is central to the carbon cycle and renewable biotechnologies. The xyloglucan (XyG), β(1→3)/β(1→4) mixed-linkage glucan (MLG) and β(1→3) glucan components of lignocellulose represent significant carbohydrate energy sources for saprophytic microorganisms. The bacterium Cellvibrio japonicus has a robust capacity for plant polysaccharide degradation, due to a genome encoding a large contingent of Carbohydrate-Active enZymes (CAZymes), many of whose specific functions remain unknown. Using a comprehensive genetic and biochemical approach, we have delineated the physiological roles of the four C. japonicus glycoside hydrolase family 3 (GH3) members on diverse β-glucans. Despite high protein sequence similarity and partially overlapping activity profiles on disaccharides, these β-glucosidases are not functionally equivalent. Bgl3A has a major role in MLG and sophorose utilization, and supports β(1→3) glucan utilization, while Bgl3B underpins cellulose utilization and supports MLG utilization. Bgl3C drives β(1→3) glucan utilization. Finally, Bgl3D is the crucial β-glucosidase for XyG utilization. This study not only sheds the light on the metabolic machinery of C. japonicus, but also expands the repertoire of characterized CAZymes for future deployment in biotechnological applications. In particular, the precise functional analysis provided here serves as a reference for informed bioinformatics on the genomes of other Cellvibrio and related species. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. Thermal experiments with the Asian bush mosquito (Aedes japonicus japonicus) (Diptera: Culicidae) and implications for its distribution in Germany.

    PubMed

    Reuss, Friederike; Wieser, Andreas; Niamir, Aidin; Bálint, Miklós; Kuch, Ulrich; Pfenninger, Markus; Müller, Ruth

    2018-02-05

    As ectothermic animals, temperature influences insects in almost every aspect. The potential disease spreading Asian bush mosquito (Aedes japonicus japonicus) is native to temperate East Asia but invasive in several parts of the world. We report on the previously poorly understood temperature-dependence of its life history under laboratory conditions to understand invasion processes and to model temperature niches. To evaluate winter survival, eggs were exposed between 1 day and 14 days to low temperatures (5 °C, 0 °C, -5 °C and -9 °C). Hatching success was drastically decreased after exposure to 0 °C and -5 °C, and the minimal hatching success of 0% was reached at -9 °C after two days. We then exposed larvae to 14 temperatures and assessed their life trait parameters. Larval survival to adulthood was only possible between 10 °C and 31 °C. Based on this, we modelled the optimal (25 °C), minimal (7 °C) and maximal (31 °C) temperature for cumulative female survival. The time to adult emergence ranges from 12 days to 58 days depending on temperature. We used an age-at-emergence-temperature model to calculate the number of potential generations per year for the Asian bush mosquito in Germany with an average of 4.72 potential generations. At lower temperatures, individuals grew larger than at higher temperatures with female R1 length ranging from 3.04 ± 0.1 mm at 31 °C to 4.26 ± 0.2 mm at 15 °C. Reduced egg hatch after exposure to sub-zero temperatures prohibits the establishment of the Asian bush mosquito in large parts of Germany. Larval overwintering is not possible at temperature ≤ 5 °C. The many potential generations displayed per year may contribute to the species' invasion success. This study on the thermal ecology of the Asian bush mosquito adds to our knowledge on the temperature dependence of the species and data could be incorporated in epidemiological and population dynamic modelling.

  15. Effect of Bacillus baekryungensis YD13 supplemented in diets on growth performance and immune response of sea cucumber ( Apostichopus japonicus)

    NASA Astrophysics Data System (ADS)

    Yan, Fajun; Tian, Xiangli; Dong, Shuanglin

    2014-10-01

    The effect of a potential probiotic on the growth performance and immune response of sea cucumber ( Apostichopus japonicus) was investigated. Bacillus baekryungensis YD13 isolated from sea cucumber culturing ponds was added to sea cucumber basal feed as a probiotic in different doses (0, the control; 1×104 (YD134), 1×106 (YD136) and 1×108 (YD138) CFU g-1 of diet), and administered orally to A. japonicus (initial mean wet weight 5.44 g ± 0.17 g). The sea cucumbers were fed in 20 aquaria, 5 each treatment, for 60 d. At the end of growth trial, 20 sea cucumbers from each treatment were challenged with Vibrio splendidus. A. japonicus in YD134 and YD136 exhibited significantly better growth performance than control ( P < 0.05). Five non-specific immune parameters including lysozyme, acid phosphatase, alkaline phosphatase, superoxide dismutase and catalase in coelomic fluid were measured to evaluate the immune response of A. japonicus to the probiotics. Results showed that all parameters were significantly improved when YD11 was supplemented in the dose of 1×106 CFU g-1 ( P < 0.05). The cumulative incidence and mortality after the Vibrio splendidus challenge decreased significantly in sea cucumbers of YD136. Accordingly, 1×106 CFU g-1 of YD13 in diet was recommended for the growth promotion and immune enhancement of A. japonicus.

  16. Metabolic rates and biochemical compositions of Apostichopus japonicus (Selenka) tissue during periods of inactivity

    NASA Astrophysics Data System (ADS)

    Bao, Jie; Dong, Shuanglin; Tian, Xiangli; Wang, Fang; Gao, Qinfeng; Dong, Yunwei

    2010-03-01

    Estivation, hibernation, and starvation are indispensable inactive states of sea cucumbers Apostichopus japonicus in nature and in culture ponds. Generally, temperature is the principal factor that induces estivation or hibernation in the sea cucumber. The present study provided insight into the physiological adaptations of A. japonicus during the three types of inactivity (hibernation, estivation, and starvation) by measuring the oxygen consumption rates ( Vo2) and biochemical compositions under laboratory conditions of low (3°C), normal (17°C) and high (24°C) temperature. The results show that the characteristics of A. japonicus in dormancy (hibernation and estivation) states were quite different from higher animals, such as fishes, amphibians, reptiles, and mammals, but more closely resembled a semi-dormant state. It was observed that the shift in the A. japonicus physiological state from normal to dormancy was a chronic rather than acute process, indicated by the gradual depression of metabolic rate. While metabolic rates declined 44.9% for the estivation group and 71.7% for the hibernation group, relative to initial rates, during the 36 d culture period, metabolic rates were not maintained at constant levels during these states. The metabolic depression processes for sea cucumbers in hibernation and estivation appeared to be a passive and an active metabolic suppression, respectively. In contrast, the metabolic rates (128.90±11.70 μg/g h) of estivating sea cucumbers were notably higher (107.85±6.31 μg/g h) than in starving sea cucumbers at 17°C, which indicated that the dormancy mechanism here, as a physiological inhibition, was not as efficient as in higher animals. Finally, the principle metabolic substrate or energy source of sea cucumbers in hibernation was lipid, whereas in estivation they mainly consumed protein in the early times and both protein and lipid thereafter.

  17. Aligning a New Reference Genetic Map of Lupinus angustifolius with the Genome Sequence of the Model Legume, Lotus japonicus

    PubMed Central

    Nelson, Matthew N.; Moolhuijzen, Paula M.; Boersma, Jeffrey G.; Chudy, Magdalena; Lesniewska, Karolina; Bellgard, Matthew; Oliver, Richard P.; Święcicki, Wojciech; Wolko, Bogdan; Cowling, Wallace A.; Ellwood, Simon R.

    2010-01-01

    We have developed a dense reference genetic map of Lupinus angustifolius (2n = 40) based on a set of 106 publicly available recombinant inbred lines derived from a cross between domesticated and wild parental lines. The map comprised 1090 loci in 20 linkage groups and three small clusters, drawing together data from several previous mapping publications plus almost 200 new markers, of which 63 were gene-based markers. A total of 171 mainly gene-based, sequence-tagged site loci served as bridging points for comparing the Lu. angustifolius genome with the genome sequence of the model legume, Lotus japonicus via BLASTn homology searching. Comparative analysis indicated that the genomes of Lu. angustifolius and Lo. japonicus are highly diverged structurally but with significant regions of conserved synteny including the region of the Lu. angustifolius genome containing the pod-shatter resistance gene, lentus. We discuss the potential of synteny analysis for identifying candidate genes for domestication traits in Lu. angustifolius and in improving our understanding of Fabaceae genome evolution. PMID:20133394

  18. Effects of rearing temperature and density on growth, survival and development of sea cucumber larvae, Apostichopus japonicus (Selenka)

    NASA Astrophysics Data System (ADS)

    Liu, Guangbin; Yang, Hongsheng; Liu, Shilin

    2010-07-01

    In laboratory conditions, effects of rearing temperature and stocking density were examined on hatching of fertilized egg and growth of auricularia larvae of Apostichopus japonicus respectively. Data series like larval length and density, metamorphic time, and survival rate of the larvae were recorded. Statistics showed that for A. japonicus, survival rate (from fertilized egg to late auricularia) decreased significantly with the increasing rearing temperature ( P<0.05). At different temperatures SGR was statistically significant as well ( P<0.05) from day 1, and maximal SGR was found on day 9 at 24°C (159.26±3.28). This study clearly indicated that at low temperature (<24°C), metamorphic rate was remarkably higher than at higher temperature (>26°C). Hatching rate was significantly different between 0.2-5 ind./ml groups and 20-50 ind./ml groups. Rearing larvae at the higher density had the smaller maximal-length, whereas needed longer time to complete metamorphosis. This study suggested that 21°C and 0.4 ind./ml can be used as the most suitable rearing temperature and stocking density for large -scale artificial breeding of A. japonicus’s larvae.

  19. Understanding mechanism of sea cucumber Apostichopus japonicus aestivation: Insights from TMT-based proteomic study.

    PubMed

    Chen, Muyan; Li, Xingke; Zhu, Aijun; Storey, Kenneth B; Sun, Lina; Gao, Tianxiang; Wang, Tianming

    2016-09-01

    Marine invertebrate aestivation is a unique strategy for summer survival in response to hot marine conditions. The sea cucumber, Apostichopus japonicus, is an excellent model marine invertebrate for studies of environmentally-induced aestivation. In the present study, we used a tandem mass tag (TMT)-coupled LC-MS/MS approach to identify and quantify the global proteome expression profile over the aestivation-arousal cycle of A. japonicus. A total of 3920 proteins were identified from the intestine of sea cucumber. Among them, 630 proteins showed significant differential expression when comparing three conditions of sea cucumbers: non-aestivating (active), deep-aestivation (at least 15days of continuous aestivation), and arousal after aestivation (renewed moving and feeding). Sea cucumbers in deep aestivation showed substantial differentially expressed proteins (143 up-regulated and 267 down-regulated proteins compared with non-aestivating controls). These differentially expressed proteins suggested that protein and phospholipid probably are major fuel sources during hypometabolism and a general attenuation of carbohydrate metabolism was observed during deep aestivation. Differentially expressed proteins also provided the first global picture of a shift in protein synthesis, protein folding, DNA binding, apoptosis, cellular transport and signaling, and cytoskeletal proteins during deep aestivation in sea cucumbers. A comparison of arousal from aestivation with deep aestivation, revealed a general reversal of the changes that occurred in aestivation for most proteins. Western blot detection further validated the significant up-regulation of HSP70 and down-regulation of methyltransferase-like protein 7A-like in deep-aestivation. Our results suggest that there is substantial post-transcriptional regulation of proteins during the aestivation-arousal cycle in sea cucumbers. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Reproductive biology of Nemipterus japonicus (Bloch, 1791) from the coastal waters of Bintulu (South China Sea), Sarawak, Malaysia.

    PubMed

    Nettely, T; Rajaee, A H; Denil, N A; Idris, M H; Nesarul, M H; Amin, S M Nurul; Hena, M K Abu

    2016-07-01

    Samples of threadfin breams Nemipterus japonicus were collected from a village in Kuala Nyalau and a fish landing centre at Bintulu from April 2013 to March 2014. A total of 360 individuals of N. japonicus (214 male and 146 female) were used in this reproductive study.? The total length (TL) of individuals were measured to the nearest 0.1 cm and body weight (BW) was recorded to the nearest 0.1 g. Month-wise distribution of the sexes was significantly higher for males in September and March, while in the month of May the number of females was significantly higher (X(2) = 6.53; P < 0.05). Males showed a preponderance in the size-class of 19.0-20.9 cm (X(2) = 80.24; P < 0.001), 21.0 -22.9 cm (X(2) = 56.39; P < 0.001) and 23.0 -24.9 cm (X(2) = 17; P < 0.001). The gonadosomatic index (GSI) values of N. japonicus ranged from 0.07 to 0.19 for males and 0.34 to 4.99 for females. Females had higher GSI than males throughout the study period. For males, a higher GSI (0.11-0.19) was observed during January to February, while it was found to be higher (2.73-4.99) for females during January to March, indicating the spawning season. The present study revealed that ovarian maturity based on histological analysis of N. japonicus was classified into seven stages namely, immature (I), immature (II), maturing (III), mature (IV), ripe (V), spawning (VI) and spent (VII). The fecundity of N. japonicus was estimated to be within a range of 19221 to 85923 with higher GSI (3.08-6.78) from the coastal waters of Bintulu, Sarawak.

  1. RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus.

    PubMed

    Yang, Aifu; Zhou, Zunchun; Pan, Yongjia; Jiang, Jingwei; Dong, Ying; Guan, Xiaoyan; Sun, Hongjuan; Gao, Shan; Chen, Zhong

    2016-06-14

    Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. In this study, we characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression. RNA sequencing of 21 cDNA libraries from various tissues and developmental stages of SUS-affected A. japonicus yielded 553 million raw reads, of which 542 million high-quality reads were generated by deep-sequencing using the Illumina HiSeq™ 2000 platform. The reference transcriptome comprised a combination of the Illumina reads, 454 sequencing data and Sanger sequences obtained from the public database to generate 93,163 unigenes (average length, 1,052 bp; N50 = 1,575 bp); 33,860 were annotated. Transcriptome comparisons between healthy and SUS-affected A. japonicus revealed greater differences in gene expression profiles in the body walls (BW) than in the intestines (Int), respiratory trees (RT) and coelomocytes (C). Clustering of expression models revealed stable up-regulation as the main pattern occurring in the BW throughout the three stages of SUS progression. Significantly affected pathways were associated with signal transduction, immune system, cellular processes, development and metabolism. Ninety-two differentially expressed genes (DEGs) were divided into four functional categories: attachment/pathogen recognition (17), inflammatory reactions (38), oxidative stress response (7) and apoptosis (30). Using quantitative real-time PCR, twenty representative DEGs were selected to validate the sequencing results. The Pearson's correlation coefficient (R) of the 20 DEGs ranged from 0.811 to 0.999, which confirmed the consistency and accuracy between these two approaches. Dynamic changes in global gene expression occur during SUS progression in A. japonicus. Elucidation of these changes is important

  2. Schizosaccharomyces japonicus: the fission yeast is a fusion of yeast and hyphae.

    PubMed

    Niki, Hironori

    2014-03-01

    The clade of Schizosaccharomyces includes 4 species: S. pombe, S. octosporus, S. cryophilus, and S. japonicus. Although all 4 species exhibit unicellular growth with a binary fission mode of cell division, S. japonicus alone is dimorphic yeast, which can transit from unicellular yeast to long filamentous hyphae. Recently it was found that the hyphal cells response to light and then synchronously activate cytokinesis of hyphae. In addition to hyphal growth, S. japonicas has many properties that aren't shared with other fission yeast. Mitosis of S. japonicas is referred to as semi-open mitosis because dynamics of nuclear membrane is an intermediate mode between open mitosis and closed mitosis. Novel genetic tools and the whole genomic sequencing of S. japonicas now provide us with an opportunity for revealing unique characters of the dimorphic yeast. © 2013 The Author. Yeast Published by John Wiley & Sons Ltd.

  3. Ontogeny of antipredator performance in hatchery-reared Japanese anchovy Engraulis japonicus larvae exposed to visual or tactile predators in relation to turbidity.

    PubMed

    Ohata, R; Masuda, R; Yamashita, Y

    2011-12-01

    Laboratory experiments revealed distinct effects of turbidity on the survival of Japanese anchovy Engraulis japonicus larvae when exposed to either visual (jack mackerel Trachurus japonicus) or tactile (moon jellyfish Aurelia aurita) predators. The experiments were conducted in 30 l tanks with three levels of turbidity obtained by dissolving 0, 50 or 300 mg l(-1) of kaolin. Predators were introduced to experimental tanks followed by larvae of E. japonicus ranging from 5 to 25 mm standard lengths (L(s) ). When exposed to T. japonicus, the mean survival rate of larvae was significantly higher in 300 mg l(-1) treatments compared to the other turbidity levels. When exposed to A. aurita, however, there was no difference in the survival rates among different turbidity treatments. The survival rates when exposed to either predator improved with larval growth. The logistic survivorship models for E. japonicus larvae when exposed to A. aurita had an inflection point at c. 12 mm L(s) , suggesting that their size refuge from A. aurita is close to this value. Comparison to a previous study suggests a high vulnerability of shirasu (long and transparent) fish larvae to jellyfish predation under turbidity. This study indicates that anthropogenic increases of turbidity in coastal waters may increase the relative effect of jellyfish predation on fish larvae. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

  4. Evolution of crop production under a pseudo-space environment using model plants, Lotus japonicus

    NASA Astrophysics Data System (ADS)

    Tomita-Yokotani, Kaori; Motohashi, Kyohei; Omi, Naomi; Sato, Seigo; Aoki, Toshio; Hashimoto, Hirofumi; Yamashita, Masamichi

    Habitation in outer space is one of our challenges. We have been studying space agriculture and/or spacecraft agriculture to provide food and oxygen for the habitation area in the space environment. However, careful investigation should be made concerning the results of exotic environmental effects on the endogenous production of biologically active substances in indi-vidual cultivated plants in a space environment. We have already reported that the production of functional substances in cultivated plants as crops are affected by gravity. The amounts of the main physiological substances in these plants grown under terrestrial control were different from that grown in a pseudo-microgravity. These results suggested that the nutrition would be changed in the plants/crops grown in the space environment when human beings eat in space. This estimation required us to investigate each of the useful components produced by each plant grown in the space environment. These estimations involved several study fields, includ-ing nutrition, plant physiology, etc. On the other hand, the analysis of model plant genomes has recently been remarkably advanced. Lotus japonicus, a leguminous plant, is also one of the model plant. The leguminosae is a large family in the plant vegetable kingdom and almost the entire genome sequence of Lotus japonicus has been determined. Nitrogen fixation would be possible even in a space environment. We are trying to determine the best conditions and evolution for crop production using the model plants.

  5. Interspecific larval competition between invasive Aedes japonicus and native Aedes triseriatus (Diptera: Culicidae) and adult longevity.

    PubMed

    Alto, Barry W

    2011-03-01

    The Asian rock pool mosquito Aedes japonicus (Theobald) inhabits natural and artificial container habitats, some of which are occupied by the native treehole mosquitoAedes triseriatus (Say), a vector of LaCrosse encephalitis virus. A laboratory experiment was used to evaluate the effects of nutrient limitation and interspecific interactions between these species. The goal was to address two related hypotheses. First, interspecific interactions between these species show competitive asymmetry with the invasive mosquito Ae. japonicus being favored over Ae. triseriatus. Second, competitive stress at the larval stage alters adult longevity. There was minimal evidence for competitive asymmetry between these two species. Mosquito and population performance showed clear negative density-dependent effects with similar effects of intra- and interspecific interactions. Only Ae. japonicus development time showed competitive asymmetry over Ae. triseriatus, providing weak support for the first hypothesis. For both species, competition resulted in lower adult longevity compared with low competition, providing support for the second hypothesis. These results suggest both species are similarly affected by intra- and interspecific competition and underscore the importance of the effects of larval competition that continue into adulthood and alter parameters important to transmission of vector-borne diseases.

  6. Effects of stomatal development on stomatal conductance and on stomatal limitation of photosynthesis in Syringa oblata and Euonymus japonicus Thunb.

    PubMed

    Wu, Bing-Jie; Chow, Wah Soon; Liu, Yu-Jun; Shi, Lei; Jiang, Chuang-Dao

    2014-12-01

    During leaf development, the increase in stomatal conductance cannot meet photosynthetic demand for CO2, thus leading to stomatal limitation of photosynthesis (Ls). Considering the crucial influences of stomatal development on stomatal conductance, we speculated whether stomatal development limits photosynthesis to some extent. To test this hypothesis, stomatal development, stomatal conductance and photosynthesis were carefully studied in both Syringa oblata (normal greening species) and Euonymus japonicus Thunb (delayed greening species). Our results show that the size of stomata increased gradually with leaf expansion, resulting in increased stomatal conductance up to the time of full leaf expansion. During this process, photosynthesis also increased steadily. Compared to that in S. oblata, the development of chloroplasts in E. japonicus Thunb was obviously delayed, leading to a delay in the improvement of photosynthetic capacity. Further analysis revealed that before full leaf expansion, stomatal limitation increased rapidly in both S. oblata and E. japonicus Thunb; after full leaf expansion, stomatal limitation continually increased in E. japonicus Thunb. Accordingly, we suggested that the enhancement of photosynthetic capacity is the main factor leading to stomatal limitation during leaf development but that stomatal development can alleviate stomatal limitation with the increase of photosynthesis by controlling gas exchange. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  7. The deubiquitinating enzyme AMSH1 is required for rhizobial infection and nodule organogenesis in Lotus japonicus.

    PubMed

    Małolepszy, Anna; Urbański, Dorian Fabian; James, Euan K; Sandal, Niels; Isono, Erika; Stougaard, Jens; Andersen, Stig Uggerhøj

    2015-08-01

    Legume-rhizobium symbiosis contributes large quantities of fixed nitrogen to both agricultural and natural ecosystems. This global impact and the selective interaction between rhizobia and legumes culminating in development of functional root nodules have prompted detailed studies of the underlying mechanisms. We performed a screen for aberrant nodulation phenotypes using the Lotus japonicus LORE1 insertion mutant collection. Here, we describe the identification of amsh1 mutants that only develop small nodule primordia and display stunted shoot growth, and show that the aberrant nodulation phenotype caused by LORE1 insertions in the Amsh1 gene may be separated from the shoot phenotype. In amsh1 mutants, rhizobia initially became entrapped in infection threads with thickened cells walls. Some rhizobia were released into plant cells much later than observed for the wild-type; however, no typical symbiosome structures were formed. Furthermore, cytokinin treatment only very weakly induced nodule organogenesis in amsh1 mutants, suggesting that AMSH1 function is required downstream of cytokinin signaling. Biochemical analysis showed that AMSH1 is an active deubiquitinating enzyme, and that AMSH1 specifically cleaves K63-linked ubiquitin chains. Post-translational ubiquitination and deubiquitination processes involving the AMSH1 deubiquitinating enzyme are thus involved in both infection and organogenesis in Lotus japonicus. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  8. Effect of food on specific dynamic action (SDA) of green and red types of sea cucumber ( Apostichopus japonicus Selenka)

    NASA Astrophysics Data System (ADS)

    Bao, Jie; Jiang, Hongbo; Dong, Shuanglin; Tian, Xiangli

    2017-10-01

    Specific dynamic action (SDA), the energy expended on all physiological processes that is associated with meal digestion and absorption, is strongly affected by food type. Effects of formulated diet (FMD), macroalgae (ALG) and sea mud (SMD) diets on the postprandial metabolic response of the green type and the red type of sea cucumber ( Apostichopus japonicus) were studied in order to understand their feeding physiology. Food offered to A. japonicus was different in protein, lipid content and energy but not in meal mass. SDA of A. japonicus resulted in a 1.3-2.7 folds of increase in oxygen consumption that can persist for up to 4.8-31.7 h after digesting three different diets. In a given type of sea cucumber, the magnitude of SDA was the highest when fed with FMD, medium with ALG, and the lowest with SMD, which is probably due to the differences in diet components and protein contents. The red type sea cucumber showed greater SDA magnitude than the green type with each diet treatment, which might result from the difference in factorial scope between the two types of sea cucumber. However, the smallest magnitude or even no difference was observed between the two types of A. japonicus in SMD group, perhaps owing to the poor nutrition and digestion of sea mud.

  9. Molecular characterization of muscle-parasitizing didymozoid from a chub mackerel, Scomber japonicus.

    PubMed

    Abe, Niichiro; Okamoto, Mitsuru

    2015-09-01

    Didymozoids found in the muscles of marine fish are almost always damaged because they are usually found after being sliced. Therefore, identifying muscle-parasitizing didymozoids is difficult because of the difficulty in collecting non-damaged worms and observing their organs as key points for morphological identification. Moreover, muscle-parasitizing didymozoids are not easily found because they parasitize at the trunk muscles. Therefore, muscle-parasitizing didymozoid classification has not progressed because there are few opportunities to detect them. Our recent report was the first to describe the usefulness of sequencing analysis for discrimination among muscle-parasitizing didymozoids. Recently, we found a didymozoid in the trunk muscle of a chub mackerel Scomber japonicus. The present study genetically compares the present isolate with other muscle-parasitizing didymozoids. The present isolate differs markedly from the previously unidentified didymozoid from an Atlantic mackerel S. scombrus by phylogenetic analysis of 18S rDNA. It also differs from other muscle-parasitizing didymozoids from other host species based on phylogenetic analyses of 18S, 28S rDNAs, and coxI loci. These results suggest that sequencing analysis is useful for the discrimination of muscle-parasitizing didymozoids. Combining the present data with earlier data for sequencing analysis, muscle-parasitizing didymozoids from seven marine fish species were classified as seven species. We proposed appellations for six distinct muscle-parasitizing didymozoids for future analysis: sweetlips fish type from Diagramma pictum and Plectorhinchus cinctus, red sea bream type from Pagrus major, flying fish type from Cypselurus heterurus, Atlantic mackerel type from Scomber scombrus, chub mackerel type from S. japonicus, and purple rockcod type from Epinephelus cyanopodus.

  10. Suppression of murine preadipocyte differentiation and reduction of visceral fat accumulation by a Petasites japonicus ethanol extract in mice fed a high-fat diet.

    PubMed

    Watanabe, Takayuki; Hata, Keishi; Hiwatashi, Kazuyuki; Hori, Kazuyuki; Suzuki, Nao; Itoh, Hideaki

    2010-01-01

    We investigated in this study the anti-obesity effect of an extract of Petasites japonicus (a culinary vegetable from Eastern Asia) on a murine adipocyte cell line (3T3-L1) and on diet-induced obesity-prone mice. An ethanol extract of P. japonicus. (PJET) suppressed 3T3-L1 preadipocyte differentiation; however, a hot water extract of P. japonicus (PJHW) exhibited no effect on cell differentiation. PJET significantly attenuated three adipogenetic transcription factors, peroxisome proliferator-activated receptor gamma2, CCAAT/enhancer-binding protein and sterol regulatory element-binding protein 1C, at the mRNA level and suppressed the gene expression of fatty acid synthetase. An experiment with diet-induced obesity-prone C57BL/6J mice showed that PJET lowered the body weight gain and visceral fat tissue accumulation, and ameliorated the plasma cholesterol concentration. These findings suggest that P. japonicus might be an effective food against obesity.

  11. Molecular and morphologic approaches to discrimination of variability patterns in chub mackerel, Scomber japonicus.

    PubMed

    Roldán; Perrotta; Cortey; Pla

    2000-10-05

    The systematic status and the evolutionary biology of chub mackerel (Scomber japonicus) in the South West Atlantic Ocean is confusing with an unknown degree of genetic differentiation and reproductive isolation between units. Simultaneous genetic and morphologic analyses were made on 227 fish collected from two areas of the South West Atlantic Ocean and one from the Mediterranean Sea. The genetic analysis was based on 36 protein-coding loci, 16 of which were variable. The morphologic analyses include six morphometric length measurements and a meristic character. Correspondence between genetic and morphologic variability patterns indicates isolated Mediterranean and Southwest Atlantic subgroups of S. japonicus and, less clearly, possible additional divergence in two regional stocks within the latter group. The most conservative approach to management is to manage the stocks independently of one another.

  12. Histological, ultrastructural and heat shock protein 70 (HSP70) responses to heat stress in the sea cucumber Apostichopus japonicus.

    PubMed

    Xu, Dongxue; Sun, Lina; Liu, Shilin; Zhang, Libin; Yang, Hongsheng

    2015-08-01

    The aquaculture industry for Apostichopus japonicus has suffered severe economic and resource losses due to high temperature in recent summers. There is increasing concern about the effect of high temperature on this species. Histological, ultrastructural and HSP70 responses to heat stress were investigated in the intestine of A. japonicus. Tissue degradation was observed in muscular, submucosal and mucosal layers, with significant decrease in plicae circulares of the mucosal layer. Ultrastructural damage intensified with increasing stress time, and indicators of cell apoptosis were evident after 192 h heat stress. Immunostaining showed HSP70 mainly in mucosa and serosa, with faint staining in non-stressed individuals (the control group) and denser staining under stress (the 6, 48 and 192 h groups). Western blot detection confirmed ocurrence of HSP70 in all groups and significant up-regulation under stress. The rapid and persistent response of HSP70 implies its critical role in the heat shock response of A. japonicus. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Dietary Cerebroside from Sea Cucumber (Stichopus japonicus): Absorption and Effects on Skin Barrier and Cecal Short-Chain Fatty Acids.

    PubMed

    Duan, Jingjing; Ishida, Marina; Aida, Kazuhiko; Tsuduki, Tsuyoshi; Zhang, Jin; Manabe, Yuki; Hirata, Takashi; Sugawara, Tatsuya

    2016-09-21

    Sphingolipids from marine sources have attracted more attention recently because of their distinctive structures and expected functions. In this study, the content and components of cerebroside from sea cucumber Stichopus japonicus were analyzed. The absorption of cerebroside from S. japonicus was investigated with an in vivo lipid absorption assay. The result revealed that S. japonicus is a rich source of cerebroside that contained considerable amounts of odd carbon chain sphingoid bases. The cumulative recoveries of d17:1- and d19:2-containing cerebrosides were 0.31 ± 0.16 and 0.32 ± 0.10%, respectively, for 24 h after administration. To the best of the authors' knowledge, this is the first work that shows sphingolipids from a marine source could be absorbed in vivo and incorporated into ceramides. In addition, dietary supplementation with sea cucumber cerebroside to hairless mouse improved the skin barrier function and increased short-chain fatty acids in cecal contents, which have shown beneficial effects on the host.

  14. Morphological and molecular characterization of a microsporidian parasite, Takaokaspora nipponicus n. gen., n. sp. from the invasive rock pool mosquito, Ochlerotatus japonicus japonicus.

    PubMed

    Andreadis, Theodore G; Takaoka, Hiroyuki; Otsuka, Yasushi; Vossbrinck, Charles R

    2013-10-01

    A new genus and species of Microsporidia, Takaokaspora nipponicus n. gen., n. sp. is described from Ochlerotatus japonicus japonicus (Theobald) and Ochlerotatus hatorii (Yamada) based on light microscope and ultrastructural morphology, developmental features, transmission cycles and comparative sequence analyses of the small subunit ribosomal DNA (SSU rDNA). The microsporidium is both vertically and horizontally transmitted, exhibits dimorphic development alternating between diplokaryotic and monokaryotic stages and produces two morphologically distinct spores, one in larvae and another in adult females. Horizontal transmission of infection to larval mosquitoes occurs via direct oral ingestion of uninucleate spores that are produced in vertically-infected larval hosts. Development in horizontally-infected hosts is diplokaryotic following karyokinesis of uninucleate schizonts and binary fission to produce small (4.3μm × 2.0μm) membrane free, ovoid, binucleate spores that are confined to adult female reproductive tissues (ovariole sheath and oviducts). Vertical transmission of the microsporidium from adult females to larval progeny takes place via surface contamination of the egg (transovum). Microsporidian development in vertically-infected larvae is haplophasic with unpaired nuclei throughout, producing rosette-shaped sporogonial plasmodia contained within a thin non-persistent sporophorous vesicle and culminating in the formation of membrane free, uninucleate, conical spores (7.0μm×2.8μm). Development is confined to host fat body tissue which appears as swollen white masses in the thorax and selected segments of the abdomen causing larvae to appear abnormally distorted and results in death during the third and fourth instar stages. The SSU rDNA sequences obtained from the two morphologically identical microsporidia isolated from Oc. j. japonicus and Oc. hatorii were nearly identical and unique when compared with GenBank entries of all other mosquito

  15. Genome-wide identification of 52 cytochrome P450 (CYP) genes in the copepod Tigriopus japonicus and their B[α]P-induced expression patterns.

    PubMed

    Han, Jeonghoon; Kim, Duck-Hyun; Kim, Hui-Su; Nelson, David R; Lee, Jae-Seong

    2017-09-01

    Cytochrome P450s (CYPs) are enzymes with a heme-binding domain that are found in all living organisms. CYP enzymes have important roles associated with detoxification of xenobiotics and endogenous compounds (e.g. steroids, fatty acids, and hormones). Although CYP enzymes have been reported in several invertebrates, including insects, little is known about copepod CYPs. Here, we identified the entire repertoire of CYP genes (n=52) from whole genome and transcriptome sequences of the benthic copepod Tigriopus japonicus, including a tandem duplication (CYP3026A3, CYP3026A4, CYP3026A5), and examined patterns of gene expression over various developmental stages and in response to benzo[α]pyrene (B[α]P) exposure. Through phylogenetic analysis, the 52 T. japonicus CYP genes were assigned to five distinct clans: CYP2 (22 genes), CYP3 (19 genes), CYP4 (two genes), CYP20 (one gene), and mitochondrial (eight genes). Developmental stage and gender-specific expression patterns of the 52 T. japonicus CYPs were analyzed. CYP3022A1 was constitutively expressed during all developmental stages. CYP genes in clans 2 and 3 were induced in response to B[α]P, suggesting that these differentially modulated CYP transcripts are likely involved in defense against exposure to B[α]P and other pollutants. This study enhances our understanding of the repertoire of CYP genes in copepods and of their potential role in development and detoxification in copepods. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Determination of triterpene glycosides in sea cucumber (Stichopus japonicus) and its related products by high-performance liquid chromatography.

    PubMed

    Dong, Ping; Xue, Chang-Hu; Yu, Lin-Fang; Xu, Jie; Chen, Shi-Guo

    2008-07-09

    A creative and sensitive method has been developed for the determination of triterpene glycosides concentrations in sea cucumber ( Stichopus japonicus) and related products by using d-quinovose (6-deoxyglucose) as the measurement standard by reverse-phase high-performance liquid chromatography (HPLC) and variable-wavelength detection. d-quinovose, which is a unique monosaccharide in holostane triterpene glycosides, was liberated by acid hydrolysis and precolumn derivatized by 1-phenyl-3-methyl-5-pyrazolone (PMP). PMP-quinovose was analyzed by HPLC with 22% acetonitrile in 0.05 M KH2PO4 aquatic solution (pH 5.2) as mobile phase. The calibration curves of d-quinovose were linear within the range of 6.56-164 mg/L (r(2) > 0.995). The contents of triterpene glycosides in various S. japonicus products were determined after appropriate pretreatment methods. The concentration of triterpene glycosides was calculated by the formula C = C(qui) x alpha (alpha = 8.5). The result showed that this method was a simple, rapid, and stable method for the determination of triterpene glycosides in S. japonicus products.

  17. Effects of water depth and substrate color on the growth and body color of the red sea cucumber, Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Jiang, Senhao; Dong, Shuanglin; Gao, Qinfeng; Ren, Yichao; Wang, Fang

    2015-05-01

    Three color variants of the sea cucumber, Apostichopus japonicus are recognized, the red one is highly valued in the market. When the red variant is cultured in ponds in China, its body color changes from red to celadon in 3-6 months. The effects of water depth and substrate color on the growth and body color of this animal were investigated. Juveniles of red A. japonicus were cultured in cages suspended at a range of water depths (20, 50, 100, 150 and 200 cm). The specific growth rate of red sea cucumbers was significantly higher in animals cultured at deeper water layers compared with those grown at shallowers. Body weights were greatest for sea cucumbers cultured at a depth of 150 cm and their survival rates were highest at a depth of 200 cm. A scale to evaluate the color of red sea cucumbers ( R value) was developed using a Pantone standard color card. All stocked animals in the 9-month trial retained a red color, however the red body color was much more intense in sea cucumbers cultured at shallower depths, while animals suspended in deeper layers became pale. In a separate trial, A. japonicus were cultured in suspended cages with seven different colored substrates. Substrate color had a significant effect on the growth and body-color of red A. japonicus. The yield were greatest for A. japonicus cultured on a yellow substrate, followed by green > white > orange > red > black and blue. All sea cucumbers in the 7-month trial retained a red color, although the red was most intense (highest R value) in animals cultured on a blue substrate and pale (lowest R value) for animals cultured on a green substrate.

  18. La Crosse Encephalitis Virus Infection in Field-Collected Aedes albopictus, Aedes japonicus, and Aedes triseriatus in Tennessee.

    PubMed

    Westby, Katie M; Fritzen, Charissa; Paulsen, Dave; Poindexter, Stephanie; Moncayo, Abelardo C

    2015-09-01

    La Crosse virus (LACV) is a mosquito-borne virus and a major cause of pediatric encephalitis in the USA. La Crosse virus emerged in Tennessee and other states in the Appalachian region in 1997. We investigated LACV infection rates and seasonal abundances of the native mosquito vector, Aedes triseriatus, and 2 recently introduced mosquito species, Ae. albopictus and Ae. japonicus, in an emerging disease focus in Tennessee. Mosquitoes were collected using multiple trapping methods specific for Aedes mosquitoes at recent human case sites. Mosquito pools were tested via reverse transcriptase-polymerase chain reaction (RT-PCR) of the S segment to detect multiple Bunyamwera and California serogroup viruses, including LACV, as well as real-time RT-PCR of the M segment. A total of 54 mosquito pools were positive, including wild-caught adult females and laboratory-reared adults, demonstrating transovarial transmission in all 3 species. Maximum likelihood estimates (per 1,000 mosquitoes) were 2.72 for Ae. triseriatus, 3.01 for Ae. albopictus, and 0.63 for Ae. japonicus. We conclude that Ae. triseriatus and Ae. albopictus are important LACV vectors and that Ae. japonicus also may be involved in virus maintenance and transmission.

  19. A new transformation-regeneration procedure in the model legume Lotus japonicus: root explants as a source of large numbers of cells susceptible to Agrobacterium-mediated transformation.

    PubMed

    Lombari, P; Ercolano, E; El Alaoui, H; Chiurazzi, M

    2003-04-01

    We describe herein a simple and efficient transformation procedure for the production of transgenic Lotus japonicus plants. In this new procedure, dedifferentiated root explants, used as starting material, are the source of a large number of cells that are competent for the regeneration procedure, with a high susceptibility to Agrobacterium infection. The application of this protocol resulted in a tenfold increase in the number of transformants produced by a single plant in comparison to the widely used hypocotyl transformation procedure. Furthermore, our procedure allowed the use of intact plants stored for a long time at 4 degrees C, thus providing a potential continuous supply of explants for transformation experiments. The overall time of incubation under tissue culture conditions required to obtain a plant transferable into soil is 4 months. The transgenic nature of the transformants was demonstrated by the detection of beta-glucuronidase (GUS) activity in the primary transformants and by molecular analysis. Stable transformation was indicated by Mendelian segregation of the hygromycin selectable marker and of the gusA activity after selfing of the transgenic plants.

  20. Growth, metabolism and physiological response of the sea cucumber, Apostichopus japonicus Selenka during periods of inactivity

    NASA Astrophysics Data System (ADS)

    Du, Rongbin; Zang, Yuanqi; Tian, Xiangli; Dong, Shuanglin

    2013-03-01

    The growth, metabolism and physiological response of the sea cucumber, Apostichopus japonicus, were investigated during periods of inactivity. The body weight, oxygen consumption rate (OCR), activities of acidic phosphatase (ACP), alkaline phosphatase (AKP), catalase (CAT) and superoxide dismutase (SOD), and content of heat shock protein 70 (Hsp70) in the body wall and coelomic fluid of A. japonicus were measured during starvation, experimental aestivation and aestivation. The results showed that the body weight of sea cucumber in the three treatments decreased significantly during the experimental period ( P < 0.05). The OCR of sea cucumber reduced in starvation and experimental aestivation treatments, but increased gradually in natural aestivation treatment. The activities of ACP and AKP of sea cucumber decreased gradually in all treatments, whereas those of SOD and CAT as well as Hsp70 content decreased in the starvation and experimental aestivation treatments and increased in natural aestivation treatment. The sea cucumber entered a state of aestivation at 24°C. To some extent, the animals in experimental aestivation were different from those in natural aestivation in metabolism and physiological response. These findings suggested that the aestivation mechanism of A. japonicus is complex and may not be attributed to the elevated temperature only.

  1. SEM and TEM study of the armed male terminal genitalia of the tapeworm Paraechinophallus japonicus (Cestoda: Bothriocephalidea).

    PubMed

    Levron, Céline; Poddubnaya, Larisa G; Kuchta, Roman; Freeman, Mark; Wang, Yan-Hai; Scholz, Tomás

    2008-08-01

    For the first time, the ultrastructure of the armed cirrus of an echinophallid cestode, Paraechinophallus japonicus (Yamaguti, 1934), has been studied with the use of scanning and transmission electron microscopy. Two sets of eversible copulatory organs (approximately 300 microm in length and approximately 130 microm in width) are present on the dorsal side of each segment near the lateral margin of the strobila. Except for the terminal portion, the cirrus is covered with large spines (up to 40 mircom long, measured from SEM photomicrographs) composed of 2 parts. The basal portion contains a lobed electron-dense outer region that gives way to a reticular meshwork of electron-dense material. The apical region of the spines, composed of a homogeneous, moderately electron-dense matrix, is slightly curved distally. Spines are covered with a cortical zone. Between the spines, the distal cytoplasm is covered with microvilli of about 1.2 microm in length. The wall of the cirrus sac, which is approximately 500 microm long and approximately 250 microm wide, is composed of 2 layers of muscles, i.e., an internal layer of circular muscles and external longitudinal muscles. Microvilli on the cirrus of P. japonicus are reported for the first time in the Cestoda, whereas the spines on the cirrus may represent a synapomorphy of bothriocephalidean cestodes of the Echinophallidae.

  2. Large-scale identification and comparative analysis of miRNA expression profile in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation.

    PubMed

    Chen, Muyan; Storey, Kenneth B

    2014-02-01

    The sea cucumber Apostichopus japonicus withstands high water temperatures in the summer by suppressing its metabolic rate and entering a state of aestivation. We hypothesized that changes in the expression of miRNAs could provide important post-transcriptional regulation of gene expression during hypometabolism via control over mRNA translation. The present study analyzed profiles of miRNA expression in the sea cucumber respiratory tree using Solexa deep sequencing technology. We identified 279 sea cucumber miRNAs, including 15 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA; after at least 15 days of continuous torpor) were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 30 differentially expressed miRNAs ([RPM (reads per million) >10, |FC| (|fold change|)≥1, FDR (false discovery rate)<0.01]) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-124, miR-124-3p, miR-79, miR-9 and miR-2010 were significantly over-expressed during deep aestivation compared with non-aestivation animals, suggesting that these miRNAs may play important roles in metabolic rate suppression during aestivation. High-throughput sequencing data and microarray data have been submitted to the GEO database with accession number: 16902695. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Iron-induced nitric oxide leads to an increase in the expression of ferritin during the senescence of Lotus japonicus nodules.

    PubMed

    Chungopast, Sirinapa; Duangkhet, Mallika; Tajima, Shigeyuki; Ma, Jian Feng; Nomura, Mika

    2017-01-01

    Iron is an essential nutrient for legume-rhizobium symbiosis and accumulates abundantly in the nodules. However, the concentration of free iron in the cells is strictly controlled to avoid toxicity. It is known that ferritin accumulates in the cells as an iron storage protein. During nodule senescence, the expression of the ferritin gene, Ljfer1, was induced in Lotus japonicus. We investigated a signal transduction pathway leading to the increase of Ljfer1 in the nodule. The Ljfer1 promoter of L. japonicus contains a conserved Iron-Dependent Regulatory Sequence (IDRS). The expression of Ljfer1 was induced by the application of iron or sodium nitroprusside, which is a nitric oxide (NO) donor. The application of iron to the nodule increased the level of NO. These data strongly suggest that iron-induced NO leads to increased expression of Ljfer1 during the senescence of L. japonicus nodules. Copyright © 2016 Elsevier GmbH. All rights reserved.

  4. Transcriptome Profiling of Lotus japonicus Roots During Arbuscular Mycorrhiza Development and Comparison with that of Nodulation

    PubMed Central

    Deguchi, Yuichi; Banba, Mari; Shimoda, Yoshikazu; Chechetka, Svetlana A.; Suzuri, Ryota; Okusako, Yasuhiro; Ooki, Yasuhiro; Toyokura, Koichi; Suzuki, Akihiro; Uchiumi, Toshiki; Higashi, Shiro; Abe, Mikiko; Kouchi, Hiroshi; Izui, Katsura; Hata, Shingo

    2007-01-01

    Abstract To better understand the molecular responses of plants to arbuscular mycorrhizal (AM) fungi, we analyzed the differential gene expression patterns of Lotus japonicus, a model legume, with the aid of a large-scale cDNA macroarray. Experiments were carried out considering the effects of contaminating microorganisms in the soil inoculants. When the colonization by AM fungi, i.e. Glomus mosseae and Gigaspora margarita, was well established, four cysteine protease genes were induced. In situ hybridization revealed that these cysteine protease genes were specifically expressed in arbuscule-containing inner cortical cells of AM roots. On the other hand, phenylpropanoid biosynthesis-related genes for phenylalanine ammonia-lyase (PAL), chalcone synthase, etc. were repressed in the later stage, although they were moderately up-regulated on the initial association with the AM fungus. Real-time RT–PCR experiments supported the array experiments. To further confirm the characteristic expression, a PAL promoter was fused with a reporter gene and introduced into L. japonicus, and then the transformants were grown with a commercial inoculum of G. mosseae. The reporter activity was augmented throughout the roots due to the presence of contaminating microorganisms in the inoculum. Interestingly, G. mosseae only colonized where the reporter activity was low. Comparison of the transcriptome profiles of AM roots and nitrogen-fixing root nodules formed with Mesorhizobium loti indicated that the PAL genes and other phenylpropanoid biosynthesis-related genes were similarly repressed in the two organs. PMID:17634281

  5. Cell wall polysaccharides released during the alcoholic fermentation by Schizosaccharomyces pombe and S. japonicus: quantification and characterization

    PubMed Central

    Domizio, P.; Liu, Y.; Bisson, L.F.; Barile, D.

    2016-01-01

    The present work demonstrates that yeasts belonging to the Schizosaccharomyces genus release a high quantity of polysaccharides of cell wall origin starting from the onset of the alcoholic fermentation. By the end of the alcoholic fermentation, all of the Schizosaccharomyces yeast strains released a quantity of polysaccharides approximately 3-7 times higher than that released by a commercial Saccharomyces cerevisiae yeast strain under the same fermentative conditions of synthetic juice. A higher content of polysaccharide was found in media fermented by Schizosaccharomyces japonicus with respect to that of Schizosaccharomyces pombe. Some of the strains evaluated were also able to produce high levels of pyruvic acid, which has been shown to be an important compound for color stability of wine. The presence of strains with different malic acid consumption patterns along with high polysaccharide release would enable production of naturally modified wines with enhanced mouth feel and reduced acidity. The chemical analysis of the released polysaccharides demonstrated divergence between the two yeast species S. pombe and S. japonicus. A different mannose/galactose ratio and a different percentage of proteins was observed on the polysaccharides released by S. pombe as compared to S. japonicus. Analysis of the proteins released in the media revealed the presence of a glycoprotein with a molecular size around 32-33 kDa only for the species S. japonicus. Mass spectrometry analysis of carbohydrate moieties showed similar proportions among the N-glycan chains released in the media by both yeast species but differences between the two species were also observed. These observations suggest a possible role of rapid MALDI-TOF screening of N-glycans compositional fingerprint as a taxonomic tool for this genus. Polysaccharides release in the media, in particular galactomannoproteins in significant amounts, could make these yeasts particularly interesting also for the industrial

  6. Fungal biodegradation and biotransformation of soluble lignocarbohydrate complexes from straw. [Aspergillus japonicus, Polyporus versicolor

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Milstein, O.A.; Vared, Y.; Sharma, A.

    1983-08-01

    Aspergillus japonicus is an efficient degrader of phenolics and carbohydrates present in a mixture of soluble lignocarbohydrate complexes extracted from wheat straw. Trichoderma species attacked part of the carbohydrate but hardly affected the aromatic portion of this solution. Polyporus versicolor had a complex effect; polymerization of low-molecular-size phenolics accompanied the degradation of aromatic and carbohydrate polymers. The addition of xylose to the medium facilitated depolymerization of lignin by the fungi tested and prevented the polymerization of low-molecular-size fractions of lignocarbohydrate complexes by P. versicolor. P. versicolor, in contrast to A. japonicus and Trichoderma species, also excreted into the medium considerablemore » amounts of laccase, but only in the absence of endogenous or exogenous carbohydrates. Apparently, laccase is involved in polymerization rather than degradation of lignin in this organism. A number of extracellular glycanases were also secreted by these fungi. 19 references« less

  7. Effects of potential probiotic Bacillus cereus EN25 on growth, immunity and disease resistance of juvenile sea cucumber Apostichopus japonicus.

    PubMed

    Zhao, Yancui; Yuan, Lei; Wan, Junli; Sun, Zhenxing; Wang, Yiyan; Sun, Hushan

    2016-02-01

    This study was conducted to determine effects of potential probiotic Bacillus cereus EN25 (isolated from mud of sea cucumber culturing water bodies) on growth, immunity and disease resistance against Vibrio splendidus infection in juvenile sea cucumbers Apostichopus japonicus. Animals were respectively fed diets with B. cereus EN25 at 0 (control), 10(5), 10(7) and 10(9) CFU/g for 30 days. Results showed that dietary B. cereus EN25 had no significant effects on growth, total coelomocytes counts and acid phosphatase activity of A. japonicus (P > 0.05). Dietary EN25 at 10(7) CFU/g had significantly improved the phagocytosis, respiratory burst activity and total nitric oxide synthase activity of animals (P < 0.05). Compared to control, dietary EN25 at 10(5) or 10(7) CFU/g had no significant effects on superoxide dismutase activity of A. japonicus (P > 0.05), whereas dietary EN25 at 10(9) CFU/g had significantly decreased its activity (P < 0.05). The cumulative mortality after V. splendidus challenge decreased significantly in sea cucumbers fed with EN25 at 10(7) CFU/g (P < 0.05). The present study confirmed dietary B. cereus EN25 at 10(7) CFU/g could significantly improve immunity and disease resistance in juvenile A. japonicus. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. First record of Neoergasilus japonicus (Poecilostomatoida: Ergasilidae), a parasitic copepod new to the Laurentian Great Lakes

    USGS Publications Warehouse

    Hudson, Patrick L.; Bowen, Charles A.

    2002-01-01

    The parasitic copepod Neoergasilus japonicus, native to eastern Asia, was first collected from 4 species of fish (fathead minnow, Pimephales promelas; largemouth bass, Micropterus salmoides; pumpkinseed sunfish, Lepomis gibbosus; and yellow perch, Perca flavescens) in July 1994 in Saginaw Bay, Lake Huron, Michigan. Further sampling in the bay in 2001 revealed infections on 7 additional species (bluegill, Lepomis macrochirus; carp, Cyprinus carpio; channel catfish, Ictalurus punctatus; goldfish, Carassius auratus; green sunfish, Lepomis cyanellus; rock bass, Ambloplites rupestris; and smallmouth bass, Micropterus dolomieu). An additional 21 species examined in 2001 were devoid of the parasite. A limited collection of fish from Lake Superior (n = 8) and Lake Michigan (n = 46) in 1994 showed no infection. Neoergasilus japonicus is most frequently found attached to the dorsal fin and, in decreasing frequency, on the anal, tail, pelvic, and pectoral fins. Prevalence generally ranged from 15 to 70 and intensity from 1 to 10. The greatest number of copepods on a single host was 44. The copepod Neoergasilus japonicus appears to disperse over long distances rather quickly, spreading across Europe in 20 yr and then moving on to North America over a span of 10 yr. Its main vehicle of transport and introduction into the Great Lakes is probably exotic fish hosts associated with the fish-culture industry.

  9. Real-time PCR Tests in Dutch Exotic Mosquito Surveys; Implementation of Aedes aegypti and Aedes albopictus Identification Tests, and the Development of Tests for the Identification of Aedes atropalpus and Aedes japonicus japonicus (Diptera: Culicidae).

    PubMed

    van de Vossenberg, B T L H; Ibáñez-Justicia, A; Metz-Verschure, E; van Veen, E J; Bruil-Dieters, M L; Scholte, E J

    2015-05-01

    Since 2009, The Netherlands Food and Consumer Product Safety Authority carries out surveys focusing on, amongst others, the presence of invasive mosquito species (IMS). Special attention is given to exotic container-breeding Aedes species Aedes aegypti (L.), Aedes albopictus (Skuse), Aedes atropalpus (Coquillett), and Aedes japonicus japonicus (Theobald). This study describes the implementation of real-time PCR tests described by Hill et al. (2008) for the identification of Ae. aegypti and Ae. albopictus, and the development of two novel real-time PCR tests for the identification of Ae. atropalpus and Ae. j. japonicus. Initial test showed that optimization of elements of the Ae. aegypti and Ae. albopictus tests was needed. Method validation tests were performed to determine if the implemented and newly developed tests are fit for routine diagnostics. Performance criteria of analytical sensitivity, analytical specificity, selectivity, repeatability, and reproducibility were determined. In addition, experiments were performed to determine the influence of environmental conditions on the usability of DNA extracted from mosquito specimens trapped in BG-Sentinel traps. The real-time PCR tests were demonstrated to be sensitive, specific, repeatable, reproducible, and are less prone to false negative results compared to partial cytochrome c oxidase I gene sequencing owing to the DNA fragmentation caused by environmental influences. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. Effects of trimethoprim on life history parameters, oxidative stress, and the expression of cytochrome P450 genes in the copepod Tigriopus japonicus.

    PubMed

    Han, Jeonghoon; Lee, Min-Chul; Kim, Duck-Hyun; Lee, Young Hwan; Park, Jun Chul; Lee, Jae-Seong

    2016-09-01

    Trimethoprim (TMP) is an antibiotic that has been detected in various environments including marine habitats; however, the toxic effects of TMP are poorly understood in non-target marine organisms. In this study, the effects of TMP on mortality, development, reproduction, intracellular reactive oxygen species (ROS) levels, and transcription levels of antioxidant and xenobiotic detoxification-related enzyme genes were investigated in the copepod Tigriopus japonicus. The TMP half lethal dose at 48 h (LC50-48 h) in nauplius and TMP LC50-96 h in adult T. japonicus copepods was determined as 156 mg/L and 200 mg/L, respectively. In TMP-exposed T. japonicus, delayed developmental time and impaired reproduction were observed as harmful effects on the life history parameters. Increased ROS levels were also shown in response to TMP exposure at the highest concentration (100 mg/L TMP) and the expression of antioxidant- (e.g. GST-kappa, GST-sigma) and xenobiotic detoxification (e.g. CYPs)-related genes were upregulated in a time and/or dose-dependent manner in response to TMP. Particularly, significant upregulation of three CYP genes (Tj-CYP3024A2, Tj-CYP3024A3 and Tj-CYP3027C2) were examined, suggesting that these CYP genes are likely playing an important role in the TMP detoxification metabolism in T. japonicus. In summary, we found that TMP induced oxidative stress via the transcriptional regulation of antioxidant- and xenobiotic detoxification-related genes, leading to changes in life history parameters such as developmental delay and reproduction impairment. Three Tj-CYP genes (Tj-CYP3024A2, Tj-CYP3024A3 and Tj-CYP3027C2) could be useful as potential T. japonicus biomarkers in response to antibiotics. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Seasonal biochemical changes in composition of body wall tissues of sea cucumber Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Gao, Fei; Xu, Qiang; Yang, Hongsheng

    2011-03-01

    Seasonal Variation in proximate, amino acid and fatty acid composition of the body wall of sea cucumber Apostichopus japonicus was evaluated. The proximate composition, except for ash content, changed significantly among seasons ( P<0.05). Alanine, glycine, glutamic acid and asparagic acid were the most abundant amino acids. Total amino acid and essential amino acid Contents both varied clearly with seasons ( P<0.05). 16:0 and 16:ln7 were the primary saturated fatty acid (SFA) and monounsaturated fatty acid (MUFA) respectively for all months. EPA (20:5n-3), AA (20:4n-6) and DHA (22:6n-3) were the major polyunsaturated fatty acids (PUFA). The proportions of SFA and PUFA yielded significant seasonal variations ( P<0.001), but MUFA did not changed significantly. The results indicated that the biochemical compositions of the body wall in A. japonicus were significantly influenced by seasons and that the body wall tissue is an excellent source of protein, MUFA and n-3 PUFA for humans.

  12. Action of trypsin on structural changes of collagen fibres from sea cucumber (Stichopus japonicus).

    PubMed

    Liu, Zi-Qiang; Tuo, Feng-Yan; Song, Liang; Liu, Yu-Xin; Dong, Xiu-Ping; Li, Dong-Mei; Zhou, Da-Yong; Shahidi, Fereidoon

    2018-08-01

    Trypsin, a representative serine proteinase, was used to hydrolyse the collagen fibres from sea cucumber (Stichopus japonicus) to highlight the role of serine proteinase in the autolysis of sea cucumber. Partial disaggregation of collagen fibres into collagen fibrils upon trypsin treatment occurred. The trypsin treatment also caused a time-dependent release of water-soluble glycosaminoglycans and proteins. Therefore, the degradation of the proteoglycan bridges between collagen fibrils might account for the disaggregation of collagen fibrils. For trypsin-treated collagen fibres (72 h), the collagen fibrils still kept their structural integrity and showed characteristic D-banding pattern, and the dissolution rate of hydroxyproline was just 0.21%. Meanwhile, Fourier transform infrared analysis showed the collagen within trypsin-treated collagen fibres (72 h) still retaining their triple-helical conformation. These results suggested that serine proteinase participated in the autolysis of S. japonicus body wall by damaging the proteoglycan bridges between collagen fibrils and disintegrating the latter. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. micro RNA 172 (miR172) signals epidermal infection and is expressed in cells primed for bacterial invasion in Lotus japonicus roots and nodules.

    PubMed

    Holt, Dennis B; Gupta, Vikas; Meyer, Dörte; Abel, Nikolaj B; Andersen, Stig U; Stougaard, Jens; Markmann, Katharina

    2015-10-01

    Legumes interact with rhizobial bacteria to form nitrogen-fixing root nodules. Host signalling following mutual recognition ensures a specific response, but is only partially understood. Focusing on the stage of epidermal infection with Mesorhizobium loti, we analysed endogenous small RNAs (sRNAs) of the model legume Lotus japonicus to investigate their involvement in host response regulation. We used Illumina sequencing to annotate the L. japonicus sRNA-ome and isolate infection-responsive sRNAs, followed by candidate-based functional characterization. Sequences from four libraries revealed 219 novel L. japonicus micro RNAs (miRNAs) from 114 newly assigned families, and 76 infection-responsive sRNAs. Unlike infection-associated coding genes such as NODULE INCEPTION (NIN), a micro RNA 172 (miR172) isoform showed strong accumulation in dependency of both Nodulation (Nod) factor and compatible rhizobia. The genetics of miR172 induction support the existence of distinct epidermal and cortical signalling events. MIR172a promoter activity followed a previously unseen pattern preceding infection thread progression in epidermal and cortical cells. Nodule-associated miR172a expression was infection-independent, representing the second of two genetically separable activity waves. The combined data provide a valuable resource for further study, and identify miR172 as an sRNA marking successful epidermal infection. We show that miR172 acts upstream of several APETALA2-type (AP2) transcription factors, and suggest that it has a role in fine-tuning AP2 levels during bacterial symbiosis. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  14. Screen and effect analysis of immunostimulants for sea cucumber, Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Li, Jiye; Sun, Xiuqin; Zheng, Fengrong; Hao, Linhua

    2009-02-01

    Immunostimulants may improve disease resistance of aquaculture animals by promoting the nonspecific immunity response of the organisms. Five types of saccharides, including chitosan, yeast polysaccharide, burdock oligosaccharide, seaweed polysaccharide and lentinus edodes polysaccharide, were screened for potential use as immunostimulants by using spectrophotometry. The saccharides were injected into Apostichopus japonicus, a sea cucumber, and the lysozyme and superoxide dismutase (SOD) activities of the coelomic fluid and epidermal slime were monitored in six consecutive days. The results show that the lysozyme activity of the animal’s coelomic fluid was significantly stimulated on day 2, day 4 and day 6 after the injection of the saccharides ( P<0.05). The effects of chitosan and yeast polysaccharide were the most notable. The lysozyme activity of the epidermal slime was significantly increased by chitosana, yeast polysaccharide, seaweed polysaccharide, and burdock oligosaccharide on day 1 and day 2 after the injection ( P<0.05). The SOD activity of the coelomic fluid was significantly promoted by the saccharides on day 2 and day 4 post-injection ( P<0.05), while the SOD activity of the epidermal slime increased on day 2. These findings indicate that chitosan and yeast polysaccharide are the most effective immunostimulants and potential healthy anti-disease feedstuff for A. japonicus.

  15. Mutagenic effects of carbon ion beam irradiations on dry Lotus japonicus seeds

    NASA Astrophysics Data System (ADS)

    Luo, Shanwei; Zhou, Libin; Li, Wenjian; Du, Yan; Yu, Lixia; Feng, Hui; Mu, Jinhu; Chen, Yuze

    2016-09-01

    Carbon ion beam irradiation is a powerful method for creating mutants and has been used in crop breeding more and more. To investigate the effects of carbon ion beams on Lotus japonicus, dry seeds were irradiated by 80 MeV/u carbon ion beam at dosages of 0, 100, 200, 300, 400, 500 and 600 Gy. The germination rate, survival rate and root length of M1 populations were explored and the dose of 400 Gy was selected as the median lethal dose (LD50) for a large-scale mutant screening. Among 2472 M2 plants, 127 morphological mutants including leaf, stem, flower and fruit phenotypic variation were found, and the mutation frequency was approximately 5.14%. Inter simple sequence repeat (ISSR) assays were utilized to investigate the DNA polymorphism between seven mutants and eight plants without phenotypic variation from M2 populations. No remarkable differences were detected between these two groups, and the total polymorphic rate was 0.567%.

  16. Gamma rays induce DNA damage and oxidative stress associated with impaired growth and reproduction in the copepod Tigriopus japonicus.

    PubMed

    Han, Jeonghoon; Won, Eun-Ji; Lee, Bo-Young; Hwang, Un-Ki; Kim, Il-Chan; Yim, Joung Han; Leung, Kenneth Mei Yee; Lee, Yong Sung; Lee, Jae-Seong

    2014-07-01

    Nuclear radioisotope accidents are potentially ecologically devastating due to their impact on marine organisms. To examine the effects of exposure of a marine organism to radioisotopes, we irradiated the intertidal copepod Tigriopus japonicus with several doses of gamma radiation and analyzed the effects on mortality, fecundity, and molting by assessing antioxidant enzyme activities and gene expression patterns. No mortality was observed at 96h, even in response to exposure to a high dose (800Gy) of radiation, but mortality rate was significantly increased 120h (5 days) after exposure to 600 or 800Gy gamma ray radiation. We observed a dose-dependent reduction in fecundity of ovigerous females; even the group irradiated with 50Gy showed a significant reduction in fecundity, suggesting that gamma rays are likely to have a population level effect. In addition, we observed growth retardation, particularly at the nauplius stage, in individuals after gamma irradiation. In fact, nauplii irradiated with more than 200Gy, though able to molt to copepodite stage 1, did not develop into adults. Upon gamma radiation, T. japonicus showed a dose-dependent increase in reactive oxygen species (ROS) levels, the activities of several antioxidant enzymes, and expression of double-stranded DNA break damage genes (e.g. DNA-PK, Ku70, Ku80). At a low level (sub-lethal dose) of gamma irradiation, we found dose-dependent upregulation of p53, implying cellular damage in T. japonicus in response to sub-lethal doses of gamma irradiation, suggesting that T. japonicus is not susceptible to sub-lethal doses of gamma irradiation. Additionally, antioxidant genes, phase II enzyme (e.g. GSTs), and cellular chaperone genes (e.g. Hsps) that are involved in cellular defense mechanisms also showed the same expression patterns for sublethal doses of gamma irradiation (50-200Gy). These findings indicate that sublethal doses of gamma radiation can induce oxidative stress-mediated DNA damage and increase

  17. Changes of exoskeleton surface roughness and expression of crucial participation genes for chitin formation and digestion in the mud crab (Macrophthalmus japonicus) following the antifouling biocide irgarol.

    PubMed

    Park, Kiyun; Nikapitiya, Chamilani; Kim, Won-Seok; Kwak, Tae-Soo; Kwak, Ihn-Sil

    2016-10-01

    Irgarol is a common antifoulant present in coastal sediment. The mud crab Macrophthalmus japonicus is one of the most abundant of the macrobenthos in the costal environment, and its exoskeleton has a protective function against various environmental threats. We evaluated the effects of irgarol toxicity on the exoskeleton of M. japonicus, which is the outer layer facing the environment. We analyzed transcriptional expression of exoskeleton, molting, and proteolysis-related genes in the gill and hepatopancreas of these exposed M. japonicus. In addition, changes in survival and exoskeleton surface characteristics were investigated. In the hepatopancreas, mRNA expression of chitinase 1 (Mj-chi1), chitinase 4 (Mj-chi4), and chitinase 5 (Mj-chi5) increased in M. japonicus exposed to all concentrations of irgarol. Mj-chi1 and Mj-chi4 expressions from 1 to 10μgL(-1) were dose- and time-dependent. Ecdysteroid receptor (Mj-EcR), trypsin (Mj-Tryp), and serine proteinase (Mj-SP) in the hepatopancreas were upregulated in response to different exposure levels of irgarol at day 1, 4, or 7. In contrast, gill Mj-chi5, Mj-Tryp, and Mj-SP exhibited late upregulated responses to 10μgL(-1) irgarol compared to the control at day 7. Mj-chi1 showed early upregulation upon exposure to 10μgL(-1) irgarol and Mj-chi4 showed no changes in transcription in the gill. Gill Mj-EcR presented generally downregulated expression patterns. In addition, decreased survival and change of exoskeleton surface roughness were observed in M. japonicus exposed to the three concentrations of irgarol. These results suggest that exposure to irgarol induces changes in the exoskeleton, molting, and proteolysis metabolism of M. japonicus. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Energy metabolism of spermatozoa of the sand dollar Clypeaster japonicus: the endogenous substrate and ultrastructural correlates.

    PubMed

    Mita, M; Yasumasu, I; Nakamura, M

    1994-07-01

    Energy metabolism in spermatozoa of the sand dollar-sea urchin Clypeaster japonicus was examined. The spermatozoa contained triglyceride and cholesterol ester besides several kinds of phospholipids and cholesterol. Glycogen and glucose were present at extremely low levels. Following incubation of spermatozoa in seawater, the triglyceride content decreased rapidly. Other lipids, however, remained at constant levels. High lipase activity was demonstrated in the spermatozoa. Also, [1-14C]oleic acid was oxidized to 14CO2. Ultrastructural study showed that lipid globules were present at the bottom of the midpiece. After incubation in seawater, morphological changes in the lipid globules were observed and vacuoles of various sizes appeared near the lipid globules. Thus, it is concluded that C. japonicus spermatozoa obtain energy through oxidation of fatty acid from triglyceride stored in the lipid globules at the midpieces.

  19. Identification and Characterization of MicroRNAs from Longitudinal Muscle and Respiratory Tree in Sea Cucumber (Apostichopus japonicus) Using High-Throughput Sequencing.

    PubMed

    Wang, Hongdi; Liu, Shikai; Cui, Jun; Li, Chengze; Hu, Yucai; Zhou, Wei; Chang, Yaqing; Qiu, Xuemei; Liu, Zhanjiang; Wang, Xiuli

    2015-01-01

    MicroRNAs (miRNAs), as a family of non-coding small RNAs, play important roles in the post-transcriptional regulation of gene expression. Sea cucumber (Apostichopus japonicus) is an important economic species which is widely cultured in East Asia. The longitudinal muscle (LTM) and respiratory tree (RPT) are two important tissues in sea cucumber, playing important roles such as respiration and movement. In this study, we identified and characterized miRNAs in the LTM and RPT of sea cucumber (Apostichopus japonicus) using Illumina HiSeq 2000 platform. A total of 314 and 221 conserved miRNAs were identified in LTM and RPT, respectively. In addition, 27 and 34 novel miRNAs were identified in the LTM and RPT, respectively. A set of 58 miRNAs were identified to be differentially expressed between LTM and RPT. Among them, 9 miRNAs (miR-31a-3p, miR-738, miR-1692, let-7a, miR-72a, miR-100b-5p, miR-31b-5p, miR-429-3p, and miR-2008) in RPT and 7 miRNAs (miR-127, miR-340, miR-381, miR-3543, miR-434-5p, miR-136-3p, and miR-300-3p) in LTM were differentially expressed with foldchange value being greater than 10. A total of 14,207 and 12,174 target genes of these miRNAs were predicted, respectively. Functional analysis of these target genes of miRNAs were performed by GO analysis and pathway analysis. This result provided in this work will be useful for understanding biological characteristics of the LTM and RPT of sea cucumber and assisting molecular breeding of sea cucumber for aquaculture.

  20. Developmental retardation, reduced fecundity, and modulated expression of the defensome in the intertidal copepod Tigriopus japonicus exposed to BDE-47 and PFOS.

    PubMed

    Han, Jeonghoon; Won, Eun-Ji; Lee, Min-Chul; Seo, Jung Soo; Lee, Su-Jae; Lee, Jae-Seong

    2015-08-01

    2,2',4,4'-tetrabromodiphenyl ether (BDE-47) and perfluorooctane sulfonate (PFOS) are widely dispersed persistent organic pollutants (POPs) in the marine ecosystem. However, their toxic effects on marine organisms are still poorly understood. In this study, we investigated the effects of BDE-47 and PFOS on development and reproduction at the organismal level and reactive oxygen species (ROS) production and gene expression patterns of the defensome at the cellular level in the intertidal copepod Tigriopus japonicus. In copepods exposed to BDE-47 and PFOS, we observed developmental retardation and reduced fecundity, suggesting repercussions on in vivo endpoints through alterations to the normal molting and reproduction system of T. japonicus. BDE-47 and PFOS increased levels of ROS in T. japonicus in a concentration-dependent manner, indicating that POPs can induce oxidative stress through the generation of ROS. Additionally, transcript profiles of genes related to detoxification (e.g., CYPs), antioxidant functions (e.g., GST- sigma, catalase, MnSOD), apoptosis (e.g., p53, Rb), and cellular proliferation (e.g., PCNA) were modulated over 72h in response to BDE-47 (120μg/L) and PFOS (1000μg/L). These findings indicate that BDE-47 and PFOS can induce oxidative stress-mediated DNA damage repair systems with transcriptional regulation of detoxification, antioxidant, and apoptosis-related genes, resulting in developmental retardation and reduced fecundity in the copepod T. japonicus. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Ultraviolet B radiation induces impaired lifecycle traits and modulates expression of cytochrome P450 (CYP) genes in the copepod Tigriopus japonicus.

    PubMed

    Puthumana, Jayesh; Lee, Min-Chul; Park, Jun Chul; Kim, Hui-Su; Hwang, Dae-Sik; Han, Jeonghoon; Lee, Jae-Seong

    2017-03-01

    To evaluate the effects of ultraviolet B (UV-B) radiation at the developmental, reproductive, and molecular levels in aquatic invertebrates, we measured UV-B-induced acute toxicity, impairments in developmental and reproductive traits, and UV-B interaction with the entire family of cytochrome P450 (CYP) genes in the intertidal benthic copepod Tigriopus japonicus. We found a significant, dose-dependent reduction (P<0.05) in the survival of T. japonicus that began as a developmental delay and decreased fecundity. The 48h LD10 and LD50 were 1.35 and 1.84kJ/m 2 , and the CYP inhibitor (PBO) elevated mortality, confirming the involvement of CYP genes in UV-B induced toxicity. Low-dose UV-B (1.5kJ/m 2 ) induced developmental delays, and higher doses (6-18kJ/m 2 ) caused reproductive impairments in ovigerous females. The significant up-regulation of CYP genes belonging to clans 2/3/MT/4/20 in T. japonicus exposed to UV-B (12kJ/m 2 ) confirmed molecular interaction between UV-B and CYP genes. Moreover, orphan CYPs, such as CYP20A1, provide good insight on the deorphanization of invertebrate CYPs. Overall, these results demonstrate the involvement of UV-B radiation in the expression of all the CYP genes in T. japonicus and their susceptibility to UV-B radiation. This will provide a better understanding of the mechanistic effects of UV-B in copepods through the predicted AhR-mediated up-regulation of CYP genes. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. ROS production in homogenate from the body wall of sea cucumber Stichopus japonicus under UVA irradiation: ESR spin-trapping study.

    PubMed

    Qi, Hang; Dong, Xiu-fang; Zhao, Ya-ping; Li, Nan; Fu, Hui; Feng, Ding-ding; Liu, Li; Yu, Chen-xu

    2016-02-01

    Sea cucumber Stichopus japonicus (S. japonicus) shows a strong ability of autolysis, which leads to severe deterioration in sea cucumber quality during processing and storage. In this study, to further characterize the mechanism of sea cucumber autolysis, hydroxyl radical production induced by ultraviolet A (UVA) irradiation was investigated. Homogenate from the body wall of S. japonicas was prepared and subjected to UVA irradiation at room temperature. Electron Spin Resonance (ESR) spectra of the treated samples were subsequently recorded. The results showed that hydroxyl radicals (OH) became more abundant while the time of UVA treatment and the homogenate concentration were increased. Addition of superoxide dismutase (SOD), catalase, EDTA, desferal, NaN3 and D2O to the homogenate samples led to different degrees of inhibition on OH production. Metal cations and pH also showed different effects on OH production. These results indicated that OH was produced in the homogenate with a possible pathway as follows: O2(-) → H2O2 → OH, suggesting that OH might be a critical factor in UVA-induced S. japonicus autolysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Aqueous extract of Orostachys japonicus A. Berger exerts immunostimulatory activity in RAW 264.7 macrophages.

    PubMed

    Park, Hye-Jin; Yang, Hye Jeong; Kim, Ki Hyun; Kim, Sang Hee

    2015-07-21

    Orostachys japonicus A. Berger (Crassulaceae) (OJ), well-known as Wa-song in Korea is a medicinal plant with immunoregulatory, anti-febrile, antidote, and anti-cancer activities. This study was aimed at evaluating the immunostimulatory effect of O. japonicus A. Berger and its possible mechanisms of action. To evaluate the effect of OJ aqueous extract on macrophage activity, we evaluated the modulation of macrophage activation state by observing structural (phagocytic activities) and the production of nitric oxide increase. The effect of OJ aqueous extract on RAW264.7 cell viability were assessed using Cell Counting Kit (CCK)-8 assay. HPLC analysis was performed to identify potential active compounds of this extract. The biological investigations indicated that OJ aqueous extract, among others, possessed the highest macrophage activation as indicated by NO production yield. The results showed that OJ aqueous extract exhibited antioxidant effects, which included scavenging activities against DPPH radicals. OJ aqueous extract increased the phagocytic activity of RAW 264.7 cells against IgG-opsonized red blood cells (RBC). The level of phosphorylated Syk kinase was increased in OJ aqueous extract-treated group as compared to control. Phosphorylation of PLC-γ was increased in the OJ aqueous extract-treated groups. Quercetin-3-O-rhamnose and kaempferol-3-O-rhamnose was detected in OJ aqueous extract by HPLC analysis. OJ aqueous extract might play a pivotal ethnopharmacologic role as an immunostimulatory agent by promoting Fc gamma receptor (FcγR)-mediated phagocytosis of IgG-opsonized RBCs. On the basis of our results, OJ aqueous extract can enhance innate immunity and may serve as an adjuvant for tumor treatment. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  4. Amino acid specificity of fibers of the facial/trigeminal complex innervating the maxillary barbel in the Japanese sea catfish, Plotosus japonicus.

