Science.gov

Sample records for japonicus identified large

  1. Genetic screening identifies cyanogenesis-deficient mutants of Lotus japonicus and reveals enzymatic specificity in hydroxynitrile glucoside metabolism.

    PubMed

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

    2010-05-01

    Cyanogenesis, the release of hydrogen cyanide from damaged plant tissues, involves the enzymatic degradation of amino acid-derived cyanogenic glucosides (alpha-hydroxynitrile glucosides) by specific beta-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 beta-glucosidase BGD2. Despite the identification of nine independent cyd2 alleles, no mutants involving the gene encoding a closely related beta-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.

  2. Expression Analysis of Immune Related Genes Identified from the Coelomocytes of Sea Cucumber (Apostichopus japonicus) in Response to LPS Challenge

    PubMed Central

    Dong, Ying; Sun, Hongjuan; Zhou, Zunchun; Yang, Aifu; Chen, Zhong; Guan, Xiaoyan; Gao, Shan; Wang, Bai; Jiang, Bei; Jiang, Jingwei

    2014-01-01

    The sea cucumber (Apostichopus japonicus) occupies a basal position during the evolution of deuterostomes and is also an important aquaculture species. In order to identify more immune effectors, transcriptome sequencing of A. japonicus coelomocytes in response to lipopolysaccharide (LPS) challenge was performed using the Illumina HiSeq™ 2000 platform. One hundred and seven differentially expressed genes were selected and divided into four functional categories including pathogen recognition (25 genes), reorganization of cytoskeleton (27 genes), inflammation (41 genes) and apoptosis (14 genes). They were analyzed to elucidate the mechanisms of host-pathogen interactions and downstream signaling transduction. Quantitative real-time polymerase chain reactions (qRT-PCRs) of 10 representative genes validated the accuracy and reliability of RNA sequencing results with the correlation coefficients from 0.88 to 0.98 and p-value <0.05. Expression analysis of immune-related genes after LPS challenge will be useful in understanding the immune response mechanisms of A. japonicus against pathogen invasion and developing strategies for resistant markers selection. PMID:25421239

  3. 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.

  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. 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

  6. Establishment of Aedes japonicus japonicus and Its Colonization of Container Habitats in Michigan

    PubMed Central

    KAUFMAN, MICHAEL G.; STANUSZEK, WILLIAM W.; BROUHARD, ELIZABETH A.; KNEPPER, RANDALL G.; WALKER, EDWARD D.

    2014-01-01

    Oviposition dynamics and colonization of container habitats by the invasive species, Aedes (Finlaya) japonicus japonicus (Theobald) were examined through the use of ovistrips placed in buckets, and larval surveys of tree holes and tires at sites in central Michigan. In general, oviposition and colonization increased during the study periods, with several sites showing large increases from <10% Ae. j. japonicus initially to over 60% in the following years. Seasonally, higher proportions of Ae. j. japonicus were found in spring and fall collection periods. Ae. j. japonicus larvae co-occurred in the artificial containers with Ae. triseriatus, Ae. hendersoni, several Culex spp., and Anopheles spp. Recent surveys of tire and tree hole habitats at our study areas in mid-Michigan revealed that Ae. j. japonicus had colonized most of these habitats, but maintained relatively low populations in tree holes occupied by Ae. triseriatus. Trends seen in tires from 2008 to 2011, and from gravid trap and New Jersey light traps in 2005–2011, suggest that Ae. j. japonicus populations are stabilizing as they integrate into native Michigan mosquito communities. PMID:23270158

  7. Layered farming for Marsupenaeus japonicus Bate

    NASA Astrophysics Data System (ADS)

    Li, Yuquan; Jiang, Lingxu; Wang, Renjie

    2014-05-01

    Marsupenaeus japonicus Bate is one of the most valuable cultured shrimp species in China and outdoor earthen pond farming is the most common method of culturing this organism. The need to increase soil usage efficiency in aquaculture has been recognized and a great deal of research effort has been directed toward development of super-intensive farming systems. However, current research and development in this field is largely devoted to Litopenaeus vannamei Boone, while to M. japonicus Bate it has been neglected. In this study, a layered farming system was designed and a 66-day study was conducted in M. japonicus Bate culture. The system comprised bracket and sand layers that divided a shrimp tank filled to a depth of 1.2 m into four water layers. Conventional tank culture (unlayered) was used as a control. The results show that survival rate, feed conversion efficiency and production of M. japonicus Bate in the layered farming system were 68%, 18%, and 0.59 kg/m2, respectively, all of which are significantly higher than in the unlayered farming system ( P <0.01). These findings confirmed the possibility of using a layered system to culture M. japonicus Bate.