    PubMed

    Caprio, John; Shimohara, Mami; Marui, Takayuki; Kohbara, Jun; Harada, Shuitsu; Kiyohara, Sadao

    2015-12-01

    The Japanese sea catfish, Plotosus japonicus, possesses taste and solitary chemoreceptor cells (SCCs) located on the external body surface that detect specific water-soluble substances. Here, we identify two major fiber types of the facial/trigeminal complex that transmit amino acid information to the medulla. Both single and few fiber preparations respond to amino acid stimulation in the 0.1 μM to mM range. One fiber type responds best to glycine and l-alanine (i.e. Gly/Ala fibers) whereas the other fiber type is best stimulated by l-proline and glycine betaine (hereafter referred to only as betaine) (i.e. Pro/Bet fibers). We demonstrate that betaine, which does not alter the pH of the seawater and therefore does not activate the animals' highly sensitive pH sensors (Caprio et al., Science 344:1154-1156, 2014), is sufficient to elicit appetitive food search behavior. We further show that the amino acid specificity of fibers of the facial/trigeminal complex in P. japonicus is different from that in Ariopsis felis (Michel and Caprio, J. Neurophysiol. 66:247-260, 1991; Michel et al., J. Comp. Physiol. A. 172:129-138, 1993), a representative member of the only other family (Ariidae) of extant marine catfishes. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Mechanical stress induces neuroendocrine and immune responses of sea cucumber ( Apostichopus japonicus)

    NASA Astrophysics Data System (ADS)

    Tan, Jie; Li, Fenghui; Sun, Huiling; Gao, Fei; Yan, Jingping; Gai, Chunlei; Chen, Aihua; Wang, Qingyin

    2015-04-01

    Grading procedure in routine sea cucumber hatchery production is thought to affect juvenile sea cucumber immunological response. The present study investigated the impact of a 3-min mechanical perturbation mimicking the grading procedure on neuroendocrine and immune parameters of the sea cucumber Apostichopus japonicus. During the application of stress, concentrations of noradrenaline and dopamine in coelomic fluid increased significantly, indicating that the mechanical perturbation resulted in a transient state of stress in sea cucumbers. Coelomocytes concentration in coelomic fluid increased transiently after the beginning of stressing, and reached the maximum in 1 h. Whereas, coelomocytes phagocytosis at 3 min, superoxide anion production from 3 min to 0.5 h, acid phosphatase activity at 0.5 h, and phenoloxidase activity from 3 min to 0.5 h were all significantly down-regulated. All of the immune parameters recovered to baseline levels after the experiment was conducted for 8 h, and an immunostimulation occurred after the stress considering the phagocytosis and acid phosphatase activity. The results suggested that, as in other marine invertebrates, neuroendocrine/immune connections exist in sea cucumber A. japonicus. Mechanical stress can elicit a profound influence on sea cucumber neuroendocrine system. Neuroendocrine messengers act in turn to modulate the immunity functions. Therefore, these effects should be considered for developing better husbandry procedures.

  6. Ultrastructure and morphology of antennal sensilla of the adult diving beetle Cybister japonicus Sharp

    PubMed Central

    Huang, Jian-Ping; Zhu, Fang; Jiang, Xiang; Zhang, Shan-Gan; Ban, Li-Ping

    2017-01-01

    The morphology and distribution of the antennal sensilla of adult diving beetle Cybister japonicus Sharp (Dytiscidae, Coleoptera), have been examined. Five types of sensilla on the antennae were identified by scanning electron microscope (SEM) and transmission electron microscope (TEM). Sensilla placodea and elongated s. placodea are the most abundant types of sensilla, distributing only on the flagellum. Both these types of sensilla carry multiple pore systems with a typical function as chemoreceptors. Three types of s. coeloconica (Type I–III) were also identified, with the characterization of the pit-in-pit style, and carrying pegs externally different from each other. Our data indicated that both type I and type II of s. coleconica contain two bipolar neurons, while the type III of s. coleconica contains three dendrites in the peg. Two sensory dendrites in the former two sensilla are tightly embedded inside the dendrite sheath, with no space left for sensilla lymph. There are no specific morphological differences in the antennal sensilla observed between males and females, except that the males have longer antennae and more sensilla than the females. PMID:28358865

  7. Production, characterization and application of monoclonal antibody to spherulocytes: A subpopulation of coelomocytes of Apostichopus japonicus

    USDA-ARS?s Scientific Manuscript database

    One monoclonal antibody (mAb 3F6) against coelomocytes of sea cucumber Apostichopus japonicus was developed by immunization of Balb/C mice. Analyzed by indirect immunofluorescence assay test (IIFAT), immunocytochemical assay (ICA),Western blotting and fluorescence-activated cell sorter (FACS), mAb 3...

  8. Cell wall polysaccharides released during the alcoholic fermentation by Schizosaccharomyces pombe and S. japonicus: quantification and characterization.

    PubMed

    Domizio, P; Liu, Y; Bisson, L F; Barile, D

    2017-02-01

    The present work demonstrates that yeasts belonging to the Schizosaccharomyces genus release a high quantity of polysaccharides of cell wall origin starting from the onset of the alcoholic fermentation. By the end of the alcoholic fermentation, all of the Schizosaccharomyces yeast strains released a quantity of polysaccharides approximately 3-7 times higher than that released by a commercial Saccharomyces cerevisiae yeast strain under the same fermentative conditions of synthetic juice. A higher content of polysaccharide was found in media fermented by Schizosaccharomyces japonicus with respect to that of Schizosaccharomyces pombe. Some of the strains evaluated were also able to produce high levels of pyruvic acid, which has been shown to be an important compound for color stability of wine. The presence of strains with different malic acid consumption patterns along with high polysaccharide release would enable production of naturally modified wines with enhanced mouth feel and reduced acidity. The chemical analysis of the released polysaccharides demonstrated divergence between the two yeast species S. pombe and S. japonicus. A different mannose/galactose ratio and a different percentage of proteins was observed on the polysaccharides released by S. pombe as compared to S. japonicus. Analysis of the proteins released in the media revealed the presence of a glycoprotein with a molecular size around 32-33 kDa only for the species S. japonicus. Mass spectrometry analysis of carbohydrate moieties showed similar proportions among the N-glycan chains released in the media by both yeast species but differences between the two species were also observed. These observations suggest a possible role of rapid MALDI-TOF screening of N-glycans compositional fingerprint as a taxonomic tool for this genus. Polysaccharides release in the media, in particular galactomannoproteins in significant amounts, could make these yeasts particularly interesting also for the industrial

  9. Long Non-Coding RNAs (lncRNAs) of Sea Cucumber: Large-Scale Prediction, Expression Profiling, Non-Coding Network Construction, and lncRNA-microRNA-Gene Interaction Analysis of lncRNAs in Apostichopus japonicus and Holothuria glaberrima During LPS Challenge and Radial Organ Complex Regeneration.

    PubMed

    Mu, Chuang; Wang, Ruijia; Li, Tianqi; Li, Yuqiang; Tian, Meilin; Jiao, Wenqian; Huang, Xiaoting; Zhang, Lingling; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin

    2016-08-01

    Long non-coding RNA (lncRNA) structurally resembles mRNA but cannot be translated into protein. Although the systematic identification and characterization of lncRNAs have been increasingly reported in model species, information concerning non-model species is still lacking. Here, we report the first systematic identification and characterization of lncRNAs in two sea cucumber species: (1) Apostichopus japonicus during lipopolysaccharide (LPS) challenge and in heathy tissues and (2) Holothuria glaberrima during radial organ complex regeneration, using RNA-seq datasets and bioinformatics analysis. We identified A. japonicus and H. glaberrima lncRNAs that were differentially expressed during LPS challenge and radial organ complex regeneration, respectively. Notably, the predicted lncRNA-microRNA-gene trinities revealed that, in addition to targeting protein-coding transcripts, miRNAs might also target lncRNAs, thereby participating in a potential novel layer of regulatory interactions among non-coding RNA classes in echinoderms. Furthermore, the constructed coding-non-coding network implied the potential involvement of lncRNA-gene interactions during the regulation of several important genes (e.g., Toll-like receptor 1 [TLR1] and transglutaminase-1 [TGM1]) in response to LPS challenge and radial organ complex regeneration in sea cucumbers. Overall, this pioneer systematic identification, annotation, and characterization of lncRNAs in echinoderm pave the way for similar studies and future genetic, genomic, and evolutionary research in non-model species.

  10. Transcription profiling using RNA-Seq demonstrates expression differences in the body walls of juvenile albino and normal sea cucumbers Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Ma, Deyou; Yang, Hongsheng; Sun, Lina; Chen, Muyan

    2014-01-01

    Sea cucumbers Apostichopus japonicus are one of the most important aquaculture species in China. Their normal body color is black to fit their surroundings. Wild albinos are rare and hard to breed. To understand the differences between albino and normal (control) sea cucumbers at the transcriptional level, we sequenced the transcriptomes in their body-wall tissues using RNA-Seq high-throughput sequencing. Approximately 4.876 million (M) and 4.884 M 200-nucleotide-long cDNA reads were produced in the cDNA libraries derived from the body walls of albino and control samples, respectively. A total of 9 561 (46.89%) putative genes were identified from among the RNA-Seq reads in both libraries. After filtering, 837 significantly differentially regulated genes were identified in the albino library compared with in the control library, and 3.6% of the differentially expressed genes (DEGs) were found to have changed those more than five-fold. The expression levels of 10 DEGs were checked by real-time PCR and the results were in full accord with the RNA-Seq expression trends, although the amplitude of the differences in expression levels was lower in all cases. A series of pathways were significantly enriched for the DEGs. These pathways were closely related to phagocytosis, the complement and coagulation cascades, apoptosis-related diseases, cytokine-cytokine receptor interaction, and cell adhesion. The differences in gene expression and enriched pathways between the albino and control sea cucumbers offer control targets for cultivating excellent albino A. japonicus strains in the future.

  11. Characterization and identification of enzyme-producing microflora isolated from the gut of sea cucumber Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Li, Fenghui; Gao, Fei; Tan, Jie; Fan, Chaojing; Sun, Huiling; Yan, Jingping; Chen, Siqing; Wang, Xiaojun

    2016-01-01

    Gut microorganisms play an important role in the digestion of their host animals. The purpose of this research was to isolate and assess the enzyme-producing microbes from the Apostichopus japonicus gut. Thirty-nine strains that can produce at least one of the three digestive enzymes (protease, amylase, and cellulase) were qualitatively screened based on their extracellular enzyme-producing abilities. The enzyme-producing strains clustered into eight groups at the genetic similarity level of 100% by analyzing the restriction patterns of 16S rDNA amplified with Mbo I. Phylogenetic analysis revealed that 37 strains belonged to the genus Bacillus and two were members of the genus Virgibacillus. Enzyme-producing capability results indicate that the main enzyme-producing microflora in the A. japonicus gut was Bacillus, which can produce protease, amylase, and cellulase. Virgibacillus, however, can only produce protease. The high enzyme-producing capability of the isolates suggests that the gut microbiota play an important role in the sea cucumber digestive process.

  12. Plate-like permanent dental laminae of upper jaw dentition in adult gobiid fish, Sicyopterus japonicus.

    PubMed

    Moriyama, Keita; Watanabe, Shun; Iida, Midori; Sahara, Noriyuki

    2010-04-01

    Sicyopterus japonicus (Teleostei, Gobiidae) possesses a unique upper jaw dentition different from that known for any other teleosts. In the adults, many (up to 30) replacement teeth, from initiation to attachment, are arranged orderly in a semicircular-like strand within a capsule of connective tissue on the labial side of each premaxillary bone. We have applied histological, ultrastructural, and three-dimensional imaging from serial sections to obtain insights into the distribution and morphological features of the dental lamina in the upper jaw dentition of adult S. japonicus. The adult fish has numerous permanent dental laminae, each of which is an infolding of the oral epithelium at the labial side of the functional tooth and forms a thin plate-like structure with a wavy contour. All replacement teeth of a semicircular-like strand are connected to the plate-like dental lamina by the outer dental epithelium and form a tooth family; neighboring tooth families are completely separated from each other. The new tooth germ directly buds off from the ventro-labial margin of the dental lamina, whereas no distinct free end of the dental lamina is present, even adjacent to this region. Cell proliferation concentrated at the ventro-labial margin of the dental lamina suggests that this region is the site for repeated tooth initiation. During tooth development, the replacement tooth migrates along a semicircular-like strand and eventually erupts through the dental lamina into the oral epithelium at the labial side of the functional tooth. This unique thin plate-like permanent dental lamina and the semicircular-like strand of replacement teeth in the upper jaw dentition of adult S. japonicus probably evolved as a dental adaptation related to the rapid replacement of teeth dictated by the specialized feeding habit of this algae-scraping fish.

  13. Phenotypic and genetic characterization of bacteria isolated from diseased cultured sea cucumber (Apostichopus japonicus) in Northeastern China

    USDA-ARS?s Scientific Manuscript database

    During the winter–spring from 2004 to 2006 in northeastern China cultured Japanese sea cucumber Apostichopus japonicus suffered from a serious disease. Clinical signs included swollen mouth, skin ulceration and massive mortality. Clinical samples taken during this period were studied. Thirty-one bac...

  14. New insight into hybridization and unidirectional introgression between Ammodytes japonicus and Ammodytes heian (Trachiniformes, Ammodytidae)

    PubMed Central

    Bae, Seung Eun; Lee, Soo Jeong; Yoon, Moon Geun

    2017-01-01

    Based on northern (NOL) and southern (SOL) mitochondrial lineages, recently, it proposed the new species Ammodytes heian and revived the species name Ammodytes japonicus to describe sand lances from the northwestern Pacific Ocean. This study used molecular methods to investigate genetic relationships between the two sand lance species in Korea and Japan. In total, 154 specimens were collected from four locations in Korea (Baengnyeongdo in the Yellow Sea, Tongyeong in the Korean Strait, and Jumunjin and Gijang in the East Sea), and 50 specimens were collected from a single location in Japan (Wakkanai in the Okhotsk Sea). Mitochondrial DNA analysis demonstrated that the individuals from Baengnyeongdo and Tongyeong all belonged to the SOL, whereas those from Gijang, Jumunjin, and Wakkanai included individuals from both the NOL and SOL (over 75% NOL). Population structure analyses were performed on the same individuals using seven microsatellite DNA markers. The population structure analysis based on 201 specimens identified two clusters (named as northern group and southern group), with the admixture proportion (q) of < 0.1 for the northern group in the Backyeongdo and Tongyeong sand lances and < 0.1 for the southern group in the Wakkanai sand lances. The high heterogeneity indicated that the former was probably A. japonicus and the latter probably A. heian. However, the admixture proportion in the Jumunjin and Gijang sand lances was 0.71–0.75 for the southern group, indicating that hybridization and unidirectional introgression from SOL to NOL occurs in southwestern margin of the East Sea. Our findings illustrate the speciation process based on different patterns of gene flow between Korean and Japanese sand lance, which is strongly influenced by both the paleo-climatic change and the contemporary local oceanic current pattern. PMID:28582394

  15. New insight into hybridization and unidirectional introgression between Ammodytes japonicus and Ammodytes heian (Trachiniformes, Ammodytidae).

    PubMed

    Kim, Jin-Koo; Bae, Seung Eun; Lee, Soo Jeong; Yoon, Moon Geun

    2017-01-01

    Based on northern (NOL) and southern (SOL) mitochondrial lineages, recently, it proposed the new species Ammodytes heian and revived the species name Ammodytes japonicus to describe sand lances from the northwestern Pacific Ocean. This study used molecular methods to investigate genetic relationships between the two sand lance species in Korea and Japan. In total, 154 specimens were collected from four locations in Korea (Baengnyeongdo in the Yellow Sea, Tongyeong in the Korean Strait, and Jumunjin and Gijang in the East Sea), and 50 specimens were collected from a single location in Japan (Wakkanai in the Okhotsk Sea). Mitochondrial DNA analysis demonstrated that the individuals from Baengnyeongdo and Tongyeong all belonged to the SOL, whereas those from Gijang, Jumunjin, and Wakkanai included individuals from both the NOL and SOL (over 75% NOL). Population structure analyses were performed on the same individuals using seven microsatellite DNA markers. The population structure analysis based on 201 specimens identified two clusters (named as northern group and southern group), with the admixture proportion (q) of < 0.1 for the northern group in the Backyeongdo and Tongyeong sand lances and < 0.1 for the southern group in the Wakkanai sand lances. The high heterogeneity indicated that the former was probably A. japonicus and the latter probably A. heian. However, the admixture proportion in the Jumunjin and Gijang sand lances was 0.71-0.75 for the southern group, indicating that hybridization and unidirectional introgression from SOL to NOL occurs in southwestern margin of the East Sea. Our findings illustrate the speciation process based on different patterns of gene flow between Korean and Japanese sand lance, which is strongly influenced by both the paleo-climatic change and the contemporary local oceanic current pattern.

  16. Expression responses of five cold tolerant related genes to two temperature dropping treatments in sea cucumber Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Li, Chengze; Chang, Yaqing; Pang, Zhenguo; Ding, Jun; Ji, Nanjing

    2015-03-01

    Environmental conditions, including ambient temperature, play important roles in survival, growth development, and reproduction of the Japanese sea cucumber, Apostichopus japonicus. Low temperatures result in slowed growth and skin ulceration disease. In a previous study, we investigated the effect of low temperature on gene expression profiles in A. japonicus by suppression subtractive hybridization (SSH). Genes encoding Ferritin, Lysozyme, Hsp70, gp96, and AjToll were selected from a subtracted cDNA library of A. japonicus under acute cold stress. The transcriptional expression profiles of these genes were investigated in different tissues (coelomocyte, respiratory tree, intestine, longitudinal muscle) after exposure to acute and mild temperature dropping treatments. The results show that (1) the five cold-tolerance-related genes were found in all four tissues and the highest mRNA levels were observed in coelomocyte and respiratory tree; (2) under the temperature dropping treatments, three types of transcriptional regulation patterns were observed: primary suppression followed by up-regulation at -2°C, suppressed expression throughout the two treatments, and more rarely an initial stimulation followed by suppression; and (3) gene expression suppression was more severe under acute temperature dropping than under mild temperature dropping treatment. The five cold-tolerance-related genes that were distributed mainly in coelomocyte and respiratory tissues were generally down-regulated by low temperature stress but an inverse up-regulation event was found at the extreme temperature (-2°C).

  17. Effects of methoprene on oviposition by Aedes japonicus and Culex spp

    USGS Publications Warehouse

    Butler, M.; Suom, C.; LeBrun, R.A.; Ginsberg, H.S.; Gettman, A.D.

    2006-01-01

    The mosquito larvicide methoprene is a juvenile growth hormone mimic that is widely used to control mosquitoes. This chemical disrupts normal mosquito development, drastically inhibiting emergence from the pupal to the adult stage. If the presence of methoprene attracts or deters mosquitoes from ovipositing it could have implications for mosquito control. This study evaluates whether methoprene attracts or deters mosquitoes likely to oviposit in catch basins. In a field experiment, methoprene formulated as liquid larvicide did not affect oviposition of either Culex spp. or Aedes japonicus in 19 liter plastic buckets.

  18. Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads

    PubMed Central

    Yano, Koji; Aoki, Seishiro; Liu, Meng; Umehara, Yosuke; Suganuma, Norio; Iwasaki, Wataru; Sato, Shusei; Soyano, Takashi; Kouchi, Hiroshi

    2017-01-01

    Abstract Legume-rhizobium symbiosis is achieved by two major events evolutionarily acquired: root hair infection and organogenesis. Infection thread (IT) development is a distinct element for rhizobial infection. Through ITs, rhizobia are efficiently transported from infection foci on root hairs to dividing meristematic cortical cells. To unveil this process, we performed genetic screening using Lotus japonicus MG-20 and isolated symbiotic mutant lines affecting nodulation, root hair morphology, and IT development. Map-based cloning identified an AP2/ERF transcription factor gene orthologous to Medicago truncatula ERN1. LjERN1 was activated in response to rhizobial infection and depended on CYCLOPS and NSP2. Legumes conserve an ERN1 homolog, ERN2, that functions redundantly with ERN1 in M. truncatula. Phylogenetic analysis showed that the lineages of ERN1 and ERN2 genes originated from a gene duplication event in the common ancestor of legume plants. However, genomic analysis suggested the lack of ERN2 gene in the L. japonicus genome, consistent with Ljern1 mutants exhibited a root hair phenotype that is observed in ern1/ern2 double mutants in M. truncatula. Molecular evolutionary analysis suggested that the nonsynonymous/synonymous rate ratios of legume ERN1 genes was almost identical to that of non-legume plants, whereas the ERN2 genes experienced a relaxed selective constraint. PMID:28028038

  19. Demographic response of cutlassfish (Trichiurus japonicus and T. nanhaiensis) to fluctuating palaeo-climate and regional oceanographic conditions in the China seas.

    PubMed

    He, Lijun; Zhang, Aibing; Weese, David; Li, Shengfa; Li, Jiansheng; Zhang, Jing

    2014-09-16

    Glacial cycles of the Quaternary have heavily influenced the demographic history of various species. To test the evolutionary impact of palaeo-geologic and climatic events on the demographic history of marine taxa from the coastal Western Pacific, we investigated the population structure and demographic history of two economically important fish (Trichiurus japonicus and T. nanhaiensis) that inhabit the continental shelves of the East China and northern South China Seas using the mitochondrial cytochrome b sequences and Bayesian Skyline Plot analyses. A molecular rate of 2.03% per million years, calibrated to the earliest flooding of the East China Sea shelf (70-140 kya), revealed a strong correlation between population sizes and primary production. Furthermore, comparison of the demographic history of T. japonicus populations from the East China and South China Seas provided evidence of the postglacial development of the Changjiang (Yangtze River) Delta. In the South China Sea, interspecific comparisons between T. japonicus and T. nanhaiensis indicated possible evolutionary responses to changes in palaeo-productivity that were influenced by East Asian winter monsoons. This study not only provides insight into the demographic history of cutlassfish but also reveals potential clues regarding the historic productivity and regional oceanographic conditions of the Western Pacific marginal seas.

  20. Demographic response of cutlassfish (Trichiurus japonicus and T. nanhaiensis) to fluctuating palaeo-climate and regional oceanographic conditions in the China seas

    PubMed Central

    He, Lijun; Zhang, Aibing; Weese, David; Li, Shengfa; Li, Jiansheng; Zhang, Jing

    2014-01-01

    Glacial cycles of the Quaternary have heavily influenced the demographic history of various species. To test the evolutionary impact of palaeo-geologic and climatic events on the demographic history of marine taxa from the coastal Western Pacific, we investigated the population structure and demographic history of two economically important fish (Trichiurus japonicus and T. nanhaiensis) that inhabit the continental shelves of the East China and northern South China Seas using the mitochondrial cytochrome b sequences and Bayesian Skyline Plot analyses. A molecular rate of 2.03% per million years, calibrated to the earliest flooding of the East China Sea shelf (70–140 kya), revealed a strong correlation between population sizes and primary production. Furthermore, comparison of the demographic history of T. japonicus populations from the East China and South China Seas provided evidence of the postglacial development of the Changjiang (Yangtze River) Delta. In the South China Sea, interspecific comparisons between T. japonicus and T. nanhaiensis indicated possible evolutionary responses to changes in palaeo-productivity that were influenced by East Asian winter monsoons. This study not only provides insight into the demographic history of cutlassfish but also reveals potential clues regarding the historic productivity and regional oceanographic conditions of the Western Pacific marginal seas. PMID:25223336

  1. Effects of endogenous cysteine proteinases on structures of collagen fibres from dermis of sea cucumber (Stichopus japonicus).

    PubMed

    Liu, Yu-Xin; Zhou, Da-Yong; Ma, Dong-Dong; Liu, Zi-Qiang; Liu, Yan-Fei; Song, Liang; Dong, Xiu-Ping; Li, Dong-Mei; Zhu, Bei-Wei; Konno, Kunihiko; Shahidi, Fereidoon

    2017-10-01

    Autolysis of sea cucumber, caused by endogenous enzymes, leads to postharvest quality deterioration of sea cucumber. However, the effects of endogenous proteinases on structures of collagen fibres, the major biologically relevant substrates in the body wall of sea cucumber, are less clear. Collagen fibres were prepared from the dermis of sea cucumber (Stichopus japonicus), and the structural consequences of degradation of the collagen fibres caused by endogenous cysteine proteinases (ECP) from Stichopus japonicus were examined. Scanning electron microscopic images showed that ECP caused partial disaggregation of collagen fibres into collagen fibrils by disrupting interfibrillar proteoglycan bridges. Differential scanning calorimetry and Fourier transform infrared analysis revealed increased structural disorder of fibrillar collagen caused by ECP. SDS-PAGE and chemical analysis indicated that ECP can liberate glycosaminoglycan, hydroxyproline and collagen fragments from collagen fibres. Thus ECP can cause disintegration of collagen fibres by degrading interfibrillar proteoglycan bridges. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Determination of three steroidal saponins from Ophiopogon japonicus (Liliaceae) via high-performance liquid chromatography with mass spectrometry.

    PubMed

    Wang, Yongyi; Xu, Jinzhong; Qu, Haibin

    2013-01-01

    A simple and accurate analytical method was developed for simultaneous quantification of three steroidal saponins in the roots of Ophiopogon japonicus via high-performance liquid chromatography (HPLC) with mass spectrometry (MS) in this study. Separation was performed on a Tigerkin C(18) column and detection was performed by mass spectrometry. A mobile phase consisted of 0.02% formic acid in water (v/v) and 0.02% formic acid in acetonitrile (v/v) was used with a flow rate of 0.5 mL min(-1). The quantitative HPLC-MS method was validated for linearity, precision, repeatability, stability, recovery, limits of detection and quantification. This developed method provides good linearity (r >0.9993), intra- and inter-day precisions (RSD <4.18%), repeatability (RSD <5.05%), stability (RSD <2.08%) and recovery (93.82-102.84%) for three steroidal saponins. It could be considered as a suitable quality control method for O. japonicus.

  3. Rapid analysis of the main components of the total glycosides of Ranunculus japonicus by UPLC/Q-TOF-MS.

    PubMed

    Rui, Wen; Chen, Hongyuan; Tan, Yuzhi; Zhong, Yanmei; Feng, Yifan

    2010-05-01

    A rapid method for the analysis of the main components of the total glycosides of Ranunculus japonicus (TGOR) was developed using ultra-performance liquid chromatography with quadrupole-time-of-flight mass spectrometry (UPLC/Q-TOF-MS). The separation analysis was performed on a Waters Acquity UPLC system and the accurate mass of molecules and their fragment ions were determined by Q-TOF MS. Twenty compounds, including lactone glycosides, flavonoid glycosides and flavonoid aglycones, were identified and tentatively deduced on the basis of their elemental compositions, MS/MS data and relevant literature. The results demonstrated that lactone glycosides and flavonoids were the main constituents of TGOR. Furthermore, an effective and rapid pattern was established allowing for the comprehensive and systematic characterization of the complex samples.

  4. Regulation of nuclear envelope dynamics via APC/C is necessary for the progression of semi-open mitosis in Schizosaccharomyces japonicus.

    PubMed

    Aoki, Keita; Shiwa, Yuh; Takada, Hiraku; Yoshikawa, Hirofumi; Niki, Hironori

    2013-09-01

    Three types of mitosis, which are open, closed or semi-open mitosis, function in eukaryotic cells, respectively. The open mitosis involves breakage of the nuclear envelope before nuclear division, whereas the closed mitosis proceeds with an intact nuclear envelope. To understand the mechanism and significance of three types of mitotic division in eukaryotes, we investigated the process of semi-open mitosis, in which the nuclear envelope is only partially broken, in the fission yeast Schizosaccharomyces japonicus. In anaphase-promoting complex/cyclosome (APC/C) mutants of Sz. japonicus, the nuclear envelope remained relatively intact during anaphase, resulting in impaired semi-open mitosis. As a suppressor of apc2 mutant, a mutation of Oar2, which was a 3-oxoacyl-[acyl carrier protein] reductase, was obtained. The level of the Oar2, which had two destruction-box motifs recognized by APC/C, was increased in APC/C mutants. Furthermore, the defective semi-open mitosis observed in an apc2 mutant was restored by mutated oar2+. Based on these findings, we propose that APC/C regulates the dynamics of the nuclear envelope through degradation of Oar2 dependent on APC/C during the metaphase-to-anaphase transition of semi-open mitosis in Sz. japonicus. © 2013 The Authors Genes to Cells © 2013 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

  5. Differential expression of acid invertase genes in roots of metallicolous and non-metallicolous populations of Rumex japonicus under copper stress.

    PubMed

    Huang, Wu-Xing; Cao, Yi; Huang, Li-Juan; Ren, Cong; Xiong, Zhi-Ting

    2011-09-01

    Recent evidence indicates that during copper (Cu) stress, the roots of metallicolous plants manifest a higher activity of acid invertase enzymes, which are rate-limiting in sucrose catabolism, than non-metallicolous plants. To test whether the higher activity of acid invertases is the result of higher expression of acid invertase genes, we isolated partial cDNAs for acid invertases from two populations of Rumex japonicus (from metalliferous and non-metalliferous soils), determined their nucleotide sequences, and designed primers to measure changes in transcript levels during Cu stress. We also determined the growth of the plants' roots, Cu accumulation, and acid invertase activities. The seedlings of R. japonicus were exposed to control or 20 μM Cu(2+) for 6d under hydroponic conditions. The transcript level and enzyme activity of acid invertases in metallicolous plants were both significantly higher than those in non-metallicolous plants when treated with 20 μM. Under Cu stress, the root length and root biomass of metallicolous plants were also significantly higher than those of non-metallicolous plants. The results suggested that under Cu stress, the expression of acid invertase genes in metallicolous plants of R. japonicus differed from those in non-metallicolous plants. Furthermore, the higher acid invertase activities of metallicolous plants under Cu stress could be due in part to elevated expression of acid invertase genes. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Characterization and application of monoclonal antibodies against Shewanella marisflavi, a novel pathogen of Apostichopus japonicus

    USDA-ARS?s Scientific Manuscript database

    Shewanella marisflavi strain AP629 was certified as a novel pathogen of the sea cucumber Apostichopus japonicus. In this study, four monoclonal antibodies (MAbs) (3C1, 3D9, 2F2, 2A8) against strain AP629 were developed by immunizing Balb/C mice. 3C1 and 3D9 recognized S. marisflavi only, showing no ...

  7. Production of the Functional Trisaccharide 1-Kestose from Cane Sugar Molasses Using Aspergillus japonicus β-Fructofuranosidase.

    PubMed

    Hirabayashi, Katsuki; Kondo, Nobuhiro; Toyota, Hiroshi; Hayashi, Sachio

    2017-01-01

    We report the production of the functional trisaccharide 1-kestose, O-β-D-fructofuranosyl-(2→1)-β-D-fructofuranosyl α-D-glucopyranoside, by β-fructofuranosidase from Aspergillus japonicus using sugar cane molasses as substrate. Sucrose in cane sugar molasses acted as a fructosyl donor and acceptor for the enzyme. The tetrasaccharide nystose, O-β-D-fructofuranosyl-(2→1)-β-D-fructofuranosyl-(2→1)-β-D-fructofuranosyl α-D-glucopyranoside, was produced from 1-kestose. Cane sugar molasses mixed with water provided a better substrate solution for β-fructofuranosidase compared to undiluted molasses due to the high concentration of product inhibitors such as glucose and fructose in molasses. The maximum concentration of 1-kestose obtained was 84.9 mg/ml and the maximum production efficiency was 32.3% after 24 h reaction at 40 °C. The maximum efficiency of combined fructo-oligosaccharide (1-kestose and nystose) production was 40.6%. 1-Kestose was therefore produced via a fructosyl-transfer reaction catalyzed by β-fructofuranosidase from A. japonicus.

  8. Deciphering of the Dual oxidase (Nox family) gene from kuruma shrimp, Marsupenaeus japonicus: full-length cDNA cloning and characterization.

    PubMed

    Inada, Mari; Kihara, Keisuke; Kono, Tomoya; Sudhakaran, Raja; Mekata, Tohru; Sakai, Masahiro; Yoshida, Terutoyo; Itami, Toshiaki

    2013-02-01

    In many physiological processes, including the innate immune system, free radicals such as nitric oxide (NO) and reactive oxygen species (ROS) play significant roles. In humans, 2 homologs of Dual oxidases (Duox) generate hydrogen peroxide (H(2)O(2)), which is a type of ROS. Here, we report the identification and characterization of a Duox from kuruma shrimp, Marsupenaeus japonicus. The full-length cDNA sequence of the M. japonicus Dual oxidase (MjDuox) gene contains 4695 bp and was generated using reverse transcriptase-polymerase chain reaction (RT-PCR) and random amplification of cDNA ends (RACE). The open reading frame of MjDuox encodes a protein of 1498 amino acids with an estimated mass of 173 kDa. In a homology analysis using amino acid sequences, MjDuox exhibited 69.3% sequence homology with the Duox of the red flour beetle, Tribolium castaneum. A transcriptional analysis revealed that the MjDuox mRNA is highly expressed in the gills of healthy kuruma shrimp. In the gills, MjDuox expression reached its peak 60 h after injection with WSSV and decreased to its normal level at 72 h. In gene knockdown experiments of free radical-generating enzymes, the survival rates decreased during the early stages of a white spot syndrome virus (WSSV) infection following the knockdown of the NADPH oxidase (MjNox) or MjDuox genes. In the present study, the identification, cloning and gene knockdown of the kuruma shrimp MjDuox are reported. Duoxes have been identified in vertebrates and some insects; however, few reports have investigated Duoxes in crustaceans. This study is the first to identify and clone a Dual oxidase from a crustacean species. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Construction of cDNA library from intestine, mesentery and coelomocyte of Apostichopus japonicus Selenka infected with Vibrio sp. and a preliminary analysis of immunity-related genes

    NASA Astrophysics Data System (ADS)

    Liu, Hongzhan; Zheng, Fengrong; Sun, Xiuqin; Cai, Yimei

    2012-06-01

    The aquaculture of sea cucumber Apostichopus japonicus (Echinodermata, Holothuroidea) has grown rapidly during recent years and has become an important sector of the marine industry in Northern China. However, with the rapid growth of the industry and the use of non-standard culture techniques, epidemic diseases of A. japonicus now pose increasing problems to the industry. To screen the genes with stress response to bacterial infection in sea cucumber at a genome wide level, we constructed a cDNA library from A. japonicus Selenka (Aspidochirotida: Stichopodidae) after infecting them with Vibrio sp. for 48 h. Total RNA was extracted from the intestine, mesentery and coelomocyte of infected sea cucumber using Trizol and mRNA was isolated by Oligotex mRNA Kits. The ligated cDNAs were transformed into DH5α, and a library of 3.24×105 clones (3.24×105 cfu mL-1) was obtained with the sizes of inserted fragments ranging from 0.8 to 2.5 kb. Sequencing the cDNA clones resulted in a total of 1106 ESTs that passed the quality control. BlastX and BlastN searches have identified 168 (31.5%) ESTs sharing significant homology with known sequences in NCBI protein or nucleotide databases. Among a panel of 25 putative immunity-related genes, serum lectin isoform, complement component 3, complement component 3-like genes were further studied by real-time PCR and they all increased more than 5 fold in response to Vibrio sp. challenge. Our library provides a valuable molecular tool for future study of invertebrate immunity against bacterial infection and our gene expression data indicates the importance of the immune system in the evolution and development of sea cucumber.

  10. Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps.

    PubMed

    Yamazaki, Yohei; Meirelles, Pedro Milet; Mino, Sayaka; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Thompson, Fabiano L; Sakai, Yuichi; Sawabe, Toko; Sawabe, Tomoo

    2016-02-24

    Gut microbiome shapes various aspects of a host's physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host's growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.

  11. Acute oral toxicity of the ethyl acetate fraction of Orostachys japonicus in mice.

    PubMed

    Kim, Seon-Hee; Ryu, Deok-Seon; Lee, Hyeong-Seon; Shin, Hye-Ryoung; Kwon, Ji-Hye; Lee, Dong-Seok

    2014-10-01

    Orostachys japonicus (Crassulaceae) is referred to as Wa-song in Korea. It is used as an anti-inflammatory, antifebrile, hemostatic, and anti cancer agent, and as an antidote. The purpose of this study was to evaluate the acute toxicity of the ethyl acetate fraction of O. japonicus (OJE) after the oral administration in Balb/c mice of both sexes. Mice were oral administered a single doses of 500, 1000, and 2000 mg/kg of body weight and were monitored for 14 d. Biochemical parameters [aspartate amino transferase (AST), alanine amino transferase (ALT), alkaline phosphatase (ALP), total protein (TP), globulin (GB), total cholesterol (TC), triglyceride (TG), blood urea nitrogen (BUN), and creatinine (CR)] and histopathological examination of liver were performed. No animals died and no toxic changes were observed in clinical signs, body weight, and organ weight. The LD50 of orally administered OJE was higher than 2000 mg/kg/d in both sexes. No toxicological findings were found in biochemical parameters. In histophathological examination, neutrophilic infiltration was observed at a dose of 2000 mg/kg group in both sexes. These finding suggest that oral administration of OJE does not produce acute toxicity. Therefore, these results could provide satisfactory preclinical evidence of safety to launch clinical trials on standardized formulation of OJE to be a biohealth product.

  12. Molecular characterization, expression analysis of the myostatin gene and its association with growth traits in sea cucumber (Apostichopus japonicus).

    PubMed

    Li, Shilei; Zhou, Zunchun; Dong, Ying; Sun, Hongjuan; Gao, Shan; Chen, Zhong; Yang, Aifu; Liu, Weidong; Wang, Qingzhi

    2016-11-01

    Myostatin (MSTN), also referred to as growth and differentiation factor-8 (GDF-8), is a member of the transforming growth factor-β superfamily (TGF-β) and an important negative regulator for skeletal muscle development and growth in vertebrates. However, its function is not clear in invertebrates. In this study, we cloned and analyzed the MSTN gene (Aj-MSTN) from sea cucumber (Apostichopus japonicus). The full-length cDNA sequence of Aj-MSTN gene was composed of 2912bp, which contained a 5' UTR of 487bp, an ORF of 1356bp encoding 452 amino acids and a 3' UTR of 1069bp. The structure of Aj-MSTN included a putative signal peptide, a TGF-β propeptide domain and a conserved TGF-β domain. Phylogenetic analysis showed that the Aj-MSTN gene was clustered in the same subgroup with the MSTN-like gene found in Strongylocentrotus purpuratus. Quantitative real-time PCR detection results indicated that the Aj-MSTN gene expressed widely in adult tissues and the highest expression level was observed in the body wall. At different developmental stages, the expression levels were increased significantly at early auricularia and doliolaria stages, and reached the peak at juvenile stage. Six SNPs were identified in 5' flanking region and exons of the Aj-MSTN gene. Association analysis showed that SNP-1, SNP-2 and SNP-4 had significant effects on dry body weight. The results suggested that Aj-MSTN gene could be used as a candidate gene for the selective breeding of A. japonicus. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Identification and characterization of 43 microsatellite markers derived from expressed sequence tags of the sea cucumber ( Apostichopus japonicus)

    NASA Astrophysics Data System (ADS)

    Jiang, Qun; Li, Qi; Yu, Hong; Kong, Lingfeng

    2011-06-01

    The sea cucumber Apostichopus japonicus is a commercially and ecologically important species in China. A total of 3056 potential unigenes were generated after assembling 7597 A. japonicus expressed sequence tags (ESTs) downloaded from Gen-Bank. Two hundred and fifty microsatellite-containing ESTs (8.18%) and 299 simple sequence repeats (SSRs) were detected. The average density of SSRs was 1 per 7.403 kb of EST after redundancy elimination. Di-nucleotide repeat motifs appeared to be the most abundant type with a percentage of 69.90%. Of the 126 primer pairs designed, 90 amplified the expected products and 43 showed polymorphism in 30 individuals tested. The number of alleles per locus ranged from 2 to 26 with an average of 7.0 alleles, and the observed and expected heterozygosities varied from 0.067 to 1.000 and from 0.066 to 0.959, respectively. These new EST-derived microsatellite markers would provide sufficient polymorphism for population genetic studies and genome mapping of this sea cucumber species.

  14. Phoretic mites and their hyperphoretic fungi associated with flying Ips typographus japonicus Niijima (Col., Scolytidae) in Japan

    Treesearch

    J.C. Moser; T.J. Perry; K. Furuta

    1997-01-01

    Flying Ips typographus japonicus from Hokkaido (Japan) carried 12 species of phoretic mites, three of which were not previously recorded in Europe. The mite biologies were diverse, including specialists feeding on microorganisms, beetle eggs, and nematodes which were common under beetle elytra. Hyperphoretic on these mites were seven distinct species of fungal spores...

  15. WAFs lead molting retardation of naupliar stages with down-regulated expression profiles of chitin metabolic pathway and related genes in the copepod Tigriopus japonicus.

    PubMed

    Hwang, Dae-Sik; Lee, Min-Chul; Kyung, Do-Hyun; Kim, Hui-Su; Han, Jeonghoon; Kim, Il-Chan; Puthumana, Jayesh; Lee, Jae-Seong

    2017-03-01

    Oil pollution is considered being disastrous to marine organisms and ecosystems. As molting is critical in the developmental process of arthropods in general and copepods, in particular, the impact will be adverse if the target of spilled oil is on molting. Thus, we investigated the harmful effects of water accommodated fractions (WAFs) of crude oil with an emphasis on inhibition of chitin metabolic pathways related genes and developmental retardation in the copepod Tigriopus japonicus. Also, we analysed the ontology and domain of chitin metabolic pathway genes and mRNA expression patterns of developmental stage-specific genes. Further, the developmental retardation followed by transcriptional modulations in nuclear receptor genes (NR) and chitin metabolic pathway-related genes were observed in the WAFs-exposed T. japonicus. As a result, the developmental time was found significantly (P<0.05) delayed in response to 40% WAFs in comparison with that of control. Moreover, the NR gene, HR3 and chitinases (CHT9 and CHT10) were up-regulated in N4-5 stages, while chitin synthase genes (CHS-1, CHS-2-1, and CHS-2-2) down-regulated in response to WAFs. In brief, a high concentration of WAFs repressed nuclear receptor genes but elicited activation of some of the transcription factors at low concentration of WAFs, resulting in suppression of chitin synthesis. Thus, we suggest that WAF can lead molting retardation of naupliar stages in T. japonicus through down-regulations of chitin metabolism. These findings will provide a better understanding of the mode of action of chitin biosynthesis associated with molting mechanism in WAF-exposed T. japonicus. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. DNA methylation levels analysis in four tissues of sea cucumber Apostichopus japonicus based on fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) during aestivation.

    PubMed

    Zhao, Ye; Chen, Muyan; Storey, Kenneth B; Sun, Lina; Yang, Hongsheng

    2015-03-01

    DNA methylation plays an important role in regulating transcriptional change in response to environmental stimuli. In the present study, DNA methylation levels of tissues of the sea cucumber Apostichopus japonicus were analyzed by the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) technique over three stages of the aestivation cycle. Overall, a total of 26,963 fragments were amplified including 9112 methylated fragments among four sea cucumber tissues using 18 pairs of selective primers. Results indicated an average DNA methylation level of 33.79% for A. japonicus. The incidence of DNA methylation was different across tissue types in the non-aestivation stage: intestine (30.16%), respiratory tree (27.61%), muscle (27.94%) and body wall (56.25%). Our results show that hypermethylation accompanied deep-aestivation in A. japonicus, which suggests that DNA methylation may have an important role in regulating global transcriptional suppression during aestivation. Further analysis indicated that the main DNA modification sites were focused on intestine and respiratory tree tissues and that full-methylation but not hemi-methylation levels exhibited significant increases in the deep-aestivation stage. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads.

    PubMed

    Yano, Koji; Aoki, Seishiro; Liu, Meng; Umehara, Yosuke; Suganuma, Norio; Iwasaki, Wataru; Sato, Shusei; Soyano, Takashi; Kouchi, Hiroshi; Kawaguchi, Masayoshi

    2017-04-01

    Legume-rhizobium symbiosis is achieved by two major events evolutionarily acquired: root hair infection and organogenesis. Infection thread (IT) development is a distinct element for rhizobial infection. Through ITs, rhizobia are efficiently transported from infection foci on root hairs to dividing meristematic cortical cells. To unveil this process, we performed genetic screening using Lotus japonicus MG-20 and isolated symbiotic mutant lines affecting nodulation, root hair morphology, and IT development. Map-based cloning identified an AP2/ERF transcription factor gene orthologous to Medicago truncatula ERN1. LjERN1 was activated in response to rhizobial infection and depended on CYCLOPS and NSP2. Legumes conserve an ERN1 homolog, ERN2, that functions redundantly with ERN1 in M. truncatula. Phylogenetic analysis showed that the lineages of ERN1 and ERN2 genes originated from a gene duplication event in the common ancestor of legume plants. However, genomic analysis suggested the lack of ERN2 gene in the L. japonicus genome, consistent with Ljern1 mutants exhibited a root hair phenotype that is observed in ern1/ern2 double mutants in M. truncatula. Molecular evolutionary analysis suggested that the nonsynonymous/synonymous rate ratios of legume ERN1 genes was almost identical to that of non-legume plants, whereas the ERN2 genes experienced a relaxed selective constraint. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  18. Effect of potential probiotic Rhodotorula benthica D30 on the growth performance, digestive enzyme activity and immunity in juvenile sea cucumber Apostichopus japonicus.

    PubMed

    Wang, Ji-hui; Zhao, Liu-qun; Liu, Jin-feng; Wang, Han; Xiao, Shan

    2015-04-01

    The effects of dietary addition of yeast Rhodotorula benthica (R. benthica) D30 which isolated from local sea mud at levels of 0 (control), 10(5), 10(6) and 10(7) CFU/g feed on the growth performance, digestive enzyme activity, immunity and disease resistance of juvenile sea cucumber Apostichopus japonicus were investigated. It was shown that dietary addition of R. benthica D30 significantly increased the growth rates of sea cucumbers (p < 0.05). The amylase activity, cellulase activity and alginase activity were increased for the animals from three probiotics treated groups. And with the supplemented concentration increased, the values of those digestive enzyme activities increased as well. Dietary addition of R. benthica D30 at the level of 10(7) CFU significantly increased the lysozyme, phagocytic and total nitric oxide synthase activity of A. japonicus (p < 0.05). While, the highest values of the phenoloxidase and alkaline phosphatase activity were found in sea cucumbers fed with R. benthica D30 at the level of 10(6) CFU. Whereas adding R. benthica D30 to diet had no significant effects on the total coelomocyte counts and acid phosphatase activity of A. japonicus (p > 0.05). It was observed that adding R. benthica D30 could significantly decrease the cumulative mortality of sea cucumbers. The present study demonstrated that dietary addition of R. benthica D30 could increase growth performance and some digestive enzyme activities, improve immunity and disease resistance of A. japonicus. And the medium (10(6) CFU) and high (10(7) CFU) additional levels showed better effects. It suggests that yeast R. benthica D30 could be a good probiotic for aquaculture. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. UV-B radiation-induced oxidative stress and p38 signaling pathway involvement in the benthic copepod Tigriopus japonicus.

    PubMed

    Kim, Bo-Mi; Rhee, Jae-Sung; Lee, Kyun-Woo; Kim, Min-Jung; Shin, Kyung-Hoon; Lee, Su-Jae; Lee, Young-Mi; Lee, Jae-Seong

    2015-01-01

    Ultraviolet B (UV-B) radiation presents an environmental hazard to aquatic organisms. To understand the molecular responses of the intertidal copepod Tigriopus japonicus to UV-B radiation, we measured the acute toxicity response to 96 h of UV-B radiation, and we also assessed the intracellular reactive oxygen species (ROS) levels, glutathione (GSH) content, and antioxidant enzyme (GST, GR, GPx, and SOD) activities after 24 h of exposure to UV-B with LD50 and half LD50 values. Also, expression patterns of p53 and hsp gene families with phosphorylation of p38 MAPK were investigated in UV-B-exposed copepods. We found that the ROS level, GSH content, and antioxidant enzyme activity levels were increased with the transcriptional upregulation of antioxidant-related genes, indicating that UV-B induces oxidative stress by generating ROS and stimulating antioxidant enzymatic activity as a defense mechanism. Additionally, we found that p53 expression was significantly increased after UV-B irradiation due to increases in the phosphorylation of the stress-responsive p38 MAPK, indicating that UV-B may be responsible for inducing DNA damage in T. japonicus. Of the hsp family genes, transcriptional levels of hsp20, hsp20.7, hsp70, and hsp90 were elevated in response to a low dose of UV-B radiation (9 kJ m(-2)), suggesting that these hsp genes may be involved in cellular protection against UV-B radiation. In this paper, we performed a pathway-oriented mechanistic analysis in response to UV-B radiation, and this analysis provides a better understanding of the effects of UV-B in the intertidal benthic copepod T. japonicus. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. The glutathione peroxidase gene family of Lotus japonicus: characterization of genomic clones, expression analyses and immunolocalization in legumes.

    PubMed

    Ramos, Javier; Matamoros, Manuel A; Naya, Loreto; James, Euan K; Rouhier, Nicolas; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

    2009-01-01

    Despite the multiple roles played by antioxidants in rhizobia-legume symbioses, little is known about glutathione peroxidases (GPXs) in legumes. Here the characterization of six GPX genes of Lotus japonicus is reported. Expression of GPX genes was analysed by quantitative reverse transcription-polymerase chain reaction in L. japonicus and Lotus corniculatus plants exposed to various treatments known to generate reactive oxygen and/or nitrogen species. LjGPX1 and LjGPX3 were the most abundantly expressed genes in leaves, roots and nodules. Compared with roots, LjGPX1 and LjGPX6 were highly expressed in leaves and LjGPX3 and LjGPX6 in nodules. In roots, salinity decreased GPX4 expression, aluminium decreased expression of the six genes, and cadmium caused up-regulation of GPX3, GPX4 and GPX5 after 1 h and down-regulation of GPX1, GPX2, GPX4 and GPX6 after 3-24 h. Exposure of roots to sodium nitroprusside (a nitric oxide donor) for 1 h increased the mRNA levels of GPX4 and GPX6 by 3.3- and 30-fold, respectively. Thereafter, the GPX6 mRNA level remained consistently higher than that of the control. Immunogold labelling revealed the presence of GPX proteins in root and nodule amyloplasts and in leaf chloroplasts of L. japonicus and other legumes. Labelling was associated with starch grains. These results underscore the differential regulation of GPX expression in response to cadmium, aluminium and nitric oxide, and strongly support a role for GPX6 and possibly other GPX genes in stress and/or metabolic signalling.

  1. Anti-fatigue activity of sea cucumber peptides prepared from Stichopus japonicus in an endurance swimming rat model.

    PubMed

    Ye, Jing; Shen, Caihong; Huang, Yayan; Zhang, Xueqin; Xiao, Meitian

    2017-10-01

    Sea cucumber (Stichopus japonicus) is a well-known nutritious and luxurious seafood in Asia which has attracted increasing attention because of its nutrition and bioactivities in recent years. In this study, the anti-fatigue activity of sea cucumber peptides (SCP) prepared from S. japonicus was evaluated in a load-induced endurance swimming model. The SCP prepared in this study was mainly made up of low-molecular-weight peptides (<2 kDa). The analysis result of amino acid composition revealed that SCP was rich in glycine, glutamic acid and proline. The endurance capability of rats to fatigue was significantly improved by SCP treatment. Meanwhile, the remarkable alterations of energy metabolic markers, antioxidant enzymes, antioxidant capacity and oxidative stress biomarkers were normalized. Moreover, administration of SCP could modulate alterations of inflammatory cytokines and downregulate the overexpression of TRL4 and NF-κB. SCP has anti-fatigue activity and it exerted its anti-fatigue effect probably through normalizing energy metabolism as well as alleviating oxidative damage and inflammatory responses. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  2. Role of crustacean hyperglycemic hormone (CHH) in the environmental stressor-exposed intertidal copepod Tigriopus japonicus.

    PubMed

    Kim, Bo-Mi; Jeong, Chang-Bum; Han, Jeonghoon; Kim, Il-Chan; Rhee, Jae-Sung; Lee, Jae-Seong

    2013-09-01

    To identify and characterize CHH (TJ-CHH) gene in the copepod Tigriopus japonicus, we analyzed the full-length cDNA sequence, genomic structure, and promoter region. The full-length TJ-CHH cDNA was 716 bp in length, encoding 136 amino acid residues. The deduced amino acid sequences of TJ-CHH showed a high similarity of the CHH mature domain to other crustaceans. Six conserved cysteine residues and five conserved structural motifs in the CHH mature peptide domain were also observed. The genomic structure of the TJ-CHH gene contained three exons and two introns in its open reading frame (ORF), and several transcriptional elements were detected in the promoter region of the TJ-CHH gene. To investigate transcriptional change of TJ-CHH under environmental stress, T. japonicus were exposed to heat treatment, UV-B radiation, heavy metals, and water-accommodated fractions (WAFs) of Iranian crude oil. Upon heat stress, TJ-CHH transcripts were elevated at 30 °C and 35 °C for 96 h in a time-course experiment. UV-B radiation led to a decreased pattern of the TJ-CHH transcript 48 h and more after radiation (12 kJ/m(2)). After exposure of a fixed dose (12 kJ/m(2)) in a time-course experiment, TJ-CHH transcript was down-regulated in time-dependent manner with a lowest value at 12h. However, the TJ-CHH transcript level was increased in response to five heavy metal exposures for 96 h. Also, the level of the TJ-CHH transcript was significantly up-regulated at 20% of WAFs after exposure to WAFs for 48 h and then remarkably reduced in a dose-dependent manner. These findings suggest that the enhanced TJ-CHH transcript level is associated with a cellular stress response of the TJ-CHH gene as shown in decapod crustaceans. This study is also helpful for a better understanding of the detrimental effects of environmental changes on the CHH-triggered copepod metabolism. Copyright © 2013 Elsevier Inc. All rights reserved.

  3. A NIN-LIKE PROTEIN mediates nitrate-induced control of root nodule symbiosis in Lotus japonicus.

    PubMed

    Nishida, Hanna; Tanaka, Sachiko; Handa, Yoshihiro; Ito, Momoyo; Sakamoto, Yuki; Matsunaga, Sachihiro; Betsuyaku, Shigeyuki; Miura, Kenji; Soyano, Takashi; Kawaguchi, Masayoshi; Suzaki, Takuya

    2018-02-05

    Legumes and rhizobia establish symbiosis in root nodules. To balance the gains and costs associated with the symbiosis, plants have developed two strategies for adapting to nitrogen availability in the soil: plants can regulate nodule number and/or stop the development or function of nodules. Although the former is accounted for by autoregulation of nodulation, a form of systemic long-range signaling, the latter strategy remains largely enigmatic. Here, we show that the Lotus japonicus NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1) gene encoding a NIN-LIKE PROTEIN transcription factor acts as a key regulator in the nitrate-induced pleiotropic control of root nodule symbiosis. NRSYM1 accumulates in the nucleus in response to nitrate and directly regulates the production of CLE-RS2, a root-derived mobile peptide that acts as a negative regulator of nodule number. Our data provide the genetic basis for how plants respond to the nitrogen environment and control symbiosis to achieve proper plant growth.

  4. Detecting points as developmental delay based on the life-history development and urosome deformity of the harpacticoid copepod, Tigriopus japonicus sensu lato, following exposure to benzo(a)pyrene.

    PubMed

    Bang, Hyun Woo; Lee, Wonchoel; Kwak, Inn-Sil

    2009-09-01

    To identify ecotoxicological responses to an endocrine disrupter, benzo(a)pyrene, we examined the life-history of the harpacticoid copepod, Tigriopus japonicus sensu lato. Based on the life-history of copepods, survival rate of nauplii (NSR) and copepodites (CSR), copepodite emergence day (CED) and adult male emergence day (AMED), sex ratio (MER), brooding success rate (BSR), and first brooding day of adult females (FBD) were measured. Significant differences were observed in the survival and development of nauplii (NSR and CED) and sex ratio (MER) of exposed and non-exposed copepods. Moreover, high concentration of BaP can be lethal to copepodite and exhibited a delay of growth. In this study, the CED and AMED among ecotoxicological response based on life-history developments were delayed and the body characteristics decreased in response to exposure to benzo(a)pyrene. The dwarfism and urosome deformity of the T. japonicus s.l. was exhibited in response to chemical exposure. Specifically, the body characteristics and biomass of dwarf copepods that had been exposed to benzo(a)pyrene were 30% and 50% lower than the control group, respectively. The incidence of abnormal urosomes was divided into two types. The first deformity type was signs of shrinkage in the middle of the urosome or the entire urosome was narrower than those of the control organisms. In the second type, the anal somite and the distal side of the urosome had abnormally swelled. Taken together, the nauplii and copepodid development of T. japonicus s.l. can be used as a useful biomaker for detecting developmental delay based on their entire life-history. In addition, the urosome deformity was used a good potential monitoring tool invading various chemicals and environmental contamination into water system.

  5. Discovery of novel antimicrobial peptides: A transcriptomic study of the sea anemone Cnidopus japonicus.

    PubMed

    Grafskaia, Ekaterina N; Polina, Nadezhda F; Babenko, Vladislav V; Kharlampieva, Daria D; Bobrovsky, Pavel A; Manuvera, Valentin A; Farafonova, Tatyana E; Anikanov, Nikolay A; Lazarev, Vassili N

    2018-04-01

    As essential conservative component of the innate immune systems of living organisms, antimicrobial peptides (AMPs) could complement pharmaceuticals that increasingly fail to combat various pathogens exhibiting increased resistance to microbial antibiotics. Among the properties of AMPs that suggest their potential as therapeutic agents, diverse peptides in the venoms of various predators demonstrate antimicrobial activity and kill a wide range of microorganisms. To identify potent AMPs, the study reported here involved a transcriptomic profiling of the tentacle secretion of the sea anemone Cnidopus japonicus. An in silico search algorithm designed to discover toxin-like proteins containing AMPs was developed based on the evaluation of the properties and structural peculiarities of amino acid sequences. The algorithm revealed new proteins of the anemone containing antimicrobial candidate sequences, and 10 AMPs verified using high-throughput proteomics were synthesized. The antimicrobial activity of the candidate molecules was experimentally estimated against Gram-positive and -negative bacteria. Ultimately, three peptides exhibited antimicrobial activity against bacterial strains, which suggests that the method can be applied to reveal new AMPs in the venoms of other predators as well.

  6. High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.

    PubMed

    Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie

    2016-06-01

    The Kuruma prawn, Marsupenaeus japonicus, is one of the most promising marine invertebrates in the industry in Asia, Europe and Australia. However, the increasing global temperatures result in considerable economic losses in M. japonicus farming. In the present study, to select genetically improved animals for the sustainable development of the Kuruma prawn industry, a high-resolution genetic linkage map and quantitative trait locus (QTL) identification were performed using the RAD technology. The maternal map contained 5849 SNP markers and spanned 3127.23 cM, with an average marker interval of 0.535 cM. Instead, the paternal map contained 3927 SNP markers and spanned 3326.19 cM, with an average marker interval of 0.847 cM. The consensus map contained 9289 SNP markers and spanned 3610.90 cM, with an average marker interval of 0.388 cM and coverage of 99.06 % of the genome. The markers were grouped into 41 linkage groups in the maps. Significantly, negative correlation was detected between high-temperature tolerance (UTT) and body weight (BW). The QTL mapping revealed 129 significant QTL loci for UTT and four significant QTL loci for BW at the genome-wide significance threshold. Among these QTLs, 129 overlapped with linked SNPs, and the remaining four were located in regions between contiguous SNPs. They explained the total phenotypic variance ranging from 8.9 to 12.4 %. Because of a significantly negative correlation between growth and high-temperature tolerance, we demonstrate that this high-resolution linkage map and QTLs would be useful for further marker-assisted selection in the genetic improvement of M. japonicus.

  7. Bioenergetic trade-offs in the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea) in response to CO2-driven ocean acidification.

    PubMed

    Yuan, Xiutang; Shao, Senlin; Yang, Xiaolong; Yang, Dazuo; Xu, Qinzeng; Zong, Humin; Liu, Shilin

    2016-05-01

    Ocean acidification (OA) caused by excessive CO2 is a potential ecological threat to marine organisms. The impacts of OA on echinoderms are well-documented, but there has been a strong bias towards sea urchins, and limited information is available on sea cucumbers. This work examined the effect of medium-term (60 days) exposure to three pH levels (pH 8.06, 7.72, and 7.41, covering present and future pH variability) on the bioenergetic responses of the sea cucumber, Apostichopus japonicus, an ecologically and economically important holothurian in Asian coasts. Results showed that the measured specific growth rate linearly decreased with decreased pH, leading to a 0.42 %·day(-1) decrease at pH 7.41 compared with that at pH 8.06. The impacts of pH on physiological energetics were variable: measured energy consumption and defecation rates linearly decreased with decreased pH, whereas maintenance energy in calculated respiration and excretion were not significantly affected. No shift in energy allocation pattern was observed in A. japonicus upon exposure to pH 7.72 compared with pH 8.06. However, a significant shift in energy budget occurred upon exposure to pH 7.41, leading to decreased energy intake and increased percentage of energy that was lost in feces, thereby resulting in a significantly lowered allocation into somatic growth. These findings indicate that adult A. japonicus is resilient to the OA scenario at the end of the twenty-first century, but further acidification may negatively influence the grazing capability and growth, thereby influencing its ecological functioning as an "ecosystem engineer" and potentially harming its culture output.

  8. Production, optimisation and characterisation of angiotensin converting enzyme inhibitory peptides from sea cucumber (Stichopus japonicus) gonad.

    PubMed

    Zhong, Chan; Sun, Le-Chang; Yan, Long-Jie; Lin, Yi-Chen; Liu, Guang-Ming; Cao, Min-Jie

    2018-01-24

    In this study, production of bioactive peptides with angiotensin converting enzyme (ACE) inhibitory activity from sea cucumber (Stichopus japonicus) gonad using commercial protamex was optimised by response surface methodology (RSM). As a result, the optimal condition to achieve the highest ACE inhibitory activity in sea cucumber gonad hydrolysate (SCGH) was hydrolysis for 1.95 h and E/S of 0.75%. For further characterisation, three individual peptides (EIYR, LF and NAPHMR) were purified and identified. The peptide NAPHMR showed the highest ACE inhibitory activity with IC 50 of 260.22 ± 3.71 μM. NAPHMR was stable against simulated gastrointestinal digestion and revealed no significant cytotoxicity toward Caco-2 cells. Molecular docking study suggested that Arg, His and Asn residues in NAPHMR interact with the S2 pocket or Zn 2+ binding motifs of ACE via hydrogen or π-bonds, potentially contributing to ACE inhibitory effect. Sea cucumber gonad is thus a potential resource to produce ACE inhibitory peptides for preparation of functional foods.

  9. Two MicroRNAs Linked to Nodule Infection and Nitrogen-Fixing Ability in the Legume Lotus japonicus1[W

    PubMed Central

    De Luis, Ana; Markmann, Katharina; Cognat, Valérie; Holt, Dennis B.; Charpentier, Myriam; Parniske, Martin; Stougaard, Jens; Voinnet, Olivier

    2012-01-01

    Legumes overcome nitrogen shortage by developing root nodules in which symbiotic bacteria fix atmospheric nitrogen in exchange for host-derived carbohydrates and mineral nutrients. Nodule development involves the distinct processes of nodule organogenesis, bacterial infection, and the onset of nitrogen fixation. These entail profound, dynamic gene expression changes, notably contributed to by microRNAs (miRNAs). Here, we used deep-sequencing, candidate-based expression studies and a selection of Lotus japonicus mutants uncoupling different symbiosis stages to identify miRNAs involved in symbiotic nitrogen fixation. Induction of a noncanonical miR171 isoform, which targets the key nodulation transcription factor Nodulation Signaling Pathway2, correlates with bacterial infection in nodules. A second candidate, miR397, is systemically induced in the presence of active, nitrogen-fixing nodules but not in that of noninfected or inactive nodule organs. It is involved in nitrogen fixation-related copper homeostasis and targets a member of the laccase copper protein family. These findings thus identify two miRNAs specifically responding to symbiotic infection and nodule function in legumes. PMID:23071252

  10. Structural and biochemical changes in dermis of sea cucumber (Stichopus japonicus) during autolysis in response to cutting the body wall.

    PubMed

    Liu, Yu-Xin; Zhou, Da-Yong; Liu, Zi-Qiang; Lu, Ting; Song, Liang; Li, Dong-Mei; Dong, Xiu-Ping; Qi, Hang; Zhu, Bei-Wei; Shahidi, Fereidoon

    2018-02-01

    The autolysis of sea cucumber body wall is caused by endogenous proteolysis of its structural elements. However, changes in collagen fibrils, collagen fibres and microfibrils, the major structural elements in sea cucumber body wall during autolysis are less clear. Autolysis of sea cucumber (S. japonicus) was induced by cutting the body wall, and the structural and biochemical changes in its dermis were investigated using electron microscopy, differential scanning calorimetry, infrared spectroscopy, electrophoresis, and chemical analysis. During autolysis, both collagen fibres and microfibrils gradually degraded. In contrast, damage to microfibrils was more pronounced. Upon massive autolysis, collagen fibres disaggregated into collagen fibril bundles and individual fibrils due to the fracture of interfibrillar bridges. Meanwhile, excessive unfolding of collagen fibrils occurred. However, there was only slight damage to collagen monomers. Therefore, structural damage in collagen fibres, collagen fibrils and microfibrils rather than monomeric collagen accounts for autolysis of S. japonicus dermis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Occurrence of Partial Nuclei in Eggs of the Sand Dollar, Clypeaster japonicus.

    PubMed

    Yoneda, M; Nemoto, S I

    1990-10-01

    Females of Clypeaster japonicus bearing eggs with multiple nuclei were occasionally found. DAPI (4'-6-diamidino-2-phenylindole) stained all these nuclei. The summed volume of the two nuclei in binucleate eggs was similar to the nuclear volume in mononucleate eggs from the same batch. On fertilization, two partial nuclei migrated to the center of the egg with a time-course similar to that taken by a single nucleus; they then participated in forming the zygote nucleus, which subsequently formed a single mitotic spindle. These multiple nuclei thus appear to function as genuine nuclei. Possibly they result from the failure of a single nucleus to form during oogenesis.

  12. DNA Damage in Euonymus japonicus Leaf Cells Caused by Roadside Pollution in Beijing

    PubMed Central

    Li, Tianxin; Zhang, Minjie; Gu, Ke; Herman, Uwizeyimana; Crittenden, John; Lu, Zhongming

    2016-01-01

    The inhalable particles from vehicle exhaust can cause DNA damage to exposed organisms. Research on DNA damage is primarily focused on the influence of specific pollutants on certain species or the effect of environmental pollution on human beings. To date, little research has quantitatively studied the relationship between roadside pollution and DNA damage. Based on an investigation of the roadside pollution in Beijing, Euonymus japonicus leaves of differing ages grown in heavily-polluted sections were chosen as biomonitors to detect DNA damage using the comet assay technique. The percentage of DNA in the tail and tail moment was chosen as the analysis index based on SPSS data analysis. The roadside samples showed significantly higher levels of DNA damage than non-roadside samples, which increased in older leaves, and the DNA damage to Euonymus japonicus leaf cells was positively correlated with haze-aggravated roadside pollution. The correlation between damage and the Air Quality Index (AQI) are 0.921 (one-year-old leaves), 0.894 (two-year-old leaves), and 0.878 (three-year-old leaves). Over time, the connection between DNA damage and AQI weakened, with the sensitivity coefficient for δyear 1 being larger than δyear 2 and δyear 3. These findings support the suitability and sensitivity of the comet assay for surveying plants for an estimation of DNA damage induced by environmental genotoxic agents. This study might be applied as a preliminary quantitative method for Chinese urban air pollution damage assessment caused by environmental stress. PMID:27455298

  13. Dianthosaponins A-F, triterpene saponins, flavonoid glycoside, aromatic amide glucoside and γ-pyrone glucoside from Dianthus japonicus.

    PubMed

    Nakano, Takahiro; Sugimoto, Sachiko; Matsunami, Katsuyoshi; Otsuka, Hideaki

    2011-01-01

    From aerial parts of Dianthus japonicus, six new and seven known oleanane-type triterpene saponins were isolated. The structures of the new saponins, named dianthosaponins A-F, were elucidated by means of high resolution mass spectrometry, and extensive inspection of one- and two-dimensional NMR spectroscopic data. A new C-glycosyl flavone, a glycosidic derivative of anthranilic acid amide and a maltol glucoside were also isolated.

  14. Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus.

    PubMed

    Sanchez, Diego H; Lippold, Felix; Redestig, Henning; Hannah, Matthew A; Erban, Alexander; Krämer, Ute; Kopka, Joachim; Udvardi, Michael K

    2008-03-01

    The model legume Lotus japonicus was subjected to non-lethal long-term salinity and profiled at the ionomic, transcriptomic and metabolomic levels. Two experimental designs with various stress doses were tested: a gradual step acclimatization and an initial acclimatization approach. Ionomic profiling by inductively coupled plasma/atomic emission spectrometry (ICP-AES) revealed salt stress-induced reductions in potassium, phosphorus, sulphur, zinc and molybdenum. Microarray profiling using the Lotus Genechip allowed the identification of 912 probesets that were differentially expressed under the acclimatization regimes. Gas chromatography/mass spectrometry-based metabolite profiling identified 147 differentially accumulated soluble metabolites, indicating a change in metabolic phenotype upon salt acclimatization. Metabolic changes were characterized by a general increase in the steady-state levels of many amino acids, sugars and polyols, with a concurrent decrease in most organic acids. Transcript and metabolite changes exhibited a stress dose-dependent response within the range of NaCl concentrations used, although threshold and plateau behaviours were also observed. The combined observations suggest a successive and increasingly global requirement for the reprogramming of gene expression and metabolic pathways to maintain ionic and osmotic homeostasis. A simple qualitative model is proposed to explain the systems behaviour of plants during salt acclimatization.

  15. Characterization and expression analysis of a complement component gene in sea cucumber ( Apostichopus japonicus)

    NASA Astrophysics Data System (ADS)

    Chen, Zhong; Zhou, Zunchun; Yang, Aifu; Dong, Ying; Guan, Xiaoyan; Jiang, Bei; Wang, Bai

    2015-12-01

    The complement system plays a crucial role in the innate immune system of animals. It can be activated by distinct yet overlapping classical, alternative and lectin pathways. In the alternative pathway, complement factor B (Bf) serves as the catalytic subunit of complement component 3 (C3) convertase, which plays the central role among three activation pathways. In this study, the Bf gene in sea cucumber ( Apostichopus japonicus), termed AjBf, was obtained by rapid amplification of cDNA ends (RACE). The full-length cDNA of AjBf was 3231 bp in length barring the poly (A) tail. It contained an open reading frame (ORF) of 2742 bp encoding 913 amino acids, a 105 bp 5'-UTR (5'-terminal untranslated region) and a 384 bp 3'-UTR. AjBf was a mosaic protein with six CCP (complement control protein) domains, a VWA (von Willebrand factor A) domain, and a serine protease domain. The deduced molecular weight of AjBf protein was 101 kDa. Quantitative real time PCR (qRT-PCR) analysis indicated that the expression level of AjBf in A. japonicus was obviously higher at larval stage than that at embryonic stage. Expression detection in different tissues showed that AjBf expressed higher in coelomocytes than in other four tissues. In addation, AjBf expression in different tissues was induced significantly after LPS or PolyI:C challenge. These results indicated that AjBf plays an important role in immune responses to pathogen infection.

  16. Dihydroagarofuranoid Sesquiterpenes as Acetylcholinesterase Inhibitors from Celastraceae Plants: Maytenus disticha and Euonymus japonicus.

    PubMed

    Alarcón, Julio; Cespedes, Carlos L; Muñoz, Evelyn; Balbontin, Cristian; Valdes, Francisco; Gutierrez, Margarita; Astudillo, Luis; Seigler, David S

    2015-12-02

    Natural cholinesterase inhibitors have been found in many biological sources. Nine compounds with agarofuran (epoxyeudesmane) skeletons were isolated from seeds and aerial parts of Maytenus disticha and Euonymus japonicus. The identification and structural elucidation of compounds were based on spectroscopic data analyses. All compounds had inhibitory acetylcholinesterase (AChE) activity. These natural compounds, which possessed mixed or uncompetitive mechanisms of inhibitory activity against AChE, may be considered as models for the design and development of new naturally occurring drugs for management strategies for neurodegenerative diseases. This is the first report of these chemical structures for seeds of M. disticha.

  17. The Seeds of Lotus japonicus Lines Transformed with Sense, Antisense, and Sense/Antisense Galactomannan Galactosyltransferase Constructs Have Structurally Altered Galactomannans in Their Endosperm Cell Walls1

    PubMed Central

    Edwards, Mary E.; Choo, Tze-Siang; Dickson, Cathryn A.; Scott, Catherine; Gidley, Michael J.; Reid, J.S. Grant

    2004-01-01

    Galactomannan biosynthesis in legume seed endosperms involves two Golgi membrane-bound glycosyltransferases, mannan synthase and galactomannan galactosyltransferase (GMGT). GMGT specificity is an important factor regulating the distribution and amount of (1→6)-α-galactose (Gal) substitution of the (1→4)-β-linked mannan backbone. The model legume Lotus japonicus is shown now to have endospermic seeds with endosperm cell walls that contain a high-Gal galactomannan (mannose [Man]/Gal = 1.2-1.3). Galactomannan biosynthesis in developing L. japonicus endosperms has been mapped, and a cDNA encoding a functional GMGT has been obtained from L. japonicus endosperms during galactomannan deposition. L. japonicus has been transformed with sense, antisense, and sense/antisense (“hairpin loop”) constructs of the GMGT cDNA. Some of the sense, antisense, and sense/antisense transgenic lines exhibited galactomannans with altered (higher) Man/Gal values in their (T1 generation) seeds, at frequencies that were consistent with posttranscriptional silencing of GMGT. For T1 generation individuals, transgene inheritance was correlated with galactomannan composition and amount in the endosperm. All the azygous individuals had unchanged galactomannans, whereas those that had inherited a GMGT transgene exhibited a range of Man/Gal values, up to about 6 in some lines. For Man/Gal values up to 4, the results were consistent with lowered Gal substitution of a constant amount of mannan backbone. Further lowering of Gal substitution was accompanied by a slight decrease in the amount of mannan backbone. Microsomal membranes prepared from the developing T2 generation endosperms of transgenic lines showed reduced GMGT activity relative to mannan synthase. The results demonstrate structural modification of a plant cell wall polysaccharide by designed regulation of a Golgi-bound glycosyltransferase. PMID:14988472

  18. Genome-wide Analyses of the Structural Gene Families Involved in the Legume-specific 5-Deoxyisoflavonoid Biosynthesis of Lotus japonicus

    PubMed Central

    Shimada, Norimoto; Sato, Shusei; Akashi, Tomoyoshi; Nakamura, Yasukazu; Tabata, Satoshi; Ayabe, Shin-ichi; Aoki, Toshio

    2007-01-01

    Abstract A model legume Lotus japonicus (Regel) K. Larsen is one of the subjects of genome sequencing and functional genomics programs. In the course of targeted approaches to the legume genomics, we analyzed the genes encoding enzymes involved in the biosynthesis of the legume-specific 5-deoxyisoflavonoid of L. japonicus, which produces isoflavan phytoalexins on elicitor treatment. The paralogous biosynthetic genes were assigned as comprehensively as possible by biochemical experiments, similarity searches, comparison of the gene structures, and phylogenetic analyses. Among the 10 biosynthetic genes investigated, six comprise multigene families, and in many cases they form gene clusters in the chromosomes. Semi-quantitative reverse transcriptase–PCR analyses showed coordinate up-regulation of most of the genes during phytoalexin induction and complex accumulation patterns of the transcripts in different organs. Some paralogous genes exhibited similar expression specificities, suggesting their genetic redundancy. The molecular evolution of the biosynthetic genes is discussed. The results presented here provide reliable annotations of the genes and genetic markers for comparative and functional genomics of leguminous plants. PMID:17452423

  19. Analysis of metabolomic profile of fermented Orostachys japonicus A. Berger by capillary electrophoresis time of flight mass spectrometry

    PubMed Central

    Das, Gitishree; Patra, Jayanta Kumar; Lee, Sun-Young; Kim, Changgeon; Park, Jae Gyu

    2017-01-01

    Microbial cell performance in food biotechnological processes has become an important concern for improving human health worldwide. Lactobacillus plantarum, which is widely distributed in nature, is a lactic acid bacterium with many industrial applications for fermented foods or functional foods (e.g., probiotics). In the present study, using capillary electrophoresis time of flight mass spectrometry, the metabolomic profile of dried Orostachys japonicus A. Berger, a perennial medicinal herb with L. plantarum was compared with that of O. japonicus fermented with L. plantarum to elucidate the metabolomic changes induced by the fermentation process. The levels of several metabolites were changed by the fermentation process, indicating their involvement in microbial performance. For example, glycolysis, the pentose phosphate pathway, the TCA cycle, the urea cycle-related metabolism, nucleotide metabolism, and lipid and amino acid metabolism were altered significantly by the fermentation process. Although the fermented metabolites were not tested using in vivo studies to increase human health benefits, our findings provide an insight into the alteration of metabolites induced by fermentation, and indicated that the metabolomic analysis for the process should be accompanied by fermenting strains and conditions. PMID:28704842

  20. Analysis of metabolomic profile of fermented Orostachys japonicus A. Berger by capillary electrophoresis time of flight mass spectrometry.

    PubMed

    Das, Gitishree; Patra, Jayanta Kumar; Lee, Sun-Young; Kim, Changgeon; Park, Jae Gyu; Baek, Kwang-Hyun

    2017-01-01

    Microbial cell performance in food biotechnological processes has become an important concern for improving human health worldwide. Lactobacillus plantarum, which is widely distributed in nature, is a lactic acid bacterium with many industrial applications for fermented foods or functional foods (e.g., probiotics). In the present study, using capillary electrophoresis time of flight mass spectrometry, the metabolomic profile of dried Orostachys japonicus A. Berger, a perennial medicinal herb with L. plantarum was compared with that of O. japonicus fermented with L. plantarum to elucidate the metabolomic changes induced by the fermentation process. The levels of several metabolites were changed by the fermentation process, indicating their involvement in microbial performance. For example, glycolysis, the pentose phosphate pathway, the TCA cycle, the urea cycle-related metabolism, nucleotide metabolism, and lipid and amino acid metabolism were altered significantly by the fermentation process. Although the fermented metabolites were not tested using in vivo studies to increase human health benefits, our findings provide an insight into the alteration of metabolites induced by fermentation, and indicated that the metabolomic analysis for the process should be accompanied by fermenting strains and conditions.

  1. Molecular cloning of hsf1 and hsbp1 cDNAs, and the expression of hsf1, hsbp1 and hsp70 under heat stress in the sea cucumber Apostichopus japonicus.

    PubMed

    Xu, Dongxue; Sun, Lina; Liu, Shilin; Zhang, Libin; Yang, Hongsheng

    2016-08-01

    The heat shock response (HSR) is known for the elevated synthesis of heat shock proteins (HSPs) under heat stress, which is mediated primarily by heat shock factor 1 (HSF1). Heat shock factor binding protein 1 (HSBP1) and feedback control of heat shock protein 70 (HSP70) are major regulators of the activity of HSF1. We obtained full-length cDNA of genes hsf1 and hsbp1 in the sea cucumber Apostichopus japonicus, which are the second available for echinoderm (after Strongylocentrotus purpuratus), and the first available for holothurian. The full-length cDNA of hsf1 was 2208bp, containing a 1326bp open reading frame encoding 441 amino acids. The full-length cDNA of hsbp1 was 2850bp, containing a 225bp open reading frame encoding 74 amino acids. The similarities of A. japonicus HSF1 with other species are low, and much higher similarity identities of A. japonicus HSBP1 were shared. Phylogenetic trees showed that A. japonicus HSF1 and HSBP1 were clustered with sequences from S. purpuratus, and fell into distinct clades with sequences from mollusca, arthropoda and vertebrata. Analysis by real-time PCR showed hsf1 and hsbp1 mRNA was expressed constitutively in all tissues examined. The expression of hsf1, hsbp1 and hsp70 in the intestine at 26°C was time-dependent. The results of this study might provide new insights into the regulation of heat shock response in this species. Copyright © 2016. Published by Elsevier Inc.

  2. Characterization of skin ulceration syndrome associated microRNAs in sea cucumber Apostichopus japonicus by deep sequencing.

    PubMed

    Li, Chenghua; Feng, Weida; Qiu, Lihua; Xia, Changge; Su, Xiurong; Jin, Chunhua; Zhou, Tingting; Zeng, Yuan; Li, Taiwu

    2012-08-01

    MicroRNAs (miRNAs) constitute a family of small RNA species which have been demonstrated to be one of key effectors in mediating host-pathogen interaction. In this study, two haemocytes miRNA libraries were constructed with deep sequenced by illumina Hiseq2000 from healthy (L1) and skin ulceration syndrome Apostichopus japonicus (L2). The high throughput solexa sequencing resulted in 9,579,038 and 7,742,558 clean data from L1 and L2, respectively. Sequences analysis revealed that 40 conserved miRNAs were found in both libraries, in which let-7 and mir-125 were speculated to be clustered together and expressed accordingly. Eighty-six miRNA candidates were also identified by reference genome search and stem-loop structure prediction. Importantly, mir-31 and mir-2008 displayed significant differential expression between the two libraries according to FPKM model, which might be considered as promising targets for elucidating the intrinsic mechanism of skin ulceration syndrome outbreak in the species. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Response to Long-Term NaHCO3-Derived Alkalinity in Model Lotus japonicus Ecotypes Gifu B-129 and Miyakojima MG-20: Transcriptomic Profiling and Physiological Characterization

    PubMed Central

    Rocco, Rubén; Bordenave, Cesar D.; Escaray, Francisco J.; Antonelli, Cristian; Calzadilla, Pablo; Gárriz, Andrés; Serna, Eva; Carrasco, Pedro; Menendez, Ana B.

    2014-01-01

    The current knowledge regarding transcriptomic changes induced by alkalinity on plants is scarce and limited to studies where plants were subjected to the alkaline salt for periods not longer than 48 h, so there is no information available regarding the regulation of genes involved in the generation of a new homeostatic cellular condition after long-term alkaline stress. Lotus japonicus is a model legume broadly used to study many important physiological processes including biotic interactions and biotic and abiotic stresses. In the present study, we characterized phenotipically the response to alkaline stress of the most widely used L. japonicus ecotypes, Gifu B-129 and MG-20, and analyzed global transcriptome of plants subjected to 10 mM NaHCO3 during 21 days, by using the Affymetrix Lotus japonicus GeneChip®. Plant growth assessment, gas exchange parameters, chlorophyll a fluorescence transient (OJIP) analysis and metal accumulation supported the notion that MG-20 plants displayed a higher tolerance level to alkaline stress than Gifu B-129. Overall, 407 and 459 probe sets were regulated in MG-20 and Gifu B-129, respectively. The number of probe sets differentially expressed in roots was higher than that of shoots, regardless the ecotype. Gifu B-129 and MG-20 also differed in their regulation of genes that could play important roles in the generation of a new Fe/Zn homeostatic cellular condition, synthesis of plant compounds involved in stress response, protein-degradation, damage repair and root senescence, as well as in glycolysis, gluconeogenesis and TCA. In addition, there were differences between both ecotypes in the expression patterns of putative transcription factors that could determine distinct arrangements of flavonoid and isoflavonoid compounds. Our results provided a set of selected, differentially expressed genes deserving further investigation and suggested that the L. japonicus ecotypes could constitute a useful model to search for common and

  4. Peroxiredoxins and NADPH-dependent thioredoxin systems in the model legume Lotus japonicus.

    PubMed

    Tovar-Méndez, Alejandro; Matamoros, Manuel A; Bustos-Sanmamed, Pilar; Dietz, Karl-Josef; Cejudo, Francisco Javier; Rouhier, Nicolas; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

    2011-07-01

    Peroxiredoxins (Prxs), thioredoxins (Trxs), and NADPH-thioredoxin reductases (NTRs) constitute central elements of the thiol-disulfide redox regulatory network of plant cells. This study provides a comprehensive survey of this network in the model legume Lotus japonicus. The aims were to identify and characterize these gene families and to assess whether the NTR-Trx systems are operative in nodules. Quantitative reverse transcription-polymerase chain reaction and immunological and proteomic approaches were used for expression profiling. We identified seven Prx, 14 Trx, and three NTR functional genes. The PrxQ1 gene was found to be transcribed in two alternative spliced variants and to be expressed at high levels in leaves, stems, petals, pods, and seeds and at low levels in roots and nodules. The 1CPrx gene showed very high expression in the seed embryos and low expression in vegetative tissues and was induced by nitric oxide and cytokinins. In sharp contrast, cytokinins down-regulated all other Prx genes, except PrxQ1, in roots and nodules, but only 2CPrxA and PrxQ1 in leaves. Gene-specific changes in Prx expression were also observed in response to ethylene, abscisic acid, and auxins. Nodules contain significant mRNA and protein amounts of cytosolic PrxIIB, Trxh1, and NTRA and of plastidic NTRC. Likewise, they express cytosolic Trxh3, Trxh4, Trxh8, and Trxh9, mitochondrial PrxIIF and Trxo, and plastidic Trxm2, Trxm4, and ferredoxin-Trx reductase. These findings reveal a complex regulation of Prxs that is dependent on the isoform, tissue, and signaling molecule and support that redox NTR-Trx systems are functional in the cytosol, mitochondria, and plastids of nodules.

  5. Production of fibrolytic enzymes by Aspergillus japonicus C03 using agro-industrial residues with potential application as additives in animal feed.

    PubMed

    Facchini, Fernanda Dell Antonio; Vici, Ana Claudia; Reis, Victor Ricardo Amin; Jorge, João Atilio; Terenzi, Héctor Francisco; Reis, Ricardo Andrade; Polizeli, Maria de Lourdes Teixeira de Moraes

    2011-03-01

    Solid-state fermentation obtained from different and low-cost carbon sources was evaluated to endocellulases and endoxylanases production by Aspergillus japonicus C03. Regarding the enzymatic production the highest levels were observed at 30 °C, using soy bran added to crushed corncob or wheat bran added to sugarcane bagasse, humidified with salt solutions, and incubated for 3 days (xylanase) or 6 days (cellulase) with 70% relative humidity. Peptone improved the xylanase and cellulase activities in 12 and 29%, respectively. The optimum temperature corresponded to 60 °C and 50-55 °C for xylanase and cellulase, respectively, both having 4.0 as optimum pH. Xylanase was fully stable up to 40 °C, which is close to the rumen temperature. The enzymes were stable in pH 4.0-7.0. Cu++ and Mn++ increased xylanase and cellulase activities by 10 and 64%, respectively. A. japonicus C03 xylanase was greatly stable in goat rumen fluid for 4 h during in vivo and in vitro experiments.

  6. Changes in endogenous plant hormones and 'H-NMR profiles and signals in Styrax japonicus seeds as influenced by warm and cold stratification

    USDA-ARS?s Scientific Manuscript database

    Germination of Styrax japonicus Sieb. et. Zucc. seeds was promoted by warm stratification (WS) at around 20 °C followed by cold stratification (CS) at around 5oC. Biochemical and physiological changes in Styrax seeds during these WS and CS treatments were not investigated. The objective of this wo...

  7. Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

    PubMed Central

    2010-01-01

    Background Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing technologies and genome backgrounds of non-model fish available. The newly developed Solexa/Illumina RNA-seq and Digital gene expression (DGE) are high-throughput sequencing approaches and are powerful tools for genomic studies at the transcriptome level. This study reports the transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus using RNA-seq and DGE in an attempt to gain insights into the immunogenetics of marine fish. Results RNA-seq analysis generated 169,950 non-redundant consensus sequences, among which 48,987 functional transcripts with complete or various length encoding regions were identified. More than 52% of these transcripts are possibly involved in approximately 219 known metabolic or signalling pathways, while 2,673 transcripts were associated with immune-relevant genes. In addition, approximately 8% of the transcripts appeared to be fish-specific genes that have never been described before. DGE analysis revealed that the host transcriptome profile of Vibrio harveyi-challenged L. japonicus is considerably altered, as indicated by the significant up- or down-regulation of 1,224 strong infection-responsive transcripts. Results indicated an overall conservation of the components and transcriptome alterations underlying innate and adaptive immunity in fish and other vertebrate models. Analysis suggested the acquisition of numerous fish-specific immune system components during early vertebrate evolution. Conclusion This study provided a global survey of host defence gene activities against bacterial challenge in a non-model marine fish. Results can contribute to the in-depth study of candidate genes in marine fish immunity, and help improve current understanding of host-pathogen interactions and evolutionary history

  8. Transcriptome Analysis and Discovery of Genes Involved in Immune Pathways from Coelomocytes of Sea Cucumber (Apostichopus japonicus) after Vibrio splendidus Challenge.

    PubMed

    Gao, Qiong; Liao, Meijie; Wang, Yingeng; Li, Bin; Zhang, Zheng; Rong, Xiaojun; Chen, Guiping; Wang, Lan

    2015-07-17

    Vibrio splendidus is identified as one of the major pathogenic factors for the skin ulceration syndrome in sea cucumber (Apostichopus japonicus), which has vastly limited the development of the sea cucumber culture industry. In order to screen the immune genes involving Vibrio splendidus challenge in sea cucumber and explore the molecular mechanism of this process, the related transcriptome and gene expression profiling of resistant and susceptible biotypes of sea cucumber with Vibrio splendidus challenge were collected for analysis. A total of 319,455,942 trimmed reads were obtained, which were assembled into 186,658 contigs. After that, 89,891 representative contigs (without isoform) were clustered. The analysis of the gene expression profiling identified 358 differentially expression genes (DEGs) in the bacterial-resistant group, and 102 DEGs in the bacterial-susceptible group, compared with that in control group. According to the reported references and annotation information from BLAST, GO and KEGG, 30 putative bacterial-resistant genes and 19 putative bacterial-susceptible genes were identified from DEGs. The qRT-PCR results were consistent with the RNA-Seq results. Furthermore, many DGEs were involved in immune signaling related pathways, such as Endocytosis, Lysosome, MAPK, Chemokine and the ERBB signaling pathway.

  9. Identifying Communication Barriers to Learning in Large Group Accounting Instruction.

    ERIC Educational Resources Information Center

    Doran, Martha S.; Golen, Steven

    1998-01-01

    Classroom communication barriers were identified by 291 financial accounting and 372 managerial accounting students. Both groups thought the greatest problems in large group instruction were too much information given in lectures, large class size, and lack of interest in the subject matter. (SK)

  10. Distribution, Innervation, and Cellular Organization of Taste Buds in the Sea Catfish, Plotosus japonicus.

    PubMed

    Nakamura, Tatsufumi; Matsuyama, Naoki; Kirino, Masato; Kasai, Masanori; Kiyohara, Sadao; Ikenaga, Takanori

    2017-01-01

    The gustatory system of the sea catfish Plotosus japonicus, like that of other catfishes, is highly developed. To clarify the details of the morphology of the peripheral gustatory system of Plotosus, we used whole-mount immunohistochemistry to investigate the distribution and innervation of the taste buds within multiple organs including the barbels, oropharyngeal cavity, fins (pectoral, dorsal, and caudal), and trunk. Labeled taste buds could be observed in all the organs examined. The density of the taste buds was higher along the leading edges of the barbels and fins; this likely increases the chance of detecting food. In all the fins, the taste buds were distributed in linear arrays parallel to the fin rays. Labeling of nerve fibers by anti-acetylated tubulin antibody showed that the taste buds within each sensory field are innervated in different ways. In the barbels, large nerve bundles run along the length of the organ, with fascicles branching off to innervate polygonally organized groups of taste buds. In the fins, nerve bundles run along the axis of fin rays to innervate taste buds lying in a line. In each case, small fascicles of fibers branch from large bundles and terminate within the basal portions of the taste buds. Serotonin immunohistochemistry demonstrated that most of the taste buds in all the organs examined contained disk-shaped serotonin-immunopositive cells in their basal region. This indicates a similar organization of the taste buds, in terms of the existence of serotonin-immunopositive basal cells, across the different sensory fields in this species. © 2017 S. Karger AG, Basel.

  11. Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus.

    PubMed

    Zhou, Xiaoxu; Cui, Jun; Liu, Shikai; Kong, Derong; Sun, He; Gu, Chenlei; Wang, Hongdi; Qiu, Xuemei; Chang, Yaqing; Liu, Zhanjiang; Wang, Xiuli

    2016-01-01

    Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such as fibroblast growth factor, transforming growth factor-β, collagen-α2 and Integrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber.

  12. The effects of dietary lead on growth, bioaccumulation and antioxidant capacity in sea cucumber, Apostichopus japonicus.

    PubMed

    Wang, Jing; Ren, Tongjun; Han, Yuzhe; Zhao, Yang; Liao, Mingling; Wang, Fuqiang; Jiang, Zhiqiang

    2015-09-01

    Three different diets amended with lead nitrate [Pb(NO3)2] (100, 500 and 1000mg Pb/kg dry weight) and a Pb-free control diet (1.03mg Pb/kg dry weight) were fed to sea cucumber (Apostichopus japonicus) for 30 days. The patterns of Pb accumulation over time were determined in various tissues (body wall, intestine and respiratory tree), as well as growth performance and antioxidant enzymes activities. Pb accumulation in body wall and intestine increased with time in all dietary Pb treatments. When fed the highest Pb diet, the body wall exhibited the greatest Pb burden (16.37mg Pb/kg tissue wet weight), while Pb content in the intestine (2.68mg Pb/kg tissue wet weight) and the respiratory tree (1.78mg Pb/kg tissue wet weight) were lower than Pb content in the body wall by day 30. The body weight gain (BWG), specific growth rate (SGR) and survival rate (SR) had not been affected by 30 days oral administration of Pb supplemented diet. However, the antioxidant enzymes activities [superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px)] of test groups were lower than control group in body wall and malondialdehyde (MDA) concentration in the body wall was opposite after 30 days in sea cucumbers. In summary, this work reports toxic effects in sea cucumber, A. japonicus, after dietary exposure to Pb. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Myeloid leukemia factor functions in anti-WSSV immune reaction of kuruma shrimp, Marsupenaeus japonicus.

    PubMed

    Feng, Xiao-Wu; Huo, Li-Jie; Sun, Jie-Jie; Xu, Ji-Dong; Niu, Guo-Juan; Wang, Jin-Xing; Shi, Xiu-Zhen

    2017-11-01

    Myeloid leukemia factor (MLF) plays an important role in development, cell cycle, myeloid differentiation, and regulates the RUNX transcription factors. However, the function of MLF in immunity is still unclear. In this study, an MLF was identified and characterized in kuruma shrimp Marsupenaeus japonicus, and named as MjMLF. The full-length cDNA of MjMLF contained 1111 nucleotides, which had an opening reading frame of 816 bp encoding a protein of 272 amino acids with an MLF1-interacting protein domain. MjMLF could be ubiquitously detected in different tissues of shrimp at the transcriptional level. The expression pattern analysis showed that MjMLF could be upregulated in shrimp hemocytes and hepatopancreas after white spot syndrome virus challenge. The RNA interference and protein injection assay showed that MjMLF could inhibit WSSV replication in vivo. Flow cytometry assay showed that MjMLF could induce hemocytes apoptosis which functioned in the shrimp antiviral reaction. All the results suggested that MjMLF played an important role in the antiviral immune reaction of kuruma shrimp. The research indicated that MjMLF might function as a novel regulator to inhibit WSSV replication in shrimp. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Transcriptional profiles of Rel/NF-κB, inhibitor of NF-κB (IκB), and lipopolysaccharide-induced TNF-α factor (LITAF) in the lipopolysaccharide (LPS) and two Vibrio sp.-exposed intertidal copepod, Tigriopus japonicus.

    PubMed

    Kim, Bo-Mi; Jeong, Chang-Bum; Rhee, Jae-Sung; Lee, Jae-Seong

    2014-02-01

    The immune system and the role of immunity-related genes have rarely been studied in copepods, even though copepods have a primitive immune response system and also have a potential in pathogen transport higher trophic levels. In this study, we firstly cloned and characterized three core immune genes such as nuclear factor κB (NF-κB), inhibitor of NF-κB (IκB), and lipopolysaccharide-induced TNF-α factor (LITAF) genes in the intertidal copepod Tigriopus japonicus. Several in silico analyses based on conserved domains, motifs, and phylogenetic relationships were supporting their annotations. To investigate the immune-related role of three genes, we exposed lipopolysaccharide (LPS) and two Vibrio sp. to T. japonicus. After exposure of different concentrations of LPS and two Vibrio sp., transcripts of TJ-IκB and TJ-LITAF genes were significantly elevated during the time course in a dose-dependent manner, while TJ-NF-κB transcripts were not significantly changed during exposure. These findings demonstrated that the copepod T. japonicus has a conserved immunity against infection. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. (-)-Epicatechin derivate from Orostachys japonicus as potential inhibitor of the human butyrylcholinesterase.

    PubMed

    Kim, Jang Hoon; Lee, Sang-Hyun; Lee, Hyun Woo; Sun, Ya Nan; Jang, Won-Hee; Yang, Seo-Young; Jang, Hae-Dong; Kim, Young Ho

    2016-10-01

    Cholinesterase inhibitors block the bioconversion of neurotransmitters by cholinesterase in the nervous system. Epicatechin derivatives (1, 3 and 5), polyphenols (6 and 7) from Orostachys japonicus, and catechin derivatives (2 and 4) from our in-house library were evaluated for their inhibitory activity on cholinesterase. Compound 5 exhibited IC50 values of 58.3±2.4 and 17.8±3.8μg/mL on AChE and BuChE, respectively. Compound 5 inhibited BuChE more strongly than AChE through a competitive behavior. In silico binding positions of 5 in the active site were predicted using Autodock 4.2 and processed in a 10000-ps molecular dynamics simulation to assess the stability of compound 5 binding. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Selection of reference genes for qRT-PCR analysis of gene expression in sea cucumber Apostichopus japonicus during aestivation

    NASA Astrophysics Data System (ADS)

    Zhao, Ye; Chen, Muyan; Wang, Tianming; Sun, Lina; Xu, Dongxue; Yang, Hongsheng

    2014-11-01

    Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a technique that is widely used for gene expression analysis, and its accuracy depends on the expression stability of the internal reference genes used as normalization factors. However, many applications of qRT-PCR used housekeeping genes as internal controls without validation. In this study, the expression stability of eight candidate reference genes in three tissues (intestine, respiratory tree, and muscle) of the sea cucumber Apostichopus japonicus was assessed during normal growth and aestivation using the geNorm, NormFinder, delta CT, and RefFinder algorithms. The results indicate that the reference genes exhibited significantly different expression patterns among the three tissues during aestivation. In general, the β-tubulin (TUBB) gene was relatively stable in the intestine and respiratory tree tissues. The optimal reference gene combination for intestine was 40S ribosomal protein S18 (RPS18), TUBB, and NADH dehydrogenase (NADH); for respiratory tree, it was β-actin (ACTB), TUBB, and succinate dehydrogenase cytochrome B small subunit (SDHC); and for muscle it was α-tubulin (TUBA) and NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 (NDUFA13). These combinations of internal control genes should be considered for use in further studies of gene expression in A. japonicus during aestivation.

  17. Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth.

    PubMed

    Gao, Lei; He, Chongbo; Bao, Xiangbo; Tian, Meilin; Ma, Zhen

    2017-01-01

    The sea cucumber (Apostichopus japonicus) is an economically important aquaculture species in China. However, the serious individual growth variation often caused financial losses to farmers and the genetic mechanisms are poorly understood. In the present study, the extensively analysis at the transcriptome level for individual growth variation in sea cucumber was carried out. A total of 118946 unigenes were assembled from 255861 transcripts, with N50 of 1700. Of all unigenes, about 23% were identified with at least one significant match to known databases. In all four pair of comparison, 1840 genes were found to be expressed differently. Global hypometabolism was found to be occurred in the slow growing population, based on which the hypothesis was raised that growth retardation in individual growth variation of sea cucumber is one type of dormancy which is used to be against to adverse circumstances. Besides, the pathways such as ECM-receptor interaction and focal adhesion were enriched in the maintenance of cell and tissue structure and communication. Further, 76645 SSRs, 765242 SNPs and 146886 ins-dels were detected in the current study providing an extensive set of data for future studies of genetic mapping and selective breeding. In summary, these results will provides deep insight into the molecular basis of individual growth variation in marine invertebrates, and be valuable for understanding the physiological differences of growth process.

  18. The taxonomic status of Japanese threadfin bream Nemipterus japonicus (Bloch, 1791) (Perciformes: Nemipteridae) with a redescription of this species from the south china sea based on morphology and DNA barcodes

    NASA Astrophysics Data System (ADS)

    Ning, Ping; Sha, Zhongli; Hebert, Paul D. N.; Russell, Barry

    2015-02-01

    Because of its importance as a food source, Nemipterus japonicus (Bloch, 1791) (Nemipteridae) or Japanese threadfin bream is the best studied of these taxa, and numerous investigations have examined its fisheries, its biology and biochemistry. Despite such intensive work, the taxonomic status of N. japonicus has never been seriously questioned and it is regarded as a common species, widely distributed throughout the Indo-Western Pacific Ocean. In fact, Bloch's description of the type specimen of N. japonicus has ambiguous collection data and lacks a designation for the type locality, though it is probably Java. In this paper, DNA barcode results based on COI gene support the existence of two geographically separated lineages of the Japanese threadfin bream, both being an Indian Ocean and western Pacific lineage, with 2.7% sequence divergence, and the results indicate a possible existing of some cryptic species. The two lineages also possess a diagnostic difference in their belly color, with specimens in the South China Sea having a silver belly, while those from the Indian Ocean isolate specimen have a yellow coloration. Based upon new collections from the South China Sea, this species from the western Pacific is morphologically redescribed and its details of DNA barcode diversity are shown for the future investigations.

  19. Scanning the Effects of Ethyl Methanesulfonate on the Whole Genome of Lotus japonicus Using Second-Generation Sequencing Analysis

    PubMed Central

    Mohd-Yusoff, Nur Fatihah; Ruperao, Pradeep; Tomoyoshi, Nurain Emylia; Edwards, David; Gresshoff, Peter M.; Biswas, Bandana; Batley, Jacqueline

    2015-01-01

    Genetic structure can be altered by chemical mutagenesis, which is a common method applied in molecular biology and genetics. Second-generation sequencing provides a platform to reveal base alterations occurring in the whole genome due to mutagenesis. A model legume, Lotus japonicus ecotype Miyakojima, was chemically mutated with alkylating ethyl methanesulfonate (EMS) for the scanning of DNA lesions throughout the genome. Using second-generation sequencing, two individually mutated third-generation progeny (M3, named AM and AS) were sequenced and analyzed to identify single nucleotide polymorphisms and reveal the effects of EMS on nucleotide sequences in these mutant genomes. Single-nucleotide polymorphisms were found in every 208 kb (AS) and 202 kb (AM) with a bias mutation of G/C-to-A/T changes at low percentage. Most mutations were intergenic. The mutation spectrum of the genomes was comparable in their individual chromosomes; however, each mutated genome has unique alterations, which are useful to identify causal mutations for their phenotypic changes. The data obtained demonstrate that whole genomic sequencing is applicable as a high-throughput tool to investigate genomic changes due to mutagenesis. The identification of these single-point mutations will facilitate the identification of phenotypically causative mutations in EMS-mutated germplasm. PMID:25660167

  20. Molecular Phylogenetics of Aedes japonicus, a Disease Vector That Recently Invaded Western Europe, North America, and the Hawaiian Islands

    DTIC Science & Technology

    2010-07-01

    the scourge of dengue fever in Central and South America , if not in North America (Gratz 2004, Paupy et al. 2009) , and has become the primary...North America , and the Hawaiian Islands EMILIE C. CAMERON,1 RICHARD C. WILKERSON,2 MOTOYOSHI MOGI,3 ICHIRO MIYAGI,4 TAKAKO TOMA,4 HEUNG-CHUL KIM,5 AND...japonicus The genus Aedes (Diptera: Culicidae) includes the principal vectors of yellow fever, dengue , and aperi- odic lymphatic filariasis (Foster

  1. Molecular cloning and mRNA expression analysis of interleukin-8 gene in Japanese sea perch (Lateolabrax japonicus).

    PubMed

    Qiu, Lihua; Zhang, Hanhua; Yang, Keng; Jiang, Shigui

    2009-05-01

    Interleukin-8 (IL-8), the first known chemokine, is a CXC chemokine, which is cable of attracting neutrophils and inducing them to release lysozomal enzymes, triggering the respiratory burst. In the present study, the cDNA of an IL-8 was cloned from Japanese sea perch Lateolabrax japonicus (designated LjIL-8) by homology cloning and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of LjIL-8 consisted of 803 nucleotides with a canonical polyadenylation signal sequence AATAAA and a poly(A) tail, and an open reading frame (ORF) of 300 bp encoding a polypeptide of 99 amino acid residues with a predicted molecular weight of 6.6 kDa. The high identity of LjIL-8 with IL-8 in other organisms indicated that LjIL-8 should be a new member of the IL-8 family. By fluorescent quantitative real-time PCR, mRNA transcript of LjIL-8 was detectable in all the examined tissues with higher level in spleen and head-kidney. The temporal expression of LjIL-8 mRNA in the spleen was up-regulated by lipopolyssacharide (LPS) stimulation and reached the maximum level at 6 h post-stimulation, and then dropped back to the original level gradually. These results indicated that LjIL-8 was a constitutive and inducible acute-phase protein that perhaps involved in the immune defense of L. japonicus.

  2. Identification and characterization of a new IgE-binding protein in mackerel ( Scomber japonicus) by MALDI-TOF-MS

    NASA Astrophysics Data System (ADS)

    Wang, Bangping; Li, Zhenxing; Zheng, Lina; Liu, Yixuan; Lin, Hong

    2011-03-01

    As fish is one source of the `big eight' food allergens, the prevalence of fish allergy has increased over the past few years. In order to better understand fish allergy, it is necessary to identify fish allergens. Based on the sera from fish-allergenic patients, a 28 kDa protein from local mackerel ( Scomber japonicus), which has not been reported as a fish allergen, was found to be reactive with most of the patients' sera. The 28 kDa protein was analyzed by MALDI-TOF-MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry). Mascot search in NCBI database (Date: 08/07/2010) showed that the top protein matched, i.e. triosephosphate isomerase (TPI) from Xiphophorus maculatus and Poecilia reticulata, had a mowse (molecular weight search) score of 98. In addition, TPI from Epinephelus coioides also matched this mackerel protein with a mowse score of 96. Because TPI is considered as an allergen in other non-fish organisms, such as lychee, wheat, latex, archaeopotamobius ( Archaeopotamobius sibiriensis) and crangon ( Crangon crangon), we consider that it may also be an allergen in mackerel.

  3. Molecular cloning of Kuruma shrimp Marsupenaeus japonicus endonuclease-reverse transcriptase and its positive role in white spot syndrome virus and Vibrio alginolyticus infection.

    PubMed

    Ma, Xiongchao; Sun, Baozhen; Zhu, Fei

    2018-02-01

    This study investigated the function of endonuclease-reverse transcriptase (mjERT) in Marsupenaeus japonicus. The 1129 bp cDNA sequence of mjERT was cloned from M. japonicus using rapid amplification of cDNA ends (RACE) PCR, and RT-qPCR analysis indicated that mjERT was highly expressed in the gills and hepatopancreas of M. japonicus. We also found that white spot syndrome virus (WSSV) or Vibrio alginolyticus challenge could enhance the expression of mjERT. When mjERT was inhibited, immune genes such as toll, p53, hemocyanin and tumor necrosis factor-α (TNF-α) were significantly down-regulated (P < .01) in the hemocytes of shrimp, while myosin was significantly up-regulated (P < .01). We demonstrated that mjERT is very important for the progression of WSSV infection and that the cumulative mortality of WSSV-infected and V. alginolyticus-infected shrimps was significantly increased following mjERT RNA interfere (RNAi). Apoptosis data provided information to suggest that mjERT-dsRNA challenge caused less apoptosis in hemocytes in both the disease-free and viral group. We also revealed that mjERT-dsRNA treatment resulted in a lower phagocytosis rate in the hemocytes of V. alginolyticus-challenged shrimp. Finally, we found that the absence of mjERT had an significantly negative impact upon shrimp phenoloxidase (PO) activity, superoxide dismutase (SOD) activity and total hemocyte count (THC) following WSSV or V. alginolyticus infection, indicating a regulative role for mjERT in the innate immunity of shrimp in response to pathogenic infection. In summary, we concluded that mjERT might promote the anti-WSSV immune response of shrimp by regulating apoptosis, PO activity, THC and SOD activity, and also exert a positive role in the immune response against V. alginolyticus by regulating phagocytosis, SOD activity, PO activity and THC. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Relation of body weight and food consumption to metabolic rate of juvenile Japanese sea bass, Lateolabrax japonicus

    NASA Astrophysics Data System (ADS)

    Xian, Wei-Wei; Zhu, Xin-Hua

    2000-12-01

    The metabolic rate of Japanese sea bass, Lateolabrax japonicus (C & V), was estimated in laboratory at temperature 25.2±0.5°C. The fresh weight of the fish was 4.64 52.28 g (average of 17.81±0.33 g). The routine metabolism was related to body weight by the exponential equation: R r =14.966 W 0.74 ( r=0.934). The rate of feeding metabolism increased linearly with food consumption. Feeding metabolic rate was 1.8 2.4 times the routine metabolic rate.

  5. Rheological and structural properties of sea cucumber Stichopus japonicus during heat treatment

    NASA Astrophysics Data System (ADS)

    Gao, Xin; Xue, Dongmei; Zhang, Zhaohui; Xu, Jiachao; Xue, Changhu

    2005-07-01

    Changes in tissue structure, rheological properties and water content of raw and heated sea cucumber meat were studied. Sea cucumber Stichopus japonicus was heated at 25°C , 70°C and 100°C water for 5 min. The structural changes were observed using a light microscope and the rheological parameters (rupture strength, adhesive strength and deformation) determined using a texture meter. Microscopic photograph revealed that the structural change of heated meat was greater than that of raw meat. The rupture strength, adhesive strength and deformation of raw meat were smaller than those of the heated meat. Meanwhile, rheological parameters showed positive correlation with heating temperature. These changes are mainly caused by thermal denaturation and gelatinization of collagen during heating. These changes were also evidenced in observations using a light microscope and differential scanning calorimetry.

  6. Transcriptome Analysis and Discovery of Genes Involved in Immune Pathways from Coelomocytes of Sea Cucumber (Apostichopus japonicus) after Vibrio splendidus Challenge

    PubMed Central

    Gao, Qiong; Liao, Meijie; Wang, Yingeng; Li, Bin; Zhang, Zheng; Rong, Xiaojun; Chen, Guiping; Wang, Lan

    2015-01-01

    Vibrio splendidus is identified as one of the major pathogenic factors for the skin ulceration syndrome in sea cucumber (Apostichopus japonicus), which has vastly limited the development of the sea cucumber culture industry. In order to screen the immune genes involving Vibrio splendidus challenge in sea cucumber and explore the molecular mechanism of this process, the related transcriptome and gene expression profiling of resistant and susceptible biotypes of sea cucumber with Vibrio splendidus challenge were collected for analysis. A total of 319,455,942 trimmed reads were obtained, which were assembled into 186,658 contigs. After that, 89,891 representative contigs (without isoform) were clustered. The analysis of the gene expression profiling identified 358 differentially expression genes (DEGs) in the bacterial-resistant group, and 102 DEGs in the bacterial-susceptible group, compared with that in control group. According to the reported references and annotation information from BLAST, GO and KEGG, 30 putative bacterial-resistant genes and 19 putative bacterial-susceptible genes were identified from DEGs. The qRT-PCR results were consistent with the RNA-Seq results. Furthermore, many DGEs were involved in immune signaling related pathways, such as Endocytosis, Lysosome, MAPK, Chemokine and the ERBB signaling pathway. PMID:26193268

  7. Soluble epoxide hydrolase inhibitory activity of components from Leonurus japonicus.

    PubMed

    Leem, Hyun Hee; Lee, Ga Young; Lee, Ji Sun; Lee, Hanna; Kim, Jang Hoon; Kim, Young Ho

    2017-10-01

    One new compound, 10-methoxy-leonurine (1), and four known compounds (2-5) were purified by silica gel, C-18, and Sephadex LH-20 column chromatography from Leonurus japonicus. Their structures were elucidated using one-dimensional (1D)/two-dimensional (2D)-nuclear magnetic resonance (NMR), high-resolution (HR)-electrospray ionization (ESI) mass spectrometry (MS). The compounds were evaluated to determine their inhibition of the catalysis of soluble epoxide hydrolase (sEH). According to the results from in vitro analyses, compounds 1 and 2, which contain guanidine and flavonoid (3), were determined to be potential inhibitors of this enzyme. All compounds were revealed to be non-competitive inhibitors according to Lineweaver-Burk plots. Furthermore, in silico molecular docking indicated that compounds 1-3 are bound to sEH in a similar fashion and have stable binding energies, as calculated by AutoDock 4.2. Molecular dynamics determined the root-mean-square deviation (RMSD), total energy, RMS fluctuation (RMSF), hydrogen bonds, and distance of the complex according to time. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. The complex physiology of Cellvibrio japonicus xylan degradation relies on a single cytoplasmic β-xylosidase for xylo-oligosaccharide utilization

    DOE PAGES

    Blake, Andrew D.; Beri, Nina R.; Guttman, Hadassa S.; ...

    2017-12-21

    Lignocellulose degradation by microbes plays a central role in global carbon cycling, human gut metabolism, and renewable energy technologies. While considerable effort has been put into understanding the biochemical aspects of lignocellulose degradation, much less work has been done to understand how these enzymes work in an in vivo context. Here in this paper, we report a systems level study of xylan degradation in the saprophytic bacterium Cellvibrio japonicus. Transcriptome analysis indicated seven genes that encode carbohydrate active enzymes were up-regulated during growth with xylan containing media. In-frame deletion analysis of these genes found that only gly43F is critical formore » utilization of xylo-oligosaccharides, xylan, and arabinoxylan. Heterologous expression of gly43F was sufficient for the utilization of xylo-oligosaccharides in Escherichia coli. Additional analysis found that the xyn11A, xyn11B, abf43L, abf43K, and abf51A gene products were critical for utilization of arabinoxylan. Furthermore, a predicted transporter (CJA_1315) was required for effective utilization of xylan substrates, and we propose this unannotated gene be called xntA (xylan transporter A). Our major findings are 1) C. japonicus employs both secreted and surface associated enzymes for xylan degradation, which differs from the strategy used for cellulose degradation, and 2) a single cytoplasmic β-xylosidase is essential for the utilization of xylo-oligosaccharides.« less

  9. The complex physiology of Cellvibrio japonicus xylan degradation relies on a single cytoplasmic β-xylosidase for xylo-oligosaccharide utilization

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Blake, Andrew D.; Beri, Nina R.; Guttman, Hadassa S.

    Lignocellulose degradation by microbes plays a central role in global carbon cycling, human gut metabolism, and renewable energy technologies. While considerable effort has been put into understanding the biochemical aspects of lignocellulose degradation, much less work has been done to understand how these enzymes work in an in vivo context. Here in this paper, we report a systems level study of xylan degradation in the saprophytic bacterium Cellvibrio japonicus. Transcriptome analysis indicated seven genes that encode carbohydrate active enzymes were up-regulated during growth with xylan containing media. In-frame deletion analysis of these genes found that only gly43F is critical formore » utilization of xylo-oligosaccharides, xylan, and arabinoxylan. Heterologous expression of gly43F was sufficient for the utilization of xylo-oligosaccharides in Escherichia coli. Additional analysis found that the xyn11A, xyn11B, abf43L, abf43K, and abf51A gene products were critical for utilization of arabinoxylan. Furthermore, a predicted transporter (CJA_1315) was required for effective utilization of xylan substrates, and we propose this unannotated gene be called xntA (xylan transporter A). Our major findings are 1) C. japonicus employs both secreted and surface associated enzymes for xylan degradation, which differs from the strategy used for cellulose degradation, and 2) a single cytoplasmic β-xylosidase is essential for the utilization of xylo-oligosaccharides.« less

  10. Identification and expression analysis of a novel stylicin antimicrobial peptide from Kuruma shrimp (Marsupenaeus japonicus).

    PubMed

    Liu, Hong-tao; Wang, Jun; Mao, Yong; Liu, Min; Niu, Su-fang; Qiao, Ying; Su, Yong-quan; Wang, Chun-zhong; Zheng, Zhi-peng

    2015-12-01

    Antimicrobial peptides (AMPs) are important components of the innate immune system and function as the first line of defense against invading pathogens. In current study we identified, cloned and characterized a novel stylicin AMP from Kuruma shrimp Marsupenaeus japonicus (Mj-sty). The full-length cDNA of Mj-sty was 428 bp with an open reading frame of 315 bp that encoded 104 amino acids. The theoretical molecular mass of mature Mj-sty was 8.693 kDa with an isoelectric point (pI) of 4.79. A proline-rich N-terminal region and a C-terminal region contained 13 cysteine residues were identified. Genomic sequence analysis with respect to its cDNA showed that Mj-sty was organized into two exons interrupted by one intron. Tissue-specific expression revealed that Mj-sty was mainly transcribed in gills and hemocytes. Expression of Mj-sty in early developmental stages demonstrated that Mj-sty mRNA were present from fertilized eggs to post-larvae of 17 days (PL17), and the expression levels showed a significant variation in different developmental stages. After challenge of white spot syndrome virus (WSSV), the time-dependent expression pattern of Mj-sty in both gills and hepatopancrease showed down-regulation at the early hours of infection, subsequently up-regulation and down-regulation, and then up-regulation at the end hours to almost the half of the controls. The results indicate that Mj-sty is potentially involved in the ontogenesis and immune responses against WSSV. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Unilateral compatibility and genotypic difference in crossability in interspecific hybridization between Dianthus caryophyllus L. and Dianthus japonicus Thunb.

    PubMed

    Nimura, M; Kato, J; Mii, M; Morioka, K

    2003-05-01

    Reciprocal interspecific crosses were carried out between six lines of Dianthus caryophyllus L. and one line of Dianthus japonicus Thunb. Although no seed was set when D. japonicus was used as the seed parent, six seedlings were successfully obtained from 2,380 immature ovules by applying the embryo-rescue technique. However, they showed seed parent-like morphology and no evidence for the hybridity by flow cytometry and RAPD analyses. When six lines of D. caryophyllus were used as seed parents, a total of 192 seedlings were successfully obtained without using the embryo-rescue technique. Among these seedlings, 12 out of 25 progenies obtained from the carnation line '98sp1651' were confirmed to be the hybrids. The remaining 13 progenies of this line, and the total 167 progenies obtained from the other carnation lines, had carnation-like morphology without any evidence of hybridity by flow cytometry and RAPD analyses. The progenies confirmed as hybrids had intermediate characters of the parents with respect to leaf width and flower size, but they had a uniform flower color, reddish purple, which was different from that of either parent. Since the hybrids obtained in the present study have some profitable characters such as vigorous growth in summer time, upright robust stem, broad leaves and early flowering, they are expected to be used for the breeding of carnation which is suitable for growing under the Japanese climate.

  12. Effects of salt stress on the expression of antioxidant genes and proteins in the model legume Lotus japonicus.

    PubMed

    Rubio, Maria C; Bustos-Sanmamed, Pilar; Clemente, Maria R; Becana, Manuel

    2009-03-01

    Salt stress negatively affects many physiological processes in plants. Some of these effects may involve the oxidative damage of cellular components, which can be promoted by reactive oxygen species and prevented by antioxidants. The protective role of antioxidants was investigated in Lotus japonicus exposed to two salinization protocols: S1 (150 mM NaCl for 7 d) and S2 (50, 100 and 150 mM NaCl, each concentration for 6 d). Several markers of salt stress were measured and the expression of antioxidant genes was analyzed using quantitative reverse transcription–polymerase chain reaction and, in some cases, immunoblots and enzyme activity assays. Leaves of S1 plants suffered from mild osmotic stress, accumulated proline but noNa+, and showed induction of many superoxide dismutase and glutathione peroxidase genes. Leaves of S2 plants showed increases in Na+ and Ca2+, decreases in K+, and accumulation of proline and malondialdehyde. In leaves and roots of S1 and S2 plants, the mRNA, protein and activity levels of the ascorbate-glutathione enzymes remained constant, with a few exceptions. Notably, there was consistent up-regulation of the gene encoding cytosolic dehydroascorbate reductase, and this was possibly related to its role in ascorbate recycling in the apoplast. The overall results indicate that L. japonicus is more tolerant to salt stress than other legumes, which can be attributed to the capacity of the plant to prevent Na+reaching the shoot and to activate antioxidant defenses.

  13. Characterization and phylogenetic analysis of lectin gene cDNA isolated from sea cucumber ( Apostichopus japonicus) body wall

    NASA Astrophysics Data System (ADS)

    Xue, Zhuang; Li, Hui; Liu, Yang; Zhou, Wei; Sun, Jing; Wang, Xiuli

    2017-12-01

    As a `living fossil' of species origin and `rich treasure' of food and nutrition development, sea cucumber has received a lot of attentions from researchers. The cDNA library construction and EST sequencing of blood had been conducted previously in our lab. The bioinformatic analysis provided a gene fragment which is highly homologous with the genes of lectin family, named AjL ( Apostichopus japonicus lectin). To characterize and determine the phylogeny of AjL genes in early evolution, we isolated a full-length cDNA of lectin gene from the body wall of A. japonicus. The open reading frame of this gene contained 489 bp and encoded a 163 amino acids secretory protein being homologous to lectins of mammals and aquatic organisms. The deduced protein included a lectin-like domain. SDS-PAGE analysis showed that AjL migrated as a specific band (about 36.09 kDa under reducing), and agglutinated against rabbit red blood cells. AjL was similar to chain A of CEL-IV in space structure. We predicted that AjL may play the same role of CEL-IV. Our results suggested that more than one lectin gene functioned in sea cucumber and most of other species, which was fused by uncertain sequences during the evolution and encoded different proteins with diverse functions. Our findings provided the insights into the function and characteristics of lectin genes invertebrates. The results will also be helpful for the identification and structural, functional, and evolutionary analyses of lectin genes.

  14. Time and order of eruption of first functional teeth in the upper jaw of post-larval life of Sicyopterus japonicus (Gobiidiae: Sicydiinae) during cranial metamorphosis at the time of river recruitment.

    PubMed

    Sahara, Noriyuki; Moriyama, Keita; Iida, Midori; Watanabe, Shun

    2016-06-01

    The present study was aimed at elucidating the time and order of eruption of first functional teeth in the upper jaw of post-larval life of Sicyopterus japonicus (S. japonicus) during cranial metamorphosis at the time of river recruitment. Fishes were caught at the post-larval stage at a river mouth and maintained for 7 days in a water tank. Each of 10 specimens was evaluated every day for 7 days by using microcomputed tomography, scanning electron microscopy, and light microscopy with peculiar attention to the development of the upper jaw teeth. Fishes caught at the river mouth were mostly transparent, with a rostral terminal mouth, and no teeth could be found in either the upper or lower jaw. At 2 days after collection, the mouth position changed from terminal to subterminal, resulting from a change in head shape. The initial eruption of first functional teeth was detected at the anterior two-thirds region of each upper jaw. These teeth erupted in adjacent positions, most had a tricuspid crown, and they represented miniature versions of adult teeth. At 5 days, the position of the mouth became further relocated from terminal rostral to ventral. The number of erupted teeth increased, followed by spreading of them anteriorly and posteriorly. At 7 days, they formed a single row of close-set tricuspid teeth along the entire length of each upper jaw. The present study demonstrated that even under laboratory conditions a rapid and drastic cranial metamorphosis took place within a week after the time of collection of post-larval S. japonicus from a river. The eruption of first functional teeth in the upper jaw of S. japonicus, which teeth are adapted to scraping algae off the substrate, was initially detected at 2 days after collection, and first functional dentition of the upper jaw was set up within 7 days after it. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. A Steroidal Saponin from Ophiopogon japonicus Extends the Lifespan of Yeast via the Pathway Involved in SOD and UTH1

    PubMed Central

    Sun, Kaiyue; Cao, Shining; Pei, Liang; Matsuura, Akira; Xiang, Lan; Qi, Jianhua

    2013-01-01

    Nolinospiroside F is a steroidal saponin isolated from Ophiopogon japonicus (O. japonicus). In this study, we found that nolinospiroside F significantly extends the replicative lifespan of K6001 yeast at doses of 1, 3 and 10 μM, indicating that it has an anti-aging effect. This may be attributed to its anti-oxidative effect, as nolinospiroside F could increase yeast survival under oxidative stress conditions and decrease the level of malondialdehyde (MDA), an oxidative stress biomarker. It could also increase anti-oxidative stress genes, SOD1 and SOD2, expression, and the activity of superoxide dismutase (SOD). It increase the activity of SIRT1, an upstream inducer of SOD2 expression. In sod1 and sod2 mutant yeast strains, nolinospiroside F failed to extend their replicative lifespan. These results indicate that SOD participates in the anti-aging effect of nolinospiroside F. Furthermore, nolinospiroside F inhibited the expression of UTH1, a yeast-aging gene that is involved in the oxidative stress of yeast, and failed to extend the replicative lifespan of uth1 or skn7 mutant yeast cells. SKN7 is the transcriptional activator of UTH1. We also demonstrate that SOD and UTH1 regulate each other’s expression. Together, these results suggest that SOD and UTH1 genes are required for and play interactive roles in nolinospiroside F-mediated yeast lifespan extension. PMID:23439553

  16. Target-strength Measurements of Sandfish Arctoscopus japonicus

    NASA Astrophysics Data System (ADS)

    Yoon, Eun-A.; Lee, Kyounghoon; Oh, Wooseok; Choi, Junghwa; Hwang, Kangseok; Kang, Myounghee

    2018-03-01

    The goal of this study was to estimate the target strength (TS) of the sandfish Arctoscopus japonicus using in-situ and ex-situ methods with an echosounder. For the in-situ TS measurement, the survey was conducted by taking hydroacoustic measurements at 38 and 120 kHz and using a coastal gill net, in Goseong, in the northeastern sea of Korea in early December 2009. Ex-situ measurement of TS used live specimens and the tethering method, and was conducted at 120 kHz. The distribution of fork length (FL) was bimodal: 14.6-19.8 cm (n = 241 individuals, mean = 17.0 cm) for males and 16.3-24.5 cm (n = 105 individuals, mean = 19.6 cm) for females. The in-situ TS ranged from -79.8 to -59.1 dB (mean = -74.3 dB for males and -64.1 dB for females) at 38 kHz and -79.9 to -56.2 dB (mean = -74.3 dB for males and -64.1 dB for females) at 120 kHz. The mean TS of females was approximately 10 dB higher than that of males at each dominant frequency. The female ex-situ TS values ranged from 68.5 to -54.6 dB, and those of males was from -67.7 to -59.3 dB. The mean TS value for females was 2.9 dB higher than that of males. These results may be used in echo-integration surveys of sandfish to estimate their abundance and seasonal distribution.

  17. Impact of hypoxia stress on the physiological responses of sea cucumber Apostichopus japonicus: respiration, digestion, immunity and oxidative damage

    PubMed Central

    Huo, Da; Ru, Xiaoshang; Zhang, Libin; Lin, Chenggang; Xin, Xiaoke

    2018-01-01

    Hypoxia is one of the most frequently occurring stressors confronted by industrial cultures of sea cucumber and can cause large economic losses and resource degradation. However, its responsive mechanisms are still lacking. In this paper, the physiological responses of Apostichopus japonicus to oxygen deficiency was illustrated, including induced oxidative response and immune defense and changed digestive enzymes activities. Significantly increased activities of alpha-amylase (AMS), acid phosphatase (ACP), lactate dehydrogenase, catalase, peroxidase, succinate dehydrogenase and higher content of malondialdehyde, and decreased activities of lipase and trypsin (TRY) were observed after hypoxia exposure (dissolved oxygen [DO] 2 mg/L). Expressions of key genes showed that AMS, peptidase, ACP, alkaline phosphatase, lysozyme, heat shock protein 70 and glutathione peroxidase were increased and TRY was decreased under hypoxia. With the decline of the DO level, the decreased tendency of oxygen consumption rates was different in varied weight groups. Moreover, respiratory trees were observed degraded under long-term hypoxia stress, thus leading a negative effect of respiration. These results could help to develop a better understanding of the responsive mechanism of sea cucumber under hypoxia stress and provide a theoretical basis for the prevention of hypoxia risk. PMID:29719735

  18. Role of animal pole protuberance and microtubules during meiosis in sea cucumber Apostichopus japonicus oocytes

    NASA Astrophysics Data System (ADS)

    Pang, Zhenguo; Chang, Yaqing; Sun, Huiling; Yu, Jiaping

    2010-05-01

    Fully grown oocytes of Apostichopus japonicus have a cytoplasmic protuberance where the oocyte attaches to the follicle. The protuberance and the oolamina located on the opposite side of the oocyte indicate the animal-vegetal axis. Two pre-meiotic centrosomes are anchored to the protuberance by microtubules between centrosomes and protuberance. After meiosis reinitiation induced by DTT solution, the germinal vesicle (GV) migrates towards the protuberance. The GV breaks down after it migrates to the oocyte membrane on the protuberance side. The protuberance then contracts back into the oocyte and the first polar body extrudes from the site of the former protuberance. The second polar body forms beneath the first. Thus the oocyte protuberance indicates the presumptive animal pole well before maturation of the oocyte.

  19. Antioxidation activities of low-molecular-weight gelatin hydrolysate isolated from the sea cucumber Stichopus japonicus

    NASA Astrophysics Data System (ADS)

    Wang, Jingfeng; Wang, Yuming; Tang, Qingjuan; Wang, Yi; Chang, Yaoguang; Zhao, Qin; Xue, Changhu

    2010-03-01

    Gelatin extracted from the body wall of the sea cucumber ( Stichopus japonicus) was hydrolyzed with flavourzyme. Low-molecular-weight gelatin hydrolysate (LMW-GH) of 700-1700 Da was produced using an ultrafiltration membrane bioreactor system. Chemiluminescence analysis revealed that LMW-GH scavenges high free radicals in a concentration-dependent manner; IC50 value for superoxide and hydroxyl radicals was 442 and 285 μg mL-1, respectively. LMW-GH exhibited excellent inhibitory characteristics against melanin synthesis and tyrosinase activity in B16 cells. Furthermore, LMW-GH notably increased intracellular glutathione (GSH), which in turn suppressed melanogenesis. LMW-GH performs antioxidation activity, holding the potential of being used as a valuable ingredient in function foods, cosmetics and pharmaceuticals or nutriceuticals.

  20. Identifying large scale structures at 1 AU using fluctuations and wavelets

    NASA Astrophysics Data System (ADS)

    Niembro, T.; Lara, A.

    2016-12-01

    The solar wind (SW) is inhomogeneous and it is dominated for two types of flows: one quasi-stationary and one related to large scale transients (such as coronal mass ejections and co-rotating interaction regions). The SW inhomogeneities can be study as fluctuations characterized by a wide range of length and time scales. We are interested in the study of the characteristic fluctuations caused by large scale transient events. To do so, we define the vector space F with the normalized moving monthly/annual deviations as the orthogonal basis. Then, we compute the norm in this space of the solar wind parameters (velocity, magnetic field, density and temperature) fluctuations using WIND data from August 1992 to August 2015. This norm gives important information about the presence of a large structure disturbance in the solar wind and by applying a wavelet transform to this norm, we are able to determine, without subjectivity, the duration of the compression regions of these large transient structures and, even more, to identify if the structure corresponds to a single or complex (or merged) event. With this method we have automatically detected most of the events identified and published by other authors.

  1. The Proteome of Seed Development in the Model Legume Lotus japonicus1[C][W

    PubMed Central

    Dam, Svend; Laursen, Brian S.; Ørnfelt, Jane H.; Jochimsen, Bjarne; Stærfeldt, Hans Henrik; Friis, Carsten; Nielsen, Kasper; Goffard, Nicolas; Besenbacher, Søren; Krusell, Lene; Sato, Shusei; Tabata, Satoshi; Thøgersen, Ida B.; Enghild, Jan J.; Stougaard, Jens

    2009-01-01

    We have characterized the development of seeds in the model legume Lotus japonicus. Like soybean (Glycine max) and pea (Pisum sativum), Lotus develops straight seed pods and each pod contains approximately 20 seeds that reach maturity within 40 days. Histological sections show the characteristic three developmental phases of legume seeds and the presence of embryo, endosperm, and seed coat in desiccated seeds. Furthermore, protein, oil, starch, phytic acid, and ash contents were determined, and this indicates that the composition of mature Lotus seed is more similar to soybean than to pea. In a first attempt to determine the seed proteome, both a two-dimensional polyacrylamide gel electrophoresis approach and a gel-based liquid chromatography-mass spectrometry approach were used. Globulins were analyzed by two-dimensional polyacrylamide gel electrophoresis, and five legumins, LLP1 to LLP5, and two convicilins, LCP1 and LCP2, were identified by matrix-assisted laser desorption ionization quadrupole/time-of-flight mass spectrometry. For two distinct developmental phases, seed filling and desiccation, a gel-based liquid chromatography-mass spectrometry approach was used, and 665 and 181 unique proteins corresponding to gene accession numbers were identified for the two phases, respectively. All of the proteome data, including the experimental data and mass spectrometry spectra peaks, were collected in a database that is available to the scientific community via a Web interface (http://www.cbs.dtu.dk/cgi-bin/lotus/db.cgi). This database establishes the basis for relating physiology, biochemistry, and regulation of seed development in Lotus. Together with a new Web interface (http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress4legumes/) collecting all protein identifications for Lotus, Medicago, and soybean seed proteomes, this database is a valuable resource for comparative seed proteomics and pathway analysis within and beyond the legume family. PMID:19129418

  2. Characteristics of the Japanese sea cucumber Apostichopus japonicus's population in the Sea of Japan (Kievka Bay)

    NASA Astrophysics Data System (ADS)

    Gavrilova, G. S.; Sukhin, I. Yu.

    2011-06-01

    In Kievka Bay of the Sea of Japan, the population of the Japanese sea cucumber Apostichopus japonicus inhabits the areas of coarse sediments and complex bottom topography. These distributional patterns are closely related to the species' ecology, i.e., to the demand for protection against the wave turbulence. The aggregationing coverage of the sea cucumber population is about 80 hectares, where ˜200 thousand animals were accounted for in the last years. The aggregation's area varies during the year, which is closely related to the species' biological peculiarities, such as their behavioral patterns and the redistribution of their food resources. A significant increase of the juvenile population occurred after the farm-reared sea cucumber spat were released in 2003.

  3. Profiling and comparison of color body wall transcriptome of normal juvenile sea cucumber ( Apostichopus japonicus) and those produced by crossing albino

    NASA Astrophysics Data System (ADS)

    Ma, Deyou; Yang, Hongsheng; Sun, Lina

    2014-12-01

    Sea cucumber ( Apostichopus japonicus) is one of the most important aquaculture animals in China. Usually its normal body color is black that fits its living environment. The juvenile individuals obtained by crossing albino sea cucumber segregated in body color. To document the transcriptome difference between albino associating sea cucumber and the control, we sequenced their transcriptomes with RNA-seq. Approximately, 4.790 million (M) and 4.884 M reads, 200 nt in length, were generated from the body wall of albino associating sea cucumber and the control, respectively, from them, 9550 (46.81%) putative genes were identified. In total, 583 genes were found to express differentially between albino associating sea cucumber and the control. Of these differentially expressed genes (DEGs), 4.8% changed more than five-folds. The expression levels of eight DEGs were confirmed with real-time PCR. The changing trend of these DEGs detected with real-time PCR agreed well with that detected with RNA-seq, although the change degree of some DEGs was different. Four significantly enriched pathways were identified for DEGs, which included phagocytosis, Staphylococcus aureus infection, ECM-receptor interaction and focal adhesion. These pathways were helpful for understanding the physiological difference between albino associating sea cucumber and the control.

  4. Anti-oxidizing effect of the dichloromethane and hexane fractions from Orostachys japonicus in LPS-stimulated RAW 264.7 cells via upregulation of Nrf2 expression and activation of MAPK signaling pathway.

    PubMed

    Lee, Hyeong-Seon; Lee, Gyeong-Seon; Kim, Seon-Hee; Kim, Hyun-Kyung; Suk, Dong-Hee; Lee, Dong-Seok

    2014-02-01

    Orostachys japonicus shows various biological activities. However, the molecular mechanisms remain unknown in LPS-stimulated macrophages. Here, we investigated the anti-oxidizing effect of the dichloromethane (DCM) and hexane fractions from O. japonicus (OJD and OJH) against oxidative stress in RAW 264.7 cells stimulated by LPS. OJD and OJH significantly increased the expression of heme oxygenase-1 (HO-1) in a dose- and time-dependent manner. Additionally, it was found that the expression of HO-1 was stimulated by Nrf2 activated via degradation of Keap1. ERK and p38 inhibitors repressed HO-1 induced by OJD and OJH in LPS-stimulated cells, respectively. In conclusion, these results suggest that OJD and OJH may block oxidative damage stimulated by LPS, via increasing the expression of HO-1 and Nrf2, and MAPK signaling pathway.

  5. Effects of the Dietary Probiotic Clostridium butyricum on Intestine Digestive and Metabolic Capacities, SCFA Content and Body Composition in Marsupenaeus japonicus

    NASA Astrophysics Data System (ADS)

    Duan, Yafei; Dong, Hongbiao; Wang, Yun; Zhang, Yue; Zhang, Jiasong

    2018-06-01

    A 56-day feeding trial was performed to evaluate the effects of dietary probiotic Clostridium butyricum (CB) on intestine digestive and metabolic capacities, intestine short-chain fatty acids (SCFA) content and body composition of kuruma shrimp Marsupenaeus japonicus. Shrimps were randomly allocated into 9 tanks, 30 each, and fed with diets containing different levels of C. butyricum (1 × 109 cfu g-1): 0 mg g-1 feed (Control), 100 mg g-1 feed (CB-100), 200 mg g-1 feed (CB-200), while each level was triplicated. The results indicated that compared with the control group, the intestine pepsin (Pep) activity and 5-hydroxytryptamine (5-HT) concentration of two C. butyricum groups were both increased. Amylase (AMY) and lipase (LPS) activities were only induced in CB-200 group. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities of two C. butyricum groups showed no significant change. The α-amylase (AMY) gene expression was induced in CB-200 group, and trypsin gene expression of two C. butyricum treated groups were both induced. Intestine SCFA content and body composition analysis showed that the contents of propionic acid, butyric acid and the crude protein of two C. butyricum groups were all higher than those of control. These results revealed that C. butyricum can modulate intestine digestive and metabolic capacities, improve intestine SCFA content and body crude protein content in M. japonicus.

  6. Transcriptional changes in epigenetic modifiers associated with gene silencing in the intestine of the sea cucumber, Apostichopus japonicus (Selenka), during aestivation

    NASA Astrophysics Data System (ADS)

    Wang, Tianming; Yang, Hongsheng; Zhao, Huan; Chen, Muyan; Wang, Bing

    2011-11-01

    The sea cucumber, Apostichopus japonicus, undergoes aestivation to improve survival during periods of high-temperature. During aestivation, the metabolic rate is depressed to reduce the consumption of reserved energy. We evaluated the role of epigenetic modification on global gene silencing during metabolic rate depression in the sea cucumber. We compared the expression of epigenetic modifiers in active and aestivating sea cucumbers. The expression of three genes involved in DNA methylation and chromatin remodeling (DNA (cytosine-5)-methyltransferase 1, Methyl-CpG-binding domain protein 2), and Chromodomain-helicase-DNA-binding protein 5) was significantly higher during aestivation (Days 20 and 40). Similarly, we observed an increase in the expression of genes involved in histone acetylation (Histone deacetylase 3) and Histone-binding protein RBBP4) during the early (Days 5 and 10) and late phases (Days 20 and 40) of aestivation. There was no change in the expression of KAT2B, a histone acetyltransferase. However, the expression of histone methylation associated modifiers (Histone-arginine methyltransferase CARMER and Histone-lysine N-methyltransferase MLL5) was significantly higher after 5 d in the aestivating group. The results suggest that the expression of epigenetic modifiers involved in DNA methylation, chromatin remodeling, histone acetylation, and histone methylation is upregulated during aestivation. We hypothesize that these changes regulate global gene silencing during aestivation in A. japonicus.

  7. Dianthosaponins G-I, triterpene saponins, an anthranilic acid amide glucoside and a flavonoid glycoside from the aerial parts of Dianthus japonicus and their cytotoxicity.

    PubMed

    Kanehira, Yuka; Kawakami, Susumu; Sugimoto, Sachiko; Matsunami, Katsuyoshi; Otsuka, Hideaki

    2016-10-01

    Extensive isolation work on the 1-BuOH-soluble fraction of a MeOH extract of the aerial parts of Dianthus japonicus afforded three further triterpene glycosyl estsers, termed dianthosaponins G-I, an anthranilic acid amide glucoside and a C-glycosyl flavonoid along with one known triterpene saponin. Their structures were elucidated from spectroscopic evidence. The cytotoxicity of the isolated compounds toward A549 cells was evaluated.

  8. Differences in morphometrics and reproductive physiology between two populations of Trissolcus japonicus, a promising biological control agent candidate for brown marmorated stink bug (Halyomorpha halys Stal) in the US

    USDA-ARS?s Scientific Manuscript database

    Trissolcus japonicus (Ashmead), a solitary egg parasitoid of Pentatomidae native to Southeast Asia, has been undergoing host-range testing in U.S. quarantine facilities since 2009 as a candidate for the biological control of brown marmorated stink bug (Halyomorpha halys Stål)(BMSB), an invasive agri...

  9. Structural and Functional Analysis of a Lytic Polysaccharide Monooxygenase Important for Efficient Utilization of Chitin in Cellvibrio japonicus*

    PubMed Central

    Forsberg, Zarah; Nelson, Cassandra E.; Dalhus, Bjørn; Mekasha, Sophanit; Loose, Jennifer S. M.; Crouch, Lucy I.; Røhr, Åsmund K.; Gardner, Jeffrey G.; Eijsink, Vincent G. H.; Vaaje-Kolstad, Gustav

    2016-01-01

    Cellvibrio japonicus is a Gram-negative soil bacterium that is primarily known for its ability to degrade plant cell wall polysaccharides through utilization of an extensive repertoire of carbohydrate-active enzymes. Several putative chitin-degrading enzymes are also found among these carbohydrate-active enzymes, such as chitinases, chitobiases, and lytic polysaccharide monooxygenases (LPMOs). In this study, we have characterized the chitin-active LPMO, CjLPMO10A, a tri-modular enzyme containing a catalytic family AA10 LPMO module, a family 5 chitin-binding module, and a C-terminal unclassified module of unknown function. Characterization of the latter module revealed tight and specific binding to chitin, thereby unraveling a new family of chitin-binding modules (classified as CBM73). X-ray crystallographic elucidation of the CjLPMO10A catalytic module revealed that the active site of the enzyme combines structural features previously only observed in either cellulose or chitin-active LPMO10s. Analysis of the copper-binding site by EPR showed a signal signature more similar to those observed for cellulose-cleaving LPMOs. The full-length LPMO shows no activity toward cellulose but is able to bind and cleave both α- and β-chitin. Removal of the chitin-binding modules reduced LPMO activity toward α-chitin compared with the full-length enzyme. Interestingly, the full-length enzyme and the individual catalytic LPMO module boosted the activity of an endochitinase equally well, also yielding similar amounts of oxidized products. Finally, gene deletion studies show that CjLPMO10A is needed by C. japonicus to obtain efficient growth on both purified chitin and crab shell particles. PMID:26858252

  10. Antiviral effects of Stichopus japonicus acid mucopolysaccharide on hepatitis B virus transgenic mice

    NASA Astrophysics Data System (ADS)

    Xin, Yongning; Li, Wei; Lu, Linlin; Zhou, Li; Victor, David W.; Xuan, Shiying

    2016-08-01

    Hepatitis B virus (HBV) is a significant global pathogen and efficient cure for HBV patients is still a challenging goal. We previously reported that acidic mucopolysaccharide from stichopus japonicus selenka (SJAMP) could inhibit HBsAg and HBeAg expression in vitro. However, the potential anti-HBV effects of SJAMP in vivo have not yet been explored. In this study, we show that SJAMP exhibits potent anti-HBV activity in HBV transgenic mice in a dose-dependent manner. Specifically, sixty HBV transgenic male BALB/c mice were randomly selected to receive the treatment of PBS, low dose SJAMP (30 mg kg-1), middle dose SJAMP (40 mg kg-1), high dose SJAMP (50 mg kg-1) and IFN (45 IU kg-1) for 30 d. SJAMP treatment suppressed serum HBV-DNA, and liver HBsAg and HBcAg levels in HBV-transgenic mice. The present study highlights the potential application of SJAMP in HBV therapy.

  11. Microbispora camponoti sp. nov., a novel actinomycete isolated from the cuticle of Camponotus japonicus Mayr.

    PubMed

    Han, Chuanyu; Liu, Chongxi; Zhao, Junwei; Guo, Lifeng; Lu, Chang; Li, Jiansong; Jia, Feiyu; Wang, Xiangjing; Xiang, Wensheng

    2016-02-01

    A novel actinomycete, designated strain 2C-HV3(T), was isolated from the cuticle of Camponotus japonicus Mayr collected from Harbin, Heilongjiang province, north China and characterised using a polyphasic approach. The 16S rRNA gene sequence of strain 2C-HV3(T) showed that it has high sequence similarities with Microbispora bryophytorum NEAU-TX2-2(T) (99.9 %), Microbispora amethystogenes JCM 3021(T) (98.9 %) and Microbispora rosea subsp. rosea JCM 3006(T) (98.6 %). Phylogenetic analysis based on 16S rRNA and gyrB gene sequences demonstrated that strain 2C-HV3(T) clusters with M. bryophytorum NEAU-TX2-2(T) using two tree-making algorithms. Moreover, key morphological and chemotaxonomic properties also confirmed the affiliation of strain 2C-HV3(T) to the genus Microbispora. Longitudinal paired spores were observed to be born on short sporophores branching from the aerial hyphae. The cell wall was found to contain meso-diaminopimelic acid as the diagnostic diamino acid; madurose was found in the whole cell hydrolysate. The polar lipid profile was found to consist of diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside, ninhydrin-positive glycophospholipids, an unidentified phospholipid and an unidentified glycolipid. The predominant menaquinones were identified as MK-9(H2) and MK-9(H4). The major fatty acids were identified as 10-methyl C17:0 and iso-C16:0. However, a combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain 2C-HV3(T) can be distinguished from its closely related relatives. Consequently, it is proposed that strain 2C-HV3(T) represents a new species of the genus Microbispora, for which the name Microbispora camponoti sp. nov. is proposed. The type strain is 2C-HV3(T) (=CGMCC 4.7281(T) = DSM 100527(T)).

  12. Peroxiredoxins and NADPH-Dependent Thioredoxin Systems in the Model Legume Lotus japonicus1[W][OA

    PubMed Central

    Tovar-Méndez, Alejandro; Matamoros, Manuel A.; Bustos-Sanmamed, Pilar; Dietz, Karl-Josef; Cejudo, Francisco Javier; Rouhier, Nicolas; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

    2011-01-01

    Peroxiredoxins (Prxs), thioredoxins (Trxs), and NADPH-thioredoxin reductases (NTRs) constitute central elements of the thiol-disulfide redox regulatory network of plant cells. This study provides a comprehensive survey of this network in the model legume Lotus japonicus. The aims were to identify and characterize these gene families and to assess whether the NTR-Trx systems are operative in nodules. Quantitative reverse transcription-polymerase chain reaction and immunological and proteomic approaches were used for expression profiling. We identified seven Prx, 14 Trx, and three NTR functional genes. The PrxQ1 gene was found to be transcribed in two alternative spliced variants and to be expressed at high levels in leaves, stems, petals, pods, and seeds and at low levels in roots and nodules. The 1CPrx gene showed very high expression in the seed embryos and low expression in vegetative tissues and was induced by nitric oxide and cytokinins. In sharp contrast, cytokinins down-regulated all other Prx genes, except PrxQ1, in roots and nodules, but only 2CPrxA and PrxQ1 in leaves. Gene-specific changes in Prx expression were also observed in response to ethylene, abscisic acid, and auxins. Nodules contain significant mRNA and protein amounts of cytosolic PrxIIB, Trxh1, and NTRA and of plastidic NTRC. Likewise, they express cytosolic Trxh3, Trxh4, Trxh8, and Trxh9, mitochondrial PrxIIF and Trxo, and plastidic Trxm2, Trxm4, and ferredoxin-Trx reductase. These findings reveal a complex regulation of Prxs that is dependent on the isoform, tissue, and signaling molecule and support that redox NTR-Trx systems are functional in the cytosol, mitochondria, and plastids of nodules. PMID:21562331

  13. Structure and rheological characteristics of fucoidan from sea cucumber Apostichopus japonicus.

    PubMed

    Yu, Long; Xue, Changhu; Chang, Yaoguang; Hu, Yanfang; Xu, Xiaoqi; Ge, Lei; Liu, Guanchen

    2015-08-01

    Sea cucumber is a traditional health food consumed in East Asia. In this study, fucoidan from sea cucumber Apostichopus japonicus (Aj-FUC) was isolated, and its structure and rheological characteristics were elucidated for the first time. Aj-FUC was a branched polysaccharide mainly composed of a novel repeating unit [α-L-Fucp2(OSO3(-))-1 → 3,(α-L-Fucp-1 → 4-α-L-Fucp-1 →)4-α-L-Fucp2(OSO3(-))-1 → 3-α-L-Fucp2(OSO3(-))], clarified by using a combination of infrared spectroscopy, methylation analysis, enzymatic degradation and nuclear magnetic resonance. In steady shear measurement, Aj-FUC manifested a non-Newtonian shear-thinning behaviour at low shear rate (1-100 S(-1)) while exhibiting a non-Newtonian shear-thickening behaviour at high shear rate (100-1000 S(-1)); salts had limited impact on its flow curve. Comparative study on viscosity and rheological behaviour of Aj-FUC and a linear fucoidan extracted from sea cucumber Acaudina molpadioides suggested that the presence of branch structure might significantly influence the rheological characteristics of fucoidan. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Speciation Analysis of Trace Mercury in Sea Cucumber Species of Apostichopus japonicus Using High-Performance Liquid Chromatography Conjunction With Inductively Coupled Plasma Mass Spectrometry.

    PubMed

    Liu, Hao; Luo, Jiaoyang; Ding, Tong; Gu, Shanyong; Yang, Shihai; Yang, Meihua

    2018-03-25

    In this paper, a simple and cost-effective method using high-performance liquid chromatography in conjunction with inductively coupled plasma mass spectrometry with a rapid ultrasound-assisted extraction was used for analysis speciation of trace mercury in sea cucumber species of Apostichopus japonicus. The effective separation of inorganic mercury, methylmercury, and ethylmercury was achieved within 10 min using Agilent ZORBAX SB-C 18 analytical and guard columns with an isocratic mobile phase consisting of 8% methanol and 92% H 2 O containing 0.12% L-cysteine (m/v) and 0.01 mol/L ammonium acetate. Mercury species were extracted from A. japonicus samples using a solution containing 2-mercaptoethanol, L-cysteine, and hydrochloric acid and sonicating for 0.5 h. The limits of detection of inorganic mercury, methylmercury, and ethylmercury were 0.12, 0.08, and 0.20 μg/L, and the minimum detectable concentrations (measured at 0.500 g sample volume in 10.00 mL) were 2.4, 1.6, and 4.0 μg/kg, respectively. Analysis of a scallop certified reference material (GBW 10024) revealed accordance between the experimental and certified values. This study provides a reference for the evaluation of mercury speciation in sea cucumber and other seafood.

  15. A brominated flame retardant 2,2',4,4' tetrabrominated diphenyl ether (BDE-47) leads to lipogenesis in the copepod Tigriopus japonicus.

    PubMed

    Lee, Min-Chul; Han, Jeonghoon; Lee, Seung-Hwi; Kim, Duck-Hyun; Kang, Hye-Min; Won, Eun-Ji; Hwang, Dae-Sik; Park, Jun Chul; Om, Ae-Son; Lee, Jae-Seong

    2016-09-01

    De novo lipogenesis (DNL) is a fatty acid synthesis process that requires several genes, including sterol regulatory element binding protein (SREBP), ATP-citrate lyase (ACLY), and acetyl-CoA carboxylase (ACC). DNL up-regulation is able to induce fat accumulation through an increase in fatty acids. To investigate the relationship between DNL up-regulation and the accumulation of fatty acids and lipid droplets in response to 2,2',4,4' tetrabrominated diphenyl ether (BDE-47), we examined DNL in the copepod Tigriopus japonicus. Transcription levels of DNL-related genes were increased after exposure to 2.5μg/L BDE-47 for 24h. After exposure to 2.5μg/L BDE-47, palmitic acid was significantly increased (P<0.05) at days 1 and 4, along with upregulation of fatty acid synthesis-related genes (e.g., desaturases and elongases). However, docosahexaenoic acid and arachidonic acid were down-regulated at days 1 and 4, showing an antagonistic effect. Lipid droplet area significantly increased in Nile red staining analysis after 24h of exposure to 2.5μg/L BDE-47 in T. japonicus, while DNL was down-regulated in response to 500μM salicylate (a lipogenesis inhibitor), indicating that BDE-47 exposure is closely associated with an increase in fatty acids in this copepod. This study provides a better understanding of the effects of BDE-47 on DNL in copepods. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Development of enzyme-linked immunosorbent assay (ELISA) for glutathione S-transferase (GST-S) protein in the intertidal copepod Tigriopus japonicus and its application for environmental monitoring.

    PubMed

    Rhee, Jae-Sung; Kim, Bo-Mi; Jeong, Chang-Bum; Leung, Kenneth Mei Yee; Park, Gyung Soo; Lee, Jae-Seong

    2013-11-01

    To utilize the GST-S protein as a useful biomarker for environmental contamination, we developed a polyclonal antibody-based enzyme-linked immunosorbent assay (ELISA) in the intertidal copepod Tigriopus japonicus. Two polyclonal antibodies, TJ-GST-S1 and TJ-GST-S2, were raised against two TJ-GST-S synthetic peptides. Also a recombinant TJ-GST-S protein was purified as a standard for ELISA development. Each polyclonal antibody was tested by Western blot analysis and indirect ELISA. Of two polyclonal antibodies, TJ-GST-S2 ELISA was further employed due to its wide range of detection and the limit of specificity compared to those of TJ-GST-S1 ELISA system. After exposure to 4 metals (Ag, As, Cd, and Cu) to T. japonicus, the amount of TJ-GST-S protein was significantly elevated in a concentration-dependent manner. Also, TJ-GST-S protein was upregulated at relative high concentrations of B[α]P, PCB, and TBT. In this paper, we suggest that T. japonicas ELISA for TJ-GST-S2 is useful as a potential indicator system for marine contaminants. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Identifying Corridors among Large Protected Areas in the United States.