  8. High degree of mitochondrial haplotype diversity in the Japanease common toad Bufo japonicus in urban Tokyo.

    PubMed

    Hase, Kazuko; Shimada, Masakazu; Nikoh, Naruo

    2012-10-01

    The Japanese common toad Bufo japonicus is widely distributed across mainland Japan and is classified into two subspecies, B. japonicus japonicus and B. japonicus formosus, in the western and eastern regions, respectively. To investigate the genetic diversity of B. japonicus at the breeding pond (local population) level, we sequenced 831 base pairs of mitochondrial DNA (mtDNA) cytochrome b (Cyt b) from 75 individuals collected from nine ponds in urban Tokyo and the surrounding area. Phylogenetic and population genetic analyses revealed high mtDNA haplotype diversity (Hd, 0.716 (mean) ± 0.230 (SD)) within local populations (breeding ponds). Most local populations had multiple haplotypes of the mitochondrial Cyt b gene, and seven of the 18 haplotypes were identified in two or more local populations. These results indicate that mitochondrial gene flow had occurred across different breeding sites. We also identified five haplotypes that belonged to the western clade and correspond to B. japonicus japonicus. Our results provide genetic evidence that B. japonicus japonicus was introduced artificially from Western Japan to Tokyo, where it occupied the natural habitat of B. japonicus formosus. The urban Tokyo area was found to represent an admixed population consisting of both native and non-native B. japonicus subspecies.

  9. 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.

  10. Identifying Mismatches in Alignments of Large Anatomical Ontologies

    PubMed Central

    Zhang, Songmao; Bodenreider, Olivier

    2007-01-01

    Objective: The objective of this study is to propose a model of matching errors for identifying mismatches in alignments of large anatomical ontologies. Methods: Three approaches to identifying mismatches are utilized: 1) lexical, based on the presence of modifiers in the names of the concepts aligned; 2) structural, identifying conflicting relations resulting from the alignment; and 3) semantic, based on disjoint top-level categories across ontologies. Results: 83% of the potential mismatches identified by the HMatch system are identified by at least one of the approaches. Conclusions: Although not a substitute for a careful validation of the matches, these approaches significantly reduce the need for manual validation by effectively characterizing most mismatches. PMID:18693957

  11. Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers.

    PubMed

    Zhou, Z C; Dong, Y; Sun, H J; Yang, A F; Chen, Z; Gao, S; Jiang, J W; Guan, X Y; Jiang, B; Wang, B

    2014-01-01

    Sea cucumber (Apostichopus japonicus) is an ecologically and economically important species in East and South-East Asia. This project aimed to identify large numbers of gene-associated markers and differentially expressed genes (DEGs) after lipopolysaccharides (LPS) challenge in A. japonicus using high-throughput transcriptome sequencing. A total of 162 million high-quality reads of 174 million raw reads were obtained by deep sequencing using Illumina HiSeq™ 2000 platform. Assembly of these reads generated 94 704 unigenes, with read length ranging from 200 to 16 153 bp (average length of 810 bp). A total of 36 005 were identified as coding sequences (CDSs), 32 479 of which were successfully annotated. Based on the assembly transcriptome, we identified 142 511 high-quality single nucleotide polymorphisms (SNPs). Among them, 33 775, 63 120 and 45 616 were located in sequences without predicted CDS (non-CDSs), CDSs and untranslated regions (UTRs), respectively. These putative SNPs included 82 664 transitions and 59 847 transversions. Totally, 89 375 (59.1%) were distributed in 15 473 known genes. A total of 6417 microsatellites were detected in 5970 unigenes, 3216 of which were annotated and 2481 were successfully subjected for primer design. The numbers of simple sequence repeats (SSRs) identified in non-CDSs, CDSs and UTRs were 2367, 2316 and 1734. These potential SNPs and SSRs are expected to provide abundant resources for genetic, evolutionary and ecological studies in sea cucumber. Transcriptome comparison revealed 1330, 1347 and 1291 DEGs in the coelomocytes of A. japonicus at 4 h, 24 h and 72 h after LPS challenge, respectively. Approximately 58.4% (1802) of total DEGs have been successfully annotated.