    PubMed

    Belote, R Travis; Dietz, Matthew S; McRae, Brad H; Theobald, David M; McClure, Meredith L; Irwin, G Hugh; McKinley, Peter S; Gage, Josh A; Aplet, Gregory H

    2016-01-01

    Conservation scientists emphasize the importance of maintaining a connected network of protected areas to prevent ecosystems and populations from becoming isolated, reduce the risk of extinction, and ultimately sustain biodiversity. Keeping protected areas connected in a network is increasingly recognized as a conservation priority in the current era of rapid climate change. Models that identify suitable linkages between core areas have been used to prioritize potentially important corridors for maintaining functional connectivity. Here, we identify the most "natural" (i.e., least human-modified) corridors between large protected areas in the contiguous Unites States. We aggregated results from multiple connectivity models to develop a composite map of corridors reflecting agreement of models run under different assumptions about how human modification of land may influence connectivity. To identify which land units are most important for sustaining structural connectivity, we used the composite map of corridors to evaluate connectivity priorities in two ways: (1) among land units outside of our pool of large core protected areas and (2) among units administratively protected as Inventoried Roadless (IRAs) or Wilderness Study Areas (WSAs). Corridor values varied substantially among classes of "unprotected" non-core land units, and land units of high connectivity value and priority represent diverse ownerships and existing levels of protections. We provide a ranking of IRAs and WSAs that should be prioritized for additional protection to maintain minimal human modification. Our results provide a coarse-scale assessment of connectivity priorities for maintaining a connected network of protected areas.

  18. Effects of triclosan (TCS) on fecundity, the antioxidant system, and oxidative stress-mediated gene expression in the copepod Tigriopus japonicus.

    PubMed

    Park, Jun Chul; Han, Jeonghoon; Lee, Min-Chul; Seo, Jung Soo; Lee, Jae-Seong

    2017-08-01

    Triclosan (TCS) is an antimicrobial agent that has been widely dispersed and detected in the marine environment. However, the effects of TCS in marine invertebrates are poorly understood. In this study, the effects of TCS on life cycle history (e.g. mortality and fecundity) along with cellular reactive oxygen species (ROS) levels, GSH content, antioxidant enzymatic activities, and mRNA expression levels of oxidative stress-mediated genes were measured in the copepod Tigriopus japonicus. The no observed effect concentration (NOEC) and median lethal concentration (LC50) of TCS in the adult stage were determined to be 300μg/L and 437.476μg/L, respectively, while in the nauplius stages the corresponding values were 20μg/L, and 51.76μg/L, respectively. Fecundity was significantly reduced (P<0.05) in response to TCS at 100μg/L. Concentration- and time-dependent analysis of ROS, GSH content (%), and antioxidant enzymatic activities (e.g. GST, GPx, and SOD) were significantly increased (P<0.05) in response to TCS exposure. Additionally, mRNA expression of detoxification (e.g., CYPs) and antioxidant (e.g., glutathione S-transferase-sigma isoforms, Cu/Zn superoxide dismutase, catalase) genes was modulated in response to TCS exposure at different concentrations over a 24h period. Our results revealed that TCS can induce reduced fecundity and oxidative stress with transcriptional regulation of oxidative stress-mediated genes with activation of the antioxidant system in the copepod T. japonicus. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. cDNA cloning, expression and immune function analysis of a novel Rac1 gene (AjRac1) in the sea cucumber Apostichopus japonicus.

    PubMed

    Li, Kaiquan; Liu, Lin; Shang, Shengnan; Wang, Yi; Zhan, Yaoyao; Song, Jian; Zhang, Xiangxiang; Chang, Yaqing

    2017-10-01

    The ras-related C3 botulinum toxin substrate 1 (Rac1) belongs to Ras homolog (Rho) small GTPases subfamily. As an important molecular switch, Rac1 regulates various processes in the cell, especially in cellular immune response. With attempt to clarify characters and functions of Rac1 in sea cucumbers, full length cDNA of a Rac1 homolog in the sea cucumber Apostichopus japonicus (AjRac1) was cloned by transcriptome database mining and rapid amplification of cDNA ends (RACE) techniques. The open reading frame of AjRac1 is 579 bp encoding a protein with a length of 192 aa. Sequence analysis showed that AjRac1 is highly conserved as compared to those from other eukaryotic species. Phylogenetic analysis revealed that amino acid sequence of AjRac1 closely related to those from Strongylocentrotus purpuratus. Results of expression analysis showed that AjRac1 exhibited a relative high expression in blastula stage, adult coelomocytes and respiratory tree in A. japonicus. The transcription of AjRac1 in adult coelomocytes altered significantly at 4 h- and 12 h-after Vibrio splendidus infection, respectively, which indicated that AjRac1 involved in sea cucumber innate immunity. All data presented in this study will deepen our understanding of characterizations and immunological functions of Rac1 in sea cucumbers. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Effects of temperature on sustained swimming performance and swimming kinematics of the chub mackerel Scomber japonicus.

    PubMed

    Dickson, Kathryn A; Donley, Jeanine M; Sepulveda, Chugey; Bhoopat, Lisa

    2002-04-01

    The effects of a 6 degrees C difference in water temperature on maximum sustained swimming speed, swimming energetics and swimming kinematics were measured in the chub mackerel Scomber japonicus (Teleostei: Scombridae), a primarily coastal, pelagic predator that inhabits subtropical and temperate transition waters of the Atlantic, Pacific and Indian Oceans. New data for chub mackerel acclimated to 18 degrees C are compared with published data from our laboratory at 24 degrees C. Twelve individuals acclimated to each of two temperatures (15.6-26.3 cm fork length, FL, and 34-179 g at 18 degrees C; 14.0-24.7 cm FL and 26-156 g at 24 degrees C) swam at a range of speeds in a temperature-controlled Brett-type respirometer, at the respective acclimation temperature. At a given fish size, the maximum speed that S. japonicus was able to maintain for a 30-min period, while swimming steadily using slow, oxidative locomotor muscle (U(max,c)), was significantly greater at 24 than at 18 degrees C (52.5-97.5 cm s(-1) at 18 degrees C and 70-120 cm s(-1) at 24 degrees C). At a given speed and fish size, the rate of oxygen consumption (VO(2)) was significantly higher at 24 than at 18 degrees C because of a higher net cost of transport (1073-4617 J km(-1) kg(-1) at 18 degrees C and 2708-14895 J km(-1) kg(-1) at 24 degrees C). Standard metabolic rate, calculated by extrapolating the logO(2) versus swimming speed relationship to zero speed, did not vary significantly with temperature or fish mass (126.4+/-67.2 mg O(2) h(-1) kg(-1) at 18 degrees C and 143.2+/-80.3 mg O(2) h(-1) kg(-1) at 24 degrees C; means +/- S.D., N=12). Swimming kinematics was quantified from high-speed (120 Hz) video recordings analyzed with a computerized, two-dimensional motion-analysis system. At a given speed and fish size, there were no significant effects of temperature on tail-beat frequency, tail-beat amplitude or stride length, but propulsive wavelength increased significantly with temperature as a result

  1. Acute and chronic toxicity study of the water accommodated fraction (WAF), chemically enhanced WAF (CEWAF) of crude oil and dispersant in the rock pool copepod Tigriopus japonicus.

    PubMed

    Lee, Kyun-Woo; Shim, Won Joon; Yim, Un Hyuk; Kang, Jung-Hoon

    2013-08-01

    We determined the toxicity of the water accommodated hydrocarbon fraction (WAF), two chemically enhanced WAFs (CEWAFs; CEWAF-C, Crude oil+Corexit 9500 and CEWAF-H, Crude oil+Hiclean) of crude oil and two dispersants (Corexit 9500 and Hiclean) to the rock pool copepod Tigriopus japonicus. In the acute toxicity test, Corexit 9500 was the most toxic of all the chemicals studied. The nauplius stage of T. japonicus was more susceptible to the toxic chemicals studied than the adult female. The toxicity data using the nauplius stage was then considered as baseline to determine the spiking concentration of chemicals for chronic toxicity tests on the copepod. As the endpoints in the chronic toxicity test, survival, sex ratio, developmental time and fecundity of the copepod were used. All chemicals used in this study resulted in increased toxicity in the F1 generation. The lowest-observed-adverse-effect (LOAE) concentrations of WAF, CEWAF-H, CEWAF-C, Hiclean and Corexit 9500 were observed to be 50%, 10%, 0.1%, 1% and 1%, respectively. The results in present study imply that copepods in marine may be negatively influenced by spilled oil and dispersant. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Identifiability of conservative linear mechanical systems. [applied to large flexible spacecraft structures

    NASA Technical Reports Server (NTRS)

    Sirlin, S. W.; Longman, R. W.; Juang, J. N.

    1985-01-01

    With a sufficiently great number of sensors and actuators, any finite dimensional dynamic system is identifiable on the basis of input-output data. It is presently indicated that, for conservative nongyroscopic linear mechanical systems, the number of sensors and actuators required for identifiability is very large, where 'identifiability' is understood as a unique determination of the mass and stiffness matrices. The required number of sensors and actuators drops by a factor of two, given a relaxation of the identifiability criterion so that identification can fail only if the system parameters being identified lie in a set of measure zero. When the mass matrix is known a priori, this additional information does not significantly affect the requirements for guaranteed identifiability, though the number of parameters to be determined is reduced by a factor of two.

  3. RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.

    PubMed

    Handa, Yoshihiro; Nishide, Hiroyo; Takeda, Naoya; Suzuki, Yutaka; Kawaguchi, Masayoshi; Saito, Katsuharu

    2015-08-01

    Gene expression during arbuscular mycorrhizal development is highly orchestrated in both plants and arbuscular mycorrhizal fungi. To elucidate the gene expression profiles of the symbiotic association, we performed a digital gene expression analysis of Lotus japonicus and Rhizophagus irregularis using a HiSeq 2000 next-generation sequencer with a Cufflinks assembly and de novo transcriptome assembly. There were 3,641 genes differentially expressed during arbuscular mycorrhizal development in L. japonicus, approximately 80% of which were up-regulated. The up-regulated genes included secreted proteins, transporters, proteins involved in lipid and amino acid metabolism, ribosomes and histones. We also detected many genes that were differentially expressed in small-secreted peptides and transcription factors, which may be involved in signal transduction or transcription regulation during symbiosis. Co-regulated genes between arbuscular mycorrhizal and root nodule symbiosis were not particularly abundant, but transcripts encoding for membrane traffic-related proteins, transporters and iron transport-related proteins were found to be highly co-up-regulated. In transcripts of arbuscular mycorrhizal fungi, expansion of cytochrome P450 was observed, which may contribute to various metabolic pathways required to accommodate roots and soil. The comprehensive gene expression data of both plants and arbuscular mycorrhizal fungi provide a powerful platform for investigating the functional and molecular mechanisms underlying arbuscular mycorrhizal symbiosis. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  4. Identifying Corridors among Large Protected Areas in the United States

    PubMed Central

    Belote, R. Travis; Dietz, Matthew S.; McRae, Brad H.; Theobald, David M.; McClure, Meredith L.; Irwin, G. Hugh; McKinley, Peter S.; Gage, Josh A.; Aplet, Gregory H.

    2016-01-01

    Conservation scientists emphasize the importance of maintaining a connected network of protected areas to prevent ecosystems and populations from becoming isolated, reduce the risk of extinction, and ultimately sustain biodiversity. Keeping protected areas connected in a network is increasingly recognized as a conservation priority in the current era of rapid climate change. Models that identify suitable linkages between core areas have been used to prioritize potentially important corridors for maintaining functional connectivity. Here, we identify the most “natural” (i.e., least human-modified) corridors between large protected areas in the contiguous Unites States. We aggregated results from multiple connectivity models to develop a composite map of corridors reflecting agreement of models run under different assumptions about how human modification of land may influence connectivity. To identify which land units are most important for sustaining structural connectivity, we used the composite map of corridors to evaluate connectivity priorities in two ways: (1) among land units outside of our pool of large core protected areas and (2) among units administratively protected as Inventoried Roadless (IRAs) or Wilderness Study Areas (WSAs). Corridor values varied substantially among classes of “unprotected” non-core land units, and land units of high connectivity value and priority represent diverse ownerships and existing levels of protections. We provide a ranking of IRAs and WSAs that should be prioritized for additional protection to maintain minimal human modification. Our results provide a coarse-scale assessment of connectivity priorities for maintaining a connected network of protected areas. PMID:27104683

  5. Characterization of xanthine dehydrogenase and aldehyde oxidase of Marsupenaeus japonicus and their response to microbial pathogen.

    PubMed

    Okamura, Yo; Inada, Mari; Elshopakey, Gehad Elsaid; Itami, Toshiaki

    2018-05-16

    Reactive oxygen species (ROS) play key roles in many physiological processes. In particular, the sterilization mechanism of bacteria using ROS in macrophages is a very important function for biological defense. Xanthine dehydrogenase (XDH) and aldehyde oxidase (AOX), members of the molybdo-flavoenzyme subfamily, are known to generate ROS. Although these enzymes occur in many vertebrates, some insects, and plants, little research has been conducted on XDHs and AOXs in crustaceans. Here, we cloned the entire cDNA sequences of XDH (MjXDH: 4328 bp) and AOX (MjAOX: 4425 bp) from Marsupenaeus japonicus (kuruma shrimp) using reverse transcriptase-polymerase chain reaction (RT-PCR) and random amplification of cDNA ends (RACE). Quantitative real-time RT-PCR transcriptional analysis revealed that MjXDH mRNA is highly expressed in heart and stomach tissues, whereas MjAOX mRNA is highly expressed in the lymphoid organ and intestinal tissues. Furthermore, expression of MjAOX was determined to be up-regulated in the lymphoid organ in response to Vibrio penaeicida at 48 and 72 h after injection; in contrast, hydrogen peroxide (H 2 O 2 ) concentrations increased significantly at 6, 12, 48, and 72 h after injection with white spot syndrome virus (WSSV) and at 72 h after injection with V. penaeicida. To the best of our knowledge, this study is the first to have identified and cloned XDH and AOX from a crustacean species.

  6. The Sulfate Transporter SST1 Is Crucial for Symbiotic Nitrogen Fixation in Lotus japonicus Root Nodules

    PubMed Central

    Krusell, Lene; Krause, Katja; Ott, Thomas; Desbrosses, Guilhem; Krämer, Ute; Sato, Shusei; Nakamura, Yasukazu; Tabata, Satoshi; James, Euan K.; Sandal, Niels; Stougaard, Jens; Kawaguchi, Masayoshi; Miyamoto, Ai; Suganuma, Norio; Udvardi, Michael K.

    2005-01-01

    Symbiotic nitrogen fixation (SNF) by intracellular rhizobia within legume root nodules requires the exchange of nutrients between host plant cells and their resident bacteria. Little is known at the molecular level about plant transporters that mediate such exchanges. Several mutants of the model legume Lotus japonicus have been identified that develop nodules with metabolic defects that cannot fix nitrogen efficiently and exhibit retarded growth under symbiotic conditions. Map-based cloning of defective genes in two such mutants, sst1-1 and sst1-2 (for symbiotic sulfate transporter), revealed two alleles of the same gene. The gene is expressed in a nodule-specific manner and encodes a protein homologous with eukaryotic sulfate transporters. Full-length cDNA of the gene complemented a yeast mutant defective in sulfate transport. Hence, the gene was named Sst1. The sst1-1 and sst1-2 mutants exhibited normal growth and development under nonsymbiotic growth conditions, a result consistent with the nodule-specific expression of Sst1. Data from a previous proteomic study indicate that SST1 is located on the symbiosome membrane in Lotus nodules. Together, these results suggest that SST1 transports sulfate from the plant cell cytoplasm to the intracellular rhizobia, where the nutrient is essential for protein and cofactor synthesis, including nitrogenase biosynthesis. This work shows the importance of plant sulfate transport in SNF and the specialization of a eukaryotic transporter gene for this purpose. PMID:15805486

  7. Absorption of metals in mulloway (Argyrosomus japonicus) after ingesting nickel-plated carbon-steel hooks.

    PubMed

    McGrath, Shane P; Reichelt-Brushett, Amanda J; Butcher, Paul A; Cairns, Stuart C

    2014-08-01

    Previous research has alluded to the potential of metals being absorbed by fish after ingesting fishing hooks, which may have adverse effects on fish health and the organisms that consume them. Subsequently, this study aimed to quantify the potential of mulloway (Argyrosomus japonicus) to absorb metals during the decay of ingested nickel-plated carbon-steel hooks. Twenty-five treatment fish were allowed to ingest nickel-plated carbon-steel hooks during angling and then monitored with 25 controls (untreated fish) for up to 42 days for hook ejection and mortality. Blood, liver and muscle samples were collected from treatment, control and 14 wild-caught individuals to determine the concentrations of chromium, cobalt, copper, iron, manganese and nickel. The results showed that increased oxidation influenced hook ejection, and that hook-ingested fish had significantly elevated concentrations of nickel in their liver and blood, but not muscle. This research has shown that there is an avenue for metal absorption from ingested hooks. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. The molecular network governing nodule organogenesis and infection in the model legume Lotus japonicus.

    PubMed

    Madsen, Lene H; Tirichine, Leïla; Jurkiewicz, Anna; Sullivan, John T; Heckmann, Anne B; Bek, Anita S; Ronson, Clive W; James, Euan K; Stougaard, Jens

    2010-04-12

    Bacterial infection of interior tissues of legume root nodules is controlled at the epidermal cell layer and is closely coordinated with progressing organ development. Using spontaneous nodulating Lotus japonicus plant mutants to uncouple nodule organogenesis from infection, we have determined the role of 16 genes in these two developmental processes. We show that host-encoded mechanisms control three alternative entry processes operating in the epidermis, the root cortex and at the single cell level. Single cell infection did not involve the formation of trans-cellular infection threads and was independent of host Nod-factor receptors and bacterial Nod-factor signals. In contrast, Nod-factor perception was required for epidermal root hair infection threads, whereas primary signal transduction genes preceding the secondary Ca2+ oscillations have an indirect role. We provide support for the origin of rhizobial infection through direct intercellular epidermal invasion and subsequent evolution of crack entry and root hair invasions observed in most extant legumes.

  9. Heavy metals induce oxidative stress and trigger oxidative stress-mediated heat shock protein (hsp) modulation in the intertidal copepod Tigriopus japonicus.

    PubMed

    Kim, Bo-Mi; Rhee, Jae-Sung; Jeong, Chang-Bum; Seo, Jung Soo; Park, Gyung Soo; Lee, Young-Mi; Lee, Jae-Seong

    2014-11-01

    Heat shock proteins (hsps) are induced by a wide range of environmental stressors including heavy metals in aquatic organisms. However, the effect of heavy metals on zooplankton at the molecular level remains still unclear. In this study, we measured the intracellular reactive oxygen species (ROS) level and the antioxidant enzyme activities for 96 h after exposure to five heavy metals: arsenic (As), cadmium (Cd), copper (Cu), silver (Ag), and zinc (Zn) in the intertidal copepod Tigriopus japonicus. Activities of the antioxidant enzymes were highly elevated in metal-exposed copepods, indicating that heavy metals can induce oxidative stress by generating ROS, and stimulate the involvement of antioxidant enzymes as cellular defense mechanisms. Subsequently, transcriptional changes in hsp gene families were further investigated in the metal-exposed groups for 96 h. The ROS level and glutathione (GSH) content were significantly increased in Ag-, As-, and Cu-exposed copepods, while they were only slightly elevated in Cd- and Zn-exposed groups. Based on the numbers of significantly modulated hsp genes and their expression levels for 96 h, we measured the effect of heavy metals to stress genes of T. japonicus in the following order: Cu > Zn > Ag > As > Cd, implying that Cu acts as a stronger oxidative stress inducer than other heavy metals. Of them, the expression of hsp20 and hsp70 genes was substantially modulated by exposure to heavy metals, indicating that these genes would provide a sensitive molecular biomarker for aquatic monitoring of heavy metal pollution. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Whole-Body Microbiota of Sea Cucumber (Apostichopus japonicus) from South Korea for Improved Seafood Management.

    PubMed

    Kim, Tae-Yoon; Lee, Jin-Jae; Kim, Bong-Soo; Choi, Sang Ho

    2017-10-28

    Sea cucumber ( Apostichopus japonicus ) is a popular seafood source in Asia, including South Korea, and its consumption has recently increased with recognition of its medicinal properties. However, because raw sea cucumber contains various microbes, its ingestion can cause foodborne illness. Therefore, analysis of the microbiota in the whole body of sea cucumber can extend our understanding of foodborne illness caused by microorganisms and help to better manage products. We collected 40 sea cucumbers from four different sites in August and November, which are known as the maximum production areas in Korea. The microbiota was analyzed by an Illumina MiSeq system, and bacterial amounts were quantified by real-time PCR. The diversity and bacterial amounts in sea cucumber were higher in August than in November. Alpha-, Beta-, and Gammaproteobacteria were common dominant classes in all samples. However, the microbiota composition differed according to sampling time and site. Staphylococcus warneri and Propionibacterium acnes were commonly detected potential pathogens in August and November samples, respectively. The effect of experimental Vibrio parahaemolyticus infection on the indigenous microbiota of sea cucumber was analyzed at different temperatures, revealing clear alterations of Psychrobacter and Moraxella ; thus, these shifts can be used as indicators for monitoring infection of sea cucumber. Although further studies are needed to clarify and understand the virulence and mechanisms of the identified pathogens of sea cucumber, our study provides a valuable reference for determining the potential of foodborne illness caused by sea cucumber ingestion and to develop monitoring strategies of products using microbiota information.

  11. Semirational Directed Evolution of Loop Regions in Aspergillus japonicus β-Fructofuranosidase for Improved Fructooligosaccharide Production

    PubMed Central

    Trollope, K. M.; Görgens, J. F.

    2015-01-01

    The Aspergillus japonicus β-fructofuranosidase catalyzes the industrially important biotransformation of sucrose to fructooligosaccharides. Operating at high substrate loading and temperatures between 50 and 60°C, the enzyme activity is negatively influenced by glucose product inhibition and thermal instability. To address these limitations, the solvent-exposed loop regions of the β-fructofuranosidase were engineered using a combined crystal structure- and evolutionary-guided approach. This semirational approach yielded a functionally enriched first-round library of 36 single-amino-acid-substitution variants with 58% retaining activity, and of these, 71% displayed improved activities compared to the parent. The substitutions yielding the five most improved variants subsequently were exhaustively combined and evaluated. A four-substitution combination variant was identified as the most improved and reduced the time to completion of an efficient industrial-like reaction by 22%. Characterization of the top five combination variants by isothermal denaturation assays indicated that these variants displayed improved thermostability, with the most thermostable variant displaying a 5.7°C increased melting temperature. The variants displayed uniquely altered, concentration-dependent substrate and product binding as determined by differential scanning fluorimetry. The altered catalytic activity was evidenced by increased specific activities of all five variants, with the most improved variant doubling that of the parent. Variant homology modeling and computational analyses were used to rationalize the effects of amino acid changes lacking direct interaction with substrates. Data indicated that targeting substitutions to loop regions resulted in improved enzyme thermostability, specific activity, and relief from product inhibition. PMID:26253664

  12. Molecular cloning and functional characterization of cathepsin D from sea cucumber Apostichopus japonicus.

    PubMed

    Yu, Cuiping; Cha, Yue; Wu, Fan; Xu, Xianbing; Qin, Lei; Du, Ming

    2017-11-01

    Cathepsin D (CTSD, EC 3.4.23.5) belongs to aspartic protease family, which is located in lysosomes and is distributed in diverse tissues and cells. CTSD has a wide variety of physiological functions, owing to its proteolytic activity in degradating proteins and peptides. In the current study, the full length cDNA of sea cucumber (Apostichopus japonicus) cathepsin D (AjCTSD) was firstly cloned, then the association between AjCTSD and sea cucumber autolysis was investigated. The full length cDNA of AjCTSD was 2896 bp, with an open reading frame (ORF) for 391 amino acids. AjCTSD was widely expressed in body wall, muscle and intestine; the expression level was the highest in intestine, followed by muscle and body wall. Compared to fresh tissues, AjCTSD expression levels were significantly increased in all examined autolytic tissues. The purified recombinant AjCTSD promoted the degradation of sea cucumber muscle. In conclusion, AjCTSD contributed to sea cucumber muscle autolysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. IBT-based quantitative proteomics identifies potential regulatory proteins involved in pigmentation of purple sea cucumber, Apostichopus japonicus.

    PubMed

    Xing, Lili; Sun, Lina; Liu, Shilin; Li, Xiaoni; Zhang, Libin; Yang, Hongsheng

    2017-09-01

    Sea cucumbers are an important economic species and exhibit high yield value among aquaculture animals. Purple sea cucumbers are very rare and beautiful and have stable hereditary patterns. In this study, isobaric tags (IBT) were first used to reveal the molecular mechanism of pigmentation in the body wall of the purple sea cucumber. We analyzed the proteomes of purple sea cucumber in early pigmentation stage (Pa), mid pigmentation stage (Pb) and late pigmentation stage (Pc), resulting in the identification of 5580 proteins, including 1099 differentially expressed proteins in Pb: Pa and 339 differentially expressed proteins in Pc: Pb. GO and KEGG analyses revealed possible differentially expressed proteins, including"melanogenesis", "melanosome", "melanoma", "pigment-biosynthetic process", "Epidermis development", "Ras-signaling pathway", "Wnt-signaling pathway", "response to UV light", and "tyrosine metabolism", involved in pigment synthesis and regulation in purple sea cucumbers. The large number of differentially expressed proteins identified here should be highly useful in further elucidating the mechanisms underlying pigmentation in sea cucumbers. Furthermore, these results may also provide the base for further identification of proteins involved in resistance mechanisms against melanoma, albinism, UV damage, and other diseases in sea cucumbers. Copyright © 2017. Published by Elsevier Inc.

  14. Anti-fibrotic effects of Orostachys japonicus A. Berger (Crassulaceae) on hepatic stellate cells and thioacetamide-induced fibrosis in rats.

    PubMed

    Koppula, Sushruta; Yum, Mun-Jeong; Kim, Jin-Seoub; Shin, Gwang-Mo; Chae, Yun-Jin; Yoon, Tony; Chun, Chi-Su; Lee, Jae-Dong; Song, MinDong

    2017-12-01

    Orostachys japonicus A. Berger (Crassulaceae) has been used in traditional herbal medicines in Korea and other Asian countries to treat various diseases, including liver disorders. In the present study, the anti-fibrotic effects of O. japonicus extract (OJE) in cellular and experimental hepatofibrotic rat models were investigated. An in vitro hepatic stellate cells (HSCs) system was used to estimate cell viability, cell cycle and apoptosis by MTT assay, flow cytometry, and Annexin V-FITC/PI staining techniques, respectively. In addition, thioacetamide (TAA)-induced liver fibrosis was established in Sprague Dawley rats. Briefly, animals were divided into five groups (n = 8): Control, TAA, OJE 10 (TAA with OJE 10 mg/kg), OJE 100 (TAA with OJE 100 mg/kg) and silymarin (TAA with Silymarin 50 mg/kg). Fibrosis was induced by treatment with TAA (200 mg/kg, i.p. ) twice per week for 13 weeks, while OJE and silymarin were administered orally two times per week from week 7 to 13. The fibrotic related gene expression serum biomarkers glutathione and hydroxyproline were estimated by RT-PCR and spectrophotometry, respectively, using commercial kits. OJE (0.5 and 0.1 mg/mL) and silymarin (0.05 mg/mL) treatment significantly ( P < 0.01 and P < 0.001) induced apoptosis (16.95% and 27.48% for OJE and 25.87% for silymarin, respectively) in HSC-T6 cells when compared with the control group (9.09%). Further, rat primary HSCs showed changes in morphology in response to OJE 0.1 mg/mL treatment. In in vivo studies, OJE (10 and 100 mg/kg) treatment significantly ameliorated TAA-induced alterations in levels of serum biomarkers, fibrotic related gene expression, glutathione, and hydroxyproline ( P < 0.05- P < 0.001) and rescued the histopathological changes. OJE can be developed as a potential agent for the treatment of hepatofibrosis.

  15. Integrated multi-omics analysis supports role of lysophosphatidylcholine and related glycerophospholipids in the Lotus japonicus-Glomus intraradices mycorrhizal symbiosis.

    PubMed

    Vijayakumar, Vinod; Liebisch, Gerhard; Buer, Benjamin; Xue, Li; Gerlach, Nina; Blau, Samira; Schmitz, Jessica; Bucher, Marcel

    2016-02-01

    Interaction of plant roots with arbuscular mycorrhizal fungi (AMF) is a complex trait resulting in cooperative interactions among the two symbionts including bidirectional exchange of resources. To study arbuscular mycorrhizal symbiosis (AMS) trait variation in the model plant Lotus japonicus, we performed an integrated multi-omics analysis with a focus on plant and fungal phospholipid (PL) metabolism and biological significance of lysophosphatidylcholine (LPC). Our results support the role of LPC as a bioactive compound eliciting cellular and molecular response mechanisms in Lotus. Evidence is provided for large interspecific chemical diversity of LPC species among mycorrhizae with related AMF species. Lipid, gene expression and elemental profiling emphasize the Lotus-Glomus intraradices interaction as distinct from other arbuscular mycorrhizal (AM) interactions. In G. intraradices, genes involved in fatty acid (FA) elongation and biosynthesis of unsaturated FAs were enhanced, while in Lotus, FA synthesis genes were up-regulated during AMS. Furthermore, FAS protein localization to mitochondria suggests FA biosynthesis and elongation may also occur in AMF. Our results suggest the existence of interspecific partitioning of PL resources for generation of LPC and novel candidate bioactive PLs in the Lotus-G. intraradices symbiosis. Moreover, the data advocate research with phylogenetically diverse Glomeromycota species for a broader understanding of the molecular underpinnings of AMS. © 2015 John Wiley & Sons Ltd.

  16. Anti-inflammatory Effects of the Natural Compounds Cortex Phellodendri and Humulus japonicus on Pelvic Inflammatory Disease in Mice

    PubMed Central

    Oh, Yeonsu; Kwon, Yong-Soo; Jung, Bae Dong

    2017-01-01

    Pelvic inflammatory disease (PID) is an inflammatory and/or infectious disorder of the upper female genital tract, including the uterus, fallopian tubes, and adjacent pelvic structures, that may spread upward to the peritoneum. Currently available treatment options have presented to produce adverse effects of various degrees, such as increased antimicrobial resistance and a limited effective duration of hormones. In the study, the Cortex Phellodendri (CP) and Humulus japonicus (HJ) among natural compounds that are believed to present biological activities with fewer side effects were tested in a PID animal model. The results suggested that the administration CP and HJ reduced clinical signs, inflammatory cytokine expression as well as secretion in uterine tissue, and neutrophil infiltration into the tissue. PMID:28824307

  17. CYTOKININ OXIDASE/DEHYDROGENASE3 Maintains Cytokinin Homeostasis during Root and Nodule Development in Lotus japonicus1[OPEN

    PubMed Central

    Heckmann, Anne B.; Kelly, Simon

    2016-01-01

    Cytokinins are required for symbiotic nodule development in legumes, and cytokinin signaling responses occur locally in nodule primordia and in developing nodules. Here, we show that the Lotus japonicus Ckx3 cytokinin oxidase/dehydrogenase gene is induced by Nod factor during the early phase of nodule initiation. At the cellular level, pCkx3::YFP reporter-gene studies revealed that the Ckx3 promoter is active during the first cortical cell divisions of the nodule primordium and in growing nodules. Cytokinin measurements in ckx3 mutants confirmed that CKX3 activity negatively regulates root cytokinin levels. Particularly, tZ and DHZ type cytokinins in both inoculated and uninoculated roots were elevated in ckx3 mutants, suggesting that these are targets for degradation by the CKX3 cytokinin oxidase/dehydrogenase. The effect of CKX3 on the positive and negative roles of cytokinin in nodule development, infection and regulation was further clarified using ckx3 insertion mutants. Phenotypic analysis indicated that ckx3 mutants have reduced nodulation, infection thread formation and root growth. We also identify a role for cytokinin in regulating nodulation and nitrogen fixation in response to nitrate as ckx3 phenotypes are exaggerated at increased nitrate levels. Together, these findings show that cytokinin accumulation is tightly regulated during nodulation in order to balance the requirement for cell divisions with negative regulatory effects of cytokinin on infection events and root development. PMID:26644503

  18. Impact of water temperature on the growth and fatty acid profiles of juvenile sea cucumber Apostichopus japonicus (Selenka).

    PubMed

    Yu, Haibo; Zhang, Cheng; Gao, Qinfeng; Dong, Shuanglin; Ye, Zhi; Tian, Xiangli

    2016-08-01

    The present study determined the changes in the fatty acid (FA) profiles of juvenile sea cucumber Apostichopus japonicus in response to the varied water temperature. Sea cucumbers with similar size (4.02±0.11g) were cultured for 8 weeks at 14°C, 18°C, 22°C and 26°C, respectively. At the end of the experiment, the specific growth rate (SGR) and the profiles of FAs in neutral lipids and phospholipids of the juvenile sea cucumbers cultured at different temperatures were determined. The SGRs of the sea cucumbers cultured at 26°C significantly decreased 46.3% compared to thos cultured at 18°C. Regression analysis showed that the SGR-temperature (T) relationship can be expressed as SGR=-0.0073T(2)+0.255T -1.0231 (R(2)=0.9936) and the highest SGR was predicted at 17.5°C. For the neutral lipids, the sum of saturated FAs (SFAs), monounsaturated FAs (MUFAs) or polyunsaturated FAs (PUFAs) of the sea cucumbers that were cultured at the water temperature from 18°C-26°C did not change significantly, indicating the insensitivity of FA profiles for the neutral lipids of sea cucumbers in response to increasing water temperature. For phospholipids, the sum of PUFAs in the sea cucumbers dramatically decreased with the gradually increased water temperature. The sum of SFAs and MUFAs of sea cucumbers, however, increased with the gradually elevated water temperature. In particular, the contents of highly unsaturated fatty acids (HUFAs), including eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA), in the phospholipids of the sea cucumbers decreased 37.2% and 26.1%, respectively, when the water temperature increased from 14°C to 26°C. In summary, the sea cucumbers A. japonicus can regulate the FA compositions, especially the contents of EPA and DHA, in the phospholipids so as to adapt to varied water temperature. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Identifiability of large-scale non-linear dynamic network models applied to the ADM1-case study.

    PubMed

    Nimmegeers, Philippe; Lauwers, Joost; Telen, Dries; Logist, Filip; Impe, Jan Van

    2017-06-01

    In this work, both the structural and practical identifiability of the Anaerobic Digestion Model no. 1 (ADM1) is investigated, which serves as a relevant case study of large non-linear dynamic network models. The structural identifiability is investigated using the probabilistic algorithm, adapted to deal with the specifics of the case study (i.e., a large-scale non-linear dynamic system of differential and algebraic equations). The practical identifiability is analyzed using a Monte Carlo parameter estimation procedure for a 'non-informative' and 'informative' experiment, which are heuristically designed. The model structure of ADM1 has been modified by replacing parameters by parameter combinations, to provide a generally locally structurally identifiable version of ADM1. This means that in an idealized theoretical situation, the parameters can be estimated accurately. Furthermore, the generally positive structural identifiability results can be explained from the large number of interconnections between the states in the network structure. This interconnectivity, however, is also observed in the parameter estimates, making uncorrelated parameter estimations in practice difficult. Copyright © 2017. Published by Elsevier Inc.

  20. Flavonoids from Orostachys japonicus A. Berger induces caspase-dependent apoptosis at least partly through activation of p38 MAPK pathway in U937 human leukemic cells.

    PubMed

    Lee, Won Sup; Yun, Jeong Won; Nagappan, Arulkumar; Jung, Ji Hyun; Yi, Sang Mi; Kim, Dong Hoon; Kim, Hye Jung; Kim, GonSup; Ryu, Chung Ho; Shin, Sung Chul; Hong, Soon Chan; Choi, Yung Hyun; Jung, Jin-Myung

    2015-01-01

    Orostachys japonicus A. Berger (A. Berger) is commonly used as a folk remedy for cancer therapy. However, the mechanisms of its anti-cancer activity are poorly investigated in human cancer cells. In this study, we investigated whether flavonoids extracted from Orostachys japonicus A. Berger (FEOJ) might have anticancer effects in human leukemia cells, focusing on cell death mechanisms. U937 human leukemic cancer cells were used. FEOJ induced apoptosis in a dose-dependent manner in human U937 cancer cells. Flow cytometry revealed significant accumulation of cells with sub-G1 DNA content at the concentrations of 200 μg/mL and 400 μg/mL. FEOJ-induced apoptosis was caspase-dependent through loss of mitochondrial membrane potential (MMP, ΔΨm) in human U937 cancer cells, which might be associated with suppression of Bcl-2 and XIAP proteins. FEOJ induced the p38 MAPK signaling pathway, playing at least in part an important role in FEOJ-induced apoptosis. This study suggested that FEOJ may induce caspase-dependent apoptosis in human leukemic cells by regulating MMP (ΔΨm) through suppressing Bcl-2 and X-IAP. In addition, the results indicated that upstream p38 MAPK signaling regulates the apoptotic effect of FEOJ. This study provides evidence that FEOJ might have anti-cancer potential for human leukemic cells.

  1. Development of observational learning during school formation in jack mackerel Trachurus japonicus juveniles.

    PubMed

    Takahashi, Kohji; Masuda, Reiji; Yamashita, Yoh

    2014-03-01

    We assessed whether the development of observational learning in jack mackerel Trachurus japonicus juveniles corresponds with that of their schooling behaviour. Schooling behaviour was quantitatively analyzed by nearest neighbour distance and separation angle in two size classes of fish, 20-mm and 40-mm in body length. Observer and non-observer fish with matching sizes were conditioned to pellets by temporarily stopping aeration. Observer fish were provided with five observation trials of other individuals feeding near an air stone when aeration was stopped. After the observation trial, fish were conditioned to pellets with the stop of aeration, and then the learning process was evaluated by the increase in the association with the feeding area when aeration was stopped. In 20-mm fish, which were at an immature stage of schooling behaviour, there was no difference in the learning process between observer and non-observer fish. In contrast, 40-mm fish were confirmed to have a well-developed schooling behaviour, and the observer learnt the feeding area more efficiently than the non-observer. This study provides evidence that observational learning develops along with the development of the social interaction. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Application of CEDA and ASPIC computer packages to the hairtail ( Trichiurus japonicus) fishery in the East China Sea

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Liu, Qun

    2013-01-01

    Surplus-production models are widely used in fish stock assessment and fisheries management due to their simplicity and lower data demands than age-structured models such as Virtual Population Analysis. The CEDA (catch-effort data analysis) and ASPIC (a surplus-production model incorporating covariates) computer packages are data-fitting or parameter estimation tools that have been developed to analyze catch-and-effort data using non-equilibrium surplus production models. We applied CEDA and ASPIC to the hairtail ( Trichiurus japonicus) fishery in the East China Sea. Both packages produced robust results and yielded similar estimates. In CEDA, the Schaefer surplus production model with log-normal error assumption produced results close to those of ASPIC. CEDA is sensitive to the choice of initial proportion, while ASPIC is not. However, CEDA produced higher R 2 values than ASPIC.

  3. Transcriptome analysis of Kuruma shrimp (Marsupenaeus japonicus) hepatopancreas in response to white spot syndrome virus (WSSV) under experimental infection.

    PubMed

    Zhong, Shengping; Mao, Yong; Wang, Jun; Liu, Min; Zhang, Man; Su, Yongquan

    2017-11-01

    Kuruma shrimp (Marsupenaeus japonicus) is one of the most valuable crustacean species in capture fisheries and mariculture in the Indo-West Pacific. White spot syndrome virus (WSSV) is a highly virulent pathogen which has seriously threatened Kuruma shrimp aquaculture sector. However, little information is available in relation to underlying mechanisms of host-virus interaction in Kuruma shrimp. In this study, we performed a transcriptome analysis from the hepatopancreas of Kuruma shrimp challenged by WSSV, using Illumina-based RNA-Seq. A total of 39,084,942 pair end (PE) reads, including 19,566,190 reads from WSSV-infected group and 19,518,752 reads from non-infected (control) group, were obtained and assembled into 33,215 unigenes with an average length of 503.7 bp and N50 of 601 bp. Approximately 17,000 unigenes were predicted and classified based on homology search, gene ontology, clusters of orthologous groups of proteins, and biological pathway mapping. Differentially expressed genes (DEGs), including 2150 up-regulated and 1931 down-regulated, were found. Among those, 805 DEGs were identified and categorized into 14 groups based on their possible functions. Many genes associated with JAK-STAT signaling pathways, Integrin-mediated signal transduction, Ras signaling pathways, apoptosis and phagocytosis were positively modified after WSSV challenge. The proteolytic cascades including Complement-like activation and Hemolymph coagulations likely participated in antiviral immune response. The transcriptome data from hepatopancreas of Kuruma shrimp under WSSV challenge provided comprehensive information for identifying novel immune related genes in this valuable crustacean species despite the absence of the genome database of crustaceans. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Hemoglobin LjGlb1-1 is involved in nodulation and regulates the level of nitric oxide in the Lotus japonicus-Mesorhizobium loti symbiosis.

    PubMed

    Fukudome, Mitsutaka; Calvo-Begueria, Laura; Kado, Tomohiro; Osuki, Ken-Ichi; Rubio, Maria Carmen; Murakami, Ei-Ichi; Nagata, Maki; Kucho, Ken-Ichi; Sandal, Niels; Stougaard, Jens; Becana, Manuel; Uchiumi, Toshiki

    2016-09-01

    Leghemoglobins transport and deliver O2 to the symbiosomes inside legume nodules and are essential for nitrogen fixation. However, the roles of other hemoglobins (Hbs) in the rhizobia-legume symbiosis are unclear. Several Lotus japonicus mutants affecting LjGlb1-1, a non-symbiotic class 1 Hb, have been used to study the function of this protein in symbiosis. Two TILLING alleles with single amino acid substitutions (A102V and E127K) and a LORE1 null allele with a retrotransposon insertion in the 5'-untranslated region (96642) were selected for phenotyping nodulation. Plants of all three mutant lines showed a decrease in long infection threads and nodules, and an increase in incipient infection threads. About 4h after inoculation, the roots of mutant plants exhibited a greater transient accumulation of nitric oxide (NO) than did the wild-type roots; nevertheless, in vitro NO dioxygenase activities of the wild-type, A102V, and E127K proteins were similar, suggesting that the mutated proteins are not fully functional in vivo The expression of LjGlb1-1, but not of the other class 1 Hb of L. japonicus (LjGlb1-2), was affected during infection of wild-type roots, further supporting a specific role for LjGlb1-1. In conclusion, the LjGlb1-1 mutants reveal that this protein is required during rhizobial infection and regulates NO levels. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  5. How large is large? Identifying large corporate ownerships in FIA datasets

    Treesearch

    Jesse Caputo; Brett Butler; Andy Hartsell

    2017-01-01

    Forest ownership size is a continuous variable, albeit one with a distinctly nonnormal distribution. Although large corporate forest ownerships are expected to differ in terms of behavior and objectives from smaller corporate ownerships, there is no clear and unambiguous means of defined these two ownership groups. We examined the distribution of the ownership size...

  6. Fucosylated chondroitin sulfate is covalently associated with collagen fibrils in sea cucumber Apostichopus japonicus body wall.

    PubMed

    Wang, Jun; Chang, Yaoguang; Wu, Fanxiu; Xu, Xiaoqi; Xue, Changhu

    2018-04-15

    Fucosylated chondroitin sulfate (fCS) is the major carbohydrate constituent of sea cucumber. However, the distribution of fCS in the sea cucumber body wall has not been fully described. We addressed this in the present study employing Apostichopus japonicus as the material, a sea cucumber species with significant commercial importance. It was found that fCS was covalently attached to collagen fibrils via O-glycosidic linkages. Transmission electron microscopy analysis revealed that fCS precipitate was present in gap regions of collagen fibrils as roughly globular or ellipsoidal dots. The fCS dots arranged circumferentially around the fibrils with an axial repeat period that matched the periodicity of the fibrils. Physicochemical analysis indicated that the presence of fCS significantly increased the negative charge of the fibrils. These findings provide novel insight into fCS distribution in the sea cucumber body wall and its supramolecular organization with other macromolecules. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Cytochrome b gene reveals panmixia among Japanese Threadfin Bream, Nemipterus japonicus (Bloch, 1791) populations along the coasts of Peninsular Malaysia and provides evidence of a cryptic species.

    PubMed

    Lim, Hong-Chiun; Ahmad, Abu Talib; Nuruddin, Ahmad Adnan; Mohd Nor, Siti Azizah

    2016-01-01

    We evaluated genetic differentiation among ten presumed Japanese threadfin bream, Nemipterus japonicus populations along the coast of Peninsular Malaysia based on the partial sequence of the mitochondrial cytochrome b gene (982 bp). Genetic divergences (Kimura-2 parameter) ranged from 0.5% to 0.8% among nine of the ten populations while these nine populations were 4.4% to 4.6% diverged from the Kuala Besar population located at the Northeast coast. The constructed Neighbour Joining (NJ) phylogenetic trees based on haplotypes showed the Kuala Besar population forming an isolated cluster. The Analysis of Molecular Variance (AMOVA) of the ten populations a priori assigned into four regions, revealed that most of the variation occurred within population with a fairly low but significant level of regional differentiation (FST = 0.07, p < 0.05, FSC = 0.00, p > 0.05 and FCT = 0.07, p < 0.05) attributed to the Kuala Besar population. p Value after Bonferroni correction revealed that only pairwise FST values involving the Kuala Besar population with the other nine populations were significant. Thus, this study revealed that the N. japonicus populations off Peninsular Malaysia were panmictic. However, the Kuala Besar population, although morphologically identical was composed of a genetically discrete taxon from the rest. These findings are important contributions in formulating sustainable fishery management policies for this important fishery in Peninsular Malaysia.

  8. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities.

    PubMed

    Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

    2016-12-06

    Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance.

  9. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

    PubMed Central

    Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

    2016-01-01

    Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance. PMID:27864511

  10. Anti-fibrotic effects of Orostachys japonicus A. Berger (Crassulaceae) on hepatic stellate cells and thioacetamide-induced fibrosis in rats

    PubMed Central

    Koppula, Sushruta; Yum, Mun-Jeong; Kim, Jin-Seoub; Shin, Gwang-Mo; Chae, Yun-Jin; Yoon, Tony; Chun, Chi-Su; Lee, Jae-Dong

    2017-01-01

    BACKGROUND/OBJECTIVE Orostachys japonicus A. Berger (Crassulaceae) has been used in traditional herbal medicines in Korea and other Asian countries to treat various diseases, including liver disorders. In the present study, the anti-fibrotic effects of O. japonicus extract (OJE) in cellular and experimental hepatofibrotic rat models were investigated. MATERIALS/METHODS An in vitro hepatic stellate cells (HSCs) system was used to estimate cell viability, cell cycle and apoptosis by MTT assay, flow cytometry, and Annexin V-FITC/PI staining techniques, respectively. In addition, thioacetamide (TAA)-induced liver fibrosis was established in Sprague Dawley rats. Briefly, animals were divided into five groups (n = 8): Control, TAA, OJE 10 (TAA with OJE 10 mg/kg), OJE 100 (TAA with OJE 100 mg/kg) and silymarin (TAA with Silymarin 50 mg/kg). Fibrosis was induced by treatment with TAA (200 mg/kg, i.p.) twice per week for 13 weeks, while OJE and silymarin were administered orally two times per week from week 7 to 13. The fibrotic related gene expression serum biomarkers glutathione and hydroxyproline were estimated by RT-PCR and spectrophotometry, respectively, using commercial kits. RESULTS OJE (0.5 and 0.1 mg/mL) and silymarin (0.05 mg/mL) treatment significantly (P < 0.01 and P < 0.001) induced apoptosis (16.95% and 27.48% for OJE and 25.87% for silymarin, respectively) in HSC-T6 cells when compared with the control group (9.09%). Further, rat primary HSCs showed changes in morphology in response to OJE 0.1 mg/mL treatment. In in vivo studies, OJE (10 and 100 mg/kg) treatment significantly ameliorated TAA-induced alterations in levels of serum biomarkers, fibrotic related gene expression, glutathione, and hydroxyproline (P < 0.05-P < 0.001) and rescued the histopathological changes. CONCLUSIONS OJE can be developed as a potential agent for the treatment of hepatofibrosis. PMID:29209457

  11. Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids.

    PubMed

    Wang, Zhicheng; Cui, Jun; Song, Jian; Wang, Haoze; Gao, Kailun; Qiu, Xuemei; Gou, Meng; Li, Xin; Hu, Ziwen; Wang, Xiuli; Chang, Yaqing

    2018-04-01

    Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.

  12. Occurrence of a new microsporidium in the skeletal muscle of the flying fish Cypselurus pinnatibarbatus japonicus (Exocoetidae) from Yakushima, Japan.

    PubMed

    Yokoyama, Hiroshi; Lee, Sun-Joung; Bell, Andrew S

    2002-01-01

    A new microsporidium was observed in the flying fish Cypselurus pinnatibarbatus japonicus (Franz) (Exocoetidae) from Yakushima, Japan. Visual examination revealed the microsporidium to form white elongate nodules in the host's trunk muscle. Monomorphic spores were ovoid to pyriform in shape, with average dimensions of 4.1 x 2.2 microm and possessing a polar tube describing 13-15 coils. Histological observations showed that each parasite focus of infection was encapsulated by a host-produced fibrous membrane. The presence of sporophorous vesicles was not clearly determined. Ribosomal DNA sequence analyses showed the microsporidium to be discrete from other known fish muscle-infecting species and to be most closely related to a clade comprising the Pleistophoridae and Glugea spp. The parasite is provisionally placed as Microsporidium cypselurus sp. n.

  13. Development of fatty acid biomarkers for the identification of wild and aquacultured sea cucumber ( Apostichopus japonicus)

    NASA Astrophysics Data System (ADS)

    Zadorozhnyj, P. A.; Pivnenko, T. N.; Kovalev, N. N.

    2016-02-01

    In this study, the fatty acids (FAs) of the organs and tissues of sea cucumber ( Apostichopus japonicus) were profiled in order to compare the FA composition of sea cucumber collected from natural habitat (wild) and cages (cultured). The differences in FA contents in dermomuscular tube, peripharyngeal annulus, gonad and intestine (with or without content) between the wild and the cultured were determined. The main fatty acids in all organs and tissues were 20:5n-3, 16:1n-7, 20:4n-6, 22:6n-3, 18:0, and 18:1n-7. The basically different FAs of body wall and digestive tube were 16:1n-7, 18:1n-9 and 20:1n-11. The ratio of saturated to mono- and polyunsaturated FAs in digestive tube was independent on inside content while there was a redistribution of the total amount of n-3 and n-6 fatty acids. The comparison of FA composition of the wild and the cultured sea cucumber showed that 20:5n-3, 16:1n-7 and 18:1n-7 predominated the wild while 20:4n-6 predominated the cultured. The content of branched-chain fatty acids in the wild was 3%-4% and about 9% in the cultured. The possible FAs for identifying the wild and the cultured sea cucumbers were selected. It was suggested that the indexes such as the ratio of either (n-3:n-6) to (n-7:n-6) or (n-3) + (n-7) to (n-6) may serve as the biomarkers distinguishing the wild and the cultured sea cucumber.

  14. Sesquiterpene furan compound CJ-01, a novel chitin synthase 2 inhibitor from Chloranthus japonicus SIEB.

    PubMed

    Yim, Nam Hui; Hwang, Eui Il; Yun, Bong Sik; Park, Ki Duk; Moon, Jae Sun; Lee, Sang Han; Sung, Nack Do; Kim, Sung Uk

    2008-05-01

    A novel sesquiterpene furan compound CJ-01 was isolated from the methanol extract of the whole plant of Chloranthus japonicus SIEB. by monitoring the inhibitory activity of chitin synthase 2 from Saccharomyces cerevisiae. Based on spectroscopic analysis, the structure of compound CJ-01 was determined as 3,4,8a-trimethyl-4a,7,8,8a-tetrahydro-4a-naphto[2,3-b]furan-9-one. The compound inhibited chitin synthase 2 of Saccharomyces cerevisiae in a dose-dependent manner with an IC50 of 39.6 microg/ml, whereas it exhibited no inhibitory activities against chitin synthase 1 and 3 of S. cerevisiae up to 280 microg/ml. CJ-01 has 1.7-fold stronger inhibitory activity than polyoxin D (IC50=70 microg/ml), a well-known chitin synthase inhibitor. These results indicate that the compound is a specific inhibitor of chitin synthase 2 from S. cerevisiae. In addition, CJ-01 showed antifungal activities against various human and phytopathogenic fungi. Therefore, the compound might be an interesting lead to develop effective antifungal agents.

  15. Circulating catecholamine and glucose concentrations in Japanese toads (Bufo japonicus) during the breeding season.

    PubMed

    Wilson, J X; Sawai, H; Kikuchi, M; Kubokawa, K; Ishii, S

    1995-06-01

    We investigated the relationship between catecholamine neurohormones and glucose during seasonal reproductive activity in Japanese toads (Bufo japonicus). Field studies found that plasma epinephrine concentration increased as toads migrated to their breeding ponds, where amplexus most frequently took place. Blood glucose concentration also increased as toads arrived at the ponds, even though these animals did not eat during the breeding season, and there was a positive correlation between epinephrine and glucose levels. Blood glucose concentration was higher in amplectic than in solitary males, whereas this relationship did not occur in females. For both males and females, plasma epinephrine concentration was elevated during amplexus. The plasma concentration of norepinephrine was lower than that of epinephrine and did not correlate with either the proximity of the animal to the breeding ponds or the blood glucose concentration. Laboratory experiments showed that systemic injection of [Trp7,Leu8]gonadotropin-releasing hormone (sGnRH) increased plasma epinephrine to levels characteristic of amplectic feral toads. These results suggest that a physiological role of GnRH-like peptides may be to stimulate epinephrine secretion and consequently to increase glucose production in toads under the starvation conditions associated with the breeding migration.

  16. Influence of Various Phenolic Compounds on Properties of Gelatin Film Prepared from Horse Mackerel Trachurus japonicus Scales.

    PubMed

    Le, Thuy; Maki, Hiroki; Okazaki, Emiko; Osako, Kazufumi; Takahashi, Kigen

    2018-06-15

    Influence of various phenolic compounds on physical properties and antioxidant activity of gelatin film from horse mackerel Trachurus japonicus scales was investigated. Tensile strength (TS) of the film was enhanced whereas elongation at break was declined by adding 1% to 5% phenolic compounds. Rutin was the most effective to improve the TS compared to the other tested phenolic compounds including ferulic acid, caffeic acid, gallic acid, and catechin. Gelatin films with the phenolic compounds showed the excellent UV barrier properties. FTIR spectra exhibited that wavenumber of amide-A band of films decreased with formation of hydrogen bonding between amino groups of gelatin and hydroxyl groups of the phenolic compounds. Gelatin film incorporated with rutin which has the largest number of hydroxyl groups among the tested compounds demonstrated the lowest wavenumber for the amide-A peak. It is indicated that hydroxyl groups contained in the phenolic compounds contribute to formation of hydrogen bonds involved in improvement of the mechanical properties of the films. The incorporation of the phenolic compounds with gelatin films also led to the increasing of total phenolic contents and DPPH radical scavenging activities. Thus, it is concluded that phenolic compounds can promote the quality of gelatin film. Properties of gelatin film derived from horse mackerel scales can be improved by adding of phenolic compounds. Phenolic compounds containing a large number of hydroxyl groups should be selected to enhance physical properties of the gelatin film. A biodegradable film prepared from horse mackerel gelatin incorporated with phenolic compounds, which has good physical properties and antioxidant properties, can solve environmental problems caused by synthetic plastic materials. © 2018 Institute of Food Technologists®.

  17. Long-term transportation, by road and air, of chub mackerel (Scomber japonicus) and atlantic bonito (Sarda sarda).

    PubMed

    Correia, João P S; Graça, José T C; Hirofumi, Morikawa; Kube, Nicole

    2011-01-01

    During the second semester of 2009, three trips were made from Olhão (Southern Portugal) to Stralsund (Northern Germany) carrying 2.122 animals, which included multiple teleosts, elasmobranchs and invertebrates. This group included scombrids, such as 1.869 Scomber japonicus and 9 Sarda sarda, which are notoriously difficult to transport. However, multiple adaptations to transport regimes adopted regularly have allowed the authors to successfully move these animals by road and air over a total of up to 25 hr. Such adaptations included maintaining oxygen saturation rates at approximately 200%, and also the constant addition of AmQuel(®) , sodium bicarbonate, and sodium carbonate. Different formulations were used during the three trips, with the best results corresponding to 20/30/30 ppm of the three aforementioned chemicals, respectively. The authors suggest, however, that a modified formula of 20/40/40 ppm will allow for an even more stable pH on future trips. © 2010 Wiley-Liss, Inc.

  18. Validity of deterministic record linkage using multiple indirect personal identifiers: linking a large registry to claims data.

    PubMed

    Setoguchi, Soko; Zhu, Ying; Jalbert, Jessica J; Williams, Lauren A; Chen, Chih-Ying

    2014-05-01

    Linking patient registries with administrative databases can enhance the utility of the databases for epidemiological and comparative effectiveness research. However, registries often lack direct personal identifiers, and the validity of record linkage using multiple indirect personal identifiers is not well understood. Using a large contemporary national cardiovascular device registry and 100% Medicare inpatient data, we linked hospitalization-level records. The main outcomes were the validity measures of several deterministic linkage rules using multiple indirect personal identifiers compared with rules using both direct and indirect personal identifiers. Linkage rules using 2 or 3 indirect, patient-level identifiers (ie, date of birth, sex, admission date) and hospital ID produced linkages with sensitivity of 95% and specificity of 98% compared with a gold standard linkage rule using a combination of both direct and indirect identifiers. Ours is the first large-scale study to validate the performance of deterministic linkage rules without direct personal identifiers. When linking hospitalization-level records in the absence of direct personal identifiers, provider information is necessary for successful linkage. © 2014 American Heart Association, Inc.

  19. A scalable method for identifying frequent subtrees in sets of large phylogenetic trees.

    PubMed

    Ramu, Avinash; Kahveci, Tamer; Burleigh, J Gordon

    2012-10-03

    We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees. We develop a heuristic solution that aims to find MFASTs in sets of many, large phylogenetic trees. Our method works in multiple phases. In the first phase, it identifies small candidate subtrees from the set of input trees which serve as the seeds of larger subtrees. In the second phase, it combines these small seeds to build larger candidate MFASTs. In the final phase, it performs a post-processing step that ensures that we find a frequent agreement subtree that is not contained in a larger frequent agreement subtree. We demonstrate that this heuristic can easily handle data sets with 1000 taxa, greatly extending the estimation of MFASTs beyond current methods. Although this heuristic does not guarantee to find all MFASTs or the largest MFAST, it found the MFAST in all of our synthetic datasets where we could verify the correctness of the result. It also performed well on large empirical data sets. Its performance is robust to the number and size of the input trees. Overall, this method provides a simple and fast way to identify strongly supported subtrees within large phylogenetic hypotheses.

  20. A scalable method for identifying frequent subtrees in sets of large phylogenetic trees

    PubMed Central

    2012-01-01

    Background We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees. Results We develop a heuristic solution that aims to find MFASTs in sets of many, large phylogenetic trees. Our method works in multiple phases. In the first phase, it identifies small candidate subtrees from the set of input trees which serve as the seeds of larger subtrees. In the second phase, it combines these small seeds to build larger candidate MFASTs. In the final phase, it performs a post-processing step that ensures that we find a frequent agreement subtree that is not contained in a larger frequent agreement subtree. We demonstrate that this heuristic can easily handle data sets with 1000 taxa, greatly extending the estimation of MFASTs beyond current methods. Conclusions Although this heuristic does not guarantee to find all MFASTs or the largest MFAST, it found the MFAST in all of our synthetic datasets where we could verify the correctness of the result. It also performed well on large empirical data sets. Its performance is robust to the number and size of the input trees. Overall, this method provides a simple and fast way to identify strongly supported subtrees within large phylogenetic hypotheses. PMID:23033843

  1. Alcohol Brine Freezing of Japanese Horse Mackerel (Trachurus japonicus) for Raw Consumption

    NASA Astrophysics Data System (ADS)

    Maeda, Toshimichi; Yuki, Atsuhiko; Sakurai, Hiroshi; Watanabe, Koichiro; Itoh, Nobuo; Inui, Etsuro; Seike, Kazunori; Mizukami, Yoichi; Fukuda, Yutaka; Harada, Kazuki

    In order to test the possible application of alcohol brine freezing to Japanese horse mackerel (Trachurus japonicus) for raw consumption, the quality and taste of fish frozen by direct immersion in 60% ethanol brine at -20, -25 and -30°C was compared with those by air freezing and fresh fish without freezing. Cracks were not found during the freezing. Smell of ethanol did not remain. K value, an indicator of freshness, of fish frozen in alcohol brine was less than 8.3%, which was at the same level as those by air freezing and fresh fish. Oxidation of lipid was at the same level as air freezing does, and lower than that of fresh fish. The pH of fish frozen in alcohol brine at -25 and -30°C was 6.5 and 6.6, respectively, which were higher than that by air freezing and that of fresh fish. Fish frozen in alcohol brine was better than that by air and at the same level as fresh fish in total evaluation of sensory tests. These results show that the alcohol brine freezing is superior to air freezing, and fish frozen in alcohol brine can be a material for raw consumption. The methods of thawing in tap water, cold water, refrigerator, and at room temperature were compared. Thawing in tap water is considered to be convenient due to the short thaw time and the quality of thawed fish that was best among the methods.

  2. Parental Effect of Long Acclimatization on Thermal Tolerance of Juvenile Sea Cucumber Apostichopus japonicus

    PubMed Central

    Dong, Yun-wei

    2015-01-01

    To evaluate the thermal resistance of marine invertebrates to elevated temperatures under scenarios of future climate change, it is crucial to understand parental effect of long acclimatization on thermal tolerance of offspring. To test whether there is parental effect of long acclimatization, adult sea cucumbers (Apostichopus japonicus) from the same broodstock were transplanted southward and acclimatized at high temperature in field mesocosms. Four groups of juvenile sea cucumbers whose parents experienced different durations of high temperature acclimatization were established. Upper thermal limits, oxygen consumption and levels of heat shock protein mRNA of juveniles was determined to compare thermal tolerance of individuals from different groups. Juvenile sea cucumbers whose parents experienced high temperature could acquire high thermal resistance. With the increase of parental exposure duration to high temperature, offspring became less sensitive to high temperature, as indicated by higher upper thermal limits (LT50), less seasonal variations of oxygen consumption, and stable oxygen consumption rates between chronic and acute thermal stress. The relatively high levels of constitutive expression of heat-shock proteins should contribute to the high thermal tolerance. Together, these results indicated that the existence of a parental effect of long acclimatization would increase thermal tolerance of juveniles and change the thermal sensitivity of sea cucumber to future climate change. PMID:26580550

  3. Parental Effect of Long Acclimatization on Thermal Tolerance of Juvenile Sea Cucumber Apostichopus japonicus.

    PubMed

    Wang, Qing-Lin; Yu, Shan-Shan; Dong, Yun-Wei

    2015-01-01

    To evaluate the thermal resistance of marine invertebrates to elevated temperatures under scenarios of future climate change, it is crucial to understand parental effect of long acclimatization on thermal tolerance of offspring. To test whether there is parental effect of long acclimatization, adult sea cucumbers (Apostichopus japonicus) from the same broodstock were transplanted southward and acclimatized at high temperature in field mesocosms. Four groups of juvenile sea cucumbers whose parents experienced different durations of high temperature acclimatization were established. Upper thermal limits, oxygen consumption and levels of heat shock protein mRNA of juveniles was determined to compare thermal tolerance of individuals from different groups. Juvenile sea cucumbers whose parents experienced high temperature could acquire high thermal resistance. With the increase of parental exposure duration to high temperature, offspring became less sensitive to high temperature, as indicated by higher upper thermal limits (LT50), less seasonal variations of oxygen consumption, and stable oxygen consumption rates between chronic and acute thermal stress. The relatively high levels of constitutive expression of heat-shock proteins should contribute to the high thermal tolerance. Together, these results indicated that the existence of a parental effect of long acclimatization would increase thermal tolerance of juveniles and change the thermal sensitivity of sea cucumber to future climate change.

  4. A Dicarboxylate Transporter, LjALMT4, Mainly Expressed in Nodules of Lotus japonicus.

    PubMed

    Takanashi, Kojiro; Sasaki, Takayuki; Kan, Tomohiro; Saida, Yuka; Sugiyama, Akifumi; Yamamoto, Yoko; Yazaki, Kazufumi

    2016-07-01

    Legume plants can establish symbiosis with soil bacteria called rhizobia to obtain nitrogen as a nutrient directly from atmospheric N2 via symbiotic nitrogen fixation. Legumes and rhizobia form nodules, symbiotic organs in which fixed-nitrogen and photosynthetic products are exchanged between rhizobia and plant cells. The photosynthetic products supplied to rhizobia are thought to be dicarboxylates but little is known about the movement of dicarboxylates in the nodules. In terms of dicarboxylate transporters, an aluminum-activated malate transporter (ALMT) family is a strong candidate responsible for the membrane transport of carboxylates in nodules. Among the seven ALMT genes in the Lotus japonicus genome, only one, LjALMT4, shows a high expression in the nodules. LjALMT4 showed transport activity in a Xenopus oocyte system, with LjALMT4 mediating the efflux of dicarboxylates including malate, succinate, and fumarate, but not tricarboxylates such as citrate. LjALMT4 also mediated the influx of several inorganic anions. Organ-specific gene expression analysis showed LjALMT4 mRNA mainly in the parenchyma cells of nodule vascular bundles. These results suggest that LjALMT4 may not be involved in the direct supply of dicarboxylates to rhizobia in infected cells but is responsible for supplying malate as well as several anions necessary for symbiotic nitrogen fixation, via nodule vasculatures.

  5. Establishment and characterization of a brain cell line from sea perch, Lateolabrax japonicus.

    PubMed

    Le, Yao; Li, Yunlong; Jin, Yilin; Jia, Peng; Jia, Kuntong; Yi, Meisheng

    2017-10-01

    A continuous cell line, designated LJB, derived from the brain of sea perch (Lateolabrax japonicus) was established. LJB cells have been subcultured for more than 60 times in Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS) since the initial primary culture. LJB cells exhibited maximum growth rate at 28°C in DMEM supplemented with 20% FBS. Cytogenetic analysis indicated that the modal chromosome number was 48, which was identical with the chromosome number of embryonic stem-like cells of sea perch. Comparison of the 18S ribosomal RNA gene sequences of LJB cells and sea perch confirmed that LJB cells originated from sea perch. After transfected with pEGFP-N3 plasmid, LJB cells showed a transfection efficiency of about 40% which was indicated by the percentage of cells expressing green fluorescence protein, indicating the potential application of LJB cells in gene expression studies. Cytopathic effect was clearly observed, and RNA-dependent RNA polymerase gene was also detected in LJB cells post red-spotted grouper nervous necrosis virus (RGNNV) infection. Furthermore, virus replication was confirmed by quantitative RT-PCR, virus titer, and transmission electron microscopy assay in RGNNV-infected LJB cells. The LJB cell line might be used as an ideal in vitro tool for analyzing and understanding the mechanisms of nervous necrosis virus-host interaction.

  6. MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

    PubMed Central

    2012-01-01

    Background The major histocompatibility complex (MHC) genes are one of the most important genetic systems in the vertebrate immune response. The diversity of MHC genes may directly influence the survival of individuals against infectious disease. However, there has been no investigation of MHC diversity in the Asiatic black bear (Ursus thibetanus). Here, we analyzed 270-bp nucleotide sequences of the entire exon 2 region of the MHC DQB gene by using 188 samples from the Japanese black bear (Ursus thibetanus japonicus) from 12 local populations. Results Among 185 of 188 samples, we identified 44 MHC variants that encoded 31 different amino acid sequences (allotypes) and one putative pseudogene. The phylogenetic analysis suggests that MHC variants detected from the Japanese black bear are derived from the DQB locus. One of the 31 DQB allotypes, Urth-DQB*01, was found to be common to all local populations. Moreover, this allotype was shared between the black bear on the Asian continent and the Japanese black bear, suggesting that Urth-DQB*01 might have been maintained in the ancestral black bear population for at least 300,000 years. Our findings, from calculating the ratio of non-synonymous to synonymous substitutions, indicate that balancing selection has maintained genetic variation of peptide-binding residues at the DQB locus of the Japanese black bear. From examination of genotype frequencies among local populations, we observed a considerably lower level of observed heterozygosity than expected. Conclusions The low level of observed heterozygosity suggests that genetic drift reduced DQB diversity in the Japanese black bear due to a bottleneck event at the population or species level. The decline of DQB diversity might have been accelerated by the loss of rare variants that have been maintained by negative frequency-dependent selection. Nevertheless, DQB diversity of the black bear appears to be relatively high compared with some other endangered mammalian

  7. MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus.

    PubMed

    Yasukochi, Yoshiki; Kurosaki, Toshifumi; Yoneda, Masaaki; Koike, Hiroko; Satta, Yoko

    2012-11-29

    The major histocompatibility complex (MHC) genes are one of the most important genetic systems in the vertebrate immune response. The diversity of MHC genes may directly influence the survival of individuals against infectious disease. However, there has been no investigation of MHC diversity in the Asiatic black bear (Ursus thibetanus). Here, we analyzed 270-bp nucleotide sequences of the entire exon 2 region of the MHC DQB gene by using 188 samples from the Japanese black bear (Ursus thibetanus japonicus) from 12 local populations. Among 185 of 188 samples, we identified 44 MHC variants that encoded 31 different amino acid sequences (allotypes) and one putative pseudogene. The phylogenetic analysis suggests that MHC variants detected from the Japanese black bear are derived from the DQB locus. One of the 31 DQB allotypes, Urth-DQB*01, was found to be common to all local populations. Moreover, this allotype was shared between the black bear on the Asian continent and the Japanese black bear, suggesting that Urth-DQB*01 might have been maintained in the ancestral black bear population for at least 300,000 years. Our findings, from calculating the ratio of non-synonymous to synonymous substitutions, indicate that balancing selection has maintained genetic variation of peptide-binding residues at the DQB locus of the Japanese black bear. From examination of genotype frequencies among local populations, we observed a considerably lower level of observed heterozygosity than expected. The low level of observed heterozygosity suggests that genetic drift reduced DQB diversity in the Japanese black bear due to a bottleneck event at the population or species level. The decline of DQB diversity might have been accelerated by the loss of rare variants that have been maintained by negative frequency-dependent selection. Nevertheless, DQB diversity of the black bear appears to be relatively high compared with some other endangered mammalian species. This result suggests that

  8. Extracellular matrix remodeling and matrix metalloproteinases (ajMMP-2 like and ajMMP-16 like) characterization during intestine regeneration of sea cucumber Apostichopus japonicus.

    PubMed

    Miao, Ting; Wan, Zixuan; Sun, Lina; Li, Xiaoni; Xing, Lili; Bai, Yucen; Wang, Fang; Yang, Hongsheng

    2017-10-01

    Remodeling of extracellular matrix (ECM) regulated by matrix metalloproteinases (MMPs) is essential for tissue regeneration. In the present study, we used immunohistochemistry (IHC) techniques against ECM components to reveal changes of ECM during intestine regeneration of Apostichopus japonicus. The expression of collagen I and laminin reduced apparently from the eviscerated intestine, while fibronectin exhibited continuous expression in all regeneration stages observed. Meanwhile, we cloned two MMP genes from A. japonicus by RACE PCR. The full-length cDNA of ajMMP-2 like is 2733bp and contains a predicted open reading frame (ORF) of 1716bp encoding 572 amino acids. The full-length cDNA of ajMMP-16 like is 2705bp and contains an ORF of 1452bp encoding 484 amino acids. The predicted protein sequences of each MMP contain two conserved domains, ZnMc_MMP and HX. Homology and phylogenetic analysis revealed that ajMMP-2 like and ajMMP-16 like share high sequence similarity with MMP-2 and MMP-16 from Strongylocentrotus purpuratus, respectively. Then we investigated spatio-temporal expression of ajMMP-2 like and ajMMP-16 like during different regeneration stages by qRT-PCR and IHC. The expression pattern of them showed a roughly opposite trend from that of ECM components. According to our results, a fibronectin-dominate temporary matrix is created in intestine regeneration, and it might provide structural integrity for matrix and promote cell movement. We also hypothesize that ajMMP-2 like and ajMMP-16 like could accelerate cell migration and regulate interaction between ECM components and growth factors. This work provides new evidence of ECM and MMPs involvement in sea cucumber regeneration. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp (Marsupenaeus japonicus) acclimated at different salinities.

    PubMed

    Koyama, Hiroki; Mizusawa, Nanami; Hoashi, Masataka; Tan, Engkong; Yasumoto, Ko; Jimbo, Mitsuru; Ikeda, Daisuke; Yokoyama, Takehiko; Asakawa, Shuichi; Piyapattanakorn, Sanit; Watabe, Shugo

    2018-06-05

    Shrimps inhabiting coastal waters can survive in a wide range of salinity. However, the molecular mechanisms involved in their acclimation to different environmental salinities have remained largely unknown. In the present study, we acclimated kuruma shrimp ( Marsupenaeus japonicus ) at 1.7%, 3.4% and 4.0% salinities. After acclimating for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA sequencing analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after 24 h of acclimation. Glutamine and alanine concentrations were markedly increased following the increase of salinity. In association with such changes, many genes related to amino acid metabolism changed their expression levels. In particular, the increase of the expression level of the gene encoding glutamate-ammonia ligase, which functions in glutamine metabolism, appeared to be associated with the increased glutamine concentration at high salinity. Furthermore, the increased alanine concentration at high salinity was likely associated with the decrease in the expression levels of the the gene encoding alanine-glyoxylate transaminase. Thus, there is a possibility that changes in the concentration of free amino acids for osmoregulation in kuruma shrimp are regulated by changes in the expression levels of genes related to amino acid metabolism. © 2018. Published by The Company of Biologists Ltd.

  10. Identifiability in N-mixture models: a large-scale screening test with bird data.

    PubMed

    Kéry, Marc

    2018-02-01

    Binomial N-mixture models have proven very useful in ecology, conservation, and monitoring: they allow estimation and modeling of abundance separately from detection probability using simple counts. Recently, doubts about parameter identifiability have been voiced. I conducted a large-scale screening test with 137 bird data sets from 2,037 sites. I found virtually no identifiability problems for Poisson and zero-inflated Poisson (ZIP) binomial N-mixture models, but negative-binomial (NB) models had problems in 25% of all data sets. The corresponding multinomial N-mixture models had no problems. Parameter estimates under Poisson and ZIP binomial and multinomial N-mixture models were extremely similar. Identifiability problems became a little more frequent with smaller sample sizes (267 and 50 sites), but were unaffected by whether the models did or did not include covariates. Hence, binomial N-mixture model parameters with Poisson and ZIP mixtures typically appeared identifiable. In contrast, NB mixtures were often unidentifiable, which is worrying since these were often selected by Akaike's information criterion. Identifiability of binomial N-mixture models should always be checked. If problems are found, simpler models, integrated models that combine different observation models or the use of external information via informative priors or penalized likelihoods, may help. © 2017 by the Ecological Society of America.

  11. Effect of high pressure processing on textural and microbiological quality of pink perch (Nemipterus japonicus) sausage during chilled storage

    NASA Astrophysics Data System (ADS)

    Kunnath, Sarika; Panda, Satyen Kumar; Jaganath, Bindu; Gudipati, Venkateshwarlu

    2015-10-01

    The non-thermal high pressure (HP) processing was studied on fish sausage to enhance the quality during chilled storage. Pink perch (Nemipterus japonicus) sausages, packed in poly amide casing under vacuum were subjected to 400, 500 and 600 MPa pressures (dwell time: 10 min and ramp rate: 300 MPa/min) and compared with heat-set samples for physico-chemical and microbial quality parameters. Pressurized samples formed softer and glossier gels with a slight reduction in water-holding capacity. HP made the texture of sausage softer, cohesive and less chewy and gummier than heat-treated ones. Folding test seen higher acceptance values in samples treated at 500 and 600 MPa, during storage. Maximum log reduction in microbial count was observed in 600 MPa immediately, and significant difference in cooked and pressurized sausages was seen only up to 7th day. This revealed the potential application of HP in replacing conventional heat treatment for sausages preparation with enhanced shelf-life.

  12. Effects of different microbes on fermenting feed for sea cucumber ( Apostichopus japonicus)

    NASA Astrophysics Data System (ADS)

    Jiang, Yan; Wang, Yingeng; Mai, Kangsen; Zhang, Zheng; Liao, Meijie; Rong, Xiaojun

    2015-10-01

    The effects of different microbes on fermenting feed for sea cucumber ( Apostichopus japonicus) were compared to select the optimal fermentation strain in this study. Saccharomgces cerevisae, Candida utilis, Bacillus subtilis and Geotrichum candidum were independently added into the experimental compound feed, while only saline was mixed with the control feed. The fermentation treatments were inoculated with 10% seed solution under the condition of 25°C and 70% water content, which lasted for 5 days to elucidate the optimal microbe strain for fermenting effect. Physicochemical indexes and sensorial characteristics were measured per day during the fermentation. The indexes included dry matter recovery (DMR), crude protein (CP), the percentage of amino acid nitrogen to total nitrogen (AA-N/tN), the percentage of ammonia nitrogen to total nitrogen (NH3-N/tN), and the ratio of fermentation strains and vibrios to the total microbes, color, smell and viscosity. The results showed that DMR, CP and AA-N/tN of the S. cerevisae group reached the highest level on day 3, but the ratio of fermentation strain was second to C. utilis group. In addition, its NH3-N/tN and the ratio of vibrios were maintained at low levels, and the sensory evaluation score including smell, color and viscosity was the highest in S. cerevisae group on day 3. Therefore, S. cerevisae could be the optimal strain for the feed fermentation for sea cucumber. This research developed a new production method of fermentation feed for sea cucumber.

  13. Toxicity of antifouling biocides to the intertidal harpacticoid copepod Tigriopus japonicus (Crustacea, Copepoda): effects of temperature and salinity.

    PubMed

    Kwok, K W H; Leung, K M Y

    2005-01-01

    Intertidal harpacticoid copepods are commonly used in eco-toxicity tests worldwide. They predominately live in mid-high shore rock pools and often experience a wide range of temperature and salinity fluctuation. Most eco-toxicity tests are conducted at fixed temperature and salinity and thus the influence of these environmental factors on chemical toxicity is largely unknown. This study investigated the combined effect of temperature and salinity on the acute toxicity of the copepod Tigriopus japonicus against two common biocides, copper (Cu) and tributyltin (TBT) using a 2 x 3 x 4 factorial design (i.e. two temperatures: 25 and 35 degrees C; three salinities: 15.0 per thousand, 34.5 per thousand and 45.0 per thousand; three levels of the biocide plus a control). Copper sulphate and tributyltin chloride were used as the test chemicals while distilled water and acetone were utilised as solvents for Cu and TBT respectively. 96 h-LC50s of Cu and TBT were 1024 and 0.149 microg l(-1) respectively (at 25 degrees C; 34.5 per thousand) and, based on these results, nominal biocide concentrations of LC0 (i.e. control), LC30, LC50 and LC70 were employed. Analysis of Covariance using 'concentration' as the covariate and both 'temperature' and 'salinity' as fixed factors, showed a significant interaction between temperature and salinity effects for Cu, mortality increasing with temperature but decreasing with elevated salinity. A similar result was revealed for TBT. Both temperature and salinity are, therefore, important factors affecting the results of acute eco-toxicity tests using these marine copepods. We recommend that such eco-toxicity tests should be conducted at a range of environmentally realistic temperature/salinity regimes, as this will enhance the sensitivity of the test and improve the safety margin in line with the precautionary principle.

  14. Dissection of Symbiosis and Organ Development by Integrated Transcriptome Analysis of Lotus japonicus Mutant and Wild-Type Plants

    PubMed Central

    Høgslund, Niels; Radutoiu, Simona; Krusell, Lene; Voroshilova, Vera; Hannah, Matthew A.; Goffard, Nicolas; Sanchez, Diego H.; Lippold, Felix; Ott, Thomas; Sato, Shusei; Tabata, Satoshi; Liboriussen, Poul; Lohmann, Gitte V.; Schauser, Leif; Weiller, Georg F.; Udvardi, Michael K.; Stougaard, Jens

    2009-01-01

    Genetic analyses of plant symbiotic mutants has led to the identification of key genes involved in Rhizobium-legume communication as well as in development and function of nitrogen fixing root nodules. However, the impact of these genes in coordinating the transcriptional programs of nodule development has only been studied in limited and isolated studies. Here, we present an integrated genome-wide analysis of transcriptome landscapes in Lotus japonicus wild-type and symbiotic mutant plants. Encompassing five different organs, five stages of the sequentially developed determinate Lotus root nodules, and eight mutants impaired at different stages of the symbiotic interaction, our data set integrates an unprecedented combination of organ- or tissue-specific profiles with mutant transcript profiles. In total, 38 different conditions sampled under the same well-defined growth regimes were included. This comprehensive analysis unravelled new and unexpected patterns of transcriptional regulation during symbiosis and organ development. Contrary to expectations, none of the previously characterized nodulins were among the 37 genes specifically expressed in nodules. Another surprise was the extensive transcriptional response in whole root compared to the susceptible root zone where the cellular response is most pronounced. A large number of transcripts predicted to encode transcriptional regulators, receptors and proteins involved in signal transduction, as well as many genes with unknown function, were found to be regulated during nodule organogenesis and rhizobial infection. Combining wild type and mutant profiles of these transcripts demonstrates the activation of a complex genetic program that delineates symbiotic nitrogen fixation. The complete data set was organized into an indexed expression directory that is accessible from a resource database, and here we present selected examples of biological questions that can be addressed with this comprehensive and powerful

  15. Dose- and time-dependent expression of aryl hydrocarbon receptor (AhR) and aryl hydrocarbon receptor nuclear translocator (ARNT) in PCB-, B[a]P-, and TBT-exposed intertidal copepod Tigriopus japonicus.

    PubMed

    Kim, Bo-Mi; Rhee, Jae-Sung; Hwang, Un-Ki; Seo, Jung Soo; Shin, Kyung-Hoon; Lee, Jae-Seong

    2015-02-01

    The aryl hydrocarbon receptor (AhR) and aryl hydrocarbon nuclear translocator (ARNT) genes from the copepod Tigriopus japonicus (Tj) were cloned to examine their potential functions in the invertebrate putative AhR-CYP signaling pathway. The amino acid sequences encoded by the Tj-AhR and Tj-ARNT genes showed high similarity to homologs of Daphnia and Drosophila, ranging from 68% and 70% similarity for the AhR genes to 56% for the ARNT genes. To determine whether Tj-AhR and Tj-ARNT are modulated by environmental pollutants, transcriptional expression of Tj-AhR and Tj-ARNT was analyzed in response to exposure to five concentrations of polychlorinated biphenyl (PCB 126) (control, 10, 50, 100, 500 μg L(-1)), benzo[a]pyrene (B[a]P) (control, 5, 10, 50, 100 μg L(-1)), and tributyltin (TBT) (control, 1, 5, 10, 20 μg L(-1)) 24h after exposure. A time-course experiment (0, 3, 6, 12, 24h) was performed to analyze mRNA expression patterns after exposure to PCB, B[a]P, and TBT. T. japonicus exhibited dose-dependent and time-dependent upregulation of Tj-AhR and Tj-ARNT in response to pollutant exposure, and the degree of expression was dependent on the pollutant, suggesting that pollutants such as PCB, B[a]P, and TBT modulate expression of Tj-AhR and Tj-ARNT genes in the putative AhR-CYP signaling pathway. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Effects of l-tryptophan on the growth, intestinal enzyme activities and non-specific immune response of sea cucumber (Apostichopus japonicus Selenka) exposed to crowding stress.

    PubMed

    Zhang, Endong; Dong, Shuanglin; Wang, Fang; Tian, Xiangli; Gao, Qinfeng

    2018-04-01

    In order to reveal the effects of l-tryptophan (Trp) on the physiology and immune response of sea cucumber (Apostichopus japonicus Selenka) exposed to crowding stress, four density groups of sea cucumbers (i.e. 4, 8, 16 and 32 individuals per 40 L water, represented as L, ML, MH and H) were fed with diets containing 0, 1, 3 and 5% l-tryptophan respectively for 75 days. The results showed that the specific growth rates (SGR) of the sea cucumber fed with diet with 3% Trp (L, 2.1; ML, 1.76; MH, 1.2; H, 0.7) were significantly higher than those fed with basal diet without Trp supplementation (P < .05). Peak amylase activity occurred at H stress density at 3% dietary Trp. Trypsin activity was higher in diet 3% in ML and MH densities than the controls, which increased by 66.4% and 53.8%. However, the lipase activity first increased and then decreased from the stocking density L to H, with highest values of 3% Trp group showed the highest value than other groups. Compared to those fed with the basal diet, sea cucumber fed diets with Trp (3%) had significantly higher phagocytic activities (0.28 OD540/10 6  cells, H) in coelomic fluid and respiratory burst activities (0.105 OD630/10 6  cells, MH) (P < .05). The results suggested that Trp cannot improve superoxide dismutase (SOD) activity at L, ML and MH densities. The alkaline phosphatase activity (AKP) significantly decreased at H stress density. Under the experimental conditions, the present results confirmed that a diet supplemented with 3% Trp was able to enhance intestinal enzyme activities, non-specific immune response and higher growth performance of A. japonicus. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Effects of dietary n-3 highly unsaturated fatty acids (HUFAs) on growth, fatty acid profiles, antioxidant capacity and immunity of sea cucumber Apostichopus japonicus (Selenka).

    PubMed

    Yu, Haibo; Gao, Qinfeng; Dong, Shuanglin; Zhou, Jishu; Ye, Zhi; Lan, Ying

    2016-07-01

    The present study was conducted to understand the effects of dietary n-3 highly unsaturated fatty acids (HUFAs) on growth, fatty acid profiles, antioxidant capacity and the immunity of sea cucumber Apostichopus japonicus (Selenka). Five experimental diets were prepared, containing graded levels of n-3 HUFAs (0.46%, 0.85%, 1.25%, 1.61% and 1.95%, respectively), and the 0.46% group was used as control group. The specific growth rates, fatty acid profiles, activities and gene expression of antioxidative enzymes and lysozyme of the sea cucumbers that were fed with the 5 experimental diets were determined. The results showed that the specific growth rate of sea cucumbers in all the treatment groups significantly increased compared to the control group (P < 0.05), indicating the positive effects of n-3 HUFAs on the growth of sea cucumbers. The contents of eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) in the body wall of the sea cucumbers gradually increased with the increasing levels of n-3 HUFAs in the diets. The suitable supplement of n-3 HUFAs in diets improved the activities of superoxide dismutase (SOD) and catalase (CAT) of sea cucumbers by up-regulating the expression of SOD and CAT mRNA in sea cucumbers. However, excess n-3 HUFAs in diets caused lipid peroxidation, inhibited the expression of lysozyme (LSZ) mRNA and decreased the activities of LSZ in sea cucumbers. In summary, the suitable supplement levels of n-3 HUFAs in diets of sea cucumbers A. japonicus were estimated between 0.85% and 1.25% considering the growth performance, cost and the indicators of antioxidant capacity and immunity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Regulation of nonsymbiotic and truncated hemoglobin genes of Lotus japonicus in plant organs and in response to nitric oxide and hormones.

    PubMed

    Bustos-Sanmamed, Pilar; Tovar-Méndez, Alejandro; Crespi, Martin; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

    2011-02-01

    • In legumes, symbiotic leghemoglobins facilitate oxygen diffusion to the bacteroids, but the roles of nonsymbiotic and truncated hemoglobins are largely unknown. Here the five hemoglobin genes of Lotus japonicus have been functionally characterized to gain insight into their regulatory mechanisms. • Plants were exposed to nitric oxide donors, stressful conditions, and hormones. Gene expression profiling was determined by quantitative PCR, and gene activities were localized using in situ hybridization and promoter-reporter gene fusions. • The LjGLB1-1, LjGLB2, and LjGLB3-1 mRNA expression levels were very high in nodules relative to other plant organs. The expression of these genes was localized in the vascular bundles, cortex, and infected tissue. LjGLB1-1 was the only gene induced by nitric oxide. Cytokinins caused nearly complete inactivation of LjGLB2 and LjGLB3-1 in nodules and induction of LjGLB1-1 in roots. Abscisic acid induced LjGLB1-1 in nodules and LjGLB1-2 and LjGLB2 in roots, whereas polyamines and jasmonic acid induced LjGLB1-1 only in roots. • The enhanced expression of the three types of hemoglobins in nodules, the colocalization of gene activities in nodule and root tissues with high metabolic rates, and their distinct regulatory mechanisms point out complementary roles of hemoglobins and strongly support the hypothesis that LjGLB1-1, LjGLB2, and LjGLB3-1 are required for symbiosis. © 2010 The Authors. New Phytologist © 2010 New Phytologist Trust.

  19. Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism

    PubMed Central

    Pérez-Delgado, Carmen M.; Moyano, Tomás C.; García-Calderón, Margarita; Canales, Javier; Gutiérrez, Rodrigo A.; Márquez, Antonio J.; Betti, Marco

    2016-01-01

    Nitrogen is one of the most important nutrients for plants and, in natural soils, its availability is often a major limiting factor for plant growth. Here we examine the effect of different forms of nitrogen nutrition and of photorespiration on gene expression in the model legume Lotus japonicus with the aim of identifying regulatory candidate genes co-ordinating primary nitrogen assimilation and photorespiration. The transcriptomic changes produced by the use of different nitrogen sources in leaves of L. japonicus plants combined with the transcriptomic changes produced in the same tissue by different photorespiratory conditions were examined. The results obtained provide novel information on the possible role of plastidic glutamine synthetase in the response to different nitrogen sources and in the C/N balance of L. japonicus plants. The use of gene co-expression networks establishes a clear relationship between photorespiration and primary nitrogen assimilation and identifies possible transcription factors connected to the genes of both routes. PMID:27117340

  20. Structural characterization of fucosylated chondroitin sulfates from sea cucumbers Apostichopus japonicus and Actinopyga mauritiana.

    PubMed

    Ustyuzhanina, Nadezhda E; Bilan, Maria I; Dmitrenok, Andrey S; Tsvetkova, Eugenia A; Shashkov, Alexander S; Stonik, Valentin A; Nifantiev, Nikolay E; Usov, Anatolii I

    2016-11-20

    Two samples of fucosylated chondroitin sulfate (FCS), AJ and AM, were isolated from holothurian species Apostichopus japonicus and Actinopyga mauritiana, respectively. Purification of FCS was performed by ion exchange chromatography followed by gel filtration. Structure of the biopolymers was elucidated using chemical and NMR spectroscopic methods. Both polysaccharides were shown to contain a typical chondroitin core built up of repeating disaccharide units →3)-β-d-GalNAc-(1→4)-β-d-GlcA-(1→ and decorated by sulfate groups and α-l-Fuc branches. Two polysaccharides were different in pattern of sulfation of GalNAc and fucosyl branches connected to O-3 of GlcA. The ratio of GalNAc4S6S:GalNAc4S for AJ was about 2:1, whereas for AM this value was approximately 1:1. AJ contained Fucp2S4S and Fucp3S4S residues linked to O-3 of GlcA in a ratio of 3:1, while for AM this ratio was 1:4. Small portions of Fucp4S units attached to O-3 of GlcA were also found in both polysaccharides. Moreover, in a structure of AM the presence of Fucp3S residues linked to O-6 of GalNAc were determined using the data of NMR spectra. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Regulation of dietary glutamine on the growth, intestinal function, immunity and antioxidant capacity of sea cucumber Apostichopus japonicus (Selenka).

    PubMed

    Yu, Haibo; Gao, Qinfeng; Dong, Shuanglin; Lan, Ying; Ye, Zhi; Wen, Bin

    2016-03-01

    The present study examined the effects of dietary glutamine (Gln) on the growth, intestinal function, immunity and antioxidant capacity of sea cucumber Apostichopus japonicus (Selenka). The specific growth rate, intestinal morphology, activity of digestive enzymes, activity and gene expression of lysozyme and antioxidative enzymes of the sea cucumbers were determined after feeding 5 experimental diets with additions of increasing levels of Gln (at 0%, 0.4%, 0.8%,1.2% and 1.6%, respectively) for 60 days. We discovered that the specific growth rate of the sea cucumbers in 0.4%, 0.8% and 1.2% groups increased 35.3%, 27.3% and 24.1%, respectively, compared to the control (0%) group with significant differences. Dietary Gln can improve the intestinal function of the sea cucumbers by increasing the activities of trypsin and lipase in the intestine and the villus height and villus density of the intestine, eventhough significant differences were not observed in some groups. 0.4%-0.8% of dietary Gln can significantly increase the activity of lysozyme (LSZ) in the coelomic fluid of the sea cucumbers. Significant improvements were observed on the SOD activity in coelomic fluid of the sea cucumbers fed diets supplemented with 0.4%-1.6% of Gln compared to the control group. Similarly, the CAT activity in coelomic fluid of the sea cucumbers significantly increased in 0.8%, 1.2% and 1.6% groups compared to the control and 0.4% groups. Change pattern of the activity of CAT was consistent with the change pattern of the expression of CAT gene, indicating the dietary Gln can up-regulate the expression of CAT gene and consequently promote the secretion of CAT. However, the down-regulation of the expression of SOD gene by dietary Gln were observed in almost all of the treatment groups, which is in contrast with the change pattern of the activity of SOD, indicating the negative feedback regulation of the secretion of SOD on the expression of SOD gene. In summary, the suitable

  2. Modeling Retention at a Large Public University: Can At-Risk Students Be Identified Early Enough to Treat?

    ERIC Educational Resources Information Center

    Singell, Larry D.; Waddell, Glen R.

    2010-01-01

    We examine the extent to which readily available data at a large public university can be used to a priori identify at-risk students who may benefit from targeted retention efforts. Although it is possible to identify such students, there remains an inevitable tradeoff in any resource allocation between not treating the students who are likely to…

  3. Streptomyces amphotericinicus sp. nov., an amphotericin-producing actinomycete isolated from the head of an ant (Camponotus japonicus Mayr).

    PubMed

    Cao, Tingting; Mu, Shan; Lu, Chang; Zhao, Shanshan; Li, Dongmei; Yan, Kai; Xiang, Wensheng; Liu, Chongxi

    2017-12-01

    A novel actinomycete, designated strain 1H-SSA8 T , was isolated from the head of an ant (Camponotus japonicus Mayr) and was found to produce amphotericin. A polyphasic approach was employed to determine the status of strain 1H-SSA8 T . Morphological and chemotaxonomic characteristics were consistent with those of members of the genus Streptomyces. The menaquinones detected were MK-9(H6), MK-9(H8) and MK-9(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylinositol mannoside. The major fatty acids were identified as iso-C16 : 0, C16 : 0, C15 : 0 and anteiso-C15 : 0. Analysis of the 16S rRNA gene sequence showed that strain 1H-SSA8 T belongs to the genus Streptomyces with high sequence similarity to Streptomyces ramulosus NRRL B-2714 T (99.2 %). Two tree-making algorithms based on 16S rRNA gene sequences showed that the isolate formed a phyletic line with Streptomyces himastatinicus ATCC 53653 T (98.7 %). The MLSA utilizing partial sequences of the housekeeping genes (atpD, gyrB, recA, rpoB and trpB) also supported the position. However, evolutionary distances were higher than the 0.007 MLSA evolutionary distance threshold proposed for species-level relatedness. Moreover, the low level of DNA-DNA relatedness and phenotypic differences allowed the novel isolate to be differentiated from its most closely related strain S. ramulosus NRRL B-2714 T and strain S. himastatinicus ATCC 53653 T . It is concluded that the organism can be classified as representing a novel species of the genus Streptomyces, for which the name Streptomyces amphotericinicus sp. nov. is proposed. The type strain is 1H-SSA8 T (=CGMCC 4.7350 T =DSM 103128 T ).

  4. A method for identifying EMI critical circuits during development of a large C3

    NASA Astrophysics Data System (ADS)

    Barr, Douglas H.

    The circuit analysis methods and process Boeing Aerospace used on a large, ground-based military command, control, and communications (C3) system are described. This analysis was designed to help identify electromagnetic interference (EMI) critical circuits. The methodology used the MIL-E-6051 equipment criticality categories as the basis for defining critical circuits, relational database technology to help sort through and account for all of the approximately 5000 system signal cables, and Macintosh Plus personal computers to predict critical circuits based on safety margin analysis. The EMI circuit analysis process systematically examined all system circuits to identify which ones were likely to be EMI critical. The process used two separate, sequential safety margin analyses to identify critical circuits (conservative safety margin analysis, and detailed safety margin analysis). These analyses used field-to-wire and wire-to-wire coupling models using both worst-case and detailed circuit parameters (physical and electrical) to predict circuit safety margins. This process identified the predicted critical circuits that could then be verified by test.

  5. Dietary supplementation of biofloc influences growth performance, physiological stress, antioxidant status and immune response of juvenile sea cucumber Apostichopus japonicus (Selenka).

    PubMed

    Chen, Jinghua; Ren, Yichao; Wang, Guodong; Xia, Bin; Li, Yuquan

    2018-01-01

    Bioflocs are rich in various probiotics and bioactive compounds, which play an important role in improving growth and health status of aquatic organisms. A 60-day experiment was conducted to investigate the effects of dietary supplementation of biofloc on growth performance, digestive enzyme activity, physiological stress, antioxidant status, expression of immune-related genes and disease resistance of sea cucumber Apostichopus japonicus. Juvenile sea cucumbers were fed five experimental diets containing graded levels of biofloc from 0% to 20% (referred as B0, B5, B10, B15 and B20, respectively). The results showed that the sea cucumbers at dietary supplementation levels of 10%-15% biofloc had significantly higher specific growth rate (SGR) compared to control group (diet B0). Digestive enzyme activity increased with the increasing of dietary biofloc level, while no significant difference was found between diets B15 and B20. Dietary supplementation of biofloc also had significant influences on physiological stress parameters except for lactate. There was no significant discrepancy in total coelomocytes counts (TCC) in coelomic fluid of sea cucumber between the treatments. Phagocytosis and respiratory burst of cellular immune at 15% and 20% biofloc levels were significantly higher than those of control group. Significant increases in superoxide dismutase (SOD), total nitric oxide synthase (T-NOS), lysozyme (LSZ), acid phosphatase (ACP) and alkaline phosphatase (AKP) activities of sea cucumber were found at highest dietary supplementation level of 20% biofloc. The expression patterns of immune-related genes (i.e., Hsp90, Hsp70, p105, Rel, NOS and LSZ) in tissues of sea cucumber were analyzed between the experimental diets, and a general trend of up-regulation was observed at higher biofloc levels. Furthermore, dietary 10%-20% biofloc significantly reduced cumulative mortality of sea cucumber after being challenged with Vibrio splendidus. In conclusion, dietary

  6. Analysis of gut microbiota revealed Lactococcus garviaeae could be an indicative of skin ulceration syndrome in farmed sea cucumber Apostichopus japonicus.

    PubMed

    Zhang, Zhen; Xing, Ronglian; Lv, Zhimeng; Shao, Yina; Zhang, Weiwei; Zhao, Xuelin; Li, Chenghua

    2018-06-02

    Accumulative evidence has supported the pivotal roles of gut microbiota in shaping host health in a wide range of animals. However, the relationship between gut microbiota and sea cucumber disease is poorly understood. Using the Illumina sequencing of bacterial 16 S rRNA gene, we investigated the divergence of gut bacterial communities between healthy and skin ulceration syndrome (SUS) diseased Apostichopus japonicus. The results showed that bacterial phylotypes in both groups were closely related at phylum level with predominant component of Proteobacteria (>90%). However, Firmicutes and Verrucomicrobia displayed opposite trends in two groups with higher abundance of Firmicutes and lower of Verrucomicrobia in diseased group. Further KEGG enrichment revealed that bacterial-mediated infectious diseases and signal transduction pathways were significantly induced in the SUS group. We also identified one OTU of Lactococcus garvieae from Firmicutes exhibited significantly different abundances in diseased sea cucumber as compared to healthy subjects. The relative abundance of the species was 27.67% ± 10.52% in diseased group compared to 2.78% ± 2.59% in healthy sea cucumber. Three virulence genes of hlyⅢ, fbp and pva encoded by L. garvieae were investigated by qPCR, and were found to be significantly induced (P < 0.05) in diseased sea cucumbers as compared to healthy ones. All our results supported that L. garvieae might be a potential pathogen for SUS outbreak and could be served as a bio-indicator for this disease monitoring. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Non-destructive geographical traceability of sea cucumber (Apostichopus japonicus) using near infrared spectroscopy combined with chemometric methods

    PubMed Central

    Cai, Rui; Wang, Shisheng; Tang, Bo; Li, Yueqing; Zhao, Weijie

    2018-01-01

    Sea cucumber is the major tonic seafood worldwide, and geographical origin traceability is an important part of its quality and safety control. In this work, a non-destructive method for origin traceability of sea cucumber (Apostichopus japonicus) from northern China Sea and East China Sea using near infrared spectroscopy (NIRS) and multivariate analysis methods was proposed. Total fat contents of 189 fresh sea cucumber samples were determined and partial least-squares (PLS) regression was used to establish the quantitative NIRS model. The ordered predictor selection algorithm was performed to select feasible wavelength regions for the construction of PLS and identification models. The identification model was developed by principal component analysis combined with Mahalanobis distance and scaling to the first range algorithms. In the test set of the optimum PLS models, the root mean square error of prediction was 0.45, and correlation coefficient was 0.90. The correct classification rates of 100% were obtained in both identification calibration model and test model. The overall results indicated that NIRS method combined with chemometric analysis was a suitable tool for origin traceability and identification of fresh sea cucumber samples from nine origins in China. PMID:29410795

  8. Non-destructive geographical traceability of sea cucumber (Apostichopus japonicus) using near infrared spectroscopy combined with chemometric methods.

    PubMed

    Guo, Xiuhan; Cai, Rui; Wang, Shisheng; Tang, Bo; Li, Yueqing; Zhao, Weijie

    2018-01-01

    Sea cucumber is the major tonic seafood worldwide, and geographical origin traceability is an important part of its quality and safety control. In this work, a non-destructive method for origin traceability of sea cucumber ( Apostichopus japonicus ) from northern China Sea and East China Sea using near infrared spectroscopy (NIRS) and multivariate analysis methods was proposed. Total fat contents of 189 fresh sea cucumber samples were determined and partial least-squares (PLS) regression was used to establish the quantitative NIRS model. The ordered predictor selection algorithm was performed to select feasible wavelength regions for the construction of PLS and identification models. The identification model was developed by principal component analysis combined with Mahalanobis distance and scaling to the first range algorithms. In the test set of the optimum PLS models, the root mean square error of prediction was 0.45, and correlation coefficient was 0.90. The correct classification rates of 100% were obtained in both identification calibration model and test model. The overall results indicated that NIRS method combined with chemometric analysis was a suitable tool for origin traceability and identification of fresh sea cucumber samples from nine origins in China.

  9. Identifying and Classifying Pollution Hotspots to Guide Watershed Management in a Large Multiuse Watershed.

    PubMed

    Su, Fangli; Kaplan, David; Li, Lifeng; Li, Haifu; Song, Fei; Liu, Haisheng

    2017-03-03

    In many locations around the globe, large reservoir sustainability is threatened by land use change and direct pollution loading from the upstream watershed. However, the size and complexity of upstream basins makes the planning and implementation of watershed-scale pollution management a challenge. In this study, we established an evaluation system based on 17 factors, representing the potential point and non-point source pollutants and the environmental carrying capacity which are likely to affect the water quality in the Dahuofang Reservoir and watershed in northeastern China. We used entropy methods to rank 118 subwatersheds by their potential pollution threat and clustered subwatersheds according to the potential pollution type. Combining ranking and clustering analyses allowed us to suggest specific areas for prioritized watershed management (in particular, two subwatersheds with the greatest pollution potential) and to recommend the conservation of current practices in other less vulnerable locations (91 small watersheds with low pollution potential). Finally, we identified the factors most likely to influence the water quality of each of the 118 subwatersheds and suggested adaptive control measures for each location. These results provide a scientific basis for improving the watershed management and sustainability of the Dahuofang reservoir and a framework for identifying threats and prioritizing the management of watersheds of large reservoirs around the world.

  10. Identifying and Classifying Pollution Hotspots to Guide Watershed Management in a Large Multiuse Watershed

    PubMed Central

    Su, Fangli; Kaplan, David; Li, Lifeng; Li, Haifu; Song, Fei; Liu, Haisheng

    2017-01-01

    In many locations around the globe, large reservoir sustainability is threatened by land use change and direct pollution loading from the upstream watershed. However, the size and complexity of upstream basins makes the planning and implementation of watershed-scale pollution management a challenge. In this study, we established an evaluation system based on 17 factors, representing the potential point and non-point source pollutants and the environmental carrying capacity which are likely to affect the water quality in the Dahuofang Reservoir and watershed in northeastern China. We used entropy methods to rank 118 subwatersheds by their potential pollution threat and clustered subwatersheds according to the potential pollution type. Combining ranking and clustering analyses allowed us to suggest specific areas for prioritized watershed management (in particular, two subwatersheds with the greatest pollution potential) and to recommend the conservation of current practices in other less vulnerable locations (91 small watersheds with low pollution potential). Finally, we identified the factors most likely to influence the water quality of each of the 118 subwatersheds and suggested adaptive control measures for each location. These results provide a scientific basis for improving the watershed management and sustainability of the Dahuofang reservoir and a framework for identifying threats and prioritizing the management of watersheds of large reservoirs around the world. PMID:28273834

  11. Functional characterization of an unusual phytochelatin synthase, LjPCS3, of Lotus japonicus.

    PubMed

    Ramos, Javier; Naya, Loreto; Gay, Marina; Abián, Joaquín; Becana, Manuel

    2008-09-01

    In plants and many other organisms, phytochelatin synthase (PCS) catalyzes the synthesis of phytochelatins from glutathione in the presence of certain metals and metalloids. We have used budding yeast (Saccharomyces cerevisiae) as a heterologous system to characterize two PCS proteins, LjPCS1 and LjPCS3, of the model legume Lotus japonicus. Initial experiments revealed that the metal tolerance of yeast cells in vivo depends on the concentrations of divalent cations in the growth medium. Detailed in vivo (intact cells) and in vitro (broken cells) assays of PCS activity were performed with yeast expressing the plant enzymes, and values of phytochelatin production for each metal tested were normalized with respect to those of cadmium to correct for the lower expression level of LjPCS3. Our results showed that lead was the best activator of LjPCS1 in the in vitro assay, whereas, for both assays, arsenic, iron, and aluminum were better activators of LjPCS3 and mercury was similarly active with the two enzymes. Most interestingly, zinc was a powerful activator, especially of LjPCS3, when assayed in vivo, whereas copper and silver were the strongest activators in the in vitro assay. We conclude that the in vivo and in vitro assays are useful and complementary to assess the response of LjPCS1 and LjPCS3 to a wide range of metals and that the differences in the C-terminal domains of the two proteins are responsible for their distinct expression levels or stabilities in heterologous systems and patterns of metal activation.

  12. Proximate composition and nutritional quality of deep sea growth sea cucumbers (Stichopus japonicus) from different origins.

    PubMed

    Gao, Yue; Li, Zhibo; Qi, Yanxia; Guo, Zhenyu; Lin, Yantong; Li, Wei; Hu, Yucai; Zhao, Qiancheng

    2016-05-01

    Deep sea growth sea cucumber (Stichopus japonicus) (DSG-SC) is considered a most nutritious and luxurious seafood in Asia. This study compared the proximate composition and nutritional quality of collagen, polysaccharides, amino acids (AAs) and fatty acids (FAs) in DSG-SCs from different origins. The contents of protein, ash, carbohydrate, fat, collagen, saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), total amino acids (TAAs), essential amino acids (EAAs), fucose and uronic acid differed among the origins. DSG-SC of Dalian origin had lower contents of ash, fat, uronic acid, TAAs and EAAs but higher contents of protein, collagen, PUFAs, eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and fucose compared with the other origins. DSG-SCs had a higher proportion of PUFAs and were richer in polysaccharides than other seafood. Glutamate and glycine were the dominant AAs, while leucine and threonine were the most abundant EAAs. DSG-SCs are a good source of collagen, polysaccharides (especially fucose), EAAs (especially leucine and threonine) and PUFAs (especially EPA and DHA). Dalian seems to be a promising origin to produce high-value sea cucumber with high PUFA, fucose, collagen and protein contents. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  13. Globally invasive, withdrawing at home: Aedes albopictus and Aedes japonicus facing the rise of Aedes flavopictus

    NASA Astrophysics Data System (ADS)

    Chaves, Luis Fernando

    2016-11-01

    It has been suggested that climate change may have facilitated the global expansion of invasive disease vectors, since several species have expanded their range as temperatures have warmed. Here, we present results from observations on two major global invasive mosquito vectors (Diptera: Culicidae), Aedes albopictus (Skuse) and Aedes japonicus (Theobald), across the altitudinal range of Mt. Konpira, Nagasaki, Japan, a location within their native range, where Aedes flavopictus Yamada, formerly a rare species, has now become dominant. Spatial abundance patterns of the three species suggest that temperature is an important factor influencing their adult distribution across the altitudinal range of Mt. Konpira. Temporal abundance patterns, by contrast, were associated with rainfall and showed signals of density-dependent regulation in the three species. The spatial and temporal analysis of abundance patterns showed that Ae. flavopictus and Ae. albopictus were negatively associated, even when accounting for differential impacts of weather and other environmental factors in their co-occurrence patterns. Our results highlight a contingency in the expansion of invasive vectors, the potential emergence of changes in their interactions with species in their native communities, and raise the question of whether these changes might be useful to predict the emergence of future invasive vectors.

  14. Variations in early life history traits of Japanese anchovy Engraulis japonicus in the Yangtze River Estuary.

    PubMed

    Liu, Chunlong; Xian, Weiwei; Liu, Shude; Chen, Yifeng

    2018-01-01

    Resources of Japanese anchovy ( Engraulis japonicus Temminck & Schlegel, 1846) are undergoing dramatic recessions in China as the consequence of intensifying anthropogenic activities. Elucidating the influences of local-scale environmental factors on early life history traits is of great importance to design strategies conserving and restoring the declining anchovy resources. In this research, we studied hatching date and early growth of anchovy in the Yangtze River Estuary (YRE) using information obtained from otolith microstructure. Onset of hatching season and growth rates of anchovy was compared to populations in Japan and Taiwan. In YRE, the hatching date of anchovy ranged from February 26th to April 6th and mean growth rate ranged from 0.27 to 0.77 mm/d. Anchovies hatching later had higher growth rates than individuals hatching earlier before the 25th day. Among populations, hatching onsets of anchovy from the higher latitude were later than populations in the lower latitude, and growth rates of anchovy in YRE were much lower than populations in Japan and Taiwan. Variations in hatching onsets and early growth patterns of anchovy thus provide important knowledge on understanding the adaptation of anchovy in YRE and designing management strategies on conserving China's anchovy resources.

  15. Transcription Factors of Lotus: Regulation of Isoflavonoid Biosynthesis Requires Coordinated Changes in Transcription Factor Activity1[W][OA

    PubMed Central

    Shelton, Dale; Stranne, Maria; Mikkelsen, Lisbeth; Pakseresht, Nima; Welham, Tracey; Hiraka, Hideki; Tabata, Satoshi; Sato, Shusei; Paquette, Suzanne; Wang, Trevor L.; Martin, Cathie; Bailey, Paul

    2012-01-01

    Isoflavonoids are a class of phenylpropanoids made by legumes, and consumption of dietary isoflavonoids confers benefits to human health. Our aim is to understand the regulation of isoflavonoid biosynthesis. Many studies have shown the importance of transcription factors in regulating the transcription of one or more genes encoding enzymes in phenylpropanoid metabolism. In this study, we coupled bioinformatics and coexpression analysis to identify candidate genes encoding transcription factors involved in regulating isoflavonoid biosynthesis in Lotus (Lotus japonicus). Genes encoding proteins belonging to 39 of the main transcription factor families were examined by microarray analysis of RNA from leaf tissue that had been elicited with glutathione. Phylogenetic analyses of each transcription factor family were used to identify subgroups of proteins that were specific to L. japonicus or closely related to known regulators of the phenylpropanoid pathway in other species. R2R3MYB subgroup 2 genes showed increased expression after treatment with glutathione. One member of this subgroup, LjMYB14, was constitutively overexpressed in L. japonicus and induced the expression of at least 12 genes that encoded enzymes in the general phenylpropanoid and isoflavonoid pathways. A distinct set of six R2R3MYB subgroup 2-like genes was identified. We suggest that these subgroup 2 sister group proteins and those belonging to the main subgroup 2 have roles in inducing isoflavonoid biosynthesis. The induction of isoflavonoid production in L. japonicus also involves the coordinated down-regulation of competing biosynthetic pathways by changing the expression of other transcription factors. PMID:22529285

  16. Statistical Analyses of Scatterplots to Identify Important Factors in Large-Scale Simulations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kleijnen, J.P.C.; Helton, J.C.

    1999-04-01

    The robustness of procedures for identifying patterns in scatterplots generated in Monte Carlo sensitivity analyses is investigated. These procedures are based on attempts to detect increasingly complex patterns in the scatterplots under consideration and involve the identification of (1) linear relationships with correlation coefficients, (2) monotonic relationships with rank correlation coefficients, (3) trends in central tendency as defined by means, medians and the Kruskal-Wallis statistic, (4) trends in variability as defined by variances and interquartile ranges, and (5) deviations from randomness as defined by the chi-square statistic. The following two topics related to the robustness of these procedures are consideredmore » for a sequence of example analyses with a large model for two-phase fluid flow: the presence of Type I and Type II errors, and the stability of results obtained with independent Latin hypercube samples. Observations from analysis include: (1) Type I errors are unavoidable, (2) Type II errors can occur when inappropriate analysis procedures are used, (3) physical explanations should always be sought for why statistical procedures identify variables as being important, and (4) the identification of important variables tends to be stable for independent Latin hypercube samples.« less

  17. miRNA-133 augments coelomocyte phagocytosis in bacteria-challenged Apostichopus japonicus via targeting the TLR component of IRAK-1 in vitro and in vivo

    PubMed Central

    Lu, Meng; Zhang, Peng-Juan; Li, Cheng-Hua; Lv, Zhi-Meng; Zhang, Wei-Wei; Jin, Chun-Hua

    2015-01-01

    In this study, we explored the potential roles of miRNA-133 in regulating TLR pathways in the sea cucumber Apostichopus japonicus. Target screening of RNA-Seq data successfully identified interleukin-1 receptor-associated kinase (AjIRAK−1) as a putative target of miR-133. This result was further validated by negative expression profiles in Vibrio splendidus-challenged coelomocytes and lipopolysaccharide (LPS)-exposed cell cultures. HEK-293T cells transfected with a dual-luciferase reporter fused to the 3′UTR of wild-type or mutant AjIRAK-1 exhibited a 52.9% reduction in luciferase activity (p < 0.01) compared to controls. Co-infection with a miR-133 mimics or a specific siRNA targeting AjIRAK-1 significantly repressed the mRNA and protein expression levels of AjIRAK-1 and its downstream molecules, such as AjTRAF6 and Ajp105, in primary coelomocytes. In contrast, a miR-133 inhibitor significantly increased the expression of these TLR pathway members. The injection of miR-133 agomir or AjIRAK-1 siRNA into sea cucumbers not only decreased the expression of AjIRAK-1 and its downstream molecules but also significantly increased V. splendidus coelomocyte phagocytosis. All of the present data provide direct evidence that miR-133 is involved in TLR cascade modulation through AjIRAK-1 targeting to promote V. splendidus coelomocyte phagocytosis in these non-model invertebrates. PMID:26223836

  18. miRNA-133 augments coelomocyte phagocytosis in bacteria-challenged Apostichopus japonicus via targeting the TLR component of IRAK-1 in vitro and in vivo.

    PubMed

    Lu, Meng; Zhang, Peng-Juan; Li, Cheng-Hua; Lv, Zhi-Meng; Zhang, Wei-Wei; Jin, Chun-Hua

    2015-07-30

    In this study, we explored the potential roles of miRNA-133 in regulating TLR pathways in the sea cucumber Apostichopus japonicus. Target screening of RNA-Seq data successfully identified interleukin-1 receptor-associated kinase (AjIRAK-1) as a putative target of miR-133. This result was further validated by negative expression profiles in Vibrio splendidus-challenged coelomocytes and lipopolysaccharide (LPS)-exposed cell cultures. HEK-293T cells transfected with a dual-luciferase reporter fused to the 3'UTR of wild-type or mutant AjIRAK-1 exhibited a 52.9% reduction in luciferase activity (p < 0.01) compared to controls. Co-infection with a miR-133 mimics or a specific siRNA targeting AjIRAK-1 significantly repressed the mRNA and protein expression levels of AjIRAK-1 and its downstream molecules, such as AjTRAF6 and Ajp105, in primary coelomocytes. In contrast, a miR-133 inhibitor significantly increased the expression of these TLR pathway members. The injection of miR-133 agomir or AjIRAK-1 siRNA into sea cucumbers not only decreased the expression of AjIRAK-1 and its downstream molecules but also significantly increased V. splendidus coelomocyte phagocytosis. All of the present data provide direct evidence that miR-133 is involved in TLR cascade modulation through AjIRAK-1 targeting to promote V. splendidus coelomocyte phagocytosis in these non-model invertebrates.

  19. Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

    PubMed Central

    Lo, Yu-Chen; Senese, Silvia; Li, Chien-Ming; Hu, Qiyang; Huang, Yong; Damoiseaux, Robert; Torres, Jorge Z.

    2015-01-01

    Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies. Current in silico target identification methods, including chemical similarity database searches, are limited to single or sequential ligand analysis that have limited capabilities for accurate deconvolution of a large number of compounds with diverse chemical structures. Here, we present CSNAP (Chemical Similarity Network Analysis Pulldown), a new computational target identification method that utilizes chemical similarity networks for large-scale chemotype (consensus chemical pattern) recognition and drug target profiling. Our benchmark study showed that CSNAP can achieve an overall higher accuracy (>80%) of target prediction with respect to representative chemotypes in large (>200) compound sets, in comparison to the SEA approach (60–70%). Additionally, CSNAP is capable of integrating with biological knowledge-based databases (Uniprot, GO) and high-throughput biology platforms (proteomic, genetic, etc) for system-wise drug target validation. To demonstrate the utility of the CSNAP approach, we combined CSNAP's target prediction with experimental ligand evaluation to identify the major mitotic targets of hit compounds from a cell-based chemical screen and we highlight novel compounds targeting microtubules, an important cancer therapeutic target. The CSNAP method is freely available and can be accessed from the CSNAP web server (http://services.mbi.ucla.edu/CSNAP/). PMID:25826798

  20. Reassimilation of Photorespiratory Ammonium in Lotus japonicus Plants Deficient in Plastidic Glutamine Synthetase

    PubMed Central

    Pérez-Delgado, Carmen M.; García-Calderón, Margarita; Márquez, Antonio J.; Betti, Marco

    2015-01-01

    It is well established that the plastidic isoform of glutamine synthetase (GS2) is the enzyme in charge of photorespiratory ammonium reassimilation in plants. The metabolic events associated to photorespiratory NH4 + accumulation were analyzed in a Lotus japonicus photorespiratory mutant lacking GS2. The mutant plants accumulated high levels of NH4 + when photorespiration was active, followed by a sudden drop in the levels of this compound. In this paper it was examined the possible existence of enzymatic pathways alternative to GS2 that could account for this decline in the photorespiratory ammonium. Induction of genes encoding for cytosolic glutamine synthetase (GS1), glutamate dehydrogenase (GDH) and asparagine synthetase (ASN) was observed in the mutant in correspondence with the diminishment of NH4 +. Measurements of gene expression, polypeptide levels, enzyme activity and metabolite levels were carried out in leaf samples from WT and mutant plants after different periods of time under active photorespiratory conditions. In the case of asparagine synthetase it was not possible to determine enzyme activity and polypeptide content; however, an increased asparagine content in parallel with the induction of ASN gene expression was detected in the mutant plants. This increase in asparagine levels took place concomitantly with an increase in glutamine due to the induction of cytosolic GS1 in the mutant, thus revealing a major role of cytosolic GS1 in the reassimilation and detoxification of photorespiratory NH4 + when the plastidic GS2 isoform is lacking. Moreover, a diminishment in glutamate levels was observed, that may be explained by the induction of NAD(H)-dependent GDH activity. PMID:26091523

  1. Relationship between luminous fish and symbiosis. I. Comparative studies of lipopolysaccharides isolated from symbiotic luminous bacteria of the luminous marine fish, Physiculus japonicus.

    PubMed

    Kuwae, T; Andoh, M; Fukasawa, S; Kurata, M

    1983-01-01

    In order to investigate the relationship between host and symbiosis in the luminous marine fish, Physiculus japonicus, the bacterial lipopolysaccharides (LPS) of symbiotic luminous bacteria were compared serologically and electrophoretically. Five symbiotic luminous bacteria (PJ strains) were separately isolated from five individuals of this fish species caught at three points, off the coasts of Chiba, Nakaminato, and Oharai. LPS preparations were made from these bacteria by Westphal's phenol-water method and highly purified by repeated ultracentrifugation. These LPSs contained little or no 2-keto-3-deoxyoctonate and had powerful mitogenic activity. In sodium dodecylsulfate polyacrylamide gel electrophoresis, these PJ-1 to -5 LPSs were separated by their electrophoretic patterns into three groups; the first group included PJ-1 and PJ-4, the second group PJ-2 and PJ-3, and the third group PJ-5 alone. The results agreed with those of the double immunodiffusion test; precipitin lines completely coalesced within each group but not with other groups. In immunoelectrophoresis, one precipitin line was observed between anti PJ-2 LPS serum and PJ-5 LPS but the electrophoretic mobility of PJ-5 LPS was clearly different from that of the PJ-2 LPS group. Furthermore, in a 50% inhibition test with PJ-2 LPS by the passive hemolysis system, the doses of PJ-2 LPS, PJ-3 LPS, and PJ-5 LPS required for 50% inhibition (ID50) in this system were 0.25, 0.25, and 21.6 micrograms/ml for each alkali-treated LPS, respectively, and the ID50's of both PJ-1 LPS and PJ-4 LPS were above 1,000 micrograms/ml. These results indicate that PJ-5 LPS has an antigenic determinant partially in common with LPS from the PJ-2 group but not with LPS from the PJ-1 group and that the symbiotic luminous bacterium PJ-5 is more closely related to the PJ-2 group than to the PJ-1 group. These results show that the species Physiculus japonicus is symbiotically associated with at least three immunologically different

  2. [Studies on preparative technology and quantitative determination for extracts of total saponin in roof of Panax japonicus].

    PubMed

    He, Yu-min; Lu, Ke-ming; Yuan, Ding; Zhang, Chang-cheng

    2008-11-01

    To explore the optimum extraction and purification condition of the total saponins in the root of Panax japonicus (RPJ), and establish its quality control methods. Designed L16 (4(5)) orthogonal test with the extraction rate of total saponins as index, to determine the rational extraction process, and the techniques of water-saturated n-butanol extraction and acetone precipitation were applied to purify the alcohol extract of RPJ. Total saponins were detected by spectrophotometry and its triterpenoidal sapogenin oleanolic acid detected by HPLC. The optimum conditions of total saponins from RPJ was as follows: the material was pulverized, dipped in 60% ethanol aqueous solution as extract solvent at 10 times of volume, and refluxed 3 times for 3 h each time. Extractant of water-saturated n-butanol with extraction times of 3 and precipitant of acetone with precipitation amount of 4-5 times were included in the purification process, which would obtain the quality products. The content of total saponins could reach to 83.48%, and oleanolic acid to 38.30%. The optimized preparative technology is stable, convenient and practical. The extract rate of RPJ was high and steady with this technology, which provided new evidence for industrializing production of the plant and developing new drug.

  3. Baculoviral mid-gut gland necrosis (BMN) of kuruma shrimp (Penaeus japonicus) larvae in Japanese intensive culture systems

    NASA Astrophysics Data System (ADS)

    Sano, T.; Nishimura, T.; Fukuda, H.; Hayashida, T.; Momoyama, K.

    1984-03-01

    In many shrimp farms in the Kyushu and Chugoku areas of Japan, the so-called mid-gut gland cloudy disease of kuruma shrimp larvae (Penaeus japonicus) has occurred since 1971. The pathological changes associated with this baculoviral mid-gut gland necrosis (BMN) are extensive cellular necrosis, collapse of mid-gut gland cells, nuclear hypertrophy and finally karyorrhexis. Electron microscopic examination revealed the presence of virions and virogenic stages in the affected nuclei. Average length and diameter of the virions detected was 310 and 72 nm, respectively; nucleocapsids were 250 nm in size. Virions enclosing 2 nucleocapsids within a single envelope were rarely found. The spirally arranged capsomeres were at an angle of 37 to 38° to a horizontal line meeting at right angles with the long axis of the virion. Infectivity trials resulted in high mortality of healthy mysis and juveniles (2nd post-larval stage). Juveniles at the 9th post-larval stage showed no mortality, although they could be infected easily by the agent. Hypertrophied nuclei in squashed and stained preparations of the affected gland cells can be considered to be of reliable presumptive diagnostic character, and fluorescent antibody staining can be employed to confirm the diagnosis of BMN.

  4. Enrichment, Distribution of Vanadium-Containing Protein in Vanadium-Enriched Sea Cucumber Apostichopus japonicus and the Ameliorative Effect on Insulin Resistance.

    PubMed

    Liu, Yanjun; Zhou, Qingxin; Zhao, Yanlei; Wang, Yiming; Wang, Yuming; Wang, Jingfeng; Xu, Jie; Xue, Changhu

    2016-05-01

    Sea cucumbers are a potential source of natural organic vanadium that may improve insulin resistance. In this work, vanadium was accumulated rapidly in blood, body wall, and intestine by sea cucumber Apostichopus japonicus. Furthermore, water-soluble vanadium-containing proteins, the main form of the organic vanadium, were tentatively accumulated and isolated by a bioaccumulation experiment. It was also designed to evaluate the beneficial effect of vanadium-containing proteins (VCPs) from sea cucumber rich in vanadium on the development of hyperglycemia and insulin resistance in C57BL/6J mice fed with a high-fat high-sucrose diet (HFSD). HFSD mice treated with VCPs significantly decreased fasting blood glucose, serum insulin, and HOMA-IR values as compared to HFSD mice, respectively. Serum adiponectin, resistin, TNF-α, and leptin levels in insulin-resistant mice were dramatically reduced by a VCP supplement. These results show an ameliorative effect on insulin resistance by treatment with VCPs. Such compound seems to be a valuable therapy to achieve and/or maintain glycemic control and therapeutic agents in the treatment arsenal for insulin resistance and type 2 diabetes.

  5. Adverse effects of methylmercury (MeHg) on life parameters, antioxidant systems, and MAPK signaling pathways in the copepod Tigriopus japonicus.

    PubMed

    Lee, Young Hwan; Kang, Hye-Min; Kim, Duck-Hyun; Wang, Minghua; Jeong, Chang-Bum; Lee, Jae-Seong

    2017-03-01

    Methylmercury (MeHg) is a concerning environmental pollutant that bioaccumulates and biomagnifies in the aquatic food web. However, the effects of MeHg on marine zooplankton are poorly understood even though zooplankton are considered key mediators of the bioaccumulation and biomagnification of MeHg in high-trophic marine organisms. Here, the toxicity of MeHg in the benthic copepod Tigriopus japonicus was assessed, and its adverse effects on growth rate and reproduction were demonstrated. Antioxidant enzymatic activities were increased in the presence of MeHg, indicating that these enzymes play an important role in the defense response to MeHg, which is regulated by a complex mechanism. Subsequent activation of different patterns of mitogen-activated protein kinase (MAPK) pathways was demonstrated, providing a mechanistic approach to understand the signaling pathways involved in the effects of MeHg. Our results provide valuable information for understanding the toxicity of MeHg and the underlying defense mechanism in response to MeHg exposure in marine zooplankton. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants.

    PubMed

    Dadaev, Tokhir; Saunders, Edward J; Newcombe, Paul J; Anokian, Ezequiel; Leongamornlert, Daniel A; Brook, Mark N; Cieza-Borrella, Clara; Mijuskovic, Martina; Wakerell, Sarah; Olama, Ali Amin Al; Schumacher, Fredrick R; Berndt, Sonja I; Benlloch, Sara; Ahmed, Mahbubl; Goh, Chee; Sheng, Xin; Zhang, Zhuo; Muir, Kenneth; Govindasami, Koveela; Lophatananon, Artitaya; Stevens, Victoria L; Gapstur, Susan M; Carter, Brian D; Tangen, Catherine M; Goodman, Phyllis; Thompson, Ian M; Batra, Jyotsna; Chambers, Suzanne; Moya, Leire; Clements, Judith; Horvath, Lisa; Tilley, Wayne; Risbridger, Gail; Gronberg, Henrik; Aly, Markus; Nordström, Tobias; Pharoah, Paul; Pashayan, Nora; Schleutker, Johanna; Tammela, Teuvo L J; Sipeky, Csilla; Auvinen, Anssi; Albanes, Demetrius; Weinstein, Stephanie; Wolk, Alicja; Hakansson, Niclas; West, Catharine; Dunning, Alison M; Burnet, Neil; Mucci, Lorelei; Giovannucci, Edward; Andriole, Gerald; Cussenot, Olivier; Cancel-Tassin, Géraldine; Koutros, Stella; Freeman, Laura E Beane; Sorensen, Karina Dalsgaard; Orntoft, Torben Falck; Borre, Michael; Maehle, Lovise; Grindedal, Eli Marie; Neal, David E; Donovan, Jenny L; Hamdy, Freddie C; Martin, Richard M; Travis, Ruth C; Key, Tim J; Hamilton, Robert J; Fleshner, Neil E; Finelli, Antonio; Ingles, Sue Ann; Stern, Mariana C; Rosenstein, Barry; Kerns, Sarah; Ostrer, Harry; Lu, Yong-Jie; Zhang, Hong-Wei; Feng, Ninghan; Mao, Xueying; Guo, Xin; Wang, Guomin; Sun, Zan; Giles, Graham G; Southey, Melissa C; MacInnis, Robert J; FitzGerald, Liesel M; Kibel, Adam S; Drake, Bettina F; Vega, Ana; Gómez-Caamaño, Antonio; Fachal, Laura; Szulkin, Robert; Eklund, Martin; Kogevinas, Manolis; Llorca, Javier; Castaño-Vinyals, Gemma; Penney, Kathryn L; Stampfer, Meir; Park, Jong Y; Sellers, Thomas A; Lin, Hui-Yi; Stanford, Janet L; Cybulski, Cezary; Wokolorczyk, Dominika; Lubinski, Jan; Ostrander, Elaine A; Geybels, Milan S; Nordestgaard, Børge G; Nielsen, Sune F; Weisher, Maren; Bisbjerg, Rasmus; Røder, Martin Andreas; Iversen, Peter; Brenner, Hermann; Cuk, Katarina; Holleczek, Bernd; Maier, Christiane; Luedeke, Manuel; Schnoeller, Thomas; Kim, Jeri; Logothetis, Christopher J; John, Esther M; Teixeira, Manuel R; Paulo, Paula; Cardoso, Marta; Neuhausen, Susan L; Steele, Linda; Ding, Yuan Chun; De Ruyck, Kim; De Meerleer, Gert; Ost, Piet; Razack, Azad; Lim, Jasmine; Teo, Soo-Hwang; Lin, Daniel W; Newcomb, Lisa F; Lessel, Davor; Gamulin, Marija; Kulis, Tomislav; Kaneva, Radka; Usmani, Nawaid; Slavov, Chavdar; Mitev, Vanio; Parliament, Matthew; Singhal, Sandeep; Claessens, Frank; Joniau, Steven; Van den Broeck, Thomas; Larkin, Samantha; Townsend, Paul A; Aukim-Hastie, Claire; Gago-Dominguez, Manuela; Castelao, Jose Esteban; Martinez, Maria Elena; Roobol, Monique J; Jenster, Guido; van Schaik, Ron H N; Menegaux, Florence; Truong, Thérèse; Koudou, Yves Akoli; Xu, Jianfeng; Khaw, Kay-Tee; Cannon-Albright, Lisa; Pandha, Hardev; Michael, Agnieszka; Kierzek, Andrzej; Thibodeau, Stephen N; McDonnell, Shannon K; Schaid, Daniel J; Lindstrom, Sara; Turman, Constance; Ma, Jing; Hunter, David J; Riboli, Elio; Siddiq, Afshan; Canzian, Federico; Kolonel, Laurence N; Le Marchand, Loic; Hoover, Robert N; Machiela, Mitchell J; Kraft, Peter; Freedman, Matthew; Wiklund, Fredrik; Chanock, Stephen; Henderson, Brian E; Easton, Douglas F; Haiman, Christopher A; Eeles, Rosalind A; Conti, David V; Kote-Jarai, Zsofia

    2018-06-11

    Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling.

  7. Contributions of molecular size, charge distribution, and specific amino acids to the iron-binding capacity of sea cucumber (Stichopus japonicus) ovum hydrolysates.

    PubMed

    Sun, Na; Cui, Pengbo; Jin, Ziqi; Wu, Haitao; Wang, Yixing; Lin, Songyi

    2017-09-01

    This study investigated the contributions of molecular size, charge distribution and specific amino acids to the iron-binding capacity of sea cucumber (Stichopus japonicus) ovum hydrolysates (SCOHs), and further explored their iron-binding sites. It was demonstrated that enzyme type and degree of hydrolysis (DH) significantly influenced the iron-binding capacity of the SCOHs. The SCOHs produced by alcalase at a DH of 25.9% possessed the highest iron-binding capacity at 92.1%. As the hydrolysis time increased, the molecular size of the SCOHs decreased, the negative charges increased, and the hydrophilic amino acids were exposed to the surface, facilitating iron binding. Furthermore, the Fourier transform infrared spectra, combined with amino acid composition analysis, revealed that iron bound to the SCOHs primarily through interactions with carboxyl oxygen of Asp, guanidine nitrogen of Arg or nitrogen atoms in imidazole group of His. The formed SCOHs-iron complexes exhibited a fold and crystal structure with spherical particles. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Epigallocatechin-3-gallate protects Kuruma shrimp Marsupeneaus japonicus from white spot syndrome virus and Vibrio alginolyticus.

    PubMed

    Wang, Zhi; Sun, Baozhen; Zhu, Fei

    2018-07-01

    Epigallocatechin-3-gallate (EGCG) is the most abundant catechin in green tea and exhibits potential antibacterial and anticancer activities. In this study, EGCG was used in pathogen-challenge experiments in shrimp to discover its effect on the innate immune system of an invertebrate. Kuruma shrimp Marsupeneaus japonicus was used as an experimental model and challenged with white spot syndrome virus (WSSV) and the Gram-negative bacterium Vibrio alginolyticus. Pathogen-challenge experiments showed that EGCG pretreatment significantly delayed and reduced mortality upon WSSV and V. alginolyticus infection, with VP-28 copies of WSSV also reduced. Quantitative reverse transcription polymerase chain reaction revealed the positive influence of EGCG on several innate immune-related genes, including IMD, proPO, QM, myosin, Rho, Rab7, p53, TNF-alpha, MAPK, and NOS, and we observed positive influences on three immune parameters, including total hemocyte count and phenoloxidase and superoxide dismutase activities, by EGCG treatment. Additionally, results showed that EGCG treatment significantly reduced apoptosis upon V. alginolyticus challenge. These results indicated the positive role of EGCG in the shrimp innate immune system as an enhancer of immune parameters and an inhibitor of apoptosis, thereby delaying and reducing mortality upon pathogen challenge. Our findings provide insight into potential therapeutic or preventive functions associated with EGCG to enhance shrimp immunity and protect shrimp from pathogen infection. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Lipolytic Potential of Aspergillus japonicus LAB01: Production, Partial Purification, and Characterisation of an Extracellular Lipase

    PubMed Central

    Souza, Lívia Tereza Andrade; Oliveira, Jamil S.; dos Santos, Vera L.; Regis, Wiliam C. B.; Santoro, Marcelo M.; Resende, Rodrigo R.

    2014-01-01

    Lipolytic potential of Aspergillus japonicus LAB01 was investigated by describing the catalytic properties and stability of a secreted extracellular lipase. Enzyme production was considered high under room temperature after 4 days using sunflower oil and a combination of casein with sodium nitrate. Lipase was partially purified by 3.9-fold, resulting in a 44.2% yield using ammonium sulphate precipitation (60%) quantified with Superose 12 HR gel filtration chromatography. The activity of the enzyme was maximised at pH 8.5, and the enzyme demonstrated stability under alkaline conditions. The optimum temperature was found to be 45°C, and the enzyme was stable for up to 100 minutes, with more than 80% of initial activity remaining after incubation at this temperature. Partially purified enzyme showed reasonable stability with triton X-100 and was activated in the presence of organic solvents (toluene, hexane, and methanol). Among the tested ions, only Cu2+, Ni2+, and Al3+ showed inhibitory effects. Substrate specificity of the lipase was higher for C14 among various p-nitrophenyl esters assayed. The KM and V max values of the purified enzyme for p-nitrophenyl palmitate were 0.13 mM and 12.58 umol/(L·min), respectively. These features render a novel biocatalyst for industrial applications. PMID:25530954

  10. Streptomyces formicae sp. nov., a novel actinomycete isolated from the head of Camponotus japonicus Mayr.

    PubMed

    Bai, Lu; Liu, Chongxi; Guo, Lifeng; Piao, Chenyu; Li, Zhilei; Li, Jiansong; Jia, Feiyu; Wang, Xiangjing; Xiang, Wensheng

    2016-02-01

    During a screening for novel and biotechnologically useful actinobacteria in insects, a novel actinomycete with antifungal activity, designated strain 1H-GS9(T), was isolated from the head of a Camponotus japonicus Mayr ant, which were collected from Northeast Agricultural University (Harbin, Heilongjiang, China). Strain 1H-GS9(T) was characterised using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. 16S rRNA gene sequence similarity studies showed that strain 1H-GS9(T) belongs to the genus Streptomyces with high sequence similarities to Streptomyces scopuliridis DSM 41917(T) (98.8 %) and Streptomyces mauvecolor JCM 5002(T) (98.6 %). However, phylogenetic analysis based on the 16S rRNA gene sequence indicated that it forms a monophyletic clade with Streptomyces kurssanovii JCM 4388(T) (98.6 %), Streptomyces xantholiticus JCM 4282(T) (98.6 %) and Streptomyces peucetius JCM 9920(T) (98.5 %). Thus, a combination of DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 1H-GS9(T) and the above-mentioned five strains, which further clarified their relatedness and demonstrated that strain 1H-GS9(T) could be distinguished from these strains. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces formicae sp. nov. is proposed. The type strain is 1H-GS9(T) (=CGMCC 4.7277(T) = DSM 100524(T)).

  11. Effects of environment factors on initiation of sperm motility in sea cucumber Apostichopus japonicus (Selenka)

    NASA Astrophysics Data System (ADS)

    Yu, Li; Shao, Mingyu; Bao, Zhenmin; Hu, Jingjie; Zhang, Zhifeng

    2011-06-01

    Sperm of sea cucumber Apostichopus japonicus (Selenka) were quiescent in electrolyte NaCl solution and artificial seawater (ASW) and nonelectrolyte glucose and mannitol solutions when the osmolality was less than 200 mOsm kg-1. The sperm started to be motile as a result of increased osmolality, indicating an osmolality-dependent initiation of sperm motility in sea cucumber. After a brief incubation in hypotonic NaCl and glucose solutions with osmolalities of 200 and 400 mOsm kg-1, sperm lost partial motile ability. Sperm became immobilized when pH was 6.0 in NaCl, glucose and mannitol solutions, suggesting that an H+ release is involved in sperm activation. The decreased pH had no effect on the percentage of motile sperm in ASW, whereas it delayed the time period to reach the maximum motility (motilitymax). Extracellular Ca2+ in electrolyte solutions was not essential for motility stimulation but shortened the time of reaching motilitymax. When Ca2+ was mixed in nonelectrolyte solutions the sperm motility was completely suppressed. The K+ channel blocker, quinine, suppressed the sperm motility in electrolyte solution, showing a possible involvement of K+ transport in the process. High K+ concentration did not affect the sperm motility in NaCl solution, but decreased it in ASW and almost entirely suppressed it in nonelectrolyte solutions. The different effects of pH and K+ in ASW and NaCl solution indicate that external ions may also regulate sperm motility.

  12. A large-scale RNA interference screen identifies genes that regulate autophagy at different stages.

    PubMed

    Guo, Sujuan; Pridham, Kevin J; Virbasius, Ching-Man; He, Bin; Zhang, Liqing; Varmark, Hanne; Green, Michael R; Sheng, Zhi

    2018-02-12

    Dysregulated autophagy is central to the pathogenesis and therapeutic development of cancer. However, how autophagy is regulated in cancer is not well understood and genes that modulate cancer autophagy are not fully defined. To gain more insights into autophagy regulation in cancer, we performed a large-scale RNA interference screen in K562 human chronic myeloid leukemia cells using monodansylcadaverine staining, an autophagy-detecting approach equivalent to immunoblotting of the autophagy marker LC3B or fluorescence microscopy of GFP-LC3B. By coupling monodansylcadaverine staining with fluorescence-activated cell sorting, we successfully isolated autophagic K562 cells where we identified 336 short hairpin RNAs. After candidate validation using Cyto-ID fluorescence spectrophotometry, LC3B immunoblotting, and quantitative RT-PCR, 82 genes were identified as autophagy-regulating genes. 20 genes have been reported previously and the remaining 62 candidates are novel autophagy mediators. Bioinformatic analyses revealed that most candidate genes were involved in molecular pathways regulating autophagy, rather than directly participating in the autophagy process. Further autophagy flux assays revealed that 57 autophagy-regulating genes suppressed autophagy initiation, whereas 21 candidates promoted autophagy maturation. Our RNA interference screen identifies identified genes that regulate autophagy at different stages, which helps decode autophagy regulation in cancer and offers novel avenues to develop autophagy-related therapies for cancer.

  13. Large Dog Relinquishment to Two Municipal Facilities in New York City and Washington, D.C.: Identifying Targets for Intervention

    PubMed Central

    Weiss, Emily; Slater, Margaret; Garrison, Laurie; Drain, Natasha; Dolan, Emily; Scarlett, Janet M.; Zawistowski, Stephen L.

    2014-01-01

    Simple Summary While the overall trend in euthanasia has been decreasing nationally, large dogs are at a higher risk of euthanasia than other-sized dogs in most animal shelters in the United States. We hypothesized that one way to increase the lives saved with regard to large dogs in shelters is to keep them home in the first place when possible. Our research is the first to collect data in New York City and Washington, D.C., identifying the process leading to the owner relinquishment of large dogs. We found that targets for interventions to decrease large dog relinquishment are likely different in each community. Abstract While the overall trend in euthanasia has been decreasing nationally, large dogs are at a higher risk of euthanasia than other sized dogs in most animal shelters in the United States. We hypothesized one way to increase the lives saved with respect to these large dogs is to keep them home when possible. In order to develop solutions to decrease relinquishment, a survey was developed to learn more about the reasons owners relinquish large dogs. The survey was administered to owners relinquishing their dogs at two large municipal facilities, one in New York City and one in Washington, D.C. There were 157 responses between the two facilities. We found both significant similarities and differences between respondents and their dogs from the two cities. We identified opportunities to potentially support future relinquishers and found that targets for interventions are likely different in each community. PMID:26480315

  14. Large-Scale Gene-Centric Analysis Identifies Novel Variants for Coronary Artery Disease

    PubMed Central

    2011-01-01

    Coronary artery disease (CAD) has a significant genetic contribution that is incompletely characterized. To complement genome-wide association (GWA) studies, we conducted a large and systematic candidate gene study of CAD susceptibility, including analysis of many uncommon and functional variants. We examined 49,094 genetic variants in ∼2,100 genes of cardiovascular relevance, using a customised gene array in 15,596 CAD cases and 34,992 controls (11,202 cases and 30,733 controls of European descent; 4,394 cases and 4,259 controls of South Asian origin). We attempted to replicate putative novel associations in an additional 17,121 CAD cases and 40,473 controls. Potential mechanisms through which the novel variants could affect CAD risk were explored through association tests with vascular risk factors and gene expression. We confirmed associations of several previously known CAD susceptibility loci (eg, 9p21.3:p<10−33; LPA:p<10−19; 1p13.3:p<10−17) as well as three recently discovered loci (COL4A1/COL4A2, ZC3HC1, CYP17A1:p<5×10−7). However, we found essentially null results for most previously suggested CAD candidate genes. In our replication study of 24 promising common variants, we identified novel associations of variants in or near LIPA, IL5, TRIB1, and ABCG5/ABCG8, with per-allele odds ratios for CAD risk with each of the novel variants ranging from 1.06–1.09. Associations with variants at LIPA, TRIB1, and ABCG5/ABCG8 were supported by gene expression data or effects on lipid levels. Apart from the previously reported variants in LPA, none of the other ∼4,500 low frequency and functional variants showed a strong effect. Associations in South Asians did not differ appreciably from those in Europeans, except for 9p21.3 (per-allele odds ratio: 1.14 versus 1.27 respectively; P for heterogeneity = 0.003). This large-scale gene-centric analysis has identified several novel genes for CAD that relate to diverse biochemical and cellular functions and

  15. Large-scale gene-centric analysis identifies novel variants for coronary artery disease.

    PubMed

    2011-09-01

    Coronary artery disease (CAD) has a significant genetic contribution that is incompletely characterized. To complement genome-wide association (GWA) studies, we conducted a large and systematic candidate gene study of CAD susceptibility, including analysis of many uncommon and functional variants. We examined 49,094 genetic variants in ∼2,100 genes of cardiovascular relevance, using a customised gene array in 15,596 CAD cases and 34,992 controls (11,202 cases and 30,733 controls of European descent; 4,394 cases and 4,259 controls of South Asian origin). We attempted to replicate putative novel associations in an additional 17,121 CAD cases and 40,473 controls. Potential mechanisms through which the novel variants could affect CAD risk were explored through association tests with vascular risk factors and gene expression. We confirmed associations of several previously known CAD susceptibility loci (eg, 9p21.3:p<10(-33); LPA:p<10(-19); 1p13.3:p<10(-17)) as well as three recently discovered loci (COL4A1/COL4A2, ZC3HC1, CYP17A1:p<5×10(-7)). However, we found essentially null results for most previously suggested CAD candidate genes. In our replication study of 24 promising common variants, we identified novel associations of variants in or near LIPA, IL5, TRIB1, and ABCG5/ABCG8, with per-allele odds ratios for CAD risk with each of the novel variants ranging from 1.06-1.09. Associations with variants at LIPA, TRIB1, and ABCG5/ABCG8 were supported by gene expression data or effects on lipid levels. Apart from the previously reported variants in LPA, none of the other ∼4,500 low frequency and functional variants showed a strong effect. Associations in South Asians did not differ appreciably from those in Europeans, except for 9p21.3 (per-allele odds ratio: 1.14 versus 1.27 respectively; P for heterogeneity = 0.003). This large-scale gene-centric analysis has identified several novel genes for CAD that relate to diverse biochemical and cellular functions and

  16. Diagnostic accuracy of clinical examination features for identifying large rotator cuff tears in primary health care

    PubMed Central

    Cadogan, Angela; McNair, Peter; Laslett, Mark; Hing, Wayne; Taylor, Stephen

    2013-01-01

    Objectives: Rotator cuff tears are a common and disabling complaint. The early diagnosis of medium and large size rotator cuff tears can enhance the prognosis of the patient. The aim of this study was to identify clinical features with the strongest ability to accurately predict the presence of a medium, large or multitendon (MLM) rotator cuff tear in a primary care cohort. Methods: Participants were consecutively recruited from primary health care practices (n = 203). All participants underwent a standardized history and physical examination, followed by a standardized X-ray series and diagnostic ultrasound scan. Clinical features associated with the presence of a MLM rotator cuff tear were identified (P<0.200), a logistic multiple regression model was derived for identifying a MLM rotator cuff tear and thereafter diagnostic accuracy was calculated. Results: A MLM rotator cuff tear was identified in 24 participants (11.8%). Constant pain and a painful arc in abduction were the strongest predictors of a MLM tear (adjusted odds ratio 3.04 and 13.97 respectively). Combinations of ten history and physical examination variables demonstrated highest levels of sensitivity when five or fewer were positive [100%, 95% confidence interval (CI): 0.86–1.00; negative likelihood ratio: 0.00, 95% CI: 0.00–0.28], and highest specificity when eight or more were positive (0.91, 95% CI: 0.86–0.95; positive likelihood ratio 4.66, 95% CI: 2.34–8.74). Discussion: Combinations of patient history and physical examination findings were able to accurately detect the presence of a MLM rotator cuff tear. These findings may aid the primary care clinician in more efficient and accurate identification of rotator cuff tears that may require further investigation or orthopedic consultation. PMID:24421626

  17. Phytochelatin synthases of the model legume Lotus japonicus. A small multigene family with differential response to cadmium and alternatively spliced variants.

    PubMed

    Ramos, Javier; Clemente, Maria R; Naya, Loreto; Loscos, Jorge; Pérez-Rontomé, Carmen; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

    2007-03-01

    The biosynthesis of phytochelatins and homophytochelatins has been studied in nodulated plants of the model legume Lotus (Lotus japonicus). In the first 6 to 24 h of treatment with cadmium (Cd), roots started to synthesize elevated amounts of both polypeptides, with a concomitant increase of glutathione and a decrease of homoglutathione, indicating the presence of active phytochelatin synthase (PCS) genes. Screening of transformation-competent artificial chromosome libraries allowed identification of a cluster of three genes, LjPCS1, LjPCS2, and LjPCS3, which were mapped at 69.0 cM on chromosome 1. The genes differ in exon-intron composition and responsiveness to Cd. Gene structures and phylogenetic analysis of the three protein products, LjPCS1-8R, LjPCS2-7N, and LjPCS3-7N, are consistent with two sequential gene duplication events during evolution of vascular plants. Two sites for alternative splicing in the primary transcripts were identified. One of them, involving intron 2 of the LjPCS2 gene, was confirmed by the finding of the two predicted mRNAs, encoding LjPCS2-7R in roots and LjPCS2-7N in nodules. The amino acid sequences of LjPCS2-7R (or LjPCS2-7N) and LjPCS3-7N share 90% identity, but have only 43% to 59% identity with respect to the typical PCS1 enzymes of Lotus and other plants. The unusual LjPCS2-7N and LjPCS3-7N proteins conferred Cd tolerance when expressed in yeast (Saccharomyces cerevisiae) cells, whereas the alternatively spliced form, LjPCS2-7R, differing only in a five-amino acid motif (GRKWK) did not. These results unveil complex regulatory mechanisms of PCS expression in legume tissues in response to heavy metals and probably to other developmental and environmental factors.

  18. Nitrogen-Fixing Nodules Are an Important Source of Reduced Sulfur, Which Triggers Global Changes in Sulfur Metabolism in Lotus japonicus.

    PubMed

    Kalloniati, Chrysanthi; Krompas, Panagiotis; Karalias, Georgios; Udvardi, Michael K; Rennenberg, Heinz; Herschbach, Cornelia; Flemetakis, Emmanouil

    2015-09-01

    We combined transcriptomic and biochemical approaches to study rhizobial and plant sulfur (S) metabolism in nitrogen (N) fixing nodules (Fix(+)) of Lotus japonicus, as well as the link of S-metabolism to symbiotic nitrogen fixation and the effect of nodules on whole-plant S-partitioning and metabolism. Our data reveal that N-fixing nodules are thiol-rich organs. Their high adenosine 5'-phosphosulfate reductase activity and strong (35)S-flux into cysteine and its metabolites, in combination with the transcriptional upregulation of several rhizobial and plant genes involved in S-assimilation, highlight the function of nodules as an important site of S-assimilation. The higher thiol content observed in nonsymbiotic organs of N-fixing plants in comparison to uninoculated plants could not be attributed to local biosynthesis, indicating that nodules are an important source of reduced S for the plant, which triggers whole-plant reprogramming of S-metabolism. Enhanced thiol biosynthesis in nodules and their impact on the whole-plant S-economy are dampened in plants nodulated by Fix(-) mutant rhizobia, which in most respects metabolically resemble uninoculated plants, indicating a strong interdependency between N-fixation and S-assimilation. © 2015 American Society of Plant Biologists. All rights reserved.