  12. 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

  13. Aedes japonicus japonicus and associated woodland species attracted to Centers for Disease Control and Prevention miniature light traps baited with carbon dioxide and the Traptech mosquito lure.

    PubMed

    Anderson, John F; McKnight, Susan; Ferrandino, Francis J

    2012-09-01

    Twelve reported mosquito attractants, alone or in combination, and 3 different types of traps were evaluated under field conditions for their attractiveness to host-seeking and oviposition-seeking female Aedes japonicus japonicus and associated woodland species in Windsor, CT, in 2010 and 2011. This study highlights the effectiveness of combining CO2 with the TrapTech Mosquito Lure in a Centers for Disease Control and Prevention (CDC) miniature light trap for collection of Ae. j. japonicus and associated woodland mammalian-feeding mosquitoes. The TrapTech Mosquito Lure is a proprietary blend of Bedoukian Research, Inc. It contained 250 mg of R-1-octen-3-ol and 1900 mg of ammonium bicarbonate, which were slowly released from a plastic disperser. On average, 567 Ae. j. japonicus individuals were collected per trap per night in the CDC miniature light traps baited with CO2 plus TrapTech Mosquito Lure. The numbers collected in this trap were 28 times and 100 times greater than the numbers of Ae. j. japonicus collected in the CDC miniature light trap baited only with CO2 and the gravid trap baited with hay infusion, 2 commonly used traps to assess abundance of Ae. j. japonicus. The average catches of other mammalian-biting species, Ae. cinereus, Ae. triseriatus, Ae. trivittatus, Ae. vexans, Anopheles punctipennis, An. quadrimaculatus, Coquillettidia perturbans, and Culex salinarius, were all significantly greater in the CDC miniature light trap baited with CO2 plus TrapTech Mosquito Lure than in traps with CO2 alone, but their average numbers were not as large as were those of Ae. j. japonicus. These data demonstrate that the TrapTech Mosquito Lure used in combination with CO2 in a CDC miniature light trap has potential to be a versatile and simple surveillance method for Ae. j. japonicus and other species.

  14. Identifying the crystal graveyards remaining after large silicic eruptions

    NASA Astrophysics Data System (ADS)

    Gelman, Sarah E.; Deering, Chad D.; Bachmann, Olivier; Huber, Christian; Gutiérrez, Francisco J.

    2014-10-01

    The formation of crystal-poor high-silica rhyolite via extraction of interstitial melt from an upper crustal mush predicts the complementary formation of large amounts of (typically unerupted) silicic cumulates. However, identification of these cumulates remains controversial. One hindrance to our ability to identify them is a lack of clear predictions for complementary chemical signatures between extracted melts and their residues. To address this discrepancy, we present a generalized geochemical model tracking the evolution of trace elements in a magma reservoir concurrently experiencing crystallization and extraction of interstitial melt. Our method uses a numerical solution rather than analytical, thereby allowing for various dependencies between crystallinity, partition coefficients for variably compatible and/or incompatible elements, and melt extraction efficiency. Results reveal unambiguous fractionation signatures for the extracted melts, while those signatures are muted for their cumulate counterparts. Our model is first applied to a well-constrained example (Searchlight pluton, USA), and provides a good fit to geochemical data. We then extrapolate our results to understanding the relationship between volcanic and plutonic silicic suites on a global scale. Utilizing the NAVDAT database to identify crystal accumulation or depletion signatures for each suite, we suggest that many large granitoids are indeed silicic cumulates, although their crystal accumulation signature is expected to be subtle.