  19. Nitrogen-Fixing Nodules Are an Important Source of Reduced Sulfur, Which Triggers Global Changes in Sulfur Metabolism in Lotus japonicus

    PubMed Central

    Kalloniati, Chrysanthi; Krompas, Panagiotis; Udvardi, Michael K.; Flemetakis, Emmanouil

    2015-01-01

    We combined transcriptomic and biochemical approaches to study rhizobial and plant sulfur (S) metabolism in nitrogen (N) fixing nodules (Fix+) of Lotus japonicus, as well as the link of S-metabolism to symbiotic nitrogen fixation and the effect of nodules on whole-plant S-partitioning and metabolism. Our data reveal that N-fixing nodules are thiol-rich organs. Their high adenosine 5′-phosphosulfate reductase activity and strong 35S-flux into cysteine and its metabolites, in combination with the transcriptional upregulation of several rhizobial and plant genes involved in S-assimilation, highlight the function of nodules as an important site of S-assimilation. The higher thiol content observed in nonsymbiotic organs of N-fixing plants in comparison to uninoculated plants could not be attributed to local biosynthesis, indicating that nodules are an important source of reduced S for the plant, which triggers whole-plant reprogramming of S-metabolism. Enhanced thiol biosynthesis in nodules and their impact on the whole-plant S-economy are dampened in plants nodulated by Fix− mutant rhizobia, which in most respects metabolically resemble uninoculated plants, indicating a strong interdependency between N-fixation and S-assimilation. PMID:26296963

  20. Effect of culture methods on individual variation in the growth of sea cucumber Apostichopus japonicus within a cohort and family

    NASA Astrophysics Data System (ADS)

    Qiu, Tianlong; Zhang, Libin; Zhang, Tao; Bai, Yucen; Yang, Hongsheng

    2014-07-01

    There is substantial individual variation in the growth rates of sea cucumber Apostichopus japonicus individuals. This necessitates additional work to grade the seed stock and lengthens the production period. We evaluated the influence of three culture methods (free-mixed, isolated-mixed, isolated-alone) on individual variation in growth and assessed the relationship between feeding, energy conversion efficiency, and individual growth variation in individually cultured sea cucumbers. Of the different culture methods, animals grew best when reared in the isolated-mixed treatment (i.e., size classes were held separately), though there was no difference in individual variation in growth between rearing treatment groups. The individual variation in growth was primarily attributed to genetic factors. The difference in food conversion efficiency caused by genetic differences among individuals was thought to be the origin of the variance. The level of individual growth variation may be altered by interactions among individuals and environmental heterogeneity. Our results suggest that, in addition to traditional seed grading, design of a new kind of substrate that changes the spatial distribution of sea cucumbers would effectively enhance growth and reduce individual variation in growth of sea cucumbers in culture.

  1. User Guide for the LORE1 Insertion Mutant Resource.

    PubMed

    Mun, Terry; Małolepszy, Anna; Sandal, Niels; Stougaard, Jens; Andersen, Stig U

    2017-01-01

    Lotus japonicus is a model legume used in the study of plant-microbe interactions, especially in the field of biological nitrogen fixation due to its ability to enter into a symbiotic relationship with a soil bacterium, Mesorhizobium loti. The LORE1 mutant population is a valuable resource for reverse genetics in L. japonicus due to its non-transgenic nature, high tagging efficiency, and low copy count. Here, we outline a workflow for identifying, ordering, and establishing homozygous LORE1 mutant lines for a gene of interest, LjFls2, including protocols for growth and genotyping of a segregating LORE1 population.

  2. Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks.

    PubMed

    Wang, Jian; Xie, Dong; Lin, Hongfei; Yang, Zhihao; Zhang, Yijia

    2012-06-21

    Many biological processes recognize in particular the importance of protein complexes, and various computational approaches have been developed to identify complexes from protein-protein interaction (PPI) networks. However, high false-positive rate of PPIs leads to challenging identification. A protein semantic similarity measure is proposed in this study, based on the ontology structure of Gene Ontology (GO) terms and GO annotations to estimate the reliability of interactions in PPI networks. Interaction pairs with low GO semantic similarity are removed from the network as unreliable interactions. Then, a cluster-expanding algorithm is used to detect complexes with core-attachment structure on filtered network. Our method is applied to three different yeast PPI networks. The effectiveness of our method is examined on two benchmark complex datasets. Experimental results show that our method performed better than other state-of-the-art approaches in most evaluation metrics. The method detects protein complexes from large scale PPI networks by filtering GO semantic similarity. Removing interactions with low GO similarity significantly improves the performance of complex identification. The expanding strategy is also effective to identify attachment proteins of complexes.

  3. Clinical Scales Do Not Reliably Identify Acute Ischemic Stroke Patients With Large-Artery Occlusion.

    PubMed

    Turc, Guillaume; Maïer, Benjamin; Naggara, Olivier; Seners, Pierre; Isabel, Clothilde; Tisserand, Marie; Raynouard, Igor; Edjlali, Myriam; Calvet, David; Baron, Jean-Claude; Mas, Jean-Louis; Oppenheim, Catherine

    2016-06-01

    It remains debated whether clinical scores can help identify acute ischemic stroke patients with large-artery occlusion and hence improve triage in the era of thrombectomy. We aimed to determine the accuracy of published clinical scores to predict large-artery occlusion. We assessed the performance of 13 clinical scores to predict large-artery occlusion in consecutive patients with acute ischemic stroke undergoing clinical examination and magnetic resonance or computed tomographic angiography ≤6 hours of symptom onset. When no cutoff was published, we used the cutoff maximizing the sum of sensitivity and specificity in our cohort. We also determined, for each score, the cutoff associated with a false-negative rate ≤10%. Of 1004 patients (median National Institute of Health Stroke Scale score, 7; range, 0-40), 328 (32.7%) had an occlusion of the internal carotid artery, M1 segment of the middle cerebral artery, or basilar artery. The highest accuracy (79%; 95% confidence interval, 77-82) was observed for National Institute of Health Stroke Scale score ≥11 and Rapid Arterial Occlusion Evaluation Scale score ≥5. However, these cutoffs were associated with false-negative rates >25%. Cutoffs associated with an false-negative rate ≤10% were 5, 1, and 0 for National Institute of Health Stroke Scale, Rapid Arterial Occlusion Evaluation Scale, and Cincinnati Prehospital Stroke Severity Scale, respectively. Using published cutoffs for triage would result in a loss of opportunity for ≥20% of patients with large-artery occlusion who would be inappropriately sent to a center lacking neurointerventional facilities. Conversely, using cutoffs reducing the false-negative rate to 10% would result in sending almost every patient to a comprehensive stroke center. Our findings, therefore, suggest that intracranial arterial imaging should be performed in all patients with acute ischemic stroke presenting within 6 hours of symptom onset. © 2016 American Heart Association

  4. Method for identifying mutagenic agents which induce large, multilocus deletions in DNA

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bradley, W.E.C.; Belouchi, A.; Dewyse, P.

    1993-07-13

    A method of identifying a mutagenic agent is described which includes a large, multilocus deletions in DNA in mammalian cells comprising: (i) exposing a class III heterozygous CHO cell line to a potential mutagenic agent under investigation, and allowing any mutation of the cell line to proceed, said cell line being characterized in that a restriction fragment length variation exists in on mutation it becomes resistant to 2,6-diaminopurine and in that the DNA sequence adjacent to the two alleles of the APRT gene such that the DNA sequence adjacent to one of the two alleles can be digested with themore » enzyme BclI but the DNA sequence variation adjacent to the other of the two alleles cannot be digested with BclI, (ii) isolating induced mutations of the cell line deficient in APRT function, (iii) isolating DNA from the induced mutants, (iv) digesting the isolated DNA with BclI enzyme to produce digested fragments including a 19 kb fragment and any 2 kb fragment, which fragments hybridize with the labeled probe derived from DNA fragment PDI, (v) separating any digested fragments, (vi) transferring the separated fragments of (v) to a solid support, (vii) hybridizing the supported separated fragments with a labeled probe derived from the clone DNA fragment PD 1, (viii) determining fragments having undergone loss of the 2 kb band identified by the probe, as an identification of parent mutants in which the loss occurred, and (ix) evaluating the mutating ability of the potential mutagenic agent.« less

  5. Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers

    PubMed Central

    2013-01-01

    Background Many large-scale studies analyzed high-throughput genomic data to identify altered pathways essential to the development and progression of specific types of cancer. However, no previous study has been extended to provide a comprehensive analysis of pathways disrupted by copy number alterations across different human cancers. Towards this goal, we propose a network-based method to integrate copy number alteration data with human protein-protein interaction networks and pathway databases to identify pathways that are commonly disrupted in many different types of cancer. Results We applied our approach to a data set of 2,172 cancer patients across 16 different types of cancers, and discovered a set of commonly disrupted pathways, which are likely essential for tumor formation in majority of the cancers. We also identified pathways that are only disrupted in specific cancer types, providing molecular markers for different human cancers. Analysis with independent microarray gene expression datasets confirms that the commonly disrupted pathways can be used to identify patient subgroups with significantly different survival outcomes. We also provide a network view of disrupted pathways to explain how copy number alterations affect pathways that regulate cell growth, cycle, and differentiation for tumorigenesis. Conclusions In this work, we demonstrated that the network-based integrative analysis can help to identify pathways disrupted by copy number alterations across 16 types of human cancers, which are not readily identifiable by conventional overrepresentation-based and other pathway-based methods. All the results and source code are available at http://compbio.cs.umn.edu/NetPathID/. PMID:23822816

  6. Characterization of sea cucumber (stichopus japonicus) ovum hydrolysates: calcium chelation, solubility and absorption into intestinal epithelial cells.

    PubMed

    Sun, Na; Cui, Pengbo; Lin, Songyi; Yu, Cuiping; Tang, Yue; Wei, Ye; Xiong, Youling; Wu, Haitao

    2017-10-01

    Sea cucumber (Stichopus japonicus) ovum hydrolysates (SCOHs) chelated with calcium were produced to investigate the characteristics of calcium binding and solubility, as well as to study any effects on calcium absorption by human intestinal epithelial cells. The results of the present study show that the calcium-binding capacity of SCOHs depended greatly on the type of proteases. The maximum level of Ca binding (0.38 mmol L -1 ) occurred when trypsin was used, with a peptide yield of 85.7%. Investigation of the possible chelating modes between SCOHs and calcium ions indicated that calcium ions bound to SCOHs primarily via interactions with carboxyl oxygen and amino nitrogen atoms of Glu and Asp and also that the phosphoserine residues might be also responsible for SCOH-calcium chelation. Moreover, SCOH-calcium complexes maintained the solubility of calcium under simulated gastrointestinal digestion, regardless of the presence of dietary components such as oxalate. Furthermore, SCOH-Ca led to higher peak intracellular [Ca 2+ ] i in both Caco-2 cells (338.3 nmol L -1 versus 269.6 nmol L -1 ) and HT-29 cells (373.9 nmol L -1 versus 271.7 nmol L -1 ) than casein phosphopeptide-Ca. Carboxyl oxygen and amino nitrogen atoms in the SCOHs could bind calcium ions, forming SCOH-calcium complexes. These complexes improved calcium solubility under simulated gastrointestinal digestion and also promoted calcium absorption in Caco-2 and HT-29 cells. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  7. CERBERUS and NSP1 of Lotus japonicus are common symbiosis genes that modulate arbuscular mycorrhiza development.

    PubMed

    Takeda, Naoya; Tsuzuki, Syusaku; Suzaki, Takuya; Parniske, Martin; Kawaguchi, Masayoshi

    2013-10-01

    Arbuscular mycorrhizal symbiosis (AMS) and root nodule symbiosis (RNS) are mutualistic plant-microbe interactions that confer nutritional benefits to both partners. Leguminous plants possess a common genetic system for intracellular symbiosis with AM fungi and with rhizobia. Here we show that CERBERUS and NSP1, which respectively encode an E3 ubiquitin ligase and a GRAS transcriptional regulator and which have previously only been implicated in RNS, are involved in AM fungal infection in Lotus japonicus. Hyphal elongation along the longitudinal axis of the root was reduced in the cerberus mutant, giving rise to a lower colonization level. Knockout of NSP1 decreased the frequency of plants colonized by AM fungi or rhizobia. CERBERUS and NSP1 showed different patterns of expression in response to infection with symbiotic microbes. A low constitutive level of CERBERUS expression was observed in the root and an increased level of NSP1 expression was detected in arbuscule-containing cells. Induction of AM marker gene was triggered in both cerberus and nsp1 mutants by infection with symbiotic microbes; however, the mutants showed a weaker induction of marker gene expression than the wild type, mirroring their lower level of colonization. The common symbiosis genes are believed to act in an early signaling pathway for recognition of symbionts and for triggering early symbiotic responses. Our quantitative analysis of symbiotic phenotypes revealed developmental defects of the novel common symbiosis mutants in both symbioses, which demonstrates that common symbiosis mechanisms also contribute to a range of functions at later or different stages of symbiont infection.

  8. Streptomyces camponoticapitis sp. nov., an actinomycete isolated from the head of an ant (Camponotus japonicus Mayr).

    PubMed

    Li, Yao; Ye, Lan; Wang, Xiangjing; Zhao, Junwei; Ma, Zhaoxu; Yan, Kai; Xiang, Wensheng; Liu, Chongxi

    2016-10-01

    A novel single-spore-producing actinomycete, designated strain 2H-TWYE14T, was isolated from the head of an ant (Camponotus japonicus Mayr) and characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 2H-TWYE14T belongs to the genus Streptomyces, with highest sequence similarity to Streptomyces niveus NRRL 2466T (98.84 %). Analysis based on the gyrB gene also indicated that strain 2H-TWYE14T should be assigned to the genus Streptomyces. The chemotaxonomic properties of strain 2H-TWYE14T were consistent with those of members of the genus Streptomyces. The cell wall contained ll-diaminopimelic acid. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C16 : 0 and iso-C15 : 0. DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 2H-TWYE14T and its phylogenetically closely related strain S. niveus JCM 4251T, which further clarified their relatedness and demonstrated that 2H-TWYE14T could be distinguished from S. niveus. Therefore, it is concluded that strain 2H-TWYE14T can be classified as representing a novel species of the genus Streptomyces, for which the name Streptomyces camponoticapitis sp. nov. is proposed. The type strain is 2H-TWYE14T (=DSM 100523T=CGMCC 4.7275T).

  9. Common symbiosis genes CERBERUS and NSP1 provide additional insight into the establishment of arbuscular mycorrhizal and root nodule symbioses in Lotus japonicus.

    PubMed

    Nagae, Miwa; Takeda, Naoya; Kawaguchi, Masayoshi

    2014-01-01

    Arbuscular mycorrhizal symbiosis (AMS) and root nodule symbiosis (RNS) share several common symbiotic components, and many of the common symbiosis mutants block the entry of symbionts into the roots. We recently reported that CERBERUS (an E3 ubiquitin ligase) and NSP1 (a GRAS family transcription factor), required for RNS, also modulate AMS development in Lotus japonicus. The novel common symbiosis mutants, cerberus and nsp1, have low colonization of arbuscular mycorrhiza (AM) fungi, caused by a defect in internal hyphal elongation and by a decreased fungal entry into the roots, respectively. Here, we showed that CERBERUS was induced at the sites of symbiotic fungal or bacterial infection. NSP1 has been implicated in a strigolactone biosynthesis gene DWARF27 expression. Nevertheless, in nsp1, DWARF27 was induced by inoculation with AM fungi, implying the existence of a NSP1-independent regulatory mechanism of strigolactone biosynthesis during AMS establishment. These results support functional analysis of CERBERUS and NSP1, and also contribute to elucidation of common mechanisms in AMS and RNS.

  10. Identifying Microlensing Events in Large, Non-Uniformly Sampled Surveys: The Case of the Palomar Transient Factory

    NASA Astrophysics Data System (ADS)

    Price-Whelan, Adrian M.; Agueros, M. A.; Fournier, A.; Street, R.; Ofek, E.; Levitan, D. B.; PTF Collaboration

    2013-01-01

    Many current photometric, time-domain surveys are driven by specific goals such as searches for supernovae or transiting exoplanets, or studies of stellar variability. These goals in turn set the cadence with which individual fields are re-imaged. In the case of the Palomar Transient Factory (PTF), several such sub-surveys are being conducted in parallel, leading to extremely non-uniform sampling over the survey's nearly 20,000 sq. deg. footprint. While the typical 7.26 sq. deg. PTF field has been imaged 20 times in R-band, ~2300 sq. deg. have been observed more than 100 times. We use the existing PTF data 6.4x107 light curves) to study the trade-off that occurs when searching for microlensing events when one has access to a large survey footprint with irregular sampling. To examine the probability that microlensing events can be recovered in these data, we also test previous statistics used on uniformly sampled data to identify variables and transients. We find that one such statistic, the von Neumann ratio, performs best for identifying simulated microlensing events. We develop a selection method using this statistic and apply it to data from all PTF fields with >100 observations to uncover a number of interesting candidate events. This work can help constrain all-sky event rate predictions and tests microlensing signal recovery in large datasets, both of which will be useful to future wide-field, time-domain surveys such as the LSST.

  11. Nitrogen and phosphorus budget of a polyculture system of sea cucumber ( Apostichopus japonicus), jellyfish ( Rhopilema esculenta) and shrimp ( Fenneropenaeus chinensis)

    NASA Astrophysics Data System (ADS)

    Li, Junwei; Dong, Shuanglin; Gao, Qinfeng; Zhu, Changbo

    2014-06-01

    The nitrogen (N) and phosphorus (P) budget and the ecological efficiency of a polyculture system of sea cucumber ( Apostichopus japonicus), jellyfish ( Rhopilema esculenta) and shrimp ( Fenneropenaeus chinensis) were studied in a cofferdam, 120.2 ha in size. The nutrients were supplied by spring tide inflow. In total, 139600 kg N yr-1 and 9730 kg P yr-1 input to the system; while 118900 kg N yr-1 and 2840 kg P yr-1 outflowed from the system concurrently, thus the outflow was 85.7% (N) and 29.2% (P) of inflow. The production of N and P was 889.5 kg yr-1 and 49.28 kg yr-1 (sea cucumber) and 204 kg yr-1 and 18.03 kg yr-1 (jellyfish and shrimp), respectively. The utilization rate of N and P by polycultured animals was 7.8‰ and 6.9‰, respectively, 21.9% and 38% higher than that of monocultured sea cucumber. Our results indicated that the polyculture system was an efficient culture system of animals and a remediation system of coastal environment as well; it scavenged 14.3% and 70.8% of N and P, respectively. Such an ecological efficiency may be improved further by increasing either the stocking density or the size of sea cucumber or both.

  12. Using Soluble Reactive Phosphorus and Ammonia to Identify Point Source Discharge from Large Livestock Facilities

    NASA Astrophysics Data System (ADS)

    Borrello, M. C.; Scribner, M.; Chessin, K.

    2013-12-01

    A growing body of research draws attention to the negative environmental impacts on surface water from large livestock facilities. These impacts are mostly in the form of excessive nutrient loading resulting in significantly decreased oxygen levels. Over-application of animal waste on fields as well as direct discharge into surface water from facilities themselves has been identified as the main contributor to the development of hypoxic zones in Lake Erie, Chesapeake Bay and the Gulf of Mexico. Some regulators claim enforcement of water quality laws is problematic because of the nature and pervasiveness of non-point source impacts. Any direct discharge by a facility is a violation of permits governed by the Clean Water Act, unless the facility has special dispensation for discharge. Previous research by the principal author and others has shown runoff and underdrain transport are the main mechanisms by which nutrients enter surface water. This study utilized previous work to determine if the effects of non-point source discharge can be distinguished from direct (point-source) discharge using simple nutrient analysis and dissolved oxygen (DO) parameters. Nutrient and DO parameters were measured from three sites: 1. A stream adjacent to a field receiving manure, upstream of a large livestock facility with a history of direct discharge, 2. The same stream downstream of the facility and 3. A stream in an area relatively unimpacted by large-scale agriculture (control site). Results show that calculating a simple Pearson correlation coefficient (r) of soluble reactive phosphorus (SRP) and ammonia over time as well as temperature and DO, distinguishes non-point source from point source discharge into surface water. The r value for SRP and ammonia for the upstream site was 0.01 while the r value for the downstream site was 0.92. The control site had an r value of 0.20. Likewise, r values were calculated on temperature and DO for each site. High negative correlations

  13. Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function

    PubMed Central

    Wild, Philipp S.; Felix, Janine F.; Schillert, Arne; Chen, Ming-Huei; Leening, Maarten J.G.; Völker, Uwe; Großmann, Vera; Brody, Jennifer A.; Irvin, Marguerite R.; Shah, Sanjiv J.; Pramana, Setia; Lieb, Wolfgang; Schmidt, Reinhold; Stanton, Alice V.; Malzahn, Dörthe; Lyytikäinen, Leo-Pekka; Tiller, Daniel; Smith, J. Gustav; Di Tullio, Marco R.; Musani, Solomon K.; Morrison, Alanna C.; Pers, Tune H.; Morley, Michael; Kleber, Marcus E.; Aragam, Jayashri; Bis, Joshua C.; Bisping, Egbert; Broeckel, Ulrich; Cheng, Susan; Deckers, Jaap W.; Del Greco M, Fabiola; Edelmann, Frank; Fornage, Myriam; Franke, Lude; Friedrich, Nele; Harris, Tamara B.; Hofer, Edith; Hofman, Albert; Huang, Jie; Hughes, Alun D.; Kähönen, Mika; investigators, KNHI; Kruppa, Jochen; Lackner, Karl J.; Lannfelt, Lars; Laskowski, Rafael; Launer, Lenore J.; Lindgren, Cecilia M.; Loley, Christina; Mayet, Jamil; Medenwald, Daniel; Morris, Andrew P.; Müller, Christian; Müller-Nurasyid, Martina; Nappo, Stefania; Nilsson, Peter M.; Nuding, Sebastian; Nutile, Teresa; Peters, Annette; Pfeufer, Arne; Pietzner, Diana; Pramstaller, Peter P.; Raitakari, Olli T.; Rice, Kenneth M.; Rotter, Jerome I.; Ruohonen, Saku T.; Sacco, Ralph L.; Samdarshi, Tandaw E.; Sharp, Andrew S.P.; Shields, Denis C.; Sorice, Rossella; Sotoodehnia, Nona; Stricker, Bruno H.; Surendran, Praveen; Töglhofer, Anna M.; Uitterlinden, André G.; Völzke, Henry; Ziegler, Andreas; Münzel, Thomas; März, Winfried; Cappola, Thomas P.; Hirschhorn, Joel N.; Mitchell, Gary F.; Smith, Nicholas L.; Fox, Ervin R.; Dueker, Nicole D.; Jaddoe, Vincent W.V.; Melander, Olle; Lehtimäki, Terho; Ciullo, Marina; Hicks, Andrew A.; Lind, Lars; Gudnason, Vilmundur; Pieske, Burkert; Barron, Anthony J.; Zweiker, Robert; Schunkert, Heribert; Ingelsson, Erik; Liu, Kiang; Arnett, Donna K.; Psaty, Bruce M.; Blankenberg, Stefan; Larson, Martin G.; Felix, Stephan B.; Franco, Oscar H.; Zeller, Tanja; Vasan, Ramachandran S.; Dörr, Marcus

    2017-01-01

    BACKGROUND. Understanding the genetic architecture of cardiac structure and function may help to prevent and treat heart disease. This investigation sought to identify common genetic variations associated with inter-individual variability in cardiac structure and function. METHODS. A GWAS meta-analysis of echocardiographic traits was performed, including 46,533 individuals from 30 studies (EchoGen consortium). The analysis included 16 traits of left ventricular (LV) structure, and systolic and diastolic function. RESULTS. The discovery analysis included 21 cohorts for structural and systolic function traits (n = 32,212) and 17 cohorts for diastolic function traits (n = 21,852). Replication was performed in 5 cohorts (n = 14,321) and 6 cohorts (n = 16,308), respectively. Besides 5 previously reported loci, the combined meta-analysis identified 10 additional genome-wide significant SNPs: rs12541595 near MTSS1 and rs10774625 in ATXN2 for LV end-diastolic internal dimension; rs806322 near KCNRG, rs4765663 in CACNA1C, rs6702619 near PALMD, rs7127129 in TMEM16A, rs11207426 near FGGY, rs17608766 in GOSR2, and rs17696696 in CFDP1 for aortic root diameter; and rs12440869 in IQCH for Doppler transmitral A-wave peak velocity. Findings were in part validated in other cohorts and in GWAS of related disease traits. The genetic loci showed associations with putative signaling pathways, and with gene expression in whole blood, monocytes, and myocardial tissue. CONCLUSION. The additional genetic loci identified in this large meta-analysis of cardiac structure and function provide insights into the underlying genetic architecture of cardiac structure and warrant follow-up in future functional studies. FUNDING. For detailed information per study, see Acknowledgments. PMID:28394258

  14. Study of nsLTPs in Lotus japonicus genome reveal a specific epidermal cell member (LjLTP10) regulated by drought stress in aerial organs with a putative role in cutin formation.

    PubMed

    Tapia, G; Morales-Quintana, L; Parra, C; Berbel, A; Alcorta, M

    2013-07-01

    The cuticle is the first defense against pathogens and the second way water is lost in plants. Hydrophobic layers covering aerial plant organs from primary stages of development form cuticle, including major classes of aliphatic wax components and cutin. Extensive research has been conducted to understand cuticle formation mechanisms in plants. However, many questions remain unresolved in the transport of lipid components to form cuticle. Database studies of the Lotus japonicus genome have revealed the presence of 24 sequences classified as putative non-specific lipid transfer proteins (nsLTPs), which were classified in seven groups; four groups were selected because of their expression in aerial organs. LjLTP8 forms a cluster with DIR1 in Arabidopsis thaliana while LjLTP6, LjLTP9, and LjLTP10 were grouped as type I LTPs. In silico studies showed a high level of structural conservation, and substrate affinity studies revealed palmitoyl-CoA as the most likely ligand for these LTPs, although the Lyso-Myristoyl Phosphatidyl Choline, Lyso-myristoyl phosphatidyl glycerol, and Lyso-stearyl phosphatidyl choline ligands also showed a high affinity with the proteins. The LjLTP6 and LjLTP10 genes were expressed in both the stems and the leaves under normal conditions and were highly induced during drought stress. LjLTP10 was the most induced gene in shoots during drought. The gene was only expressed in the epidermal cells of stems, primordial leaves, and young leaflets. LjLTP10 was positively regulated by MeJA but repressed by abscisic acid (ABA), ethylene, and H2O2, while LjLTP6 was weakly induced by MeJA, repressed by H2O2, and not affected by ABA and ethylene. We suggest that LjLTP10 is involved in plant development of stem and leaf cuticle, but also in acclimation to tolerate drought stress in L. japonicus.

  15. Heat and microbial treatments for nutritional upgrading of wheat straw

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Milstein, O.; Vered, Y.; Sharma, A.

    1986-03-01

    The ligninolytic activities of four cellulolytic organisms were compared using straw. Only Aspergillus japonicus and Polyporous versicolor appreciably degraded lignin with A. japonicus yielding the most protein. In solid culture, most protein was produced by P. versicolor, closely followed by A. japonicus. Pertreatment of the straw by hot water facilitated biodegradation and protein production. The nutritional value of the residual straw was also increased by some fungal cultures. The greatest amount of degradable polysaccharide in the straw was made available by A. japonicus in liquid media and Pleurotus ostreatus in solid media. 29 references.

  16. Streptomyces capitiformicae sp. nov., a novel actinomycete producing angucyclinone antibiotics isolated from the head of Camponotus japonicus Mayr.

    PubMed

    Jiang, Shanwen; Piao, Chenyu; Yu, Yang; Cao, Peng; Li, Chenxu; Yang, Fan; Li, Mutong; Xiang, Wensheng; Liu, Chongxi

    2018-01-01

    A novel actinomycete, designated strain 1H-SSA4 T , was isolated from the head of an ant (Camponotus japonicus Mayr) and was found to produce angucyclinone antibiotics. A polyphasic approach was used to determine the taxonomic status of strain 1H-SSA4 T . The DNA G+C content of the draft genome sequence, consisting of 11.4 Mbp, was 70.0 mol%. 16S rRNA gene sequence similarity studies showed that strain 1H-SSA4 T belongs to the genus Streptomyces with the highest sequence similarity to Streptomyces hygroscopicus subsp. ossamyceticus NBRC 13983 T (98.9 %), and phylogenetically clustered with this species, Streptomyces torulosus LMG 20305 T (98.8 %), Streptomyces ipomoeae NBRC 13050 T (98.5 %) and Streptomyces decoyicus NRRL 2666 T (98.4 %). The morphological and chemotaxonomic properties of the strain were also consistent with those members of the genus Streptomyces. A combination of DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 1H-SSA4 T and the above-mentioned strains, which further clarified their relatedness and demonstrated that strain 1H-SSA4 T could be distinguished from these strains. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces capitiformicae sp. nov. is proposed. The type strain is 1H-SSA4 T (=CGMCC 4.7403 T =DSM 104537 T ).

  17. Temperature-dependent performance of competitive native and alien invasive plant species

    NASA Astrophysics Data System (ADS)

    Song, Uhram

    2017-10-01

    To assess the likely impacts of environmental change, the responses of two well-known invasive plant species, native Pueraria lobata and alien Humulus japonicus, to differences in growth temperature were studied in South Korea. Habitat preferences, physiological responses such as photosynthetic rates and chlorophyll contents, growth rates, and nutrient contents were quantified for each species. A competition experiment was conducted to evaluate the temperature preferences of the two species. All results indicated that the alien species H. japonicus can take advantage of elevated temperatures (35 °C) to enhance its competitive advantage against the native species P. lobata. While H. japonicus took advantage of elevated temperatures and preferred high-temperature areas, P. lobata showed reduced performance and dominance in high-temperature areas. Therefore, in future, due to global warming and urbanization, there are possibilities that H. japonicus takes advantage of elevated temperature against P. lobata that could lead to increased H. japonicus coverage over time. Therefore, consistent monitoring of both species especially where P. lobata is dominated are required because both species are found in every continents in the world. Controlling P. lobata requires thorough inspection of H. japonicus presence of the habitat in advance to prevent post P. lobata management invasion of H. japonicus.

  18. Pepsin-solubilised collagen (PSC) from Red Sea cucumber (Stichopus japonicus) regulates cell cycle and the fibronectin synthesis in HaCaT cell migration.

    PubMed

    Park, Soo-Yeong; Lim, Hee Kyoung; Lee, Seogjae; Hwang, Hyeong Cheol; Cho, Somi K; Cho, Moonjae

    2012-05-01

    Pepsin-solubilised collagen (PSC) from Red Sea cucumber (Stichopus japonicus) was studied with respect to its wound-healing effects on a human keratinocyte (HaCaT) cell line. Disaggregated collagen fibres were treated with 0.1M NaOH for 24h and digested with pepsin for 72h to reach maximum yield of 26.6%. The results of an in vitro wound-healing test showed that migration of HaCaT cells was 1.5-fold faster on PSC-coated plates than on untreated plates. The migration rate of sea cucumber PSC was similar to that of rat PSC, but five times higher than that of bovine gelatin. HaCaT cells grown on PSC-coated plates revealed increased fibronectin synthesis (6-fold and 3-fold compared to gelatin and rat PSC, respectively). Additionally, sea cucumber PSCs induced HaCaT cell proliferation by decreasing the G1 phase by 5% and maintaining a larger population (8%) of cells in mitosis. Collagen from Red Sea cucumber might be useful as an alternative to mammalian collagen in the nutraceutical and pharmaceutical industries. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. Holocentric chromosomes of psocids (Insecta, Psocoptera) analysed by C-banding, silver impregnation and sequence specific fluorochromes CMA3 and DAPI.

    PubMed

    Golub, Natalia V; Nokkala, Seppo; Kuznetsova, Valentina G

    2004-01-01

    The pattern of nucleolus attachment and C-heterochromatin distribution and molecular composition in the karyotypes of psocid species Psococerastis gibbosa (2n = 16+X), Blaste conspurcata (2n = 16+X) and Amphipsocus japonicus (2n = 14+neo-XY) were studied by C-banding, silver impregnation and sequence specific fluorochromes CMA3 and DAPI. Every species was found to have a single nucleolus in male meiosis. In P. gibbosa the nucleolus is attached to an autosomal bivalent; in B. conspurcata to the X-chromosome; in A. japonicus to the neo-XY bivalent. The species show a rather small amount of constitutive heterochromatin, C-blocks demonstrating telomeric localization with rare exceptions. P. gibbosa is characterized by a polymorphism for C-blocks occurrence and distribution. In the autosomes of this species, C-heterochromatin consists of AT-rich DNA except for the nucleolus organizing region, which is also GC-rich; the X-chromosome shows both AT- and GC-rich clusters. In A. japonicus and B. conspurcata, C-heterochromatin of the autosomes and sex chromosomes consists of both GC-rich and AT-rich DNA clusters, which are largely co-localized.

  20. Identifying opportunities to advance practice at a large academic medical center using the ASHP Ambulatory Care Self-Assessment Tool.

    PubMed

    Martirosov, Amber Lanae; Michael, Angela; McCarty, Melissa; Bacon, Opal; DiLodovico, John R; Jantz, Arin; Kostoff, Diana; MacDonald, Nancy C; Mikulandric, Nancy; Neme, Klodiana; Sulejmani, Nimisha; Summers, Bryant B

    2018-05-29

    The use of the ASHP Ambulatory Care Self-Assessment Tool to advance pharmacy practice at 8 ambulatory care clinics of a large academic medical center is described. The ASHP Ambulatory Care Self-Assessment Tool was developed to help ambulatory care pharmacists assess how their current practices align with the ASHP Practice Advancement Initiative. The Henry Ford Hospital Ambulatory Care Advisory Group (ACAG) opted to use the "Practitioner Track" sections of the tool to assess pharmacy practices within each of 8 ambulatory care clinics individually. The responses to self-assessment items were then compiled and discussed by ACAG members. The group identified best practices and ways to implement action items to advance ambulatory care practice throughout the institution. Three recommended action items were common to most clinics: (1) identify and evaluate solutions to deliver financially viable services, (2) develop technology to improve patient care, and (3) optimize the role of pharmacy technicians and support personnel. The ACAG leadership met with pharmacy administrators to discuss how action items that were both feasible and deemed likely to have a medium-to-high impact aligned with departmental goals and used this information to develop an ambulatory care strategic plan. This process informed and enabled initiatives to advance ambulatory care pharmacy practice within the system. The ASHP Ambulatory Care Self-Assessment Tool was useful in identifying opportunities for practice advancement in a large academic medical center. Copyright © 2018 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

  1. Effects of Pseudoalteromonas sp. BC228 on digestive enzyme activity and immune response of juvenile sea cucumber ( Apostichopus japonicus)

    NASA Astrophysics Data System (ADS)

    Ma, Yuexin; Sun, Feixue; Zhang, Congyao; Bao, Pengyun; Cao, Shuqing; Zhang, Meiyan

    2014-12-01

    A marine bacterium, Pseudoalteromonas sp. BC228 was supplemented to feed in a feeding experiment aiming to determine its ability of enhancing the digestive enzyme activity and immune response of juvenile Apostichopus japonicus. Sea cucumber individuals were fed with the diets containing 0 (control), 105, 107 and 109 CFU g-1 diet of BC228 for 45 days. Results showed that intestinal trypsin and lipase activities were significantly enhanced by 107 and 109 CFU g-1 diet of BC228 in comparison with control ( P < 0.01). The phagocytic activity in the coelomocytes of sea cucumber fed the diet supplemented with 107 CFU g-1 diet of BC228 was significantly higher than that of those fed control diet ( P < 0.05). In addition, 105 and 107 CFU g-1 diet of BC228 significantly enhanced lysozyme and phenoloxidase activities in the coelomic fluid of sea cucumber, respectively, in comparison with other diets ( P < 0.01). Sea cucumbers, 10 each diet, were challenged with Vibrio splendidus NB13 after 45 days of feeding. It was found that the cumulative incidence and mortality of sea cucumber fed with BC228 containing diets were lower than those of animals fed control diet. Our findings evidenced that BC228 supplemented in diets improved the digestive enzyme activity of juvenile sea cucumber, stimulated its immune response and enhanced its resistance to the infection of V. splendidus.

  2. The preparation and characterization of chitin and chitosan under large-scale submerged fermentation level using shrimp by-products as substrate.

    PubMed

    Zhang, Hongcai; Yun, Sanyue; Song, Lingling; Zhang, Yiwen; Zhao, Yanyun

    2017-03-01

    The crustacean shells of crabs and shrimps produces quantities of by-products, leading to seriously environmental pollution and human health problems during industrial processing, yet they turned into high-value useful products, such as chitin and chitosan. To prepare them under large-scale submerged fermentation level, shrimp shell powders (SSPs) was fermented by successive three-step fermentation of Serratia marcescens B742, Lactobacillus plantarum ATCC 8014 and Rhizopus japonicus M193 to extract chitin and chitosan based on previously optimal conditions. Moreover, the key parameters was investigated to monitor the changes of resulted products during fermentation process. The results showed that the yield of prepared chitin and chitosan reached 21.35 and 13.11% with the recovery rate of 74.67 and 63.42%, respectively. The degree of deacetylation (DDA) and molecular mass (MM) of produced chitosan were 81.23% and 512.06kDa, respectively. The obtained chitin and chitosan was characterized using Fourier transform infrared spectrometer (FT-IR) and X-ray diffraction (XRD) analysis. The established microbial fermentation method can be applied for the industrial large-scale production of chitin and chitosan, while the use of chemical reagents was significantly reduced. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Large-Scale Phenomics Identifies Primary and Fine-Tuning Roles for CRKs in Responses Related to Oxidative Stress

    PubMed Central

    Rayapuram, Channabasavangowda; Idänheimo, Niina; Hunter, Kerri; Kimura, Sachie; Merilo, Ebe; Vaattovaara, Aleksia; Oracz, Krystyna; Kaufholdt, David; Pallon, Andres; Anggoro, Damar Tri; Glów, Dawid; Lowe, Jennifer; Zhou, Ji; Mohammadi, Omid; Puukko, Tuomas; Albert, Andreas; Lang, Hans; Ernst, Dieter; Kollist, Hannes; Brosché, Mikael; Durner, Jörg; Borst, Jan Willem; Collinge, David B.; Karpiński, Stanisław; Lyngkjær, Michael F.; Robatzek, Silke; Wrzaczek, Michael; Kangasjärvi, Jaakko

    2015-01-01

    Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins characterized by the presence of two domains of unknown function 26 (DUF26) in their ectodomain. The CRKs form one of the largest groups of receptor-like protein kinases in plants, but their biological functions have so far remained largely uncharacterized. We conducted a large-scale phenotyping approach of a nearly complete crk T-DNA insertion line collection showing that CRKs control important aspects of plant development and stress adaptation in response to biotic and abiotic stimuli in a non-redundant fashion. In particular, the analysis of reactive oxygen species (ROS)-related stress responses, such as regulation of the stomatal aperture, suggests that CRKs participate in ROS/redox signalling and sensing. CRKs play general and fine-tuning roles in the regulation of stomatal closure induced by microbial and abiotic cues. Despite their great number and high similarity, large-scale phenotyping identified specific functions in diverse processes for many CRKs and indicated that CRK2 and CRK5 play predominant roles in growth regulation and stress adaptation, respectively. As a whole, the CRKs contribute to specificity in ROS signalling. Individual CRKs control distinct responses in an antagonistic fashion suggesting future potential for using CRKs in genetic approaches to improve plant performance and stress tolerance. PMID:26197346

  4. Effects of heat treatment on the gel properties of the body wall of sea cucumber (Apostichopus japonicus).

    PubMed

    Zhang, Kai; Hou, Hu; Bu, Lin; Li, Bafang; Xue, Changhu; Peng, Zhe; Su, Shiwei

    2017-03-01

    The sensory texture of sea cucumber ( Apostichopus japonicus ) was dramatically affected by heat treatment. In this study, sea cucumbers were heated under different thermal conditions (HSC), and divided into five groups (HSC-80, HSC-90, HSC-100, HSC-110, and HSC-120) according to the heating temperature (from 80 to 120 °C). The changes in texture, moisture, gel structure, and biochemical parameters of the HSC were investigated. With increasing heating time (from 10 to 80 min), the hardness and gel structure changed slightly, and the water activity decreased as the proportion of T 21 increased by 133.33, 55.56, and 59.09% in the HSC-80, HSC-90, and HSC-100 groups, respectively. This indicated that moderate heating conditions (below 100 °C) caused gelation of sea cucumbers in HSC-80, HSC-90, and HSC-100 groups. However, as the water activity increased, the hardness declined rapidly by 2.56 and 2.7% in the HSC-110 and HSC-120 groups, with heating time increased from 10 to 80 min. Meanwhile, free hydroxyproline and ammonia nitrogen contents increased by 81.24 and 63.16% in the HSC-110 group; and by 63.09 and 54.99% in the HSC-120 group, as the gel structure of the sea cucumbers decomposed in these two groups. These results demonstrated that, severe heat treatment (above 100 °C) destroyed the chemical bonds, triggered the disintegration of collagen fibers and the gel structure of sea cucumbers, and transformed the migration and distribution of moisture, finally causing the deterioration of the sensory texture of the sea cucumbers.

  5. Large data series: Modeling the usual to identify the unusual

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Downing, D.J.; Fedorov, V.V.; Lawkins, W.F.

    {open_quotes}Standard{close_quotes} approaches such as regression analysis, Fourier analysis, Box-Jenkins procedure, et al., which handle a data series as a whole, are not useful for very large data sets for at least two reasons. First, even with computer hardware available today, including parallel processors and storage devices, there are no effective means for manipulating and analyzing gigabyte, or larger, data files. Second, in general it can not be assumed that a very large data set is {open_quotes}stable{close_quotes} by the usual measures, like homogeneity, stationarity, and ergodicity, that standard analysis techniques require. Both reasons dictate the necessity to use {open_quotes}local{close_quotes} data analysismore » methods whereby the data is segmented and ordered, where order leads to a sense of {open_quotes}neighbor,{close_quotes} and then analyzed segment by segment. The idea of local data analysis is central to the study reported here.« less

  6. The seesaw space, a vector space to identify and characterize large-scale structures at 1 AU

    NASA Astrophysics Data System (ADS)

    Lara, A.; Niembro, T.

    2017-12-01

    We introduce the seesaw space, an orthonormal space formed by the local and the global fluctuations of any of the four basic solar parameters: velocity, density, magnetic field and temperature at any heliospheric distance. The fluctuations compare the standard deviation of a moving average of three hours against the running average of the parameter in a month (consider as the local fluctuations) and in a year (global fluctuations) We created this new vectorial spaces to identify the arrival of transients to any spacecraft without the need of an observer. We applied our method to the one-minute resolution data of WIND spacecraft from 1996 to 2016. To study the behavior of the seesaw norms in terms of the solar cycle, we computed annual histograms and fixed piecewise functions formed by two log-normal distributions and observed that one of the distributions is due to large-scale structures while the other to the ambient solar wind. The norm values in which the piecewise functions change vary in terms of the solar cycle. We compared the seesaw norms of each of the basic parameters due to the arrival of coronal mass ejections, co-rotating interaction regions and sector boundaries reported in literature. High seesaw norms are due to large-scale structures. We found three critical values of the norms that can be used to determined the arrival of coronal mass ejections. We present as well general comparisons of the norms during the two maxima and the minimum solar cycle periods and the differences of the norms due to large-scale structures depending on each period.

  7. Selection of sourdough lactobacilli with antifungal activity for use as biopreservatives in bakery products.

    PubMed

    Garofalo, Cristiana; Zannini, Emanuele; Aquilanti, Lucia; Silvestri, Gloria; Fierro, Olga; Picariello, Gianluca; Clementi, Francesca

    2012-08-08

    Two hundred and sixteen LAB cultures from sourdoughs and dough for bread and panettone production were screened for in vitro antifungal properties against three indicator cultures ascribed to Aspergillus japonicus , Eurotium repens , and Penicillium roseopurpureum , isolated from bakery environment and moldy panettone. Nineteen preselected isolates were subjected to minimum inhibitory concentration determination against the indicator cultures. Sourdoughs prepared with the two most promising strains, identified as Lactobacillus rossiae LD108 and Lactobacillus paralimentarius PB127, were characterized. The sourdough extracts were subjected to HPLC analysis coupled with a microtiter plate bioassay against A. japonicus to identify the active fractions. MALDI-TOF MS analysis revealed the occurrence of a series of peptides corresponding to wheat α-gliadin proteolysis fragments in the active fraction from L. rossiae LD108 sourdough. The ability to prevent mold growth on bread was demonstrated for both strains, whereas L. rossiae LD108 also inhibited mold growth on panettone.

  8. Morphological Differentiation of the Eggs of North American Container-Inhabiting Aedes Mosquitoes.

    PubMed

    Bova, Jake; Paulson, Sally; Paulson, Greg

    2016-09-01

    Aedes aegypti , Ae. albopictus, Ae. japonicus japonicus, and Ae. triseriatus eggs are described with the aid of color images and images from scanning electron microscopy. All eggs were broadly cigar shaped with Ae. triseriatus and Ae. j japonicus eggs being dull or matte black, while Ae. albopictus and Ae. aegypti eggs were shiny jet black. Aedes triseriatus eggs were lighter in color and had a rougher appearance when compared to those of Ae. j. japonicus. Aedes albopictus and Ae. aegypti eggs can be differentiated by the distinct presence of micropylar collars in Ae. aegypti. Our results reduce the need to rear these mosquitoes, reducing labor and time while providing an accurate identification of the vector mosquitoes.

  9. Analysis of Apoptosis in Ultraviolet-Induced Sea Cucumber (Stichopus japonicus) Melting Using Terminal Deoxynucleotidyl-Transferase-Mediated dUTP Nick End-Labeling Assay and Cleaved Caspase-3 Immunohistochemistry.

    PubMed

    Yang, Jing-Feng; Gao, Rong-Chun; Wu, Hai-Tao; Li, Peng-Fei; Hu, Xian-Shu; Zhou, Da-Yong; Zhu, Bei-Wei; Su, Yi-Cheng

    2015-11-04

    The sea cucumber body wall melting phenomenon occurs under certain circumstances, and the mechanism of this phenomenon remains unclear. This study investigated the apoptosis in the ultraviolet (UV)-induced sea cucumber melting phenomenon. Fresh sea cucumbers (Stichopus japonicus) were exposed to UV radiation for half an hour at an intensity of 0.056 mW/cm(2) and then held at room temperature for melting development. The samples were histologically processed into formalin-fixed paraffin-embedded tissues. The apoptosis of samples was analyzed with the terminal deoxynucleotidyl-transferase-mediated dUTP nick end-labeling (TUNEL) assay and cleaved caspase-3 immunohistochemistry. The emergence of TUNEL-positive cells speeds up between 0.5 and 2 h after UV irradiation. Cleaved caspase-3 positive cells were obviously detected in sample tissues immediately after the UV irradiation. These results demonstrated that sea cucumber melting induced by UV irradiation was triggered by the activation of caspase-3 followed by DNA fragmentation in sea cucumber tissue, which was attributed to apoptosis but was not a consequence of autolysis activity.

  10. Two White Spot Syndrome Virus MicroRNAs Target the Dorsal Gene To Promote Virus Infection in Marsupenaeus japonicus Shrimp

    PubMed Central

    Ren, Qian; Huang, Xin; Cui, Yalei; Sun, Jiejie; Wang, Wen

    2017-01-01

    ABSTRACT In eukaryotes, microRNAs (miRNAs) serve as regulators of many biological processes, including virus infection. An miRNA can generally target diverse genes during virus-host interactions. However, the regulation of gene expression by multiple miRNAs has not yet been extensively explored during virus infection. This study found that the Spaztle (Spz)-Toll-Dorsal-antilipopolysaccharide factor (ALF) signaling pathway plays a very important role in antiviral immunity against invasion of white spot syndrome virus (WSSV) in shrimp (Marsupenaeus japonicus). Dorsal, the central gene in the Toll pathway, was targeted by two viral miRNAs (WSSV-miR-N13 and WSSV-miR-N23) during WSSV infection. The regulation of Dorsal expression by viral miRNAs suppressed the Spz-Toll-Dorsal-ALF signaling pathway in shrimp in vivo, leading to virus infection. Our study contributes novel insights into the viral miRNA-mediated Toll signaling pathway during the virus-host interaction. IMPORTANCE An miRNA can target diverse genes during virus-host interactions. However, the regulation of gene expression by multiple miRNAs during virus infection has not yet been extensively explored. The results of this study indicated that the shrimp Dorsal gene, the central gene in the Toll pathway, was targeted by two viral miRNAs during infection with white spot syndrome virus. Regulation of Dorsal expression by viral miRNAs suppressed the Spz-Toll-Dorsal-ALF signaling pathway in shrimp in vivo, leading to virus infection. Our study provides new insight into the viral miRNA-mediated Toll signaling pathway in virus-host interactions. PMID:28179524

  11. Changes in Postfermentation Quality during the Distribution Process of Anchovy ( Engraulis japonicus) Fish Sauce.

    PubMed

    Joung, Byung Chun; Min, Jin Gi

    2018-06-01

    In the present study, we evaluated the changes in quality that can occur during the distribution of nonheated anchovy ( Engraulis japonicus) fish sauce after packaging. The pH values of all samples ranged from 5.5 to 5.8, and there were no significant differences ( P > 0.05) in pH among the samples during storage regardless of storage temperature or salt concentration. The initial total volatile base nitrogen concentration in all samples after bottling was 115 to 121 mg/100 mL, but this concentration increased gradually with storage time. After 1 year of storage, total volatile base nitrogen concentration had increased to approximately 170% of the initial concentration (166 to 194 mg/100 mL). Amino nitrogen increased slightly during storage but was significantly lower than the increase in amino nitrogen during general anchovy fish sauce fermentation with anchovy flesh. Most of the free amino acids increased slightly during the storage period regardless of storage temperature or salt concentration, but tyrosine and histidine increased and then decreased during the storage period. The histamine concentration of the anchovy fish sauce at a salt concentration of 20% was 43.3 mg/100 mL initially, but after 1 year the histamine concentration was 89.7 mg/100 mL in samples stored at 10°C, 102.6 mg/100 mL in samples stored at 25°C, and 116.8 mg/100 mL in samples stored at 35°C . Changes in putrescine and cadaverine concentrations were similar to those in histamine; concentrations increased about twofold from the initial concentrations after 1 year of storage. However, the rate of increase in putrescine from 4 months after storage was very high, and cadaverine slightly decreased by 12 months of storage. High scores for umami and aroma sensory characteristics were given to samples stored at 10°C, but samples stored 35°C were given high scores for rancid. Despite the overall low scores for aroma and umami for samples stored at 35°C, the quality of the anchovy fish sauce

  12. Wuhan large pig roundworm virus identified in human feces in Brazil.

    PubMed

    Luchs, Adriana; Leal, Elcio; Komninakis, Shirley Vasconcelos; de Pádua Milagres, Flavio Augusto; Brustulin, Rafael; da Aparecida Rodrigues Teles, Maria; Gill, Danielle Elise; Deng, Xutao; Delwart, Eric; Sabino, Ester Cerdeira; da Costa, Antonio Charlys

    2018-03-28

    We report here the complete genome sequence of a bipartite virus, herein denoted WLPRV/human/BRA/TO-34/201, from a sample collected in 2015 from a two-year-old child in Brazil presenting acute gastroenteritis. The virus has 98-99% identity (segments 2 and 1, respectively) with the Wuhan large pig roundworm virus (unclassified RNA virus) that was recently discovered in the stomachs of pigs from China. This is the first report of a Wuhan large pig roundworm virus detected in human specimens, and the second genome described worldwide. However, the generation of more sequence data and further functional studies are required to fully understand the ecology, epidemiology, and evolution of this new unclassified virus.

  13. Gibberellins interfere with symbiosis signaling and gene expression and alter colonization by arbuscular mycorrhizal fungi in Lotus japonicus.

    PubMed

    Takeda, Naoya; Handa, Yoshihiro; Tsuzuki, Syusaku; Kojima, Mikiko; Sakakibara, Hitoshi; Kawaguchi, Masayoshi

    2015-02-01

    Arbuscular mycorrhiza is a mutualistic plant-fungus interaction that confers great advantages for plant growth. Arbuscular mycorrhizal (AM) fungi enter the host root and form symbiotic structures that facilitate nutrient supplies between the symbionts. The gibberellins (GAs) are phytohormones known to inhibit AM fungal infection. However, our transcriptome analysis and phytohormone quantification revealed GA accumulation in the roots of Lotus japonicus infected with AM fungi, suggesting that de novo GA synthesis plays a role in arbuscular mycorrhiza development. We found pleiotropic effects of GAs on the AM fungal infection. In particular, the morphology of AM fungal colonization was drastically altered by the status of GA signaling in the host root. Exogenous GA treatment inhibited AM hyphal entry into the host root and suppressed the expression of Reduced Arbuscular Mycorrhization1 (RAM1) and RAM2 homologs that function in hyphal entry and arbuscule formation. On the other hand, inhibition of GA biosynthesis or suppression of GA signaling also affected arbuscular mycorrhiza development in the host root. Low-GA conditions suppressed arbuscular mycorrhiza-induced subtilisin-like serine protease1 (SbtM1) expression that is required for AM fungal colonization and reduced hyphal branching in the host root. The reduced hyphal branching and SbtM1 expression caused by the inhibition of GA biosynthesis were recovered by GA treatment, supporting the theory that insufficient GA signaling causes the inhibitory effects on arbuscular mycorrhiza development. Most studies have focused on the negative role of GA signaling, whereas our study demonstrates that GA signaling also positively interacts with symbiotic responses and promotes AM colonization of the host root. © 2015 American Society of Plant Biologists. All Rights Reserved.

  14. Maximum sustainable speeds and cost of swimming in juvenile kawakawa tuna (Euthynnus affinis) and chub mackerel (Scomber japonicus).

    PubMed

    Sepulveda, C; Dickson, K A

    2000-10-01

    Tunas (Scombridae) have been assumed to be among the fastest and most efficient swimmers because they elevate the temperature of the slow-twitch, aerobic locomotor muscle above the ambient water temperature (endothermy) and because of their streamlined body shape and use of the thunniform locomotor mode. The purpose of this study was to test the hypothesis that juvenile tunas swim both faster and more efficiently than their ectothermic relatives. The maximum sustainable swimming speed (U(max), the maximum speed attained while using a steady, continuous gait powered by the aerobic myotomal muscle) and the net cost of transport (COT(net)) were compared at 24 degrees C in similar-sized (116-255 mm fork length) juvenile scombrids, an endothermic tuna, the kawakawa (Euthynnus affinis) and the ectothermic chub mackerel (Scomber japonicus). U(max) and COT(net) were measured by forcing individual fish to swim in a temperature-controlled, variable-speed swimming tunnel respirometer. There were no significant interspecific differences in the relationship between U(max) and body mass or fork length or in the relationship between COT(net) and body mass or fork length. Muscle temperatures were elevated by 1.0-2.3 degrees C and 0.1-0.6 degrees C above water temperature in the kawakawa and chub mackerel, respectively. The juvenile kawakawa had significantly higher standard metabolic rates than the chub mackerel, because the total rate of oxygen consumption at a given swimming speed was higher in the kawakawa when the effects of fish size were accounted for. Thus, juvenile kawakawa are not capable of higher sustainable swimming speeds and are not more efficient swimmers than juvenile chub mackerel.

  15. Identifying Critical Habitat for Australian Freshwater Turtles in a Large Regulated Floodplain: Implications for Environmental Water Management

    NASA Astrophysics Data System (ADS)

    Ocock, J. F.; Bino, G.; Wassens, S.; Spencer, J.; Thomas, R. F.; Kingsford, R. T.

    2018-03-01

    Freshwater turtles face many threats, including habitat loss and river regulation reducing occupancy and contributing to population decline. Limited knowledge of hydrological conditions required to maintain viable turtle populations in large floodplain wetlands hinders effective adaptive management of environmental water in regulated rivers. We surveyed three turtle species over 4 years across the Lower Murrumbidgee River floodplain, a large wetland complex with a long history of water resource development. Using site and floodplain metrics and generalized linear models, within a Bayesian Model Averaging framework, we quantified the main drivers affecting turtle abundance. We also used a hierarchical modeling approach, requiring large sample sizes, quantifying possible environmental effects while accounting for detection probabilities of the eastern long-necked turtle ( Chelodina longicollis). The three species varied in their responses to hydrological conditions and connectivity to the main river channel. Broad-shelled turtles ( Chelodina expansa) and Macquarie River turtles ( Emydura macquarii macquarii) had restricted distributions, centered on frequently inundated wetlands close to the river, whereas the eastern long-necked turtles were more widely distributed, indicating an ability to exploit variable habitats. We conclude that turtle communities would benefit from long-term management strategies that maintain a spatiotemporal mosaic of hydrological conditions. More specifically, we identified characteristics of refuge habitats and stress the importance of maintaining their integrity during dry periods. Neighboring habitats can be targeted during increased water availability years to enhance feeding and dispersal opportunities for freshwater turtles.

  16. Increasing critical sensitivity of the Load/Unload Response Ratio before large earthquakes with identified stress accumulation pattern

    NASA Astrophysics Data System (ADS)

    Yu, Huai-zhong; Shen, Zheng-kang; Wan, Yong-ge; Zhu, Qing-yong; Yin, Xiang-chu

    2006-12-01

    The Load/Unload Response Ratio (LURR) method is proposed for short-to-intermediate-term earthquake prediction [Yin, X.C., Chen, X.Z., Song, Z.P., Yin, C., 1995. A New Approach to Earthquake Prediction — The Load/Unload Response Ratio (LURR) Theory, Pure Appl. Geophys., 145, 701-715]. This method is based on measuring the ratio between Benioff strains released during the time periods of loading and unloading, corresponding to the Coulomb Failure Stress change induced by Earth tides on optimally oriented faults. According to the method, the LURR time series usually climb to an anomalously high peak prior to occurrence of a large earthquake. Previous studies have indicated that the size of critical seismogenic region selected for LURR measurements has great influence on the evaluation of LURR. In this study, we replace the circular region usually adopted in LURR practice with an area within which the tectonic stress change would mostly affect the Coulomb stress on a potential seismogenic fault of a future event. The Coulomb stress change before a hypothetical earthquake is calculated based on a simple back-slip dislocation model of the event. This new algorithm, by combining the LURR method with our choice of identified area with increased Coulomb stress, is devised to improve the sensitivity of LURR to measure criticality of stress accumulation before a large earthquake. Retrospective tests of this algorithm on four large earthquakes occurred in California over the last two decades show remarkable enhancement of the LURR precursory anomalies. For some strong events of lesser magnitudes occurred in the same neighborhoods and during the same time periods, significant anomalies are found if circular areas are used, and are not found if increased Coulomb stress areas are used for LURR data selection. The unique feature of this algorithm may provide stronger constraints on forecasts of the size and location of future large events.

  17. Expert systems identify fossils and manage large paleontological databases

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Beightol, D.S.; Conrad, M.A.

    EXPAL is a computer program permitting creation and maintenance of comprehensive databases in marine paleontology. It is designed to assist specialists and non-specialists. EXPAL includes a powerful expert system based on the morphological descriptors specific to a given group of fossils. The expert system may be used, for example, to describe and automatically identify an unknown specimen. EXPAL was first applied to Dasycladales (Calcareous green algae). Projects are under way for corresponding expert systems and databases on planktonic foraminifers and calpionellids. EXPAL runs on an IBM XT or compatible microcomputer.

  18. A novel C-type lectin from the sea cucumber Apostichopus japonicus (AjCTL-2) with preferential binding of d-galactose.

    PubMed

    Wang, Hui; Xue, Zhuang; Liu, Zhaoqun; Wang, Weilin; Wang, Feifei; Wang, Ying; Wang, Lingling; Song, Linsheng

    2018-05-15

    C-type lectins (CTLs) are Ca 2+ dependent carbohydrate-binding proteins that share structural homology in their carbohydrate-recognition domains (CRDs). In the present study, a novel CTL was identified from sea cucumber Apostichopus japonicus (named as AjCTL-2). The deduced amino acid sequence of AjCTL-2 was homologous to CTLs from other animals with the identities ranging from 33% to 40%. It contained a canonical signal peptide at the N-terminus, a low density lipoprotein receptor class A (LDLa), a C1r/C1s/Uegf/bone morphogenetic protein 1 (CUB), and a CRD with two motifs Glu-Pro-Asn (EPN) and Trp-Asn-Asp (WND) in Ca 2+ binding site 2. The mRNA transcripts of AjCTL-2 were extensively expressed in all the tested tissues including respiratory tree, muscle, gut, coelomocyte, tube-foot, body wall and gonad, and the highest expression level of AjCTL-2 in coelomocyte was about 4.2-fold (p < 0.05) of that in body wall. The mRNA expression level of AjCTL-2 in coelomocyte increased significantly after Vibrio splendidus stimulation, and dramatically peaked at 12 h, which was 206.4-fold (p < 0.05) of that in control group. AjCTL-2 protein was mainly detected in cytoplasm of coelomocyte by immunofluorescence. The recombinant AjCTL-2 (rAjCTL-2) displayed binding activity to d-galactose independent of Ca 2+ , while the binding activity to other tested pathogen-associated molecular patterns (PAMPs) including lipopolysaccharide (LPS), peptidoglycan (PGN), and mannose (Man) could not be detected. Surface plasmon resonance (SPR) analysis further revealed the high binding specificity and moderate binding affinity of rAjCTL-2 to d-galactose (KD = 4.093 × 10 -6  M). After rAjCTL-2 was blocked by its polyclonal antibody, the binding activity to d-galactose could not be detected by using a blocking ELISA (B-ELISA). Moreover, rAjCTL-2 could bind various microorganisms including V. splendidus, V. anguillarum, Staphylococcus aureus, Bifidobacterium breve and Yarrowia

  19. tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote

    PubMed Central

    Iben, James R.; Maraia, Richard J.

    2012-01-01

    tRNA genes are interspersed throughout eukaryotic DNA, contributing to genome architecture and evolution in addition to translation of the transcriptome. Codon use correlates with tRNA gene copy number in noncomplex organisms including yeasts. Synonymous codons impact translation with various outcomes, dependent on relative tRNA abundances. Availability of whole-genome sequences allowed us to examine tRNA gene copy number variation (tgCNV) and codon use in four Schizosaccharomyces species and Saccharomyces cerevisiae. tRNA gene numbers vary from 171 to 322 in the four Schizosaccharomyces despite very high similarity in other features of their genomes. In addition, we performed whole-genome sequencing of several related laboratory strains of Schizosaccharomyces pombe and found tgCNV at a cluster of tRNA genes. We examined for the first time effects of wobble rules on correlation of tRNA gene number and codon use and showed improvement for S. cerevisiae and three of the Schizosaccharomyces species. In contrast, correlation in Schizosaccharomyces japonicus is poor due to markedly divergent tRNA gene content, and much worsened by the wobble rules. In japonicus, some tRNA iso-acceptor genes are absent and others are greatly reduced relative to the other yeasts, while genes for synonymous wobble iso-acceptors are amplified, indicating wobble use not apparent in any other eukaryote. We identified a subset of japonicus-specific wobbles that improves correlation of codon use and tRNA gene content in japonicus. We conclude that tgCNV is high among Schizo species and occurs in related laboratory strains of S. pombe (and expectedly other species), and tRNAome-codon analyses can provide insight into species-specific wobble decoding. PMID:22586155

  20. Identifying genetic variants that affect viability in large cohorts

    PubMed Central

    Berisa, Tomaz; Day, Felix R.; Perry, John R. B.

    2017-01-01

    A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness. As a step towards this goal, we developed a method to examine whether individual genetic variants, or sets of genetic variants, currently influence viability. The approach consists in testing whether the frequency of an allele varies across ages, accounting for variation in ancestry. We applied it to the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort and to the parents of participants in the UK Biobank. Across the genome, we found only a few common variants with large effects on age-specific mortality: tagging the APOE ε4 allele and near CHRNA3. These results suggest that when large, even late-onset effects are kept at low frequency by purifying selection. Testing viability effects of sets of genetic variants that jointly influence 1 of 42 traits, we detected a number of strong signals. In participants of the UK Biobank of British ancestry, we found that variants that delay puberty timing are associated with a longer parental life span (P~6.2 × 10−6 for fathers and P~2.0 × 10−3 for mothers), consistent with epidemiological studies. Similarly, variants associated with later age at first birth are associated with a longer maternal life span (P~1.4 × 10−3). Signals are also observed for variants influencing cholesterol levels, risk of coronary artery disease (CAD), body mass index, as well as risk of asthma. These signals exhibit consistent effects in the GERA cohort and among participants of the UK Biobank of non-British ancestry. We also found marked differences between males and females, most notably at the CHRNA3 locus, and variants associated with risk of CAD and cholesterol levels. Beyond our findings, the analysis serves as a proof of principle for how upcoming biomedical data sets can be used to learn about selection effects in contemporary humans. PMID:28873088

  1. Two White Spot Syndrome Virus MicroRNAs Target the Dorsal Gene To Promote Virus Infection in Marsupenaeus japonicus Shrimp.

    PubMed

    Ren, Qian; Huang, Xin; Cui, Yalei; Sun, Jiejie; Wang, Wen; Zhang, Xiaobo

    2017-04-15

    In eukaryotes, microRNAs (miRNAs) serve as regulators of many biological processes, including virus infection. An miRNA can generally target diverse genes during virus-host interactions. However, the regulation of gene expression by multiple miRNAs has not yet been extensively explored during virus infection. This study found that the Spaztle (Spz)-Toll-Dorsal-antilipopolysaccharide factor (ALF) signaling pathway plays a very important role in antiviral immunity against invasion of white spot syndrome virus (WSSV) in shrimp ( Marsupenaeus japonicus ). Dorsal , the central gene in the Toll pathway, was targeted by two viral miRNAs (WSSV-miR-N13 and WSSV-miR-N23) during WSSV infection. The regulation of Dorsal expression by viral miRNAs suppressed the Spz-Toll-Dorsal-ALF signaling pathway in shrimp in vivo , leading to virus infection. Our study contributes novel insights into the viral miRNA-mediated Toll signaling pathway during the virus-host interaction. IMPORTANCE An miRNA can target diverse genes during virus-host interactions. However, the regulation of gene expression by multiple miRNAs during virus infection has not yet been extensively explored. The results of this study indicated that the shrimp Dorsal gene, the central gene in the Toll pathway, was targeted by two viral miRNAs during infection with white spot syndrome virus. Regulation of Dorsal expression by viral miRNAs suppressed the Spz-Toll-Dorsal-ALF signaling pathway in shrimp in vivo , leading to virus infection. Our study provides new insight into the viral miRNA-mediated Toll signaling pathway in virus-host interactions. Copyright © 2017 American Society for Microbiology.

  2. Gibberellins Interfere with Symbiosis Signaling and Gene Expression and Alter Colonization by Arbuscular Mycorrhizal Fungi in Lotus japonicus1

    PubMed Central

    Takeda, Naoya; Handa, Yoshihiro; Tsuzuki, Syusaku; Kojima, Mikiko; Sakakibara, Hitoshi; Kawaguchi, Masayoshi

    2015-01-01

    Arbuscular mycorrhiza is a mutualistic plant-fungus interaction that confers great advantages for plant growth. Arbuscular mycorrhizal (AM) fungi enter the host root and form symbiotic structures that facilitate nutrient supplies between the symbionts. The gibberellins (GAs) are phytohormones known to inhibit AM fungal infection. However, our transcriptome analysis and phytohormone quantification revealed GA accumulation in the roots of Lotus japonicus infected with AM fungi, suggesting that de novo GA synthesis plays a role in arbuscular mycorrhiza development. We found pleiotropic effects of GAs on the AM fungal infection. In particular, the morphology of AM fungal colonization was drastically altered by the status of GA signaling in the host root. Exogenous GA treatment inhibited AM hyphal entry into the host root and suppressed the expression of Reduced Arbuscular Mycorrhization1 (RAM1) and RAM2 homologs that function in hyphal entry and arbuscule formation. On the other hand, inhibition of GA biosynthesis or suppression of GA signaling also affected arbuscular mycorrhiza development in the host root. Low-GA conditions suppressed arbuscular mycorrhiza-induced subtilisin-like serine protease1 (SbtM1) expression that is required for AM fungal colonization and reduced hyphal branching in the host root. The reduced hyphal branching and SbtM1 expression caused by the inhibition of GA biosynthesis were recovered by GA treatment, supporting the theory that insufficient GA signaling causes the inhibitory effects on arbuscular mycorrhiza development. Most studies have focused on the negative role of GA signaling, whereas our study demonstrates that GA signaling also positively interacts with symbiotic responses and promotes AM colonization of the host root. PMID:25527715

  3. Effects of a Potential Autochthonous Probiotic Bacillus subtilis 2-1 on the Growth and Intestinal Microbiota of Juvenile Sea Cucumber, Apostichopus japonicus Selenka

    NASA Astrophysics Data System (ADS)

    Zhao, Yancui; Yuan, Lei; Wan, Junli; Sun, Hushan; Wang, Yiyan; Zhang, Qin

    2018-04-01

    The effects of Bacillus subtilis 2-1 from the intestine of healthy sea cucumber on the growth, digestive enzyme activities and intestinal microbiota of juvenile sea cucumber ( Apostichopus japonicus) were determined in the present study. Sea cucumber was fed with Sargassum thunbergii powder supplemented with B. subtilis 2-1 at different concentrations varying among 0 (control), 105, 107, and 109 CFU g-1 for 8 weeks. Results showed that the growth performance and intestinal amylase and trypsin activities were significantly increased by dietary B. subtilis 2-1 at 109 CFU g-1 ( P < 0.05). However, dietary B. subtilis 2-1 had no significant influence on the lipase activity in sea cucumber ( P > 0.05). The polymerase chain reaction denaturing gradient gel electrophoresis and 16S rRNA gene sequencing analysis indicated that dietary B. subtilis 2-1 at 105 and 107 CFU g-1 inhibited most of the Proteobacteria including those in genus Vibrio. Dietary B. subtilis 2-1 at 109 CFU g-1 not only decreased the abundance and species of genus Vibrio, but also increased the intensity of genera Psychrobacter and Bacillus. A specific dosage of dietary B. subtilis 2-1 could increase the growth and modulate the intestinal microbiota of sea cucumber; thus it might be a novel probiotic for keeping the health of sea cucumber.

  4. Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons

    PubMed Central

    2012-01-01

    Background A central goal in Huntington's disease (HD) research is to identify and prioritize candidate targets for neuroprotective intervention, which requires genome-scale information on the modifiers of early-stage neuron injury in HD. Results Here, we performed a large-scale RNA interference screen in C. elegans strains that express N-terminal huntingtin (htt) in touch receptor neurons. These neurons control the response to light touch. Their function is strongly impaired by expanded polyglutamines (128Q) as shown by the nearly complete loss of touch response in adult animals, providing an in vivo model in which to manipulate the early phases of expanded-polyQ neurotoxicity. In total, 6034 genes were examined, revealing 662 gene inactivations that either reduce or aggravate defective touch response in 128Q animals. Several genes were previously implicated in HD or neurodegenerative disease, suggesting that this screen has effectively identified candidate targets for HD. Network-based analysis emphasized a subset of high-confidence modifier genes in pathways of interest in HD including metabolic, neurodevelopmental and pro-survival pathways. Finally, 49 modifiers of 128Q-neuron dysfunction that are dysregulated in the striatum of either R/2 or CHL2 HD mice, or both, were identified. Conclusions Collectively, these results highlight the relevance to HD pathogenesis, providing novel information on the potential therapeutic targets for neuroprotection in HD. PMID:22413862

  5. Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons.

    PubMed

    Lejeune, François-Xavier; Mesrob, Lilia; Parmentier, Frédéric; Bicep, Cedric; Vazquez-Manrique, Rafael P; Parker, J Alex; Vert, Jean-Philippe; Tourette, Cendrine; Neri, Christian

    2012-03-13

    A central goal in Huntington's disease (HD) research is to identify and prioritize candidate targets for neuroprotective intervention, which requires genome-scale information on the modifiers of early-stage neuron injury in HD. Here, we performed a large-scale RNA interference screen in C. elegans strains that express N-terminal huntingtin (htt) in touch receptor neurons. These neurons control the response to light touch. Their function is strongly impaired by expanded polyglutamines (128Q) as shown by the nearly complete loss of touch response in adult animals, providing an in vivo model in which to manipulate the early phases of expanded-polyQ neurotoxicity. In total, 6034 genes were examined, revealing 662 gene inactivations that either reduce or aggravate defective touch response in 128Q animals. Several genes were previously implicated in HD or neurodegenerative disease, suggesting that this screen has effectively identified candidate targets for HD. Network-based analysis emphasized a subset of high-confidence modifier genes in pathways of interest in HD including metabolic, neurodevelopmental and pro-survival pathways. Finally, 49 modifiers of 128Q-neuron dysfunction that are dysregulated in the striatum of either R/2 or CHL2 HD mice, or both, were identified. Collectively, these results highlight the relevance to HD pathogenesis, providing novel information on the potential therapeutic targets for neuroprotection in HD. © 2012 Lejeune et al; licensee BioMed Central Ltd.

  6. Effects of Mulching Tolerant Plant Straw on Soil Surface on Growth and Cadmium Accumulation of Galinsoga parviflora

    PubMed Central

    Lin, Lijin; Liao, Ming’an; Ren, Yajun; Luo, Li; Zhang, Xiao; Yang, Daiyu; He, Jing

    2014-01-01

    Pot and field experiments were conducted to study the effects of mulching with straw of cadmium (Cd) tolerant plants (Ranunculus sieboldii, Mazus japonicus, Clinopodium confine and Plantago asiatica) on growth and Cd accumulation of Galinsoga parviflora in Cd-contaminated soil. In the pot experiment, mulching with M. japonicus straw increased the root biomass, stem biomass, leaf biomass, shoot biomass, plant height and activities of antioxidant enzymes (superoxide dismutase, peroxidase and catalase) of G. parviflora compared with the control, whereas mulching with straws of R. sieboldii, C. confine and P. asiatica decreased these parameters. Straws of the four Cd-tolerant plants increased the Cd content in roots of G. parviflora compared with the control. However, only straws of M. japonicus and P. asiatica increased the Cd content in shoots of G. parviflora, reduced the soil pH, and increased the soil exchangeable Cd concentration. Straw of M. japonicus increased the amount of Cd extraction in stems, leaves and shoots of G. parviflora by 21.11%, 29.43% and 24.22%, respectively, compared with the control, whereas straws of the other three Cd-tolerant plants decreased these parameters. In the field experiment, the M. japonicus straw also increased shoot biomass, Cd content in shoots, and amount of Cd extraction in shoots of G. parviflora compared with the control. Therefore, straw of M. japonicus can be used to improve the Cd extraction ability of G. parviflora from Cd-contaminated soil. PMID:25490210

  7. I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chard, Kyle; D'Arcy, Mike; Heavner, Benjamin D.

    Big data workflows often require the assembly and exchange of complex, multi-element datasets. For example, in biomedical applications, the input to an analytic pipeline can be a dataset consisting thousands of images and genome sequences assembled from diverse repositories, requiring a description of the contents of the dataset in a concise and unambiguous form. Typical approaches to creating datasets for big data workflows assume that all data reside in a single location, requiring costly data marshaling and permitting errors of omission and commission because dataset members are not explicitly specified. We address these issues by proposing simple methods and toolsmore » for assembling, sharing, and analyzing large and complex datasets that scientists can easily integrate into their daily workflows. These tools combine a simple and robust method for describing data collections (BDBags), data descriptions (Research Objects), and simple persistent identifiers (Minids) to create a powerful ecosystem of tools and services for big data analysis and sharing. We present these tools and use biomedical case studies to illustrate their use for the rapid assembly, sharing, and analysis of large datasets.« less

  8. A GEOSPATIAL STUDY OF THE POTENTIAL OF TWO EXOTIC SPECIES OF MOSQUITOES TO IMPACT THE EPIDEMIOLOGY OF WEST NITLE VIRUS IN MARYLAND

    EPA Science Inventory


    Geospatial techniques were used to study the potential impact of two exotic mosquitoes, the Asian tiger mosquito, Aedes albopictus (Skuse) and Ochlerotatus japonicus japonicus (Theobald), on the epidemiology of West Nile virus in Maryland. These two species have established p...

  9. Large-scale GWAS identifies multiple loci for hand grip strength providing biological insights into muscular fitness.

    PubMed

    Willems, Sara M; Wright, Daniel J; Day, Felix R; Trajanoska, Katerina; Joshi, Peter K; Morris, John A; Matteini, Amy M; Garton, Fleur C; Grarup, Niels; Oskolkov, Nikolay; Thalamuthu, Anbupalam; Mangino, Massimo; Liu, Jun; Demirkan, Ayse; Lek, Monkol; Xu, Liwen; Wang, Guan; Oldmeadow, Christopher; Gaulton, Kyle J; Lotta, Luca A; Miyamoto-Mikami, Eri; Rivas, Manuel A; White, Tom; Loh, Po-Ru; Aadahl, Mette; Amin, Najaf; Attia, John R; Austin, Krista; Benyamin, Beben; Brage, Søren; Cheng, Yu-Ching; Cięszczyk, Paweł; Derave, Wim; Eriksson, Karl-Fredrik; Eynon, Nir; Linneberg, Allan; Lucia, Alejandro; Massidda, Myosotis; Mitchell, Braxton D; Miyachi, Motohiko; Murakami, Haruka; Padmanabhan, Sandosh; Pandey, Ashutosh; Papadimitriou, Ioannis; Rajpal, Deepak K; Sale, Craig; Schnurr, Theresia M; Sessa, Francesco; Shrine, Nick; Tobin, Martin D; Varley, Ian; Wain, Louise V; Wray, Naomi R; Lindgren, Cecilia M; MacArthur, Daniel G; Waterworth, Dawn M; McCarthy, Mark I; Pedersen, Oluf; Khaw, Kay-Tee; Kiel, Douglas P; Pitsiladis, Yannis; Fuku, Noriyuki; Franks, Paul W; North, Kathryn N; van Duijn, Cornelia M; Mather, Karen A; Hansen, Torben; Hansson, Ola; Spector, Tim; Murabito, Joanne M; Richards, J Brent; Rivadeneira, Fernando; Langenberg, Claudia; Perry, John R B; Wareham, Nick J; Scott, Robert A

    2017-07-12

    Hand grip strength is a widely used proxy of muscular fitness, a marker of frailty, and predictor of a range of morbidities and all-cause mortality. To investigate the genetic determinants of variation in grip strength, we perform a large-scale genetic discovery analysis in a combined sample of 195,180 individuals and identify 16 loci associated with grip strength (P<5 × 10 -8 ) in combined analyses. A number of these loci contain genes implicated in structure and function of skeletal muscle fibres (ACTG1), neuronal maintenance and signal transduction (PEX14, TGFA, SYT1), or monogenic syndromes with involvement of psychomotor impairment (PEX14, LRPPRC and KANSL1). Mendelian randomization analyses are consistent with a causal effect of higher genetically predicted grip strength on lower fracture risk. In conclusion, our findings provide new biological insight into the mechanistic underpinnings of grip strength and the causal role of muscular strength in age-related morbidities and mortality.

  10. Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation

    PubMed Central

    Christophersen, Ingrid E.; Rienstra, Michiel; Roselli, Carolina; Yin, Xiaoyan; Geelhoed, Bastiaan; Barnard, John; Lin, Honghuang; Arking, Dan E.; Smith, Albert V.; Albert, Christine M.; Chaffin, Mark; Tucker, Nathan R.; Li, Molong; Klarin, Derek; Bihlmeyer, Nathan A; Low, Siew-Kee; Weeke, Peter E.; Müller-Nurasyid, Martina; Smith, J. Gustav; Brody, Jennifer A.; Niemeijer, Maartje N.; Dörr, Marcus; Trompet, Stella; Huffman, Jennifer; Gustafsson, Stefan; Schurman, Claudia; Kleber, Marcus E.; Lyytikäinen, Leo-Pekka; Seppälä, Ilkka; Malik, Rainer; Horimoto, Andrea R. V. R.; Perez, Marco; Sinisalo, Juha; Aeschbacher, Stefanie; Thériault, Sébastien; Yao, Jie; Radmanesh, Farid; Weiss, Stefan; Teumer, Alexander; Choi, Seung Hoan; Weng, Lu-Chen; Clauss, Sebastian; Deo, Rajat; Rader, Daniel J.; Shah, Svati; Sun, Albert; Hopewell, Jemma C.; Debette, Stephanie; Chauhan, Ganesh; Yang, Qiong; Worrall, Bradford B.; Paré, Guillaume; Kamatani, Yoichiro; Hagemeijer, Yanick P.; Verweij, Niek; Siland, Joylene E.; Kubo, Michiaki; Smith, Jonathan D.; Van Wagoner, David R.; Bis, Joshua C.; Perz, Siegfried; Psaty, Bruce M.; Ridker, Paul M.; Magnani, Jared W.; Harris, Tamara B.; Launer, Lenore J.; Shoemaker, M. Benjamin; Padmanabhan, Sandosh; Haessler, Jeffrey; Bartz, Traci M.; Waldenberger, Melanie; Lichtner, Peter; Arendt, Marina; Krieger, Jose E.; Kähönen, Mika; Risch, Lorenz; Mansur, Alfredo J.; Peters, Annette; Smith, Blair H.; Lind, Lars; Scott, Stuart A.; Lu, Yingchang; Bottinger, Erwin B.; Hernesniemi, Jussi; Lindgren, Cecilia M.; Wong, Jorge; Huang, Jie; Eskola, Markku; Morris, Andrew P.; Ford, Ian; Reiner, Alex P.; Delgado, Graciela; Chen, Lin Y.; Chen, Yii-Der Ida; Sandhu, Roopinder K.; Li, Man; Boerwinkle, Eric; Eisele, Lewin; Lannfelt, Lars; Rost, Natalia; Anderson, Christopher D.; Taylor, Kent D.; Campbell, Archie; Magnusson, Patrik K.; Porteous, David; Hocking, Lynne J.; Vlachopoulou, Efthymia; Pedersen, Nancy L.; Nikus, Kjell; Orho-Melander, Marju; Hamsten, Anders; Heeringa, Jan; Denny, Joshua C.; Kriebel, Jennifer; Darbar, Dawood; Newton-Cheh, Christopher; Shaffer, Christian; Macfarlane, Peter W.; Heilmann, Stefanie; Almgren, Peter; Huang, Paul L.; Sotoodehnia, Nona; Soliman, Elsayed Z.; Uitterlinden, Andre G.; Hofman, Albert; Franco, Oscar H.; Völker, Uwe; Jöckel, Karl-Heinz; Sinner, Moritz F.; Lin, Henry J.; Guo, Xiuqing; Dichgans, Martin; Ingelsson, Erik; Kooperberg, Charles; Melander, Olle; Loos, Ruth J. F.; Laurikka, Jari; Conen, David; Rosand, Jonathan; van der Harst, Pim; Lokki, Marja-Liisa; Kathiresan, Sekar; Pereira, Alexandre; Jukema, J. Wouter; Hayward, Caroline; Rotter, Jerome I.; März, Winfried; Lehtimäki, Terho; Stricker, Bruno H.; Chung, Mina K.; Felix, Stephan B.; Gudnason, Vilmundur; Alonso, Alvaro; Roden, Dan M.; Kääb, Stefan; Chasman, Daniel I.; Heckbert, Susan R.; Benjamin, Emelia J.; Tanaka, Toshihiro; Lunetta, Kathryn L.; Lubitz, Steven A.; Ellinor, Patrick T.

    2017-01-01

    Atrial fibrillation affects more than 33 million people worldwide and increases the risk of stroke, heart failure, and death.1,2 Fourteen genetic loci have been associated with atrial fibrillation in European and Asian ancestry groups.3–7 To further define the genetic basis of atrial fibrillation, we performed large-scale, multi-racial meta-analyses of common and rare variant association studies. The genome-wide association studies (GWAS) included 18,398 individuals with atrial fibrillation and 91,536 referents; the exome-wide association studies (ExWAS) and rare variant association studies (RVAS) involved 22,806 cases and 132,612 referents. We identified 12 novel genetic loci that exceeded genome-wide significance, implicating genes involved in cardiac electrical and structural remodeling. Our results nearly double the number of known genetic loci for atrial fibrillation, provide insights into the molecular basis of atrial fibrillation, and may facilitate new potential targets for drug discovery.8 PMID:28416818

  11. A new identified complication of intracystic hemorrhage in a large pineal gland cyst.

    PubMed

    Mehrzad, Raman; Mishra, Suprav; Feinstein, Alexander; Ho, Michael G

    2014-01-01

    Pineal gland cysts are typically asymptomatic, benign cysts most commonly found incidentally in adults. In rare cases, a large pineal gland cyst can be complicated by intracystic hemorrhage, which could then manifest with neurological symptoms. We report a new complication of intracystic hemorrhage in a large pineal gland cyst in a 40-year-old man with new onset seizures. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. The Ethylene Responsive Factor Required for Nodulation 1 (ERN1) Transcription Factor Is Required for Infection-Thread Formation in Lotus japonicus.

    PubMed

    Kawaharada, Yasuyuki; James, Euan K; Kelly, Simon; Sandal, Niels; Stougaard, Jens

    2017-03-01

    Several hundred genes are transcriptionally regulated during infection-thread formation and development of nitrogen-fixing root nodules. We have characterized a set of Lotus japonicus mutants impaired in root-nodule formation and found that the causative gene, Ern1, encodes a protein with a characteristic APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription-factor domain. Phenotypic characterization of four ern1 alleles shows that infection pockets are formed but root-hair infection threads are absent. Formation of root-nodule primordia is delayed and no normal transcellular infection threads are found in the infected nodules. Corroborating the role of ERN1 (ERF Required for Nodulation1) in nodule organogenesis, spontaneous nodulation induced by an autoactive CCaMK and cytokinin-induced nodule primordia were not observed in ern1 mutants. Expression of Ern1 is induced in the susceptible zone by Nod factor treatment or rhizobial inoculation. At the cellular level, the pErn1:GUS reporter is highly expressed in root epidermal cells of the susceptible zone and in the cortical cells that form nodule primordia. The genetic regulation of this cellular expression pattern was further investigated in symbiotic mutants. Nod factor induction of Ern1 in epidermal cells was found to depend on Nfr1, Cyclops, and Nsp2 but was independent of Nin and Nf-ya1. These results suggest that ERN1 functions as a transcriptional regulator involved in the formation of infection threads and development of nodule primordia and may coordinate these two processes.

  13. Ecological effects of co-culturing the sea cucumber Apostichopus japonicus with the Chinese white shrimp Fenneropenaeus chinensis in an earthen pond

    NASA Astrophysics Data System (ADS)

    Zhou, Shun; Ren, Yichao; Pearce, Christopher M.; Dong, Shuanglin; Tian, Xiangli; Gao, Qinfeng; Wang, Fang

    2017-01-01

    Using net enclosures in an earthen pond, we established three culture treatments with the sea cucumber Apostichopus japonicus and the Chinese white shrimp Fenneropenaeus chinensis: monoculture of sea cucumbers (C), monoculture of shrimp (S), and co-culture of the two species (CS). We measured levels of suspended particulate matter in the water column; total organic matter, total organic carbon, total nitrogen, and carbon/nitrogen ratios in both settling particles and the sediment; and chlorophyll a levels in the sediment. We then compared these variables between the three treatments. We also examined growth, survival, and yield of the two species in the different treatments. From June to September, the mean monthly suspended particulate matter sedimentation rates in the CS and S treatments were significantly ( P<0.05) greater than those in the C treatment. From August to November, the mean monthly total organic matter, total organic carbon, total nitrogen, and chlorophyll a contents in the sediment in the CS and S treatments were significantly ( P <0.05) greater than those in the C treatment. Final wet weight, specific growth rate, survival rate, and total yield of sea cucumbers in co-culture were all significantly greater than those of sea cucumbers in monoculture. There were no significant differences among any of these variables for shrimp reared in the two systems. The bioturbation of the sediment and fecal production of the shrimp likely supplied natural food for the sea cucumbers. Co-culture of the two species is a viable option for increasing yield per unit area, maximizing use of the water body, and diversifying crop production.

  14. Update on Comparative Genomics of Legumes

    USDA-ARS?s Scientific Manuscript database

    This year marks the essential completion of the genome sequences of Glycine max, Medicago truncatula, and Lotus japonicus (soybean, barrel medic, and birdsfoot trefoil, respectively). The impact of these assembled, annotated genomes will be enormous. L. japonicus and M. truncatula, both forage crop...

  15. Cooperativity in the two-domain arginine kinase from the sea anemone Anthopleura japonicus. II. Evidence from site-directed mutagenesis studies.

    PubMed

    Tada, Hiroshi; Suzuki, Tomohiko

    2010-08-01

    The arginine kinase (AK) from the sea anemone Anthopleura japonicus has an unusual two-domain structure (contiguous dimer; denoted by D1-D2). In a previous report, we suggested cooperativity in the contiguous dimer, which may be a result of domain-domain interactions, using MBP-fused enzymes. To further understand this observation, we inserted six-Lys residues into the linker region of the two-domain AK (D1-K6-D2 mutant) using His-tagged enzyme. The dissociation constants, K(a) and K(ia), of the mutant were similar to those of the wild-type enzyme but the catalytic constant, k(cat), was decreased to 28% that of the wild-type, indicating that some of the domain-domain interactions are lost due to the six-Lys insertion. Y68 plays a major role in arginine binding in the catalytic pocket in Limulus AK, and introduction of mutation at the Y68 position virtually abolishes catalytic activity. Thus, the constructed D1(Y68G)-D2 and D1-D2(Y68G) mutants mimic the D1(inactive)-D2(active) and D1(active)-D2(inactive) enzymes, respectively. The k(cat) values of both Y68 mutants were decreased to 13-18% that of the wild-type enzyme, which is much less than the 50% level of the two-domain enzyme. Thus, it is clear that substrate-binding to both domains is necessary for full expression of activity. In other words, substrate-binding appears to act as the trigger of the functional cooperativity in two-domain AK. Copyright 2010 Elsevier B.V. All rights reserved.

  16. The Skill of Identifying Argumentation.

    ERIC Educational Resources Information Center

    van Eemeren, Frans H.; And Others

    1989-01-01

    Investigates 14-year-old students' ability to recognize argumentation without having systematic instruction; and whether the identification of argumentation is an independent skill. Finds that after a 20-minute explanation, a large proportion of 14-year-olds could not identify simple argumentation. Concludes that identifying argumentation is a…

  17. High-Throughput Genetic Screens Identify a Large and Diverse Collection of New Sporulation Genes in Bacillus subtilis.

    PubMed

    Meeske, Alexander J; Rodrigues, Christopher D A; Brady, Jacqueline; Lim, Hoong Chuin; Bernhardt, Thomas G; Rudner, David Z

    2016-01-01

    The differentiation of the bacterium Bacillus subtilis into a dormant spore is among the most well-characterized developmental pathways in biology. Classical genetic screens performed over the past half century identified scores of factors involved in every step of this morphological process. More recently, transcriptional profiling uncovered additional sporulation-induced genes required for successful spore development. Here, we used transposon-sequencing (Tn-seq) to assess whether there were any sporulation genes left to be discovered. Our screen identified 133 out of the 148 genes with known sporulation defects. Surprisingly, we discovered 24 additional genes that had not been previously implicated in spore formation. To investigate their functions, we used fluorescence microscopy to survey early, middle, and late stages of differentiation of null mutants from the B. subtilis ordered knockout collection. This analysis identified mutants that are delayed in the initiation of sporulation, defective in membrane remodeling, and impaired in spore maturation. Several mutants had novel sporulation phenotypes. We performed in-depth characterization of two new factors that participate in cell-cell signaling pathways during sporulation. One (SpoIIT) functions in the activation of σE in the mother cell; the other (SpoIIIL) is required for σG activity in the forespore. Our analysis also revealed that as many as 36 sporulation-induced genes with no previously reported mutant phenotypes are required for timely spore maturation. Finally, we discovered a large set of transposon insertions that trigger premature initiation of sporulation. Our results highlight the power of Tn-seq for the discovery of new genes and novel pathways in sporulation and, combined with the recently completed null mutant collection, open the door for similar screens in other, less well-characterized processes.

  18. High-Throughput Genetic Screens Identify a Large and Diverse Collection of New Sporulation Genes in Bacillus subtilis

    PubMed Central

    Brady, Jacqueline; Lim, Hoong Chuin; Bernhardt, Thomas G.; Rudner, David Z.

    2016-01-01

    The differentiation of the bacterium Bacillus subtilis into a dormant spore is among the most well-characterized developmental pathways in biology. Classical genetic screens performed over the past half century identified scores of factors involved in every step of this morphological process. More recently, transcriptional profiling uncovered additional sporulation-induced genes required for successful spore development. Here, we used transposon-sequencing (Tn-seq) to assess whether there were any sporulation genes left to be discovered. Our screen identified 133 out of the 148 genes with known sporulation defects. Surprisingly, we discovered 24 additional genes that had not been previously implicated in spore formation. To investigate their functions, we used fluorescence microscopy to survey early, middle, and late stages of differentiation of null mutants from the B. subtilis ordered knockout collection. This analysis identified mutants that are delayed in the initiation of sporulation, defective in membrane remodeling, and impaired in spore maturation. Several mutants had novel sporulation phenotypes. We performed in-depth characterization of two new factors that participate in cell–cell signaling pathways during sporulation. One (SpoIIT) functions in the activation of σE in the mother cell; the other (SpoIIIL) is required for σG activity in the forespore. Our analysis also revealed that as many as 36 sporulation-induced genes with no previously reported mutant phenotypes are required for timely spore maturation. Finally, we discovered a large set of transposon insertions that trigger premature initiation of sporulation. Our results highlight the power of Tn-seq for the discovery of new genes and novel pathways in sporulation and, combined with the recently completed null mutant collection, open the door for similar screens in other, less well-characterized processes. PMID:26735940

  19. How do you assign persistent identifiers to extracts from large, complex, dynamic data sets that underpin scholarly publications?

    NASA Astrophysics Data System (ADS)

    Wyborn, Lesley; Car, Nicholas; Evans, Benjamin; Klump, Jens

    2016-04-01

    Persistent identifiers in the form of a Digital Object Identifier (DOI) are becoming more mainstream, assigned at both the collection and dataset level. For static datasets, this is a relatively straight-forward matter. However, many new data collections are dynamic, with new data being appended, models and derivative products being revised with new data, or the data itself revised as processing methods are improved. Further, because data collections are becoming accessible as services, researchers can log in and dynamically create user-defined subsets for specific research projects: they also can easily mix and match data from multiple collections, each of which can have a complex history. Inevitably extracts from such dynamic data sets underpin scholarly publications, and this presents new challenges. The National Computational Infrastructure (NCI) has been experiencing and making progress towards addressing these issues. The NCI is large node of the Research Data Services initiative (RDS) of the Australian Government's research infrastructure, which currently makes available over 10 PBytes of priority research collections, ranging from geosciences, geophysics, environment, and climate, through to astronomy, bioinformatics, and social sciences. Data are replicated to, or are produced at, NCI and then processed there to higher-level data products or directly analysed. Individual datasets range from multi-petabyte computational models and large volume raster arrays, down to gigabyte size, ultra-high resolution datasets. To facilitate access, maximise reuse and enable integration across the disciplines, datasets have been organized on a platform called the National Environmental Research Data Interoperability Platform (NERDIP). Combined, the NERDIP data collections form a rich and diverse asset for researchers: their co-location and standardization optimises the value of existing data, and forms a new resource to underpin data-intensive Science. New publication

  20. Key to Nearctic Trissolcus Ashmead

    USDA-ARS?s Scientific Manuscript database

    Trissolcus japonicus (Ashmead) and T. cultratus (Mayr) comb. rev. are under study as classical biological agents to control the brown marmorated stink bug Halyomorpha halys (Stål) in North America. Here we present diagnoses for all Nearctic species of Trissolcus, including T. japonicus and T. cultra...

  1. Comparative genome analysis of a large Dutch Legionella pneumophila strain collection identifies five markers highly correlated with clinical strains

    PubMed Central

    2010-01-01

    Background Discrimination between clinical and environmental strains within many bacterial species is currently underexplored. Genomic analyses have clearly shown the enormous variability in genome composition between different strains of a bacterial species. In this study we have used Legionella pneumophila, the causative agent of Legionnaire's disease, to search for genomic markers related to pathogenicity. During a large surveillance study in The Netherlands well-characterized patient-derived strains and environmental strains were collected. We have used a mixed-genome microarray to perform comparative-genome analysis of 257 strains from this collection. Results Microarray analysis indicated that 480 DNA markers (out of in total 3360 markers) showed clear variation in presence between individual strains and these were therefore selected for further analysis. Unsupervised statistical analysis of these markers showed the enormous genomic variation within the species but did not show any correlation with a pathogenic phenotype. We therefore used supervised statistical analysis to identify discriminating markers. Genetic programming was used both to identify predictive markers and to define their interrelationships. A model consisting of five markers was developed that together correctly predicted 100% of the clinical strains and 69% of the environmental strains. Conclusions A novel approach for identifying predictive markers enabling discrimination between clinical and environmental isolates of L. pneumophila is presented. Out of over 3000 possible markers, five were selected that together enabled correct prediction of all the clinical strains included in this study. This novel approach for identifying predictive markers can be applied to all bacterial species, allowing for better discrimination between strains well equipped to cause human disease and relatively harmless strains. PMID:20630115

  2. Swim bladder function and buoyancy control in pink snapper (Pagrus auratus) and mulloway (Argyrosomus japonicus).

    PubMed

    Stewart, John; Hughes, Julian M

    2014-04-01

    Physoclist fish are able to regulate their buoyancy by secreting gas into their hydrostatic organ, the swim bladder, as they descend through the water column and by resorbing gas from their swim bladder as they ascend. Physoclists are restricted in their vertical movements due to increases in swim bladder gas volume that occur as a result of a reduction in hydrostatic pressure, causing fish to become positively buoyant and risking swim bladder rupture. Buoyancy control, rates of swim bladder gas exchange and restrictions to vertical movements are little understood in marine teleosts. We used custom-built hyperbaric chambers and laboratory experiments to examine these aspects of physiology for two important fishing target species in southern Australia, pink snapper (Pagrus auratus) and mulloway (Argyrosomus japonicus). The swim bladders of pink snapper and mulloway averaged 4.2 and 4.9 % of their total body volumes, respectively. The density of pink snapper was not significantly different to the density of seawater (1.026 g/ml), whereas mulloway were significantly denser than seawater. Pink snapper secreted gas into their swim bladders at a rate of 0.027 ± 0.005 ml/kg/min (mean ± SE), almost 4 times faster than mulloway (0.007 ± 0.001 ml/kg/min). Rates of swim bladder gas resorption were 11 and 6 times faster than the rates of gas secretion for pink snapper and mulloway, respectively. Pink snapper resorbed swim bladder gas at a rate of 0.309 ± 0.069 ml/kg/min, 7 times faster than mulloway (0.044 ± 0.009 ml/kg/min). Rates of gas exchange were not affected by water pressure or water temperature over the ranges examined in either species. Pink snapper were able to acclimate to changes in hydrostatic pressure reasonably quickly when compared to other marine teleosts, taking approximately 27 h to refill their swim bladders from empty. Mulloway were able to acclimate at a much slower rate, taking approximately 99 h to refill their swim bladders. We estimated that the

  3. Condition of larval and early juvenile Japanese temperate bass Lateolabrax japonicus related to spatial distribution and feeding in the Chikugo estuarine nursery ground in the Ariake Bay, Japan

    NASA Astrophysics Data System (ADS)

    Islam, Md. Shahidul; Hibino, Manabu; Nakayama, Kouji; Tanaka, Masaru

    2006-02-01

    The present study investigates feeding and condition of larval and juvenile Japanese temperate bass Lateolabrax japonicus in relation to spatial distribution in the Chikugo estuary (Japan). Larvae were collected in a wide area covering the nursery grounds of the species in 2002 and 2003. Food habits of the fish were analysed by examining their gut contents. Fish condition was evaluated by using morphometric (the length-weight relationship and condition factor) and biochemical (the RNA:DNA ratio and other nucleic acid based parameters) indices and growth rates. The nucleic-acid contents in individually frozen larvae and juveniles were quantified by standard fluorometric methods. Two distinct feeding patterns, determined by the distribution of prey copepods, were identified. The first pattern showed dependence on the calanoid copepod Sinocalanus sinensis, which was the single dominant prey in low-saline upper river areas. The second pattern involved a multi-specific dietary habit mainly dominated by Acartia omorii, Oithona davisae, and Paracalanus parvus. As in the gut contents analyses, two different sets of values were observed for RNA, DNA, total protein, growth rates and for all the nucleic acid-based indices: one for the high-saline downstream areas and a second for the low-saline upstream areas, which was significantly higher than the first. The proportion of starving fish was lower upstream than downstream. Values of the allometric coefficient ( b) and the condition factor ( K) obtained from the length-weight relationships increased gradually from the sea to the upper river. Clearly, fish in the upper river had a better condition than those in the lower estuary. RNA:DNA ratios correlated positively with temperature and negatively with salinity. We hypothesise that by migration to the better foraging grounds of the upper estuary (with higher prey biomass, elevated temperature and reduced salinity), the fish reduce early mortality and attain a better condition

  4. Development of monoclonal antibodies against IgM of sea bass (Lateolabrax japonicus) and analysis of phagocytosis by mIgM+ lymphocytes.

    PubMed

    Yang, Shun; Tang, Xiaoqian; Sheng, Xiuzhen; Xing, Jing; Zhan, Wenbin

    2018-07-01

    B cells in some fish were recently found to have potent phagocytic activities. Sea bass (Lateolabrax japonicus) as an important economical marine fish species, it could be used as an appropriate model to study the functions of B cells in phagocytosis. In the paper, three positive hybridomas designated as 1E11, 2H4 and 3F3 secreting monoclonal antibodies (MAbs) against sea bass immunoglobulin M (IgM) were produced and used as research tools. Indirect enzyme-linked immunosorbent assay showed that all the three MAbs had a high binding capacity with sea bass serum IgM. Western blotting analysis showed that all the three MAbs were specific for the heavy chain of sea bass IgM. Indirect immunofluorescence assay (IFA) analysis suggested that both MAbs 1E11 and 2H4 could recognize membrane-bound IgM (mIgM) molecule of sea bass. Specificity analysis showed that three MAbs had no cross-reactions with other six teleosts IgMs. Flow cytometric analysis exhibited that the percentages of sea bass mIgM + lymphocytes in peripheral blood, spleen and pronephros were 25.6%, 21.1%, and 17.5%, respectively. Moreover, we found that the mIgM + lymphocytes of sea bass could phagocytose fluorescence microspheres and Lactococcus lactis, but lower phagocytosis rates of L. lactis was observed. These results demonstrated that the MAbs produced in this paper could be used as tools to study secretory IgM and mIgM + lymphocytes of sea bass, and mIgM + lymphocytes might also play an important role in innate immunity of sea bass. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Vibrio japonicus sp. nov., a novel member of the Nereis clade in the genus Vibrio isolated from the coast of Japan

    PubMed Central

    2017-01-01

    A novel Vibrio strain, JCM 31412T, was isolated from seawater collected from the Inland Sea (Setonaikai), Japan, and characterized as a Gram-negative, oxidase-positive, catalase-negative, facultatively anaerobic, motile, ovoid-shaped bacterium with one polar flagellum. Based on 16S rDNA gene identity, strain JCM 31412T showed a close relationship with type strains of Vibrio brasiliensis (LMG 20546T, 98.2% identity), V. harveyi (NBRC 15634T, 98.2%), V. caribbeanicus (ATCC BAA-2122T, 97.8%) and V. proteolyticus (NBRC 13287T, 97.8%). The G+C content of strain JCM 31412T DNA was 46.8%. Multi-locus sequence analysis (MLSA) of eight loci (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA; 5535bp) further clustered strain JCM 31412T in the Nereis clade, genus Vibrio. Phenotypically, strain JCM 31412T differed from the closest related Vibrio species in its utilization of melibiose and raffinose, and its lack of casein and gelatin hydrolysis. It was further differentiated based on its fatty acid composition, specifically properties of C12:03OH and summed features, which were significantly different from those of V. brasiliensis, V. nigripulchritudo and V. caribbeanicus type strains. Overall, the results of DNA-DNA hybridization, and physiological and biochemical analysis differentiated strain JCM 31412T from other described species of the genus Vibrio. Based on these polyphasic taxonomic findings, it was therefore concluded that JCM 31412T was a novel Vibrio species, for which the name Vibrio japonicus sp. nov. was proposed, with JCM 31412T (= LMG 29636T = ATCC TSD-62T) as the type strain. PMID:28231272

  6. Dim-light photoreceptor of chub mackerel Scomber japonicus and the photoresponse upon illumination with LEDs of different wavelengths.

    PubMed

    Jang, Jun-Chul; Choi, Mi-Jin; Yang, Yong-Soo; Lee, Hyung-Been; Yu, Young-Moon; Kim, Jong-Myoung

    2016-06-01

    To study the absorption characteristics of rhodopsin, a dim-light photoreceptor, in chub mackerel (Scomber japonicus) and the relationship between light wavelengths on the photoresponse, the rod opsin gene was cloned into an expression vector, pMT4. Recombinant opsin was transiently expressed in COS-1 cells and reconstituted with 11-cis-retinal. Cells containing the regenerated rhodopsin were solubilized and subjected to UV/Vis spectroscopic analysis in the dark and upon illumination. Difference spectra from the lysates indicated an absorption maximum of mackerel rhodopsin around 500 nm. Four types of light-emitting diode (LED) modules with different wavelengths (red, peak 627 nm; cyan, 505 nm; blue, 442 nm; white, 447 + 560 nm) were constructed to examine their effects on the photoresponse in chub mackerel. Behavioral responses of the mackerels, including speed and frequencies acclimated in the dark and upon LED illumination, were analyzed using an underwater acoustic camera. Compared to an average speed of 22.25 ± 1.57 cm/s of mackerel movement in the dark, speed increased to 22.97 ± 0.29, 24.66 ± 1.06, 26.28 ± 2.28, and 25.19 ± 1.91 cm/s upon exposure to red, blue, cyan, and white LEDs, respectively. There were increases of 103.48 ± 1.58, 109.37 ± 5.29, 118.48 ± 10.82, and 109.43 ± 3.92 %, respectively, in the relative speed of the fishes upon illumination with red, blue, cyan, and white LEDs compared with that in the dark (set at 100 %). Similar rate of wavelength-dependent responses was observed in a frequency analysis. These results indicate that an LED emitting a peak wavelength close to an absorption maximum of rhodopsin is more effective at eliciting a response to light.

  7. Effects of tussah immunoreactive substances on growth, immunity, disease resistance against Vibrio splendidus and gut microbiota profile of Apostichopus japonicus.

    PubMed

    Ma, Shuhui; Sun, Yongxin; Wang, Fuqiang; Mi, Rui; Wen, Zhixin; Li, Xuejun; Meng, Nan; Li, Yajie; Du, Xingfan; Li, Shuying

    2017-04-01

    Tussah immunoreactive substance (TIS) comprises a number of active chemicals with various bioactivities. The current study investigated the effects of these substances on the sea cucumber Apostichopus japonicus. The specific growth rate (SGR) of TIS-fed sea cucumbers was significantly enhanced, whereas no significant difference in SGR was observed between those soaked in antibiotics and those fed with basal diet only. TIS also improved the immune response of the animals when given at a dose of 1.0% or 2.0%, as shown by increased phagocytic, lysozyme, superoxide dismutase, alkaline phosphatase, acid phosphatase, and catalase activities following injection with live Vibrio splendidus. At a dose of 1.0% or 2.0%, TIS significantly enhanced the immune ability (P < 0.05) of the sea cucumbers, but except for lysozyme activity, other immune indices were reduced one day after the animals were injected with Vibrio splendidus. However, the values of these immune indexes were still significantly higher compared to those of the control groups (P < 0.05). Intestinal micro flora counts and high-throughput sequencing showed that dietary TIS could improve the amount of probiotic bacteria, yielding a 6-fold increase in Bacillus and 10-fold increase in Lactobacillus for sea cucumbers fed with 2.0% TIS diet compared to the control. Furthermore, TIS-containing diet also greatly reduced the number of harmful bacteria, with the number of Vibrio in sea cucumbers fed with 1%TIS diet decreased by 67% compared to the control. The results thus indicated that TIS increased the growth of sea cucumbers and enhanced their resistance to V. splendidus infection by improving the immunity of the animals. TIS also improved the gut microbiota profiles of the animals by increasing the probiotics and reducing the harmful bacteria within their guts. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Identifying anomalously early spring onsets in the CESM large ensemble project

    NASA Astrophysics Data System (ADS)

    Labe, Zachary; Ault, Toby; Zurita-Milla, Raul

    2017-06-01

    Seasonal transitions from winter to spring impact a wide variety of ecological and physical systems. While the effects of early springs across North America are widely documented, changes in their frequency and likelihood under the combined influences of climate change and natural variability are poorly understood. Extremely early springs, such as March 2012, can lead to severe economical losses and agricultural damage when these are followed by hard freeze events. Here we use the new Community Earth System Model Large Ensemble project and Extended Spring Indices to simulate historical and future spring onsets across the United States and in the particular the Great Lakes region. We found a marked increase in the frequency of March 2012-like springs by midcentury in addition to an overall trend towards earlier spring onsets, which nearly doubles that of observational records. However, changes in the date of last freeze do not occur at the same rate, therefore, causing a potential increase in the threat of plant tissue damage. Although large-scale climate modes, such as the Pacific Decadal Oscillation, have previously dominated decadal to multidecadal spring onset trends, our results indicate a decreased role in natural climate variability and hence a greater forced response by the end of the century for modulating trends. Without a major reduction in greenhouse gas emissions, our study suggests that years like 2012 in the US could become normal by mid-century.

  9. Detection of a large unnamed Babesia piroplasm originally identified in dogs in North Carolina in a dog with no history of travel to that state.

    PubMed

    Holman, Patricia J; Backlund, Brianna B; Wilcox, Angela L; Stone, Richard; Stricklin, Andrew L; Bardin, Kendall E

    2009-10-01

    A 12-year-old 46-kg (101.2-lb) sexually intact male Labrador Retriever was evaluated because of lymphadenomegaly. The dog resided in Texas, and its travel history included many southeastern and eastern shore states but not North Carolina. Following evaluation of the dog, a diagnosis of stage IVa intermediate- to large-cell lymphoma was made. A cyclophosphamide-hydroxydaunorubicin (doxorubicin)-vincristine-prednisone chemotherapy protocol was initiated. One week after the first chemotherapeutic treatment, a routine blood smear evaluation revealed single and paired intraerythrocytic large piroplasms that resembled Babesia canis. Via molecular testing, the organism was identified as a Babesia sp that had been detected previously in dogs in North Carolina. The dog was administered imidocarb diproprionate (7 mg/kg [3.2 mg/lb], IM) on 2 occasions (3-week interval). At 1, 4, 15, and 50 weeks after the second treatment, blood samples were analyzed specifically for the North Carolina Babesia sp via PCR assay; the result of each assay was positive. Because of the morphologic similarity of the large piroplasm detected in dogs in North Carolina to B canis, molecular testing of large piroplasms detected in dogs is needed to definitively identify the infective Babesia sp. In the dog of this report, the infection was not eliminated following treatment with imidocarb diproprionate, which may have been a result of the immunocompromised state of the dog or the drug's ineffectiveness against this parasite. If imidocarb diproprionate is ineffective against the North Carolina Babesia sp, treated dogs may act as reservoirs of infection.

  10. Phagocytic activities of hemocytes from the deep-sea symbiotic mussels Bathymodiolus japonicus, B. platifrons, and B. septemdierum.

    PubMed

    Tame, Akihiro; Yoshida, Takao; Ohishi, Kazue; Maruyama, Tadashi

    2015-07-01

    Deep-sea mytilid mussels harbor symbiotic bacteria in their gill epithelial cells that are horizontally or environmentally transmitted to the next generation of hosts. To understand the immune defense system in deep-sea symbiotic mussels, we examined the hemocyte populations of the symbiotic Bathymodiolus mussel species Bathymodiolus japonicus, Bathymodiolus platifrons, and Bathymodiolus septemdierum, and characterized three types of hemocytes: agranulocytes (AGs), basophilic granulocytes (BGs), and eosinophilic granulocytes (EGs). Of these, the EG cells were the largest (diameter, 8.4-10.0 μm) and had eosinophilic cytoplasm with numerous eosinophilic granules (diameter, 0.8-1.2 μm). Meanwhile, the BGs were of medium size (diameter, 6.7-8.0 μm) and contained small basophilic granules (diameter, 0.3-0.4 μm) in basophilic cytoplasm, and the AGs, the smallest of the hemocytes (diameter, 4.8-6.0 μm), had basophilic cytoplasm lacking granules. A lectin binding assay revealed that concanavalin A bound to all three hemocyte types, while wheat germ agglutinin bound exclusively to EGs and BGs. The total hemocyte population densities within the hemolymph of all three Bathymodiolus mussel species were similar (8.4-13.3 × 10(5) cells/mL), and the percentages of circulating AGs, BGs, and EGs in the hemolymph of these organisms were 44.7-48.5%, 14.3-17.6%, and 34.3-41.0%, respectively. To analyze the functional differences between these hemocytes, the phagocytic activity and post-phagocytic phagosome-lysosome fusion events were analyzed in each cell type using a fluorescent Alexa Fluor(®) 488-conjugated Escherichia coli bioparticle and a LysoTracker(®) lysosomal marker, respectively. While the AGs exhibited no phagocytic activity, both types of granulocytes were phagocytic. Of the three hemocyte types, the EGs exhibited the highest level of phagocytic activity as well as rapid phagosome-lysosome fusion, which occurred within 2 h of incubation. Meanwhile, the BGs showed

  11. [Characteristics of ichthyoplankton assemblages in Yangtze Estuary and adjacent waters in spring].

    PubMed

    Liu, Shu-De; Xian, Wei-Wei; Liu, Dong

    2008-10-01

    Based on the investigation data of ichthyoplankton assemblages and environmental factors in Yangtze Estuary and adjacent waters in May 1999 and 2001, the characteristics of ichthyoplankton assemblages in these areas in spring were studied by using TWINSPAN (two-way indicator species analysis) and CCA (canonical correspondence analysis). A total of 11 540 ichthyoplankton individuals were taxonomically identified, belonging to 11 orders, 18 families and 32 species, of which, Coilia mystus, Engraulis japonicus, Chaeturichthys hexanema, Allanetta bleekeri, and Trachidermis fasciatus were the dominant species. The ichthyoplankton communities were classified into three assemblages by using TWINSPAN, i.e., estuarine assemblage dominated by C. mystus, coastal assemblage dominated by A. bleekeri and T. fasciatus; and shelf assemblage featured by E. japonicus and C. hexanema. The CCA ordination of the interrelations among the three assemblages and their correlations to the environmental variables revealed that salinity, depth, dissolved oxygen, and total suspended particulate matter were the major factors affecting the ichthyoplankton assemblages in the study areas.

  12. Identifying the Source of Large-Scale Atmospheric Variability in Jupiter

    NASA Astrophysics Data System (ADS)

    Orton, Glenn

    2011-01-01

    We propose to use the unique mid-infrared filtered imaging and spectroscopic capabilities of the Subaru COMICS instrument to determine the mechanisms associated with recent unusual rapid albedo and color transformations of several of Jupiter's bands, particularly its South Equatorial Belt (SEB), as a means to understand the coupling between its dynamics and chemistry. These observations will characterize the temperature, degree of cloud cover, and distribution of minor gases that serve as indirect tracers of vertical motions in regions that will be undergoing unusual large-scale changes in dynamics and chemistry: the SEB, as well as regions near the equator and Jupiter's North Temperate Belt. COMICS is ideal for this investigation because of its efficiency in doing both imaging and spectroscopy, its 24.5-mum filter that is unique to 8-meter-class telescopes, its wide field of view that allows imaging of nearly all of Jupiter's disk, coupled with a high diffraction-limited angular resolution and optimal mid-infrared atmospheric transparency.

  13. Development of unidentified dna-specific hif 1α gene of lizard (hemidactylus platyurus) which plays a role in tissue regeneration process

    NASA Astrophysics Data System (ADS)

    Novianti, T.; Sadikin, M.; Widia, S.; Juniantito, V.; Arida, E. A.

    2018-03-01

    Development of unidentified specific gene is essential to analyze the availability these genes in biological process. Identification unidentified specific DNA of HIF 1α genes is important to analyze their contribution in tissue regeneration process in lizard tail (Hemidactylus platyurus). Bioinformatics and PCR techniques are relatively an easier method to identify an unidentified gene. The most widely used method is BLAST (Basic Local Alignment Sequence Tools) method for alignment the sequences from the other organism. BLAST technique is online software from website https://blast.ncbi.nlm.nih.gov/Blast.cgi that capable to generate the similar sequences from closest kinship to distant kindship. Gecko japonicus is a species that it has closest kinship with H. platyurus. Comparing HIF 1 α gene sequence of G. japonicus with the other species used multiple alignment methods from Mega7 software. Conserved base areas were identified using Clustal IX method. Primary DNA of HIF 1 α gene was design by Primer3 software. HIF 1α gene of lizard (H. platyurus) was successfully amplified using a real-time PCR machine by primary DNA that we had designed from Gecko japonicus. Identification unidentified gene of HIF 1a lizard has been done successfully with multiple alignment method. The study was conducted by analyzing during the growth of tail on day 1, 3, 5, 7, 10, 13 and 17 of lizard tail after autotomy. Process amplification of HIF 1α gene was described by CT value in real time PCR machine. HIF 1α expression of gene is quantified by Livak formula. Chi-square statistic test is 0.000 which means that there is a different expression of HIF 1 α gene in every growth day treatment.

  14. [Removal efficiency of red tide organisms by modified clay and its impacts on cultured organisms].

    PubMed

    Cao, Xi-hua; Song, Xiu-xian; Yu, Zhi-ming

    2004-09-01

    Removal efficiencies of Prorocentrum donghaiense (Prorocentrum dentatum) by Hexadecyltrimethylammonium (HDTMA) bromide and organo-clay modified by HDTMA were identified. Moreover the toxicity of the unbound HDTMA and HDTMA plus clay to aquacultural organisms, Penaeus japonicus, was also tested. The results suggested that (1) The unbound HDTMA had an excellent ability to remove the red tide organisms. However, its strong toxicity to Penaeus japonicus would restrict its practical use in red tide control. (2) The toxicity of HDTMA could be remarkably decreased by addition of clay and the organo-clay complex had a good ability to removal red tide organisms. At the same time the availability of organo-clay to remove the red tide of P. donghaiense and Heterosigma akashiwo in the lab-imitated cultures were studied. The results indicated that the organo-clay complex could remove 100% P. donghaiense at the dosage of 0.03 g/L and effectively control H. akashiwo at 0.09 g/L while the survival rate of Penaeus japonicus larvae, which were cultured in the red tide seawater, is kept 100%. According to the results in laboratory, the mesocosm tests (CEPEX) in East China Sea were conducted in April and May of 2003. The removal efficiencies of original clay, organic clay and inorganic clay were compared during the CEPEX tests. The results revealed that both inorganic clay and organic clay could remove red tide organisms more effectively than the original clay.

  15. Changes in blood glucose and insulin responses to intravenous glucose tolerance tests and blood biochemical values in adult female Japanese black bears (Ursus thibetanus japonicus).

    PubMed

    Kamine, Akari; Shimozuru, Michito; Shibata, Haruki; Tsubota, Toshio

    2012-02-01

    The metabolic mechanisms to circannual changes in body mass of bears have yet to be elucidated. We hypothesized that the Japanese black bear (Ursus thibetanus japonicus) has a metabolic mechanism that efficiently converts carbohydrates into body fat by altering insulin sensitivity during the hyperphagic stage before hibernation. To test this hypothesis, we investigated the changes in blood biochemical values and glucose and insulin responses to intravenous glucose tolerance tests (IVGTT) during the active season (August, early and late November). Four, adult, female bears (5-17 years old) were anesthetized with 6 mg/kg TZ (tiletamine HCl and zolazepam HCl) in combination with 0.1 mg/kg acepromazine maleate. The bears were injected intravenously with glucose (0.5 g/kg of body mass), and blood samples were obtained before, at, and intermittently after glucose injection. The basal triglycerides concentration decreased significantly with increase in body mass from August to November. Basal levels of plasma glucose and serum insulin concentrations were not significantly different among groups. The results of IVGTT demonstrated the increased peripheral insulin sensitivity and glucose tolerance in early November. In contrast, peripheral insulin resistance was indicated by the exaggerated insulin response in late November. Our findings suggest that bears shift their glucose and lipid metabolism from the stage of normal activity to the hyperphagic stage in which they show lipogenic-predominant metabolism and accelerate glucose uptake by increasing the peripheral insulin sensitivity.

  16. Scalable persistent identifier systems for dynamic datasets

    NASA Astrophysics Data System (ADS)

    Golodoniuc, P.; Cox, S. J. D.; Klump, J. F.

    2016-12-01

    Reliable and persistent identification of objects, whether tangible or not, is essential in information management. Many Internet-based systems have been developed to identify digital data objects, e.g., PURL, LSID, Handle, ARK. These were largely designed for identification of static digital objects. The amount of data made available online has grown exponentially over the last two decades and fine-grained identification of dynamically generated data objects within large datasets using conventional systems (e.g., PURL) has become impractical. We have compared capabilities of various technological solutions to enable resolvability of data objects in dynamic datasets, and developed a dataset-centric approach to resolution of identifiers. This is particularly important in Semantic Linked Data environments where dynamic frequently changing data is delivered live via web services, so registration of individual data objects to obtain identifiers is impractical. We use identifier patterns and pattern hierarchies for identification of data objects, which allows relationships between identifiers to be expressed, and also provides means for resolving a single identifier into multiple forms (i.e. views or representations of an object). The latter can be implemented through (a) HTTP content negotiation, or (b) use of URI querystring parameters. The pattern and hierarchy approach has been implemented in the Linked Data API supporting the United Nations Spatial Data Infrastructure (UNSDI) initiative and later in the implementation of geoscientific data delivery for the Capricorn Distal Footprints project using International Geo Sample Numbers (IGSN). This enables flexible resolution of multi-view persistent identifiers and provides a scalable solution for large heterogeneous datasets.

  17. Beneficial Effects of Rhodotorula sp. C11 on Growth and Disease Resistance of Juvenile Japanese Spiky Sea Cucumber Apostichopus japonicus.

    PubMed

    Yang, ZhiPing; Sun, JianMing; Xu, Zhe

    2015-06-01

    The purpose of this study was to evaluate the effects of dietary administration of the live yeast, Rhodotorula sp. C11, on growth and disease resistance against Vibrio splendidus infection in juvenile Japanese spiky sea cucumber Apostichopus japonicus. Sea cucumbers were fed diets containing Rhodotorula sp. C11 at 0 (control), 10⁴, 10⁵, and 10⁶ CFU/g of feed for 45 d. There were three replicate tanks per dietary treatment. The specific growth rates were higher in all sea cucumbers treated with Rhodotorula sp. C11 than in the controls. Following a challenge with V. splendidus NB13, the cumulative prevalence and mortality of sea cucumbers fed diets supplemented with Rhodotorula sp. C11 were lower than in animals fed the basal diet. In sea cucumbers fed diets supplemented with Rhodotorula sp. C11 for 42 d, the only viable yeast found in the intestine was Rhodotorula sp. C11, which had counts of 1.58-1.98 × 10⁴CFU/g. No yeast was isolated from the intestine of animals fed the basal diet. For the colonization study, 20 sea cucumbers from each dietary treatment were removed to separate tanks and fed the control diet from day 16 to day 46. The viable yeast (Rhodotorula sp. C11) counts in the intestine decreased to 60-80 CFU/g by day 37. Moreover, as demonstrated by denaturing gradient gel electrophoresis, Rhodotorula sp. C11 colonization of the intestine could be detected until day 46. The differences in culture and PCR-denaturing gradient gel electrophoresis may be due to differences in the sensitivity of both methods. The present result showed that Rhodotorula sp. C11 was able to successfully colonize the intestine of juvenile Japanese spiky sea cucumbers by dietary supplementation, which improved its growth and disease resistance.

  18. Proteinaceous toxins from three species of scorpaeniform fish (lionfish Pterois lunulata, devil stinger Inimicus japonicus and waspfish Hypodytes rubripinnis): close similarity in properties and primary structures to stonefish toxins.

    PubMed

    Kiriake, Aya; Suzuki, Yasuko; Nagashima, Yuji; Shiomi, Kazuo

    2013-08-01

    The crude toxins from three species of venomous fish (lionfish Pterois lunulata, devil stinger Inimicus japonicus and waspfish Hypodytes rubripinnis) belonging to the order Scorpaeniformes exhibited mouse-lethal, hemolytic, edema-forming and nociceptive activities. In view of the antigenic cross-reactivity with the stonefish toxins, the primary structures of the stonefish toxin-like toxins from the three scorpaeniform fish were determined by cDNA cloning using primers designed from the highly conserved sequences of the stonefish toxins. Based on the data obtained in gel filtration, immunoblotting and cDNA cloning, each toxin was judged to be a 160 kDa heterodimer composed of 80 kDa α- and β-subunits. The three scorpaeniform fish toxins contain a B30.2/SPRY domain (∼200 amino acid residues) in the C-terminal region of each subunit, as reported for the toxins from two species of lionfish and two species of stonefish. With respect to the amino acid sequence similarity, the scorpaeniform fish toxins are divided into the following two groups: toxins from three species of lionfish and those from devil stinger, two species of stonefish and waspfish. The phylogenetic tree generated also clearly supports the classification of the toxins. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

    PubMed Central

    Voight, Benjamin F; Scott, Laura J; Steinthorsdottir, Valgerdur; Morris, Andrew P; Dina, Christian; Welch, Ryan P; Zeggini, Eleftheria; Huth, Cornelia; Aulchenko, Yurii S; Thorleifsson, Gudmar; McCulloch, Laura J; Ferreira, Teresa; Grallert, Harald; Amin, Najaf; Wu, Guanming; Willer, Cristen J; Raychaudhuri, Soumya; McCarroll, Steve A; Langenberg, Claudia; Hofmann, Oliver M; Dupuis, Josée; Qi, Lu; Segrè, Ayellet V; van Hoek, Mandy; Navarro, Pau; Ardlie, Kristin; Balkau, Beverley; Benediktsson, Rafn; Bennett, Amanda J; Blagieva, Roza; Boerwinkle, Eric; Bonnycastle, Lori L; Boström, Kristina Bengtsson; Bravenboer, Bert; Bumpstead, Suzannah; Burtt, Noisël P; Charpentier, Guillaume; Chines, Peter S; Cornelis, Marilyn; Couper, David J; Crawford, Gabe; Doney, Alex S F; Elliott, Katherine S; Elliott, Amanda L; Erdos, Michael R; Fox, Caroline S; Franklin, Christopher S; Ganser, Martha; Gieger, Christian; Grarup, Niels; Green, Todd; Griffin, Simon; Groves, Christopher J; Guiducci, Candace; Hadjadj, Samy; Hassanali, Neelam; Herder, Christian; Isomaa, Bo; Jackson, Anne U; Johnson, Paul R V; Jørgensen, Torben; Kao, Wen H L; Klopp, Norman; Kong, Augustine; Kraft, Peter; Kuusisto, Johanna; Lauritzen, Torsten; Li, Man; Lieverse, Aloysius; Lindgren, Cecilia M; Lyssenko, Valeriya; Marre, Michel; Meitinger, Thomas; Midthjell, Kristian; Morken, Mario A; Narisu, Narisu; Nilsson, Peter; Owen, Katharine R; Payne, Felicity; Perry, John R B; Petersen, Ann-Kristin; Platou, Carl; Proença, Christine; Prokopenko, Inga; Rathmann, Wolfgang; Rayner, N William; Robertson, Neil R; Rocheleau, Ghislain; Roden, Michael; Sampson, Michael J; Saxena, Richa; Shields, Beverley M; Shrader, Peter; Sigurdsson, Gunnar; Sparsø, Thomas; Strassburger, Klaus; Stringham, Heather M; Sun, Qi; Swift, Amy J; Thorand, Barbara; Tichet, Jean; Tuomi, Tiinamaija; van Dam, Rob M; van Haeften, Timon W; van Herpt, Thijs; van Vliet-Ostaptchouk, Jana V; Walters, G Bragi; Weedon, Michael N; Wijmenga, Cisca; Witteman, Jacqueline; Bergman, Richard N; Cauchi, Stephane; Collins, Francis S; Gloyn, Anna L; Gyllensten, Ulf; Hansen, Torben; Hide, Winston A; Hitman, Graham A; Hofman, Albert; Hunter, David J; Hveem, Kristian; Laakso, Markku; Mohlke, Karen L; Morris, Andrew D; Palmer, Colin N A; Pramstaller, Peter P; Rudan, Igor; Sijbrands, Eric; Stein, Lincoln D; Tuomilehto, Jaakko; Uitterlinden, Andre; Walker, Mark; Wareham, Nicholas J; Watanabe, Richard M; Abecasis, Gonçalo R; Boehm, Bernhard O; Campbell, Harry; Daly, Mark J; Hattersley, Andrew T; Hu, Frank B; Meigs, James B; Pankow, James S; Pedersen, Oluf; Wichmann, H-Erich; Barroso, Inês; Florez, Jose C; Frayling, Timothy M; Groop, Leif; Sladek, Rob; Thorsteinsdottir, Unnur; Wilson, James F; Illig, Thomas; Froguel, Philippe; van Duijn, Cornelia M; Stefansson, Kari; Altshuler, David; Boehnke, Michael; McCarthy, Mark I

    2011-01-01

    By combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals with combinedP < 5 × 10−8. These include a second independent signal at the KCNQ1 locus; the first report, to our knowledge, of an X-chromosomal association (near DUSP9); and a further instance of overlap between loci implicated in monogenic and multifactorial forms of diabetes (at HNF1A). The identified loci affect both beta-cell function and insulin action, and, overall, T2D association signals show evidence of enrichment for genes involved in cell cycle regulation. We also show that a high proportion of T2D susceptibility loci harbor independent association signals influencing apparently unrelated complex traits. PMID:20581827

  20. Identifying the Root Causes of Wait States in Large-Scale Parallel Applications

    DOE PAGES

    Böhme, David; Geimer, Markus; Arnold, Lukas; ...

    2016-07-20

    Driven by growing application requirements and accelerated by current trends in microprocessor design, the number of processor cores on modern supercomputers is increasing from generation to generation. However, load or communication imbalance prevents many codes from taking advantage of the available parallelism, as delays of single processes may spread wait states across the entire machine. Moreover, when employing complex point-to-point communication patterns, wait states may propagate along far-reaching cause-effect chains that are hard to track manually and that complicate an assessment of the actual costs of an imbalance. Building on earlier work by Meira Jr. et al., we present amore » scalable approach that identifies program wait states and attributes their costs in terms of resource waste to their original cause. Ultimately, by replaying event traces in parallel both forward and backward, we can identify the processes and call paths responsible for the most severe imbalances even for runs with hundreds of thousands of processes.« less

  1. Identifying the Root Causes of Wait States in Large-Scale Parallel Applications

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Böhme, David; Geimer, Markus; Arnold, Lukas

    Driven by growing application requirements and accelerated by current trends in microprocessor design, the number of processor cores on modern supercomputers is increasing from generation to generation. However, load or communication imbalance prevents many codes from taking advantage of the available parallelism, as delays of single processes may spread wait states across the entire machine. Moreover, when employing complex point-to-point communication patterns, wait states may propagate along far-reaching cause-effect chains that are hard to track manually and that complicate an assessment of the actual costs of an imbalance. Building on earlier work by Meira Jr. et al., we present amore » scalable approach that identifies program wait states and attributes their costs in terms of resource waste to their original cause. Ultimately, by replaying event traces in parallel both forward and backward, we can identify the processes and call paths responsible for the most severe imbalances even for runs with hundreds of thousands of processes.« less

  2. Identifying Challenges to the Integration of Computer-Based Surveillance Information Systems in a Large City Health Department: A Case Study.

    PubMed

    Jennings, Jacky M; Stover, Jeffrey A; Bair-Merritt, Megan H; Fichtenberg, Caroline; Munoz, Mary Grace; Maziad, Rafiq; Ketemepi, Sherry Johnson; Zenilman, Jonathan

    2009-01-01

    Integrated infectious disease surveillance information systems have the potential to provide important new surveillance capacities and business efficiencies for local health departments. We conducted a case study at a large city health department of the primary computer-based infectious disease surveillance information systems during a 10-year period to identify the major challenges for information integration across the systems. The assessment included key informant interviews and evaluations of the computer-based surveillance information systems used for acute communicable diseases, human immunodeficiency virus/acquired immunodeficiency syndrome, sexually transmitted diseases, and tuberculosis. Assessments were conducted in 1998 with a follow-up in 2008. Assessments specifically identified and described the primary computer-based surveillance information system, any duplicative information systems, and selected variables collected. Persistent challenges to information integration across the information systems included the existence of duplicative data systems, differences in the variables used to collect similar information, and differences in basic architecture. The assessments identified a number of challenges for information integration across the infectious disease surveillance information systems at this city health department. The results suggest that local disease control programs use computer-based surveillance information systems that were not designed for data integration. To the extent that integration provides important new surveillance capacities and business efficiencies, we recommend that patient-centric information systems be designed that provide all the epidemiologic, clinical, and research needs in one system. In addition, the systems should include a standard system of elements and fields across similar surveillance systems.

  3. Air quality models and unusually large ozone increases: Identifying model failures, understanding environmental causes, and improving modeled chemistry

    NASA Astrophysics Data System (ADS)

    Couzo, Evan A.

    Several factors combine to make ozone (O3) pollution in Houston, Texas, unique when compared to other metropolitan areas. These include complex meteorology, intense clustering of industrial activity, and significant precursor emissions from the heavily urbanized eight-county area. Decades of air pollution research have borne out two different causes, or conceptual models, of O 3 formation. One conceptual model describes a gradual region-wide increase in O3 concentrations "typical" of many large U.S. cities. The other conceptual model links episodic emissions of volatile organic compounds to spatially limited plumes of high O3, which lead to large hourly increases that have exceeded 100 parts per billion (ppb) per hour. These large hourly increases are known to lead to violations of the federal O 3 standard and impact Houston's status as a non-attainment area. There is a need to further understand and characterize the causes of peak O 3 levels in Houston and simulate them correctly so that environmental regulators can find the most cost-effective pollution controls. This work provides a detailed understanding of unusually large O 3 increases in the natural and modeled environments. First, we probe regulatory model simulations and assess their ability to reproduce the observed phenomenon. As configured for the purpose of demonstrating future attainment of the O3 standard, the model fails to predict the spatially limited O3 plumes observed in Houston. Second, we combine ambient meteorological and pollutant measurement data to identify the most likely geographic origins and preconditions of the concentrated O3 plumes. We find evidence that the O3 plumes are the result of photochemical activity accelerated by industrial emissions. And, third, we implement changes to the modeled chemistry to add missing formation mechanisms of nitrous acid, which is an important radical precursor. Radicals control the chemical reactivity of atmospheric systems, and perturbations to

  4. Interspecies differences in the accumulation of tributyltin and its metabolites under dietary exposure in sea perch, Lateolabrax japonicus, and red sea bream, Pagrus major.

    PubMed

    Uno, Seiichi; Murakami, Masayo; Kokushi, Emiko; Koyama, Jiro

    2011-02-01

    Interspecies differences in the accumulation of dietary tributyltin (TBT) between sea perch, Lateolabrax japonicus, and red sea bream, Pagrus major, were studied. Although TBTs in both species reached steady-state condition in low-concentration group (L-group, 200 ng/g nominal concentration) by 1 week, it increased up to the end of exposure in high-concentration group (H-group, 3000 ng/g nominal concentration). In H-group, the accumulation rate of TBT in sea perch from 1 to 2 weeks was much higher than in red sea bream, which were 2.4-fold for sea perch and 1.7-fold for red sea bream, although TBT concentrations were similar between sea perch and red sea bream in L-group. Furthermore, in the H-group, the concentrations of TBT at 1 and 2 weeks were about 1.3- and 1.9-fold, respectively, higher in the sea perch than in the red sea bream. On the other hand, DBT residue in red sea bream was about 1.4-fold higher in sea perch for the L-group but concentrations were similar in both fishes for the H-group. These results suggest that red sea bream could metabolize faster the TBT to DBT than sea perch. This study also reveals that fish probably could absorb TBT through the food chain. The uptake of TBT by fish should be regarded in the real environment, because TBT concentration in seawater has been decreasing and now already at significantly low level. Copyright © 2009 Wiley Periodicals, Inc.

  5. Large-scale genotyping identifies 41 new loci associated with breast cancer risk.

    PubMed

    Michailidou, Kyriaki; Hall, Per; Gonzalez-Neira, Anna; Ghoussaini, Maya; Dennis, Joe; Milne, Roger L; Schmidt, Marjanka K; Chang-Claude, Jenny; Bojesen, Stig E; Bolla, Manjeet K; Wang, Qin; Dicks, Ed; Lee, Andrew; Turnbull, Clare; Rahman, Nazneen; Fletcher, Olivia; Peto, Julian; Gibson, Lorna; Dos Santos Silva, Isabel; Nevanlinna, Heli; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Czene, Kamila; Irwanto, Astrid; Liu, Jianjun; Waisfisz, Quinten; Meijers-Heijboer, Hanne; Adank, Muriel; van der Luijt, Rob B; Hein, Rebecca; Dahmen, Norbert; Beckman, Lars; Meindl, Alfons; Schmutzler, Rita K; Müller-Myhsok, Bertram; Lichtner, Peter; Hopper, John L; Southey, Melissa C; Makalic, Enes; Schmidt, Daniel F; Uitterlinden, Andre G; Hofman, Albert; Hunter, David J; Chanock, Stephen J; Vincent, Daniel; Bacot, François; Tessier, Daniel C; Canisius, Sander; Wessels, Lodewyk F A; Haiman, Christopher A; Shah, Mitul; Luben, Robert; Brown, Judith; Luccarini, Craig; Schoof, Nils; Humphreys, Keith; Li, Jingmei; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Couch, Fergus J; Wang, Xianshu; Vachon, Celine; Stevens, Kristen N; Lambrechts, Diether; Moisse, Matthieu; Paridaens, Robert; Christiaens, Marie-Rose; Rudolph, Anja; Nickels, Stefan; Flesch-Janys, Dieter; Johnson, Nichola; Aitken, Zoe; Aaltonen, Kirsimari; Heikkinen, Tuomas; Broeks, Annegien; Veer, Laura J Van't; van der Schoot, C Ellen; Guénel, Pascal; Truong, Thérèse; Laurent-Puig, Pierre; Menegaux, Florence; Marme, Frederik; Schneeweiss, Andreas; Sohn, Christof; Burwinkel, Barbara; Zamora, M Pilar; Perez, Jose Ignacio Arias; Pita, Guillermo; Alonso, M Rosario; Cox, Angela; Brock, Ian W; Cross, Simon S; Reed, Malcolm W R; Sawyer, Elinor J; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Henderson, Brian E; Schumacher, Fredrick; Le Marchand, Loic; Andrulis, Irene L; Knight, Julia A; Glendon, Gord; Mulligan, Anna Marie; Lindblom, Annika; Margolin, Sara; Hooning, Maartje J; Hollestelle, Antoinette; van den Ouweland, Ans M W; Jager, Agnes; Bui, Quang M; Stone, Jennifer; Dite, Gillian S; Apicella, Carmel; Tsimiklis, Helen; Giles, Graham G; Severi, Gianluca; Baglietto, Laura; Fasching, Peter A; Haeberle, Lothar; Ekici, Arif B; Beckmann, Matthias W; Brenner, Hermann; Müller, Heiko; Arndt, Volker; Stegmaier, Christa; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Figueroa, Jonine; Lissowska, Jolanta; Brinton, Louise; Goldberg, Mark S; Labrèche, France; Dumont, Martine; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Brauch, Hiltrud; Hamann, Ute; Brüning, Thomas; Radice, Paolo; Peterlongo, Paolo; Manoukian, Siranoush; Bonanni, Bernardo; Devilee, Peter; Tollenaar, Rob A E M; Seynaeve, Caroline; van Asperen, Christi J; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Bogdanova, Natalia V; Antonenkova, Natalia N; Dörk, Thilo; Kristensen, Vessela N; Anton-Culver, Hoda; Slager, Susan; Toland, Amanda E; Edge, Stephen; Fostira, Florentia; Kang, Daehee; Yoo, Keun-Young; Noh, Dong-Young; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Sueta, Aiko; Wu, Anna H; Tseng, Chiu-Chen; Van Den Berg, David; Stram, Daniel O; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Teo, Soo Hwang; Yip, Cheng Har; Phuah, Sze Yee; Cornes, Belinda K; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Sng, Jen-Hwei; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Shen, Chen-Yang; Hsiung, Chia-Ni; Wu, Pei-Ei; Ding, Shian-Ling; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Blot, William J; Signorello, Lisa B; Cai, Qiuyin; Zheng, Wei; Deming-Halverson, Sandra; Shrubsole, Martha; Long, Jirong; Simard, Jacques; Garcia-Closas, Montse; Pharoah, Paul D P; Chenevix-Trench, Georgia; Dunning, Alison M; Benitez, Javier; Easton, Douglas F

    2013-04-01

    Breast cancer is the most common cancer among women. Common variants at 27 loci have been identified as associated with susceptibility to breast cancer, and these account for ∼9% of the familial risk of the disease. We report here a meta-analysis of 9 genome-wide association studies, including 10,052 breast cancer cases and 12,575 controls of European ancestry, from which we selected 29,807 SNPs for further genotyping. These SNPs were genotyped in 45,290 cases and 41,880 controls of European ancestry from 41 studies in the Breast Cancer Association Consortium (BCAC). The SNPs were genotyped as part of a collaborative genotyping experiment involving four consortia (Collaborative Oncological Gene-environment Study, COGS) and used a custom Illumina iSelect genotyping array, iCOGS, comprising more than 200,000 SNPs. We identified SNPs at 41 new breast cancer susceptibility loci at genome-wide significance (P < 5 × 10(-8)). Further analyses suggest that more than 1,000 additional loci are involved in breast cancer susceptibility.

  6. Large-scale genotyping identifies 41 new loci associated with breast cancer risk

    PubMed Central

    Michailidou, Kyriaki; Hall, Per; Gonzalez-Neira, Anna; Ghoussaini, Maya; Dennis, Joe; Milne, Roger L; Schmidt, Marjanka K; Chang-Claude, Jenny; Bojesen, Stig E; Bolla, Manjeet K; Wang, Qin; Dicks, Ed; Lee, Andrew; Turnbull, Clare; Rahman, Nazneen; Fletcher, Olivia; Peto, Julian; Gibson, Lorna; Silva, Isabel dos Santos; Nevanlinna, Heli; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Czene, Kamila; Irwanto, Astrid; Liu, Jianjun; Waisfisz, Quinten; Meijers-Heijboer, Hanne; Adank, Muriel; van der Luijt, Rob B; Hein, Rebecca; Dahmen, Norbert; Beckman, Lars; Meindl, Alfons; Schmutzler, Rita K; Müller-Myhsok, Bertram; Lichtner, Peter; Hopper, John L; Southey, Melissa C; Makalic, Enes; Schmidt, Daniel F; Uitterlinden, Andre G; Hofman, Albert; Hunter, David J; Chanock, Stephen J; Vincent, Daniel; Bacot, François; Tessier, Daniel C; Canisius, Sander; Wessels, Lodewyk F A; Haiman, Christopher A; Shah, Mitul; Luben, Robert; Brown, Judith; Luccarini, Craig; Schoof, Nils; Humphreys, Keith; Li, Jingmei; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Couch, Fergus J; Wang, Xianshu; Vachon, Celine; Stevens, Kristen N; Lambrechts, Diether; Moisse, Matthieu; Paridaens, Robert; Christiaens, Marie-Rose; Rudolph, Anja; Nickels, Stefan; Flesch-Janys, Dieter; Johnson, Nichola; Aitken, Zoe; Aaltonen, Kirsimari; Heikkinen, Tuomas; Broeks, Annegien; Van’t Veer, Laura J; van der Schoot, C Ellen; Guénel, Pascal; Truong, Thérèse; Laurent-Puig, Pierre; Menegaux, Florence; Marme, Frederik; Schneeweiss, Andreas; Sohn, Christof; Burwinkel, Barbara; Zamora, M Pilar; Perez, Jose Ignacio Arias; Pita, Guillermo; Alonso, M Rosario; Cox, Angela; Brock, Ian W; Cross, Simon S; Reed, Malcolm W R; Sawyer, Elinor J; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Henderson, Brian E; Schumacher, Fredrick; Le Marchand, Loic; Andrulis, Irene L; Knight, Julia A; Glendon, Gord; Mulligan, Anna Marie; Lindblom, Annika; Margolin, Sara; Hooning, Maartje J; Hollestelle, Antoinette; van den Ouweland, Ans M W; Jager, Agnes; Bui, Quang M; Stone, Jennifer; Dite, Gillian S; Apicella, Carmel; Tsimiklis, Helen; Giles, Graham G; Severi, Gianluca; Baglietto, Laura; Fasching, Peter A; Haeberle, Lothar; Ekici, Arif B; Beckmann, Matthias W; Brenner, Hermann; Müller, Heiko; Arndt, Volker; Stegmaier, Christa; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Figueroa, Jonine; Lissowska, Jolanta; Brinton, Louise; Goldberg, Mark S; Labrèche, France; Dumont, Martine; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Brauch, Hiltrud; Hamann, Ute; Brüning, Thomas; Radice, Paolo; Peterlongo, Paolo; Manoukian, Siranoush; Bonanni, Bernardo; Devilee, Peter; Tollenaar, Rob A E M; Seynaeve, Caroline; van Asperen, Christi J; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Bogdanova, Natalia V; Antonenkova, Natalia N; Dörk, Thilo; Kristensen, Vessela N; Anton-Culver, Hoda; Slager, Susan; Toland, Amanda E; Edge, Stephen; Fostira, Florentia; Kang, Daehee; Yoo, Keun-Young; Noh, Dong-Young; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Sueta, Aiko; Wu, Anna H; Tseng, Chiu-Chen; Van Den Berg, David; Stram, Daniel O; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Teo, Soo Hwang; Yip, Cheng Har; Phuah, Sze Yee; Cornes, Belinda K; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Sng, Jen-Hwei; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Shen, Chen-Yang; Hsiung, Chia-Ni; Wu, Pei-Ei; Ding, Shian-Ling; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Blot, William J; Signorello, Lisa B; Cai, Qiuyin; Zheng, Wei; Deming-Halverson, Sandra; Shrubsole, Martha; Long, Jirong; Simard, Jacques; Garcia-Closas, Montse; Pharoah, Paul D P; Chenevix-Trench, Georgia; Dunning, Alison M; Benitez, Javier; Easton, Douglas F

    2013-01-01

    Breast cancer is the most common cancer among women. Common variants at 27 loci have been identified as associated with susceptibility to breast cancer, and these account for ~9% of the familial risk of the disease. We report here a meta-analysis of 9 genome-wide association studies, including 10,052 breast cancer cases and 12,575 controls of European ancestry, from which we selected 29,807 SNPs for further genotyping. These SNPs were genotyped in 45,290 cases and 41,880 controls of European ancestry from 41 studies in the Breast Cancer Association Consortium (BCAC). The SNPs were genotyped as part of a collaborative genotyping experiment involving four consortia (Collaborative Oncological Gene-environment Study, COGS) and used a custom Illumina iSelect genotyping array, iCOGS, comprising more than 200,000 SNPs. We identified SNPs at 41 new breast cancer susceptibility loci at genome-wide significance (P < 5 × 10−8). Further analyses suggest that more than 1,000 additional loci are involved in breast cancer susceptibility. PMID:23535729

  7. Influence of cryoprotectant levels on storage stability of surimi from Nemipterus japonicus and quality of surimi-based products.

    PubMed

    U, Parvathy; George, Sajan

    2014-05-01

    A study was undertaken with the aim of reducing the concentration of cryoprotectants in surimi without adversely affecting frozen storage stability. Minced meat from a tropical fish, Nemipterus japonicus, was strained, water leached and mixed with different levels of sucrose-sorbitol (1:1) mixture (henceforth called sugar mixture), quick frozen at -35 °C and frozen stored at -20 °C. The surimi samples were subjected to storage stability studies for a period of 5 months. Water leaching resulted in slight absorption of water by meat and reduction in protein, fat and mineral contents. Surimi was found to have moderately white colour. Sensory evaluation studies were conducted on three products, viz., sausage, patty and cake, prepared using surimi containing different concentrations of sugar mixture. Sugar mixture content varying from 0% (control) to 4% in surimi resulted in products that were more acceptable to the taste panelists compared those with 6% and 8% sugar mixture. During frozen storage of surimi pH and total plate count remained nearly steady for all sugar mixture concentrations and throughout the storage period. Moisture content appeared to remain constant during storage, but decreased with increase in sugar concentration. The salt soluble nitrogen content of surimi and gel strength of sausage prepared from it decreased with storage period in all surimi samples, and increased with sugar mixture concentration. Expressible water content of surimi sausage showed an increasing trend with storage period of surimi and a decreasing trend with sugar mixture concentration. Sensory evaluation parameters-elasticity, sweetness and preference-remained more or less steady during storage. However elasticity and sweetness increased and preference decreased with sugar mixture concentration beyond 4%. Elasticity and gel strength of surimi sausage seemed to be much lower for control compared to even the lowest concentration of sugar (2%) used. A concentration of 2 to 4

  8. Characterization and comparison of proteomes of albino sea cucumber Apostichopus japonicus (Selenka) by iTRAQ analysis.

    PubMed

    Xia, Chang-Ge; Zhang, Dijun; Ma, Chengnv; Zhou, Jun; He, Shan; Su, Xiu-Rong

    2016-04-01

    Sea cucumber is a commercially important marine organism in China. Of the different colored varieties sold in China, albino sea cucumber has the greatest appeal among consumers. Identification of factors contributing to albinism in sea cucumber is therefore likely to provide a scientific basis for improving the cultivability of these strains. In this study, two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification labeling was used for the first time to quantitatively define the proteome of sea cucumbers and reveal proteomic characteristics unique to albino sea cucumbers. A total of 549 proteins were identified and quantified in albino sea cucumber and the functional annotations of 485 proteins have been exhibited based on COG database. Compared with green sea cucumber, 12 proteins were identified as differentially expressed in the intestine and 16 proteins in the body wall of albino sea cucumber. Among them, 5 proteins were up-regulated in the intestine and 8 proteins were down-regulated in body wall. Gene ontology annotations of these differentially expressed proteins consisted mostly of 'biological process'. The large number of differentially expressed proteins identified here should be highly useful in further elucidating the mechanisms underlying albinism in sea cucumber. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Surveys of Gynaecotyla squatarolae and Microphallus koreana (Digenea: Microphallidae) metacercariae in two species of estuarine crabs in western coastal areas, Korea.

    PubMed

    Lee, Hye Jung; Chai, Jong-Yil; Lee, Jin-Woo; Jin, Ho; Min, Kwan-Hong; Cho, Yong-Jun; Seo, Min

    2010-03-01

    To figure out the geographical distribution of Gynaecotyla squatarolae and Microphallus koreana metacercariae in Korea, shore crabs of southwestern coastal areas were examined. Eight coastal areas in Inchon-si (A), Gyeonggi-do (B), Chungcheongnam-do (C, D, and E), Jeollabuk-do (F), and Jeollanam-do (G and H) were selected, and 2 kinds of crabs, Macrophthalmus dilatatus and/or Macrophthalmus japonicus, were caught. After transportation to the laboratory, 15 crabs per each group were grouped and ground in a mortar and pestle, and examined for microphallid metacercariae. In M. dilatatus, G. squatarolae metacercariae were recovered from 3 (C, E, and H) out of 6 regions, but M. koreana metacercariae were not recovered. In the case of M. japonicus, G. squatarolae metacercariae were recovered from 6 (B, D, E, F, G, and H) of 7 areas surveyed, and M. koreana matacercariae were detected from 5 regions (A, B, D, F, and H). These results indicate that the life cycle of G. squatarolae is maintained in the western coastal areas using M. dilatatus and M. japonicus as intermediate hosts, while that of M. koreana is maintained only using M. japonicus.

  10. Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods.

    PubMed

    Katano, Izumi; Harada, Ken; Doi, Hideyuki; Souma, Rio; Minamoto, Toshifumi

    2017-01-01

    Environmental DNA (eDNA) has recently been used for detecting the distribution of macroorganisms in various aquatic habitats. In this study, we applied an eDNA method to estimate the distribution of the Japanese clawed salamander, Onychodactylus japonicus, in headwater streams. Additionally, we compared the detection of eDNA and hand-capturing methods used for determining the distribution of O. japonicus. For eDNA detection, we designed a qPCR primer/probe set for O. japonicus using the 12S rRNA region. We detected the eDNA of O. japonicus at all sites (with the exception of one), where we also observed them by hand-capturing. Additionally, we detected eDNA at two sites where we were unable to observe individuals using the hand-capturing method. Moreover, we found that eDNA concentrations and detection rates of the two water sampling areas (stream surface and under stones) were not significantly different, although the eDNA concentration in the water under stones was more varied than that on the surface. We, therefore, conclude that eDNA methods could be used to determine the distribution of macroorganisms inhabiting headwater systems by using samples collected from the surface of the water.

  11. Exome sequencing of a large family identifies potential candidate genes contributing risk to bipolar disorder.

    PubMed

    Zhang, Tianxiao; Hou, Liping; Chen, David T; McMahon, Francis J; Wang, Jen-Chyong; Rice, John P

    2018-03-01

    Bipolar disorder is a mental illness with lifetime prevalence of about 1%. Previous genetic studies have identified multiple chromosomal linkage regions and candidate genes that might be associated with bipolar disorder. The present study aimed to identify potential susceptibility variants for bipolar disorder using 6 related case samples from a four-generation family. A combination of exome sequencing and linkage analysis was performed to identify potential susceptibility variants for bipolar disorder. Our study identified a list of five potential candidate genes for bipolar disorder. Among these five genes, GRID1(Glutamate Receptor Delta-1 Subunit), which was previously reported to be associated with several psychiatric disorders and brain related traits, is particularly interesting. Variants with functional significance in this gene were identified from two cousins in our bipolar disorder pedigree. Our findings suggest a potential role for these genes and the related rare variants in the onset and development of bipolar disorder in this one family. Additional research is needed to replicate these findings and evaluate their patho-biological significance. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Multigenerational effects of 4-methylbenzylidene camphor (4-MBC) on the survival, development and reproduction of the marine copepod Tigriopus japonicus.

    PubMed

    Chen, Leyun; Li, Xiaolin; Hong, Haizheng; Shi, Dalin

    2018-01-01

    One of the most widely used organic UV filters, 4-methylbenzylidene camphor (4-MBC), is present at high concentrations in offshore waters. The marine copepod Tigriopus japonicus was exposed to different concentrations of 4-MBC (i.e., 0, 0.5, 1, 5 and 10μgL -1 ) for 4 consecutive generations (F0-F3) to evaluate the impact of 4-MBC on marine ecosystems. The results showed that in the F0 generation, 4-MBC caused significant lethal toxicity in T. japonicas at concentrations of 5 and 10μgL -1 and the nauplii were more sensitive to 4-MBC toxicity than the adults. However in the F1-F3 generations, 4-MBC exposure did not affect the survival rate. The hatching rate and the developmental duration from the nauplii to the copepodite (N-C) and from the nauplii to adult (N-A) decreased significantly in the F1-F2 generations and in the F2-F3 generations, respectively, even at the lowest exposure concentration (0.5μgL -1 ). In the subsequent two generations (i.e., the F4-F5 generations) of recovery exposure in clean seawater, the growth rates of the original 4-MBC exposure groups were still faster than the control in both the N-C and N-A stages, suggesting possible transgenerational genetic and/or epigenetic changes upon chronic 4-MBC exposure. The expression of the ecdysone receptor gene was up-regulated by 4-MBC, which was consistent with the decrease of the N-C/N-A duration. In addition, 4-MBC may induce oxidative stress and trigger apoptosis in T. japonicas, resulting in developmental, reproductive and even lethal toxicity. A preliminary risk assessment suggested that under environmentally realistic concentrations, 4-MBC had significant potential to pose a threat to marine crustaceans and marine ecosystems. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. RNA extraction from various recalcitrant plant tissues with a cethyltrimethylammonium bromide-containing buffer followed by an acid guanidium thiocyanate-phenol-chloroform treatment.

    PubMed

    Suzuki, Yuji; Mae, Tadahiko; Makino, Amane

    2008-07-01

    High-quality total RNA was extracted using a cethyltrimethylammonium bromide-containing buffer followed by an acid guanidium thiocyanate-phenol-chloroform treatment from recalcitrant plant tissues such as tree leaves (pine, Norway spruce, ginkgo, Japanese cedar, rose), flowers (rose, Lotus japonicus) and storage tissues (seeds of Lotus japonicus and rice, sweet potato tuber, banana fruit). This protocol greatly reduced the time required for RNA extraction.

  14. Evaluation of matrix-assisted laser desorption/ionization time of flight mass spectrometry for the identification of ceratopogonid and culicid larvae.

    PubMed

    Steinmann, I C; Pflüger, V; Schaffner, F; Mathis, A; Kaufmann, C

    2013-03-01

    Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) was evaluated for the rapid identification of ceratopogonid larvae. Optimal sample preparation as evaluated with laboratory-reared biting midges Culicoides nubeculosus was the homogenization of gut-less larvae in 10% formic acid, and analysis of 0.2 mg/ml crude protein homogenate mixed with SA matrix at a ratio of 1:1.5. Using 5 larvae each of 4 ceratopogonid species (C. nubeculosus, C. obsoletus, C. decor, and Dasyhelea sp.) and of 2 culicid species (Aedes aegypti, Ae. japonicus), biomarker mass sets between 27 and 33 masses were determined. In a validation study, 67 larvae belonging to the target species were correctly identified by automated database-based identification (91%) or manual full comparison (9%). Four specimens of non-target species did not yield identification. As anticipated for holometabolous insects, the biomarker mass sets of adults cannot be used for the identification of larvae, and vice versa, because they share only very few similar masses as shown for C. nubeculosus, C. obsoletus, and Ae. japonicus. Thus, protein profiling by MALDI-TOF as a quick, inexpensive and accurate alternative tool is applicable to identify insect larvae of vector species collected in the field.

  15. Photometric brown-dwarf classification. I. A method to identify and accurately classify large samples of brown dwarfs without spectroscopy

    NASA Astrophysics Data System (ADS)

    Skrzypek, N.; Warren, S. J.; Faherty, J. K.; Mortlock, D. J.; Burgasser, A. J.; Hewett, P. C.

    2015-02-01

    Aims: We present a method, named photo-type, to identify and accurately classify L and T dwarfs onto the standard spectral classification system using photometry alone. This enables the creation of large and deep homogeneous samples of these objects efficiently, without the need for spectroscopy. Methods: We created a catalogue of point sources with photometry in 8 bands, ranging from 0.75 to 4.6 μm, selected from an area of 3344 deg2, by combining SDSS, UKIDSS LAS, and WISE data. Sources with 13.0 0.8, were then classified by comparison against template colours of quasars, stars, and brown dwarfs. The L and T templates, spectral types L0 to T8, were created by identifying previously known sources with spectroscopic classifications, and fitting polynomial relations between colour and spectral type. Results: Of the 192 known L and T dwarfs with reliable photometry in the surveyed area and magnitude range, 189 are recovered by our selection and classification method. We have quantified the accuracy of the classification method both externally, with spectroscopy, and internally, by creating synthetic catalogues and accounting for the uncertainties. We find that, brighter than J = 17.5, photo-type classifications are accurate to one spectral sub-type, and are therefore competitive with spectroscopic classifications. The resultant catalogue of 1157 L and T dwarfs will be presented in a companion paper.

  16. Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci

    USDA-ARS?s Scientific Manuscript database

    Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholest...

  17. BDE-47 causes developmental retardation with down-regulated expression profiles of ecdysteroid signaling pathway-involved nuclear receptor (NR) genes in the copepod Tigriopus japonicus.

    PubMed

    Hwang, Dae-Sik; Han, Jeonghoon; Won, Eun-Ji; Kim, Duck-Hyun; Jeong, Chang-Bum; Hwang, Un-Ki; Zhou, Bingsheng; Choe, Joonho; Lee, Jae-Seong

    2016-08-01

    2,2',4,4'-Tetrabromodiphenyl ether (BDE-47) is a persistent organic pollutant (POP) in marine environments. Despite its adverse effects (e.g. developmental retardation) in ecdysozoa, the effects of BDE-47 on transcription of ecdysteroid signaling pathway-involved-nuclear receptor (NR) genes and metamorphosis-related genes have not been examined in copepods. To examine the deleterious effect of BDE-47 on copepod molting and metamorphosis, BDE-47 was exposed to the harpacticoid copepod Tigriopus japonicus, followed by monitoring developmental retardation and transcriptional alteration of NR genes. The developmental rate was significantly inhibited (P<0.05) in response to BDE-47 and the agricultural insecticide gamma-hexachlorocyclohexane. Conversely, the ecdysteroid agonist ponasterone A (PoA) led to decreased molting and metamorphosis time (P<0.05) from the nauplius stage to the adult stage. In particular, expression profiles of all NR genes were the highest at naupliar stages 5-6 except for SVP, FTZ-F1, and HR96 genes. Nuclear receptor USP, HR96, and FTZ-F1 genes also showed significant sex differences (P<0.05) in gene expression levels over different developmental stages, indicating that these genes may be involved in vitellogenesis. NR gene expression patterns showed significant decreases (P<0.05) in response to BDE-47 exposure, implying that molting and metamorphosis retardation is likely associated with NR gene expression. In summary, BDE-47 leads to molting and metamorphosis retardation and suppresses transcription of NR genes. This information will be helpful in understanding the molting and metamorphosis delay mechanism in response to BDE-47 exposure. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Antibiotic Resistance of Bacteria Isolated from the Internal Organs of Edible Snow Crabs

    PubMed Central

    Kim, Misoon; Kwon, Tae-Hyung; Jung, Su-Mi; Cho, Seung-Hak; Jin, Seon Yeong; Park, Nyun-Ho; Kim, Choong-Gon; Kim, Jong-Shik

    2013-01-01

    Antibiotic resistance and microbiota within edible snow crabs are important for the Chionoecetes (snow crab) fishing industry. We investigated these parameters using culture methods and antibiotic susceptibility tests with six internal organs from three species of Chionoecetes. Each sample revealed many unexpected microbial species within Chionoecetes internal organs. On the basis of 16S rRNA sequence analysis of 381 isolates, the most abundant genera identified in Chionoecetes opilio were Acinetobacter spp. (24%), Bacillus spp. (4%), Pseudomonas spp. (34%), Stenotrophomonas spp. (28%), and Agreia spp. (11%). In Chionoecetes sp. crabs, Acinetobacter spp. (23%), Bacillus spp. (12%), and Psychrobacter spp. (20%) were most prevalent, while Agreia spp. (11%), Bacillus spp. (31%), Microbacterium spp. (10%), Rhodococcus spp. (12%), and Agrococcus spp. (6%) were most abundant in C. japonicus. Our antibiotic resistance test found resistance to all nine antibiotics tested in 19, 14, and two of the isolates from C. opilio, Chionoecetes sp., and, C. japonicus respectively. Our results are the first to show that microbes with antibiotic resistance are widely distributed throughout the internal organs of natural snow crabs. PMID:23990916

  19. Social Network Analysis and Mining to Monitor and Identify Problems with Large-Scale Information and Communication Technology Interventions

    PubMed Central

    da Silva, Aleksandra do Socorro; de Brito, Silvana Rossy; Vijaykumar, Nandamudi Lankalapalli; da Rocha, Cláudio Alex Jorge; Monteiro, Maurílio de Abreu; Costa, João Crisóstomo Weyl Albuquerque; Francês, Carlos Renato Lisboa

    2016-01-01

    The published literature reveals several arguments concerning the strategic importance of information and communication technology (ICT) interventions for developing countries where the digital divide is a challenge. Large-scale ICT interventions can be an option for countries whose regions, both urban and rural, present a high number of digitally excluded people. Our goal was to monitor and identify problems in interventions aimed at certification for a large number of participants in different geographical regions. Our case study is the training at the Telecentros.BR, a program created in Brazil to install telecenters and certify individuals to use ICT resources. We propose an approach that applies social network analysis and mining techniques to data collected from Telecentros.BR dataset and from the socioeconomics and telecommunications infrastructure indicators of the participants’ municipalities. We found that (i) the analysis of interactions in different time periods reflects the objectives of each phase of training, highlighting the increased density in the phase in which participants develop and disseminate their projects; (ii) analysis according to the roles of participants (i.e., tutors or community members) reveals that the interactions were influenced by the center (or region) to which the participant belongs (that is, a community contained mainly members of the same region and always with the presence of tutors, contradicting expectations of the training project, which aimed for intense collaboration of the participants, regardless of the geographic region); (iii) the social network of participants influences the success of the training: that is, given evidence that the degree of the community member is in the highest range, the probability of this individual concluding the training is 0.689; (iv) the North region presented the lowest probability of participant certification, whereas the Northeast, which served municipalities with similar

  20. Social Network Analysis and Mining to Monitor and Identify Problems with Large-Scale Information and Communication Technology Interventions.

    PubMed

    da Silva, Aleksandra do Socorro; de Brito, Silvana Rossy; Vijaykumar, Nandamudi Lankalapalli; da Rocha, Cláudio Alex Jorge; Monteiro, Maurílio de Abreu; Costa, João Crisóstomo Weyl Albuquerque; Francês, Carlos Renato Lisboa

    2016-01-01

    The published literature reveals several arguments concerning the strategic importance of information and communication technology (ICT) interventions for developing countries where the digital divide is a challenge. Large-scale ICT interventions can be an option for countries whose regions, both urban and rural, present a high number of digitally excluded people. Our goal was to monitor and identify problems in interventions aimed at certification for a large number of participants in different geographical regions. Our case study is the training at the Telecentros.BR, a program created in Brazil to install telecenters and certify individuals to use ICT resources. We propose an approach that applies social network analysis and mining techniques to data collected from Telecentros.BR dataset and from the socioeconomics and telecommunications infrastructure indicators of the participants' municipalities. We found that (i) the analysis of interactions in different time periods reflects the objectives of each phase of training, highlighting the increased density in the phase in which participants develop and disseminate their projects; (ii) analysis according to the roles of participants (i.e., tutors or community members) reveals that the interactions were influenced by the center (or region) to which the participant belongs (that is, a community contained mainly members of the same region and always with the presence of tutors, contradicting expectations of the training project, which aimed for intense collaboration of the participants, regardless of the geographic region); (iii) the social network of participants influences the success of the training: that is, given evidence that the degree of the community member is in the highest range, the probability of this individual concluding the training is 0.689; (iv) the North region presented the lowest probability of participant certification, whereas the Northeast, which served municipalities with similar

  1. Localization and dynamic expression of a 27.8 kDa receptor protein for lymphocystis disease virus infection in sea bass ( Lateolabrax japonicus) tissues

    NASA Astrophysics Data System (ADS)

    Wu, Ronghua; Sheng, Xiuzhen; Tang, Xiaoqian; Xing, Jing; Zhan, Wenbin

    2017-10-01

    Lymphocystis disease virus (LCDV) infects target cells by attaching to a 27.8 kDa receptor (27.8R) protein in flounder Paralichthys olivaceus, and anti-27.8R monoclonal antibodies (MAbs) have been developed. However, the 27.8R existence in tissues of sea bass ( Lateolabrax japonicus) and its role in LCDV infection have remained unclear. In this study, the results of western blotting demonstrated that the same 27.8R was shared by flounder and sea bass. LCDV-free sea bass individuals were intramuscularly injected with LCDV, and viral copies were detected in tissues from 3 h post infection and showed a time-dependent increase during 9 days infection. Distribution and synthesis of 27.8R in sea bass tissues were investigated by using anti-27.8R MAbs as probes. It was found that 27.8R was distributed in all the tested tissues. The levels of 27.8R protein were highest in gill and skin, then a bit lowly in stomach, head kidney and heart, followed by spleen, intestine, blood cells, gonad and liver, and least in kidney and brain in healthy sea bass. Upon LCDV infection, 27.8R synthesis was up-regulated in each tissue, and higher in the tissues with higher LCDV copies. The 27.8R and LCDV were detected in some peripheral blood leukocytes but not in red blood cells. These results suggested that 27.8R was widely distributed in sea bass tissues, and it served as a receptor and correlated with tissue tropism of LCDV infection. Furthermore, leukocytes had the potential of being a LCDV carrier and were responsible for a systemic infection of LCDV in sea bass.

  2. New ultracool subdwarfs identified in large-scale surveys using Virtual Observatory tools

    NASA Astrophysics Data System (ADS)

    Lodieu, N.; Espinoza Contreras, M.; Zapatero Osorio, M. R.; Solano, E.; Aberasturi, M.; Martín, E. L.; Rodrigo, C.

    2017-02-01

    Aims: We aim to develop an efficient method to search for late-type subdwarfs (metal-depleted dwarfs with spectral types ≥M5) to improve the current statistics. Our objectives are to improve our knowledge of metal-poor low-mass dwarfs, bridge the gap between the late-M and L types, determine their surface density, and understand the impact of metallicity on the stellar and substellar mass function. Methods: We carried out a search cross-matching the Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) and the Two Micron All Sky Survey (2MASS), and different releases of SDSS and the United Kingdom InfraRed Telescope (UKIRT) Infrared Deep Sky Survey (UKIDSS) using STILTS, Aladin, and Topcat developed as part of the Virtual Observatory tools. We considered different photometric and proper motion criteria for our selection. We identified 29 and 71 late-type subdwarf candidates in each cross-correlation over 8826 and 3679 sq. deg, respectively (2312 sq. deg overlap). We obtained our own low-resolution optical spectra for 71 of our candidates: 26 were observed with the Gran Telescopio de Canarias (GTC; R 350, λλ5000-10 000 Å), six with the Nordic Optical Telescope (NOT; R 450, λλ5000-10 700 Å), and 39 with the Very Large Telescope (VLT; R 350, λλ6000-11 000 Å). We also retrieved spectra for 30 of our candidates from the SDSS spectroscopic database (R 2000 and λλ 3800-9400 Å), nine of these 30 candidates with an independent spectrum in our follow-up. We classified 92 candidates based on 101 optical spectra using two methods: spectral indices and comparison with templates of known subdwarfs. Results: We developed an efficient photometric and proper motion search methodology to identify metal-poor M dwarfs. We confirmed 86% and 94% of the candidates as late-type subdwarfs from the SDSS vs. 2MASS and SDSS vs. UKIDSS cross-matches, respectively. These subdwarfs have spectral types ranging between M5 and L0.5 and SDSS magnitudes in the r = 19.4-23.3 mag range

  3. Large truck crashes in Texas : a predictive approach for identifying those at higher risk

    DOT National Transportation Integrated Search

    2007-08-01

    The objective of this research is to characterize large truck safety levels in Texas on the basis of driver, vehicle, cargo, and carrier traits while controlling for the effects of crash and operating environment conditions. Data to support this inve...

  4. Study Identifies New Lymphoma Treatment Target

    Cancer.gov

    NCI researchers have identified new therapeutic targets for diffuse large B-cell lymphoma. Drugs that hit these targets are under clinical development and the researchers hope to begin testing them in clinical trials of patients with DLBCL.

  5. Influence of dietary probiotic Bacillus TC22 and Prebiotic fructooligosaccharide on growth, immune responses and disease resistance against Vibrio splendidus infection in sea cucumber Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Zhao, Yancui; Mai, Kangsen; Xu, Wei; Zhang, Wenbing; Ai, Qinghui; Zhang, Yanjiao; Wang, Xiaojie; Liufu, Zhiguo

    2011-09-01

    The effects of probiotic Bacillus TC22 (isolated from intestine of infected sea cucumber) and prebiotic fructooligosaccharide (FOS) on growth, immunity and disease resistance in sea cucumber Apostichopus japonicus were studied. Six experimental diets were formulated with combinations of three levels of TC22 (0, 107 and 109 CFU g-1 diet) and two levels of FOS (0 and 0.5%) in a 3 × 2 factorial experiment. At the end of the 8-week feeding trial, animals were challenged by injecting Vibrio splendidus. The results revealed that the specific growth rates (SGR) of sea cucumbers were not affected by TC22 and FOS, or the interaction between TC22 and FOS ( P > 0.05). However, there were significant interactions between TC22 and FOS for immune response and disease resistance in sea cucumbers ( P < 0.05). When sea cucumbers were fed with TC22 at 109 CFU g-1 feed and 0.5% FOS alone or in combination, the phagocytosis, respiratory burst and phenoloxidase activity of sea cucumber coelomocytes were significantly enhanced; the disease resistance against V. splendidus infection was also increased significantly ( P < 0.05). However, dietary combination of TC22 at 109 CFU g-1 diet and 0.5% FOS did not yield significantly higher efficiency than either TC22 at 109 CFU g-1 diet or 0.5% FOS used alone ( P > 0.05). Therefore, further studies should examine the effects of combinations of other levels of FOS (> 0.5% or < 0.5%) and TC22 on the immunity and disease resistance of sea cucumbers.

  6. Regulation of growth, intestinal microbiota, non-specific immune response and disease resistance of sea cucumber Apostichopus japonicus (Selenka) in biofloc systems.

    PubMed

    Chen, Jinghua; Ren, Yichao; Li, Yuquan; Xia, Bin

    2018-06-01

    Bioflocs are not only a source of supplemental nutrition but also provide substantial probiotic bacteria and bioactive compounds, which play an important role in improving physiological health of aquatic organisms. A 60-day experiment was conducted to investigate the growth, intestinal microbiota, non-specific immune response and disease resistance of sea cucumber in biofloc systems with different carbon sources (glucose, sucrose and starch). Control (no biofloc) and three biofloc systems were set up, and each group has three replicates. The results showed that biofloc volume (BFV) and total suspended solids (TSS) increased in the sequences of glucose > sucrose > starch and green sea cucumber > white sea cucumber during the experiment. The highest specific growth rates (SGRs) were observed in biofloc system with glucose as carbon source, which also had relatively lower glucose, lactate and cortisol levels in coelomic fluid and higher glycogen content in muscle compared to other groups. There were significant increased Bacillus and Lactobacillus counts of sea cucumber intestine in biofloc systems, and the activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) also showed obvious ascending trends. Significant increases in total coelomocytes counts (TCC), phagocytosis, respiratory burst, complement C3 content and lysozyme (LSZ) and acid phosphatase (ACP) activities of sea cucumber were all found in biofloc system (glucose). The expression patterns of most immune-related genes (i.e. Hsp90, Hsp70, c-type lectin (CL), toll-like receptor (TLR)) were up-regulated, suggesting the promotion of pathogen recognition ability and immune signaling pathways activation by biofloc. Furthermore, green and white sea cucumber had significantly higher survival rates in biofloc systems during the 14-day challenge test. In conclusion, biofloc technology could improve growth and physiological health of A. japonicus, by optimizing intestinal

  7. External Validation of Fatty Liver Index for Identifying Ultrasonographic Fatty Liver in a Large-Scale Cross-Sectional Study in Taiwan

    PubMed Central

    Fang, Kuan-Chieh; Wang, Yuan-Chen; Huo, Teh-Ia; Huang, Yi-Hsiang; Yang, Hwai-I; Su, Chien-Wei; Lin, Han-Chieh; Lee, Fa-Yauh; Wu, Jaw-Ching; Lee, Shou-Dong

    2015-01-01

    Background and Aims The fatty liver index (FLI) is an algorithm involving the waist circumference, body mass index, and serum levels of triglyceride and gamma-glutamyl transferase to identify fatty liver. Although some studies have attempted to validate the FLI, few studies have been conducted for external validation among Asians. We attempted to validate FLI to predict ultrasonographic fatty liver in Taiwanese subjects. Methods We enrolled consecutive subjects who received health check-up services at the Taipei Veterans General Hospital from 2002 to 2009. Ultrasonography was applied to diagnose fatty liver. The ability of the FLI to detect ultrasonographic fatty liver was assessed by analyzing the area under the receiver operating characteristic (AUROC) curve. Results Among the 29,797 subjects enrolled in this study, fatty liver was diagnosed in 44.5% of the population. Subjects with ultrasonographic fatty liver had a significantly higher FLI than those without fatty liver by multivariate analysis (odds ratio 1.045; 95% confidence interval, CI 1.044–1.047, p< 0.001). Moreover, FLI had the best discriminative ability to identify patients with ultrasonographic fatty liver (AUROC: 0.827, 95% confidence interval, 0.822–0.831). An FLI < 25 (negative likelihood ratio (LR−) 0.32) for males and <10 (LR− 0.26) for females rule out ultrasonographic fatty liver. Moreover, an FLI ≥ 35 (positive likelihood ratio (LR+) 3.12) for males and ≥ 20 (LR+ 4.43) for females rule in ultrasonographic fatty liver. Conclusions FLI could accurately identify ultrasonographic fatty liver in a large-scale population in Taiwan but with lower cut-off value than the Western population. Meanwhile the cut-off value was lower in females than in males. PMID:25781622

  8. Germline whole exome sequencing and large-scale replication identifies FANCM as a likely high grade serous ovarian cancer susceptibility gene.

    PubMed

    Dicks, Ed; Song, Honglin; Ramus, Susan J; Oudenhove, Elke Van; Tyrer, Jonathan P; Intermaggio, Maria P; Kar, Siddhartha; Harrington, Patricia; Bowtell, David D; Group, Aocs Study; Cicek, Mine S; Cunningham, Julie M; Fridley, Brooke L; Alsop, Jennifer; Jimenez-Linan, Mercedes; Piskorz, Anna; Goranova, Teodora; Kent, Emma; Siddiqui, Nadeem; Paul, James; Crawford, Robin; Poblete, Samantha; Lele, Shashi; Sucheston-Campbell, Lara; Moysich, Kirsten B; Sieh, Weiva; McGuire, Valerie; Lester, Jenny; Odunsi, Kunle; Whittemore, Alice S; Bogdanova, Natalia; Dürst, Matthias; Hillemanns, Peter; Karlan, Beth Y; Gentry-Maharaj, Aleksandra; Menon, Usha; Tischkowitz, Marc; Levine, Douglas; Brenton, James D; Dörk, Thilo; Goode, Ellen L; Gayther, Simon A; Pharoah, D P Paul

    2017-08-01

    We analyzed whole exome sequencing data in germline DNA from 412 high grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas Project and identified 5,517 genes harboring a predicted deleterious germline coding mutation in at least one HGSOC case. Gene-set enrichment analysis showed enrichment for genes involved in DNA repair (p = 1.8×10 -3 ). Twelve DNA repair genes - APEX1, APLF, ATX, EME1, FANCL, FANCM, MAD2L2, PARP2, PARP3, POLN, RAD54L and SMUG1 - were prioritized for targeted sequencing in up to 3,107 HGSOC cases, 1,491 cases of other epithelial ovarian cancer (EOC) subtypes and 3,368 unaffected controls of European origin. We estimated mutation prevalence for each gene and tested for associations with disease risk. Mutations were identified in both cases and controls in all genes except MAD2L2 , where we found no evidence of mutations in controls. In FANCM we observed a higher mutation frequency in HGSOC cases compared to controls (29/3,107 cases, 0.96 percent; 13/3,368 controls, 0.38 percent; P=0.008) with little evidence for association with other subtypes (6/1,491, 0.40 percent; P=0.82). The relative risk of HGSOC associated with deleterious FANCM mutations was estimated to be 2.5 (95% CI 1.3 - 5.0; P=0.006). In summary, whole exome sequencing of EOC cases with large-scale replication in case-control studies has identified FANCM as a likely novel susceptibility gene for HGSOC, with mutations associated with a moderate increase in risk. These data may have clinical implications for risk prediction and prevention approaches for high-grade serous ovarian cancer in the future and a significant impact on reducing disease mortality.

  9. Attack and Success of Native and Exotic Parasitoids on Eggs of Halyomorpha halys in Three Maryland Habitats

    PubMed Central

    Herlihy, Megan V.; Talamas, Elijah J.; Weber, Donald C.

    2016-01-01

    Egg parasitoids of the exotic invasive brown marmorated stink bug, Halyomorpha halys (Stål), were investigated using lab-reared fresh (live) and frozen (killed) lab-reared sentinel egg masses deployed for 72h on foliage in three habitats—woods, orchard, and soybean field—in Maryland, USA, in summer 2014. Four native hymenopteran species, Telenomus podisi Ashmead (Scelionidae), Trissolcus euschisti (Ashmead) and Tr. brochymenae Ashmead (Scelionidae), and Anastatus reduvii (Howard) (Eupelmidae), developed and emerged from H. halys eggs. One exotic parasitoid, Trissolcus japonicus (Ashmead), emerged, providing the first known occurrence of this species in North America. Native parasitoids emerged from frozen eggs significantly more often than from fresh eggs (89.3% of egg masses and 98.1% of individual eggs), whereas the exotic Tr. japonicus did not show a similar difference, strongly suggesting adaptation to H. halys as a host by Tr. japonicus but not by the native species. Parasitoids were habitat-specific: all three Trissolcus species were significantly more likely to occur in the woods habitat, whereas Te. podisi was found exclusively in the soybean field. Further investigations are required to elucidate evolving host-parasitoid relationships, habitat specificity, and non-target effects of Tr. japonicus over the expanded range of H. halys in North America. PMID:26983012

  10. The Effect of Eating Sea Cucumber Jelly on Candida Load in the Oral Cavity of Elderly Individuals in a Nursing Home

    PubMed Central

    Yano, Akira; Abe, Akiko; Aizawa, Fumie; Yamada, Hidetoshi; Minami, Kentaro; Matsui, Miki; Kishi, Mitsuo

    2013-01-01

    We conducted a double-blind randomized controlled study of elderly individuals in a nursing home to investigate the effect of the consumption of jelly containing sea cucumber on their oral Candida load. The jelly contained a hydrolysate of the sea cucumber Stichopus japonicus, which contained triterpene glycosides called holotoxins. The holotoxins worked as a fungicide, and their minimum inhibitory concentrations for Candida albicans were 7 µg/mL. Eight individuals in the nursing home took the sea cucumber jelly for a week and their oral Candida were counted before and after the intervention. Nine individuals took a control jelly without S. japonicus. The sea cucumber jelly showed inhibitory effects on the oral Candida. Thus, daily consumption of the S. japonicus jelly has the potential to reduce the oral Candida load in the elderly in nursing homes. PMID:24335524

  11. Distributed design approach in persistent identifiers systems

    NASA Astrophysics Data System (ADS)

    Golodoniuc, Pavel; Car, Nicholas; Klump, Jens

    2017-04-01

    The need to identify both digital and physical objects is ubiquitous in our society. Past and present persistent identifier (PID) systems, of which there is a great variety in terms of technical and social implementations, have evolved with the advent of the Internet, which has allowed for globally unique and globally resolvable identifiers. PID systems have catered for identifier uniqueness, integrity, persistence, and trustworthiness, regardless of the identifier's application domain, the scope of which has expanded significantly in the past two decades. Since many PID systems have been largely conceived and developed by small communities, or even a single organisation, they have faced challenges in gaining widespread adoption and, most importantly, the ability to survive change of technology. This has left a legacy of identifiers that still exist and are being used but which have lost their resolution service. We believe that one of the causes of once successful PID systems fading is their reliance on a centralised technical infrastructure or a governing authority. Golodoniuc et al. (2016) proposed an approach to the development of PID systems that combines the use of (a) the Handle system, as a distributed system for the registration and first-degree resolution of persistent identifiers, and (b) the PID Service (Golodoniuc et al., 2015), to enable fine-grained resolution to different information object representations. The proposed approach solved the problem of guaranteed first-degree resolution of identifiers, but left fine-grained resolution and information delivery under the control of a single authoritative source, posing risk to the long-term availability of information resources. Herein, we develop these approaches further and explore the potential of large-scale decentralisation at all levels: (i) persistent identifiers and information resources registration; (ii) identifier resolution; and (iii) data delivery. To achieve large-scale decentralisation

  12. Evolutionary history of mitogen-activated protein kinase (MAPK) genes in Lotus, Medicago, and Phaseolus

    PubMed Central

    Neupane, Achal; Nepal, Madhav P; Benson, Benjamin V; MacArthur, Kenton J; Piya, Sarbottam

    2013-01-01

    Mitogen-Activated Protein Kinase (MAPK) genes encode proteins that mediate various signaling pathways associated with biotic and abiotic stress responses in eukaryotes. The MAPK genes form a 3-tier signal transduction cascade between cellular stimuli and physiological responses. Recent identification of soybean MAPKs and availability of genome sequences from other legume species allowed us to identify their MAPK genes. The main objectives of this study were to identify MAPKs in 3 legume species, Lotus japonicus, Medicago truncatula, and Phaseolus vulgaris, and to assess their phylogenetic relationships. We used approaches in comparative genomics for MAPK gene identification and named the newly identified genes following Arabidopsis MAPK nomenclature model. We identified 19, 18, and 15 MAPKs and 7, 4, and 9 MAPKKs in the genome of Lotus japonicus, Medicago truncatula, and Phaseolus vulgaris, respectively. Within clade placement of MAPKs and MAPKKs in the 3 legume species were consistent with those in soybean and Arabidopsis. Among 5 clades of MAPKs, 4 founder clades were consistent to MAPKs of other plant species and orthologs of MAPK genes in the fifth clade-"Clade E" were consistent with those in soybean. Our results also indicated that some gene duplication events might have occurred prior to eudicot-monocot divergence. Highly diversified MAPKs in soybean relative to those in 3 other legume species are attributable to the polyploidization events in soybean. The identification of the MAPK genes in the legume species is important for the legume crop improvement; and evolutionary relationships and functional divergence of these gene members provide insights into plant genome evolution. PMID:24317362

  13. An Evaluation on the Ratio of Plant to Animal Protein in the Diet of Juvenile Sea Cucumber (Apostichopus japonicus): Growth, Nutrient Digestibility and Nonspecific Immunity

    NASA Astrophysics Data System (ADS)

    Bao, Pengyun; Li, Xiaoyu; Xu, Yongping

    2018-05-01

    This study was conducted to evaluate the effects of plant/animal (P/A) protein ratios (viz.1:4, 1:3, 1:2, 1:1,2:1, 3:1, 4:1) on growth performance, body composition, apparent digestibility of diets, and nonspecific immunity of juvenile sea cucumber (Apostichopus japonicus). Sea cucumbers were divided into 21 plastic tanks, and each tank was stocked with 15 individuals (initial weight: about 23.73 g). Each feed was allocated to three replicates of sea cucumbers. The feeding experiment lasted for 50 days. Results indicated that weight gain rate (WGR) and body wall weight (BWW) significantly increased as dietary ratio of P/A increased from 1:4 to 3:1, and then decreased significantly with further increase of this ratio (P < 0.05). The body wall coefficient (BWC) showed a similar tendency to WGR and BWW, but no significance was detected among dietary treatments (P > 0.05). The apparent digestibility of dry matter, protein and lipid increased with ratio of P/A increasing from 1:4 to 2:1 (P < 0.05), and then decreased with further increase of this ratio. Correspondingly, activities of trypsin and amylase were significantly increased as P/A increased from 1:4 to 2:1 (P < 0.05). The activities of SOD and CAT showed a similar trend with WGR, with the highest value observed in the ratio of 1:2 and 1:1, respectively. Results above showed that moderate or relatively higher ratio of P/A protein (1:1-3:1) significantly increased the growth performance, apparent digestibility, and nonspecific immunity of sea cucumber. This will contribute to improving the feed formulation for juvenile cucumbers.

  14. Effects of dietary β-glucan and glycyrrhizin on non-specific immunity and disease resistance of the sea cucumber ( Apostichopus japonicus Selenka) challenged with Vibrio splendidus

    NASA Astrophysics Data System (ADS)

    Chang, Jie; Zhang, Wenbing; Mai, Kangsen; Ma, Hongming; Xu, Wei

    2010-12-01

    Sea cucumbers, Apostichopus japonicus Selenka, were fed diets containing non-immunostimulant (basal diet), 0.2% β-glucan and 0.02% glycyrrhizin in a recirculatory water system for 45 days, and subsequently challenged with Vibrio splendidus by injection at 1.0×108 cfu / sea cucumber for 15 days. Phagocytic capacity (PC), intracellular superoxide anion production (ISAP), lysozyme (LSZ) activity and superoxide dismutase (SOD) activity in the coelomic fluid were analyzed on the 0th, 5th, 10th and 15th days after injection. Results showed that after the 45-day feeding period, PC, ISAP, LSZ activity and SOD activity in sea cucumbers fed with dietary β-glucan or glycyrrhizin were significantly higher than in those fed with the basal diet. On the 5th day after infection, all the immune parameters examined in the sea cucumbers injected with V. splendidus decreased in value significantly. On the 15th day, PC, ISAP and LSZ activity returned to levels similar to those on the 0th day. For the sea cucumbers injected with saline, there were no significant differences in all the immune parameters examined and in the cumulative morbidity during the 15-day challenging trial. After injecting with V. splendidus, the cumulative morbidity of sea cucumbers fed with the basal diet was significantly higher than those fed with dietary β-glucan or glycyrrhizin when challenged with V. splendidus challenged sea cucumber fed with the basal diet was significantly higher than those fed with dietary β-glucan or glycyrrhizin. There was no significant difference in cumulative morbidity between the dietary β-glucan and glycyrrhizin treatments over time.

  15. Recurrent TERT promoter mutations identified in a large-scale study of multiple tumor types are associated with increased TERT expression and telomerase activation

    PubMed Central

    Huang, Dong-Sheng; Wang, Zhaohui; He, Xu-Jun; Diplas, Bill H.; Yang, Rui; Killela, Patrick J.; Liang, Junbo; Meng, Qun; Ye, Zai-Yuan; Wang, Wei; Jiang, Xiao-Ting; Xu, Li; He, Xiang-Lei; Zhao, Zhong-Sheng; Xu, Wen-Juan; Wang, Hui-Ju; Ma, Ying-Yu; Xia, Ying-Jie; Li, Li; Zhang, Ru-Xuan; Jin, Tao; Zhao, Zhong-Kuo; Xu, Ji; Yu, Sheng; Wu, Fang; Wang, Si-Zhen; Jiao, Yu-Chen; Yan, Hai; Tao, Hou-Quan

    2015-01-01

    Background Several somatic mutation hotspots were recently identified in the TERT promoter region in human cancers. Large scale studies of these mutations in multiple tumor types are limited, in particular in Asian populations. This study aimed to: analyze TERT promoter mutations in multiple tumor types in a large Chinese patient cohort, investigate novel tumor types and assess the functional significance of the mutations. Methods TERT promoter mutation status was assessed by Sanger sequencing for 13 different tumor types and 799 tumor tissues from Chinese cancer patients. Thymic epithelial tumors, gastrointestinal leiomyoma, and gastric schwannoma were included, for which the TERT promoter has not been previously sequenced. Functional studies included TERT expression by RT-qPCR, telomerase activity by the TRAP assay, and promoter activity by the luciferase reporter assay. Results TERT promoter mutations were highly frequent in glioblastoma (83.9%), urothelial carcinoma (64.5%), oligodendroglioma (70.0%), medulloblastoma (33.3%), and hepatocellular carcinoma (31.4%). C228T and C250T were the most common mutations. In urothelial carcinoma, several novel rare mutations were identified. TERT promoter mutations were absent in GIST, thymic epithelial tumors, gastrointestinal leiomyoma, gastric schwannoma, cholangiocarcinoma, gastric and pancreatic cancer. TERT promoter mutations highly correlated with upregulated TERT mRNA expression and telomerase activity in adult gliomas. These mutations differentially enhanced the transcriptional activity of the TERT core promoter. Conclusions TERT promoter mutations are frequent in multiple tumor types and have similar distributions in Chinese cancer patients. The functional significance of these mutations reflect the importance to telomere maintenance and hence tumorigenesis, making them potential therapeutic targets. PMID:25843513

  16. Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr.

    PubMed

    Piao, Chenyu; Zheng, Weiwei; Li, Yao; Liu, Chongxi; Jin, Liying; Song, Wei; Yan, Kai; Wang, Xiangjing; Xiang, Wensheng

    2017-09-01

    Two novel actinomycetes, designated strains 2C-SSA16(2) T and 1C-GS8 T , were isolated from the cuticle of Camponotus japonicus Mayr, collected from Northeast Agricultural University, Heilongjiang Province, north China. Both of them contained genes (involved in antibiotics biosynthesis) of the ketosynthase (KS) and methyl malonyl transferase domains (PKS-I) and the adenylation domain (NRPS). A polyphasic study was carried out to establish the taxonomic positions of these strains. The 16S rRNA gene sequence analysis showed that the two novel isolates 2C-SSA16(2) T and 1C-GS8 T exhibited 98.8% similarity with each other and that they are most closely related to Streptomyces umbrinus JCM 4521 T (99.0, 98.6%), Streptomyces ederensis JCM 4958 T (98.9, 98.7%), Streptomyces aurantiacus JCM 4453 T (98.6, 98.2%), Streptomyces glomeroaurantiacus JCM 4677 T (98.6, 98.1%), Streptomyces tauricus JCM4837 T (98.2, 98.0%) and Streptomyces phaeochromogenes JCM 4070 T (98.2, 99.2%). The corresponding phylogenetic analysis based on partial gyrB gene sequences showed that strains 2C-SSA16(2) T and 1C-GS8 T formed a cluster with the above-mentioned strains. The DNA-DNA hybridization data and phenotypic characteristics indicated that strains 2C-SSA16(2) T and 1C-GS8 T could be readily distinguished from each other and their closest phylogenetic relatives. Therefore, these two strains are suggested to represent two novel species of the genus Streptomyces, for which the names Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. are proposed. The type strains are 2C-SSA16(2) T (=CGMCC 4.7276 T  = DSM 100522 T ) and 1C-GS8 T (=CGMCC 4.7348 = DSM 103127 T ), respectively.

  17. Protective effects of chicken egg yolk antibody (IgY) against experimental Vibrio splendidus infection in the sea cucumber (Apostichopus japonicus).

    PubMed

    Li, Xiaoyu; Jing, Kailin; Wang, Xitao; Li, Yuan; Zhang, Meixia; Li, Zhen; Xu, Le; Wang, Lili; Xu, Yongping

    2016-01-01

    Vibrio splendidus is one of the most harmful pathogens associated with skin ulceration syndrome in the sea cucumber (Apostichopus japonicus) due to its high virulence and frequency of appearance. The objective of this study was to determine the effectiveness of chicken egg yolk antibody (IgY) against V. splendidus infection in the sea cucumber. Whole V. splendidus cells were used as an immunogen to immunize 20 White Leghorn hens (25 weeks old). IgY was produced from egg yolks obtained from these immunized hens using water dilution, two-step salt precipitation and ultrafiltration. The purity of the IgY produced was approximately 83%. Enzyme-linked Immunosorbent Assay indicated a high specificity for IgY with a maximum antibody titer of 320,000. The growth of V. splendidus in liquid medium was significantly inhibited by IgY in a dose-dependent manner at concentrations ranging from 1 to 10 mg/mL. The protective effects of IgY were evaluated in sea cucumber by intraperitoneally injecting anti-V. splendidus IgY antibodies (10 mg/mL) or immersing the sea cucumber in aqueous IgY (1 g/L) after an intraperitoneal injection of V. splendidus. Intraperitoneal injection resulted in an 80% survival while immersion resulted in a 75% survival during the 11-day experimental period. The survival rates were significantly higher than the positive control and the non-specific IgY group (P < 0.05). As well, the bacterial burden in the respiratory tree, intestine and coelomic liquid was significantly (P < 0.05) lower in sea cucumber treated with specific IgY than those treated with non-specific IgY. The phagocytosis of coelomocytes for V. splendidus in the presence of specific IgY was significantly (P < 0.05) higher than that obtained with non-specific IgY or without IgY, suggesting that specific IgY enhanced phagocytic activity. The current work suggests that specific IgY has potential for protecting sea cucumbers against V. splendidus infection. Copyright © 2015

  18. Impact of an Alien Invasive Shrub on Ecology of Native and Alien Invasive Mosquito Species (Diptera: Culicidae).

    PubMed

    Muturi, Ephantus J; Gardner, Allison M; Bara, Jeffrey J

    2015-10-01

    We examined how leaf litter of alien invasive honeysuckle (Lonicera maackii Rupr.) either alone or in combination with leaf litter of one of two native tree species, sugar maple (Acer saccharum Marshall) and northern red oak (Quercus rubra L.), affects the ecology of Culex restuans Theobald, Ochlerotatus triseriatus Say, and Ochlerotatus japonicus Theobald. Experimental mesocosms containing single species litter or a mixture of honeysuckle and one of two native tree species litter were established at South Farms and Trelease Woods study sites in Urbana, IL, and examined for their effect on 1) oviposition site selection by the three mosquito species, and 2) adult production and body size of Oc. triseriatus and Oc. japonicus. There were no significant effects of study site and leaf treatment on Oc. japonicus and Oc. triseriatus oviposition preference and adult production. In contrast, significantly more Cx. restuans eggs rafts were collected at South Farms relative to Trelease Woods and in honeysuckle litter relative to native tree species litter. Significantly larger adult females of Oc. japonicus and Oc. triseriatus were collected at South Farms relative to Trelease Woods and in honeysuckle litter relative to native tree species litter. Combining honeysuckle litter with native tree species litter had additive effects on Cx. restuans oviposition preference and Oc. japonicus and Oc. triseriatus body size, with the exception of honeysuckle and northern red oak litter combination, which had antagonistic effects on Oc. triseriatus body size. We conclude that input of honeysuckle litter into container aquatic habitats may alter the life history traits of vector mosquito species. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  19. Generically large nongaussianity in small multifield inflation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bramante, Joseph

    If forthcoming measurements of cosmic photon polarization restrict the primordial tensor-to-scalar ratio to r<0.01, small field inflation will be a principal candidate for the origin of the universe. Here we show that small multifield inflation, without the hybrid mechanism, typically results in large squeezed nongaussianity. Small multifield potentials contain multiple flat field directions, often identified with the gauge invariant field directions in supersymmetric potentials. We find that unless these field directions have equal slopes, large nongaussianity arises. After identifying relevant differences between large and small two-field potentials, we demonstrate that the latter naturally fulfill the Byrnes-Choi-Hall large nongaussianity conditions. Computationsmore » of the primordial power spectrum, spectral index, and squeezed bispectrum, reveal that small two-field models which otherwise match observed primordial perturbations, produce excludably large nongaussianity if the inflatons’ field directions have unequal slopes.« less

  20. Generically large nongaussianity in small multifield inflation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bramante, Joseph, E-mail: josephbramante@gmail.com

    If forthcoming measurements of cosmic photon polarization restrict the primordial tensor-to-scalar ratio to r < 0.01, small field inflation will be a principal candidate for the origin of the universe. Here we show that small multifield inflation, without the hybrid mechanism, typically results in large squeezed nongaussianity. Small multifield potentials contain multiple flat field directions, often identified with the gauge invariant field directions in supersymmetric potentials. We find that unless these field directions have equal slopes, large nongaussianity arises. After identifying relevant differences between large and small two-field potentials, we demonstrate that the latter naturally fulfill the Byrnes-Choi-Hall large nongaussianity conditions. Computationsmore » of the primordial power spectrum, spectral index, and squeezed bispectrum, reveal that small two-field models which otherwise match observed primordial perturbations, produce excludably large nongaussianity if the inflatons' field directions have unequal slopes.« less

  1. Recurrent TERT promoter mutations identified in a large-scale study of multiple tumour types are associated with increased TERT expression and telomerase activation.

    PubMed

    Huang, Dong-Sheng; Wang, Zhaohui; He, Xu-Jun; Diplas, Bill H; Yang, Rui; Killela, Patrick J; Meng, Qun; Ye, Zai-Yuan; Wang, Wei; Jiang, Xiao-Ting; Xu, Li; He, Xiang-Lei; Zhao, Zhong-Sheng; Xu, Wen-Juan; Wang, Hui-Ju; Ma, Ying-Yu; Xia, Ying-Jie; Li, Li; Zhang, Ru-Xuan; Jin, Tao; Zhao, Zhong-Kuo; Xu, Ji; Yu, Sheng; Wu, Fang; Liang, Junbo; Wang, Sizhen; Jiao, Yuchen; Yan, Hai; Tao, Hou-Quan

    2015-05-01

    Several somatic mutation hotspots were recently identified in the telomerase reverse transcriptase (TERT) promoter region in human cancers. Large scale studies of these mutations in multiple tumour types are limited, in particular in Asian populations. This study aimed to: analyse TERT promoter mutations in multiple tumour types in a large Chinese patient cohort, investigate novel tumour types and assess the functional significance of the mutations. TERT promoter mutation status was assessed by Sanger sequencing for 13 different tumour types and 799 tumour tissues from Chinese cancer patients. Thymic epithelial tumours, gastrointestinal leiomyoma, and gastric schwannoma were included, for which the TERT promoter has not been previously sequenced. Functional studies included TERT expression by reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR), telomerase activity by the telomeric repeat amplification protocol (TRAP) assay and promoter activity by the luciferase reporter assay. TERT promoter mutations were highly frequent in glioblastoma (83.9%), urothelial carcinoma (64.5%), oligodendroglioma (70.0%), medulloblastoma (33.3%) and hepatocellular carcinoma (31.4%). C228T and C250T were the most common mutations. In urothelial carcinoma, several novel rare mutations were identified. TERT promoter mutations were absent in gastrointestinal stromal tumour (GIST), thymic epithelial tumours, gastrointestinal leiomyoma, gastric schwannoma, cholangiocarcinoma, gastric and pancreatic cancer. TERT promoter mutations highly correlated with upregulated TERT mRNA expression and telomerase activity in adult gliomas. These mutations differentially enhanced the transcriptional activity of the TERT core promoter. TERT promoter mutations are frequent in multiple tumour types and have similar distributions in Chinese cancer patients. The functional significance of these mutations reflect the importance to telomere maintenance and hence tumourigenesis, making them

  2. Modeling connectivity to identify current and future anthropogenic barriers to movement of large carnivores: A case study in the American Southwest.

    PubMed

    McClure, Meredith L; Dickson, Brett G; Nicholson, Kerry L

    2017-06-01

    This study sought to identify critical areas for puma ( Puma concolor ) movement across the state of Arizona in the American Southwest and to identify those most likely to be impacted by current and future human land uses, particularly expanding urban development and associated increases in traffic volume. Human populations in this region are expanding rapidly, with the potential for urban centers and busy roads to increasingly act as barriers to demographic and genetic connectivity of large-bodied, wide-ranging carnivores such as pumas, whose long-distance movements are likely to bring them into contact with human land uses and whose low tolerance both for and from humans may put them at risk unless opportunities for safe passage through or around human-modified landscapes are present. Brownian bridge movement models based on global positioning system collar data collected during bouts of active movement and linear mixed models were used to model habitat quality for puma movement; then, a wall-to-wall application of circuit theory models was used to produce a continuous statewide estimate of connectivity for puma movement and to identify pinch points, or bottlenecks, that may be most at risk of impacts from current and future traffic volume and expanding development. Rugged, shrub- and scrub-dominated regions were highlighted as those offering high quality movement habitat for pumas, and pinch points with the greatest potential impacts from expanding development and traffic, although widely distributed, were particularly prominent to the north and east of the city of Phoenix and along interstate highways in the western portion of the state. These pinch points likely constitute important conservation opportunities, where barriers to movement may cause disproportionate loss of connectivity, but also where actions such as placement of wildlife crossing structures or conservation easements could enhance connectivity and prevent detrimental impacts before they occur.

  3. Persistence of nondysplastic Barrett's esophagus identifies patients at lower risk for esophageal adenocarcinoma: results from a large multicenter cohort.

    PubMed

    Gaddam, Srinivas; Singh, Mandeep; Balasubramanian, Gokulakrishnan; Thota, Prashanthi; Gupta, Neil; Wani, Sachin; Higbee, April D; Mathur, Sharad C; Horwhat, John D; Rastogi, Amit; Young, Patrick E; Cash, Brooks D; Bansal, Ajay; Vargo, John J; Falk, Gary W; Lieberman, David A; Sampliner, Richard E; Sharma, Prateek

    2013-09-01

    Recent population-based studies have shown a low risk of esophageal adenocarcinoma (EAC) in patients with nondysplastic Barrett's esophagus (NDBE). We evaluated whether persistence of NDBE over multiple consecutive surveillance endoscopic examinations could be used in risk stratification of patients with Barrett's esophagus (BE). We performed a multicenter outcomes study of a large cohort of patients with BE. Based on the number of consecutive surveillance endoscopies showing NDBE, we identified 5 groups of patients. Patients in group 1 were found to have NDBE at their first esophagogastroduodenoscopy (EGD). Patients in group 2 were found to have NDBE on their first 2 consecutive EGDs. Similarly, patients in groups 3, 4, and 5 were found to have NDBE on 3, 4, and 5 consecutive surveillance EGDs. A logistic regression model was built to determine whether persistence of NDBE independently protected against development of cancer. Of a total of 3515 patients with BE, 1401 patients met the inclusion criteria (93.3% white; 87.5% men; median age, 60 ±17 years). The median follow-up period was 5 ± 3.9 years (7846 patient-years). The annual risk of EAC in groups 1 to 5 was 0.32%, 0.27%, 0.16%, 0.2%, and 0.11%, respectively (P for trend = .03). After adjusting for age, sex, and length of BE, persistence of NDBE, based on multiple surveillance endoscopies, was associated with a gradually lower likelihood of progression to EAC. Persistence of NDBE over several endoscopic examinations identifies patients who are at low risk for development of EAC. These findings support lengthening surveillance intervals or discontinuing surveillance of patients with persistent NDBE. Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.

  4. Effects of light on direct and indirect defences against herbivores of young plants of Mallotus japonicus demonstrate a trade-off between two indirect defence traits

    PubMed Central

    Yamawo, Akira; Hada, Yoshio

    2010-01-01

    Background and Aims Although most studies on plant defence strategies have focused on a particular defence trait, some plant species develop multiple defence traits. To clarify the effects of light on the development of multiple defence traits, the production of direct and indirect defence traits of young plants of Mallotus japonicus were examined experimentally under different light conditions. Methods The young plants were cultivated under three light conditions in the experimental field for 3 months from May to July. Numbers of ants and pearl bodies on leaves in July were examined. After cultivation, the plants were collected and the developments of trichomes and pellucid dots, and extrafloral nectaries (EFNs) on the leaves were examined. On plants without nectar-collecting insects, the size of EFNs and the volume of extrafloral nectar secreted from the EFNs were examined. Key results Densities of trichomes and pellucid dots did not differ significantly among the plants under the different light conditions, suggesting that the chemical and physical defences function under both high and low light availability. The number of EFNs on the leaves did not differ significantly among the plants under the different light conditions, but there appeared to be a trade-off between the size of EFNs and the number of pearl bodies; the largest EFNs and the smallest number of pearl bodies were found under high light availability. EFN size was significantly correlated with the volume of extrafloral nectar secreted for 24 h. The number of ants on the plants was smaller under low light availability than under high and moderate light availability. Conclusions These results suggest that direct defence traits function regardless of light conditions, but light conditions affected the development of indirect defence traits. PMID:20472698

  5. A characteristic chondroitin sulfate trisaccharide unit with a sulfated fucose branch exhibits neurite outgrowth-promoting activity: Novel biological roles of fucosylated chondroitin sulfates isolated from the sea cucumber Apostichopus japonicus.

    PubMed

    Shida, Miharu; Mikami, Tadahisa; Tamura, Jun-Ichi; Kitagawa, Hiroshi

    2017-06-03

    Chondroitin sulfate (CS) is a class of sulfated glycosaminoglycan (GAG) chains that consist of repeating disaccharide unit composed of glucuronic acid (GlcA) and N-acetylgalactosamine (GalNAc). CS chains are found throughout the pericellular and extracellular spaces and contribute to the formation of functional microenvironments for numerous biological events. However, their structure-function relations remain to be fully characterized. Here, a fucosylated CS (FCS) was isolated from the body wall of the sea cucumber Apostichopus japonicus. Its promotional effects on neurite outgrowth were assessed by using isolated polysaccharides and the chemically synthesized FCS trisaccharide β-D-GalNAc(4,6-O-disulfate) (1-4)[α-l-fucose (2,4-O-disulfate) (1-3)]-β-D-GlcA. FCS polysaccharides contained the E-type disaccharide unit GlcA-GalNAc(4,6-O-disulfate) as a CS major backbone structure and carried distinct sulfated fucose branches. Despite their relatively lower abundance of E unit, FCS polysaccharides exhibited neurite outgrowth-promoting activity comparable to squid cartilage-derived CS-E polysaccharides, which are characterized by their predominant E units, suggesting potential roles of the fucose branch in neurite outgrowth. Indeed, the chemically synthesized FCS trisaccharide was as effective as CS-E tetrasaccharide in stimulating neurite elongation in vitro. In conclusion, FCS trisaccharide units with 2,4-O-disulfated fucose branches may provide new insights into understanding the structure-function relations of CS chains. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Fusions between green fluorescent protein and beta-glucuronidase as sensitive and vital bifunctional reporters in plants.

    PubMed

    Quaedvlieg, N E; Schlaman, H R; Admiraal, P C; Wijting, S E; Stougaard, J; Spaink, H P

    1998-07-01

    By fusing the genes encoding green fluorescent protein (GFP) and beta-glucuronidase (GUS) we have created a set of bifunctional reporter constructs which are optimized for use in transient and stable expression studies in plants. This approach makes it possible to combine the advantage of GUS, its high sensitivity in histochemical staining, with the advantages of GFP as a vital marker. The fusion proteins were functional in transient expression studies in tobacco using either DNA bombardment or potato virus X as a vector, and in stably transformed Arabidopsis thaliana and Lotus japonicus plants. The results show that high level of expression does not interfere with efficient stable transformation in A. thaliana and L. japonicus. Using confocal laser scanning microscopy we show that the fusion constructs are very suitable for promoter expression studies in all organs of living plants, including root nodules. The use of these reporter constructs in the model legume L. japonicus offers exciting new possibilities for the study of the root nodulation process.

  7. Fusions between green fluorescent protein and beta-glucuronidase as sensitive and vital bifunctional reporters in plants.

    PubMed

    Quaedvlieg, N E; Schlaman, H R; Admiraal, P C; Wijting, S E; Stougaard, J; Spaink, H P

    1998-11-01

    By fusing the genes encoding green fluorescent protein (GFP) and beta-glucuronidase (GUS) we have created a set of bifunctional reporter constructs which are optimized for use in transient and stable expression studies in plants. This approach makes it possible to combine the advantage of GUS, its high sensitivity in histochemical staining, with the advantages of GFP as a vital marker. The fusion proteins were functional in transient expression studies in tobacco using either DNA bombardment or potato virus X as a vector, and in stably transformed Arabidopsis thaliana and Lotus japonicus plants. The results show that high level of expression does not interfere with efficient stable transformation in A. thaliana and L. japonicus. Using confocal laser scanning microscopy we show that the fusion constructs are very suitable for promoter expression studies in all organs of living plants, including root nodules. The use of these reporter constructs in the model legume L. japonicus offers exciting new possibilities for the study of the root nodulation process.

  8. Predator size divergence depends on community context.

    PubMed

    Okuzaki, Yutaka; Sota, Teiji

    2018-05-09

    Body size is a multi-functional trait related to various fitness components, but the relative importance of different selection pressures is seldom resolved. In Carabus japonicus beetles, of which the larvae exclusively prey on earthworms, adult body size is related to the presence/absence of a larger congener and habitat temperature. In sympatry, C. japonicus consistently exhibits smaller body size which is effective for avoiding interspecific mating, but in allopatry, it shows size variation unrelated to temperature. Here, we show that this predator-size variation is attributed to prey-size variation, associated with high phylogenetic diversity in earthworm communities. In allopatry, the predator size was larger where larger prey occurred. Larger adult size may have been selected because larger females produce larger larvae, which can subdue larger prey. Thus, in the absence of a larger congener, variation in prey body size had a pronounced effect on geographic body size divergence in C. japonicus. © 2018 John Wiley & Sons Ltd/CNRS.

  9. The challenge of monitoring elusive large carnivores: An accurate and cost-effective tool to identify and sex pumas (Puma concolor) from footprints.

    PubMed

    Alibhai, Sky; Jewell, Zoe; Evans, Jonah

    2017-01-01

    Acquiring reliable data on large felid populations is crucial for effective conservation and management. However, large felids, typically solitary, elusive and nocturnal, are difficult to survey. Tagging and following individuals with VHF or GPS technology is the standard approach, but costs are high and these methodologies can compromise animal welfare. Such limitations can restrict the use of these techniques at population or landscape levels. In this paper we describe a robust technique to identify and sex individual pumas from footprints. We used a standardized image collection protocol to collect a reference database of 535 footprints from 35 captive pumas over 10 facilities; 19 females (300 footprints) and 16 males (235 footprints), ranging in age from 1-20 yrs. Images were processed in JMP data visualization software, generating one hundred and twenty three measurements from each footprint. Data were analyzed using a customized model based on a pairwise trail comparison using robust cross-validated discriminant analysis with a Ward's clustering method. Classification accuracy was consistently > 90% for individuals, and for the correct classification of footprints within trails, and > 99% for sex classification. The technique has the potential to greatly augment the methods available for studying puma and other elusive felids, and is amenable to both citizen-science and opportunistic/local community data collection efforts, particularly as the data collection protocol is inexpensive and intuitive.

  10. New deep-sea free-living marine nematodes from the Sea of Japan: the genera Siphonolaimus and Halichoanolaimus (Nematoda: Chromadorea) with keys to species identifications.

    PubMed

    Zograf, Julia; Trebukhova, Yulia; Pavlyuk, Olga

    2015-01-16

    In deep-sea sediments from the Sea of Japan, two new species, Halichoanolaimus brandtae sp. n. and Siphonolaimus japonicus sp. n., were found and described. Siphonolaimus japonicus sp. n. is characterized by having short anterior sensillae, body length of 3670-4500 μm, buccal cavity with axial spear, and length of the spicules. Halichoanolaimus brandtae sp.n is characterized by the number of amphideal rings, long spicules, five precloacal supplements and by having a long cylindrical part of the tail. Keys to species level are provided. 

  11. Distinct types of primary cutaneous large B-cell lymphoma identified by gene expression profiling.

    PubMed

    Hoefnagel, Juliette J; Dijkman, Remco; Basso, Katia; Jansen, Patty M; Hallermann, Christian; Willemze, Rein; Tensen, Cornelis P; Vermeer, Maarten H

    2005-05-01

    In the European Organization for Research and Treatment of Cancer (EORTC) classification 2 types of primary cutaneous large B-cell lymphoma (PCLBCL) are distinguished: primary cutaneous follicle center cell lymphomas (PCFCCL) and PCLBCL of the leg (PCLBCL-leg). Distinction between both groups is considered important because of differences in prognosis (5-year survival > 95% and 52%, respectively) and the first choice of treatment (radiotherapy or systemic chemotherapy, respectively), but is not generally accepted. To establish a molecular basis for this subdivision in the EORTC classification, we investigated the gene expression profiles of 21 PCLBCLs by oligonucleotide microarray analysis. Hierarchical clustering based on a B-cell signature (7450 genes) classified PCLBCL into 2 distinct subgroups consisting of, respectively, 8 PCFCCLs and 13 PCLBCLsleg. PCLBCLs-leg showed increased expression of genes associated with cell proliferation; the proto-oncogenes Pim-1, Pim-2, and c-Myc; and the transcription factors Mum1/IRF4 and Oct-2. In the group of PCFCCL high expression of SPINK2 was observed. Further analysis suggested that PCFCCLs and PCLBCLs-leg have expression profiles similar to that of germinal center B-cell-like and activated B-cell-like diffuse large B-cell lymphoma, respectively. The results of this study suggest that different pathogenetic mechanisms are involved in the development of PCFCCLs and PCLBCLs-leg and provide molecular support for the subdivision used in the EORTC classification.

  12. Using lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Osenton, P.C.; Price, R.W.

    1995-01-01

    Avian lice may link fledgling Brown-headed Cowbirds to the host species that raised them. Lice, if host-specific and transferred to nestling cowbirds, could serve to identify the principal host species raising cowbirds in a local area. This approach of trapping cowbird fledglings in a feeding flock, then collecting and identifying the lice they carry is economical. The alternative requires a team of people to locate large numbers of parasitized host nests. We trapped 250 cowbird fledglings during June-August 1994 on Patuxent Research Center, and from them we collected 426 lice identified as representing 6 genera and 12 species. We. also collected and identified 347 lice from 30 known host species that were mist-netted on our Center. The lice found on cowbird fledglings in this population can be linked to Wood Thrush, Red-eyed Vireo, Common Yellowthroat, Rufous-sided Towhee, Red-winged Blackbird, Common Grackle, Song Sparrow, Field Sparrow, and Tree sparrow, based on this study and also on published reports.

  13. Functional groupings and food web of an artificial reef used for sea cucumber aquaculture in northern China

    NASA Astrophysics Data System (ADS)

    Xu, Qinzeng; Zhang, Libin; Zhang, Tao; Zhang, Xuelei; Yang, Hongsheng

    2017-01-01

    Artificial reef is considered as a useful tool to remodel habitats in coastal and estuarine area. Some artificial reefs (ARs) were conducted in Shandong Peninsula for sea cucumber Apostichopus japonicus integrated multi-trophic aquaculture (IMTA). Little is known about the main feeding type and food resources of living organisms in this IMTA ecosystem. Neither is the information about other animals competing food with A. japonicus. Functional group (FG) and their food resources of mobile organisms and epifauna in ARs area were investigated. There were three types of food resources and five FGs within two trophic levels in studied area. Particle organic matter (POM), seaweed detritus and sediment were considered to be the main food resources. The first three FGs were primary consumers and were mainly epifauna, while the other two FGs were secondary consumers. FG 1 species were filter feeders, and group 2 was all deposit feeders and A. japonicus was in this group. FG 2 contained few species and this indicated that A. japonicus had few food competitors. FG 3 contained most epifauna species which were detritus feeders and this result implied that the artificial oyster shell reed can retain detritus effectively. The food sources of group 4 were complex. Species of group 5, mostly fish, occupied the top trophic level and fed primarily on species of FG 1 and FG 2. This kind of ARs can retain detritus effectively and provide suitable habitat to epifauna and surrounding natural fauna community.

  14. The Citizen Science Project ‘Mueckenatlas’ Helps Monitor the Distribution and Spread of Invasive Mosquito Species in Germany

    PubMed Central

    Walther, Doreen; Kampen, Helge

    2017-01-01

    Abstract The citizen science project ‘Mueckenatlas’ (mosquito atlas) was implemented in early 2012 to improve mosquito surveillance in Germany. Citizens are asked to support the spatiotemporal mapping of culicids by submitting mosquito specimens collected in their private surroundings. The Mueckenatlas has developed into an efficient tool for data collection with close to 30,000 mosquitoes submitted by the end of 2015. While the vast majority of submissions included native mosquito species, a small percentage represented invasive species. The discovery of Aedes albopictus (Skuse) (Diptera: Culicidae), Aedes japonicus japonicus (Theobald) (Diptera: Culicidae) and Aedes koreicus (Edwards) (Diptera: Culicidae) specimens via the Mueckenatlas project prompted targeted monitoring activities in the field which produced additional information on the distribution of these species in Germany. Among others, Mueckenatlas submissions led to the detection of three populations of Ae. j. japonicus in West, North and Southeast Germany in 2012, 2013, and 2015, respectively. As demonstrated by on-site monitoring, the origins of Ae. j. japonicus specimens submitted to the Mueckenatlas mirror the distribution areas of the four presently known German populations as found by active field sampling (the fourth population already reported prior to the launch of the Mueckenatlas). The data suggest that a citizen science project such as the Mueckenatlas may aid in detecting changes in the mosquito fauna and can therefore be used to guide the design of more targeted field surveillance activities. PMID:29029273

  15. The Citizen Science Project 'Mueckenatlas' Helps Monitor the Distribution and Spread of Invasive Mosquito Species in Germany.

    PubMed

    Walther, Doreen; Kampen, Helge

    2017-11-07

    The citizen science project 'Mueckenatlas' (mosquito atlas) was implemented in early 2012 to improve mosquito surveillance in Germany. Citizens are asked to support the spatiotemporal mapping of culicids by submitting mosquito specimens collected in their private surroundings. The Mueckenatlas has developed into an efficient tool for data collection with close to 30,000 mosquitoes submitted by the end of 2015. While the vast majority of submissions included native mosquito species, a small percentage represented invasive species. The discovery of Aedes albopictus (Skuse) (Diptera: Culicidae), Aedes japonicus japonicus (Theobald) (Diptera: Culicidae) and Aedes koreicus (Edwards) (Diptera: Culicidae) specimens via the Mueckenatlas project prompted targeted monitoring activities in the field which produced additional information on the distribution of these species in Germany. Among others, Mueckenatlas submissions led to the detection of three populations of Ae. j. japonicus in West, North and Southeast Germany in 2012, 2013, and 2015, respectively. As demonstrated by on-site monitoring, the origins of Ae. j. japonicus specimens submitted to the Mueckenatlas mirror the distribution areas of the four presently known German populations as found by active field sampling (the fourth population already reported prior to the launch of the Mueckenatlas). The data suggest that a citizen science project such as the Mueckenatlas may aid in detecting changes in the mosquito fauna and can therefore be used to guide the design of more targeted field surveillance activities. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

  16. Two evolved supernova remnants with newly identified Fe-rich cores in the Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Kavanagh, P. J.; Sasaki, M.; Bozzetto, L. M.; Points, S. D.; Crawford, E. J.; Dickel, J.; Filipović, M. D.; Haberl, F.; Maggi, P.; Whelan, E. T.

    2016-02-01

    Aims: We present a multi-wavelength analysis of the evolved supernova remnants MCSNR J0506-7025 and MCSNR J0527-7104 in the Large Magellanic Cloud. Methods: We used observational data from XMM-Newton, the Australian Telescope Compact Array, and the Magellanic Cloud Emission Line Survey to study their broad-band emission and used Spitzer and H I data to gain a picture of the environment into which the remnants are expanding. We performed a multi-wavelength morphological study and detailed radio and X-ray spectral analyses to determine their physical characteristics. Results: Both remnants were found to have bright X-ray cores, dominated by Fe L-shell emission, which is consistent with reverse shock-heated ejecta with determined Fe masses in agreement with Type Ia explosion yields. A soft X-ray shell, which is consistent with swept-up interstellar medium, was observed in MCSNR J0506-7025, suggestive of a remnant in the Sedov phase. Using the spectral fit results and the Sedov self-similar solution, we estimated the age of MCSNR J0506-7025 to be ~16-28 kyr, with an initial explosion energy of (0.07-0.84) × 1051 erg. A soft shell was absent in MCSNR J0527-7104, with only ejecta emission visible in an extremely elongated morphology that extends beyond the optical shell. We suggest that the blast wave has broken out into a low density cavity, allowing the shock heated ejecta to escape. We find that the radio spectral index of MCSNR J0506-7025 is consistent with the standard -0.5 for supernova remnants. Radio polarisation at 6 cm indicates a higher degree of polarisation along the western front and at the eastern knot with a mean fractional polarisation across the remnant of P ≅ (20 ± 6)%. Conclusions: The detection of Fe-rich ejecta in the remnants suggests that both resulted from Type Ia explosions. The newly identified Fe-rich cores in MCSNR J0506-7025 and MCSNR J0527-7104 make them members of the expanding class of evolved Fe-rich remnants in the Magellanic Clouds

  17. Data Identifiers, Versioning, and Micro-citation

    NASA Astrophysics Data System (ADS)

    Parsons, M. A.; Duerr, R. E.

    2012-12-01

    Data citation, especially using Digital Object Identifiers (DOIs), is an increasingly accepted scientific practice. For example, the AGU Council asserts that data "publications" should "be credited and cited like the products of any other scientific activity," and Thomson Reuters has recently announced a data citation index built from DOIs assigned to data sets. Correspondingly, formal guidelines for how to cite a data set (using DOIs or similar identifiers/locators) have recently emerged, notably those from the international DataCite consortium, the UK Digital Curation Centre, and the US Federation of Earth Science Information Partners. These different data citation guidelines are largely congruent. They agree on the basic practice and elements of data citation, especially for relatively static, whole data collections. There is less agreement on some of the more subtle nuances of data citation. They define different methods for handling different data set versions, especially for the very dynamic, growing data sets that are common in Earth Sciences. They also differ in how people should cite specific, arbitrarily large elements, "passages," or subsets of a larger data collection, i.e., the precise data records actually used in a study. This detailed "micro-citation", and careful reference to exact versions of data are essential to ensure scientific reproducibility. Identifiers such as DOIs are necessary but not sufficient for the precise, detailed, references necessary. Careful practice must be coupled with the use of curated identifiers. In this paper we review the pros and cons of different approaches to versioning and micro-citation. We suggest a workable solution for most existing Earth science data and suggest a more rigorous path forward for the future.

  18. Neurobehavioral Mutants Identified in an ENU Mutagenesis Project

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cook, Melloni N.; Dunning, Jonathan P; Wiley, Ronald G

    2007-01-01

    We report on a behavioral screening test battery that successfully identified several neurobehavioral mutants among a large-scale ENU-mutagenized mouse population. Large numbers of ENU mutagenized mice were screened for abnormalities in central nervous system function based on abnormal performance in a series of behavior tasks. We developed and employed a high-throughput screen of behavioral tasks to detect behavioral outliers. Twelve mutant pedigrees, representing a broad range of behavioral phenotypes, have been identified. Specifically, we have identified two open field mutants (one displaying hyper-locomotion, the other hypo-locomotion), four tail suspension mutants (all displaying increased immobility), one nociception mutant (displaying abnormal responsivenessmore » to thermal pain), two prepulse inhibition mutants (displaying poor inhibition of the startle response), one anxiety-related mutant (displaying decreased anxiety in the light/dark test), and one learning and memory mutant (displaying reduced response to the conditioned stimulus) These findings highlight the utility of a set of behavioral tasks used in a high throughput screen to identify neurobehavioral mutants. Further analysis (i.e., behavioral and genetic mapping studies) of mutants is in progress with the ultimate goal of identification of novel genes and mouse models relevant to human disorders as well as the identification of novel therapeutic targets.« less

  19. The effect of temperature and body weight on the routine metabolic rate and postprandial metabolic response in mulloway, Argyrosomus japonicus.

    PubMed

    Pirozzi, Igor; Booth, Mark A

    2009-09-01

    Specific dynamic action (SDA) is the energy expended on the physiological processes associated with meal digestion and is strongly influenced by the characteristics of the meal and the body weight (BW) and temperature of the organism. This study assessed the effects of temperature and body weight on the routine metabolic rate (RMR) and postprandial metabolic response in mulloway, Argyrosomus japonicus. RMR and SDA were established at 3 temperatures (14, 20 and 26 degrees C). 5 size classes of mulloway ranging from 60 g to 1.14 kg were used to establish RMR with 3 of the 5 size classes (60, 120 and 240 g) used to establish SDA. The effect of body size on the mass-specific RMR (mg O(2) kg(-1) h(-1)) varied significantly depending on the temperature; there was a greater relative increase in the mass-specific RMR for smaller mulloway with increasing temperature. No statistical differences were found between the mass exponent (b) values at each temperature when tested against H(0): b=0.8. The gross RMR of mulloway (mg O(2) fish(-1) h(-1)) can be described as function of temperature (T; 14-26 degrees C) as: (0.0195T-0.0454)BW(g)(0.8) and the mass-specific RMR (mg O(2) kg(-1) h(-1)) can be described as: (21.042T-74.867)BW(g)(-0.2). Both SDA duration and time to peak SDA were influenced by temperature and body weight; SDA duration occurred within 41-89 h and peak time occurred within 17-38 h of feeding. The effect of body size on peak metabolic rate varied significantly depending on temperature, generally increasing with temperature and decreasing with increasing body size. Peak gross oxygen consumption (MO(2): mg O(2) fish(-1) h(-1)) scaled allometrically with BW. Temperature, but not body size, significantly affected SDA scope, although the difference was numerically small. There was a trend for MO(2) above RMR over the SDA period to increase with temperature; however, this was not statistically significant. The average proportion of energy expended over the SDA period

  20. Characterization of the Heme Pocket Structure and Ligand Binding Kinetics of Non-symbiotic Hemoglobins from the Model Legume Lotus japonicus.

    PubMed

    Calvo-Begueria, Laura; Cuypers, Bert; Van Doorslaer, Sabine; Abbruzzetti, Stefania; Bruno, Stefano; Berghmans, Herald; Dewilde, Sylvia; Ramos, Javier; Viappiani, Cristiano; Becana, Manuel

    2017-01-01

    Plant hemoglobins (Hbs) are found in nodules of legumes and actinorhizal plants but also in non-symbiotic organs of monocots and dicots. Non-symbiotic Hbs (nsHbs) have been classified into two phylogenetic groups. Class 1 nsHbs show an extremely high O 2 affinity and are induced by hypoxia and nitric oxide (NO), whereas class 2 nsHbs have moderate O 2 affinity and are induced by cold and cytokinins. The functions of nsHbs are still unclear, but some of them rely on the capacity of hemes to bind diatomic ligands and catalyze the NO dioxygenase (NOD) reaction (oxyferrous Hb + NO → ferric Hb + nitrate). Moreover, NO may nitrosylate Cys residues of proteins. It is therefore important to determine the ligand binding properties of the hemes and the role of Cys residues. Here, we have addressed these issues with the two class 1 nsHbs (LjGlb1-1 and LjGlb1-2) and the single class 2 nsHb (LjGlb2) of Lotus japonicus , which is a model legume used to facilitate the transfer of genetic and biochemical information into crops. We have employed carbon monoxide (CO) as a model ligand and resonance Raman, laser flash photolysis, and stopped-flow spectroscopies to unveil major differences in the heme environments and ligand binding kinetics of the three proteins, which suggest non-redundant functions. In the deoxyferrous state, LjGlb1-1 is partially hexacoordinate, whereas LjGlb1-2 shows complete hexacoordination (behaving like class 2 nsHbs) and LjGlb2 is mostly pentacoordinate (unlike other class 2 nsHbs). LjGlb1-1 binds CO very strongly by stabilizing it through hydrogen bonding, but LjGlb1-2 and LjGlb2 show lower CO stabilization. The changes in CO stabilization would explain the different affinities of the three proteins for gaseous ligands. These affinities are determined by the dissociation rates and follow the order LjGlb1-1 > LjGlb1-2 > LjGlb2. Mutations LjGlb1-1 C78S and LjGlb1-2 C79S caused important alterations in protein dynamics and stability, indicating a structural