  15. Genome-wide identification and transcript profile of the whole cathepsin superfamily in the intertidal copepod Tigriopus japonicus.

    PubMed

    Jeong, Chang-Bum; Kim, Bo-Mi; Choi, Hyeon-Jeong; Baek, Inseon; Souissi, Sami; Park, Heum Gi; Lee, Jae-Seong; Rhee, Jae-Sung

    2015-11-01

    Modulation of expression of cathepsins in innate immune response has previously been reported in mollusks and large crustaceans including crabs, lobsters, and shrimps in response to immune challenges. However, similar responses in copepods and the related cathepsin members remain under-investigated. To understand molecular and innate immune responses in the intertidal copepod Tigriopus japonicus, we identified the full spectra of cathepsin members (2 aspartyl proteases, 18 cysteine proteases, and 4 serine proteases) and also analyzed transcriptional expression of cathepsin (Tj-cathepsin) genes in developmental stages, lipopolysaccharide (LPS)- and two Vibrio species-exposed T. japonicus. The transcriptional levels of most Tj-cathepsin genes were highly increased during the molting transition from the nauplius to the copepodid stages. LPS treatment induced innate immune response via significant transcriptional increase of serine cathepsin (e.g., cathepsin As) members with induction of several cysteine cathepsin genes. However, Tj-aspartyl cathepsin E-like and a novel cysteine cathepsin were slightly reduced in response to LPS exposure. Interestingly, Vibrio species showed very low transcriptional sensitivity in the expression of entire cathepsins, while LPS induced several cathepsin gene-involved primitive immune responses in T. japonicus. In this paper, we discuss how whole cathepsin expression profiling can be linked to host defense mechanism to better understand and uncover the underlying mechanism of copepods' innate immunity.

  16. Large screen approaches to identify novel malaria vaccine candidates

    PubMed Central

    Davies, D. Huw; Duffy, Patrick; Bodmer, Jean-Luc; Felgner, Philip L.; Doolan, Denise L.

    2016-01-01

    Until recently, malaria vaccine development efforts have focused almost exclusively on a handful of well characterized Plasmodium falciparum antigens. Despite dedicated work by many researchers on different continents spanning more than half a century, a successful malaria vaccine remains elusive. Sequencing of the P. falciparum genome has revealed more than five thousand genes, providing the foundation for systematic approaches to discover candidate vaccine antigens. We are taking advantage of this wealth of information to discover new antigens that may be more effective vaccine targets. Herein, we describe different approaches to large-scale screening of the P. falciparum genome to identify targets of either antibody responses or T cell responses using human specimens collected in Controlled Human Malaria Infections (CHMI) or under conditions of natural exposure in the field. These genome, proteome and transcriptome based approaches offer enormous potential for the development of an efficacious malaria vaccine. PMID:26428458

  17. Chemically peculiar stars identified in large photometric surveys

    NASA Astrophysics Data System (ADS)

    Paunzen, Ernst; Netopil, Martin; Bernhard, Klaus; Hümmerich, Stefan

    2016-01-01

    The chemically peculiar (CP) stars of the upper main sequence are mainly characterized by strong overabundances of heavy elements. Two subgroups (CP2 and CP4) have strong local magnetic fields which make them interesting targets for astrophysical studies. This star group, in general, is often used for the analysis of stellar formation and evolution in the context of diffusion as well as meridional circulation. The overabundant elements in CP2/4 star atmospheres are concentrated into large spot regions that persist for decades to centuries. Periodic variations of the brightness, spectrum, and magnetic field are observed. The stars are slow rotators and it is believed that the slow rotation is owed to the strong magnetic field. Recent and future surveys that aim to obtain photometric time series are ideally suited to provide a detailed view of the stars' rotational behaviour. We present our efforts to analyze the rotational periods of CP stars and to identify new candidates in the Kepler, SuperWASP, and ASAS-3 surveys, but also in the photometric data that were extracted as valuable by-product of the STEREO satellite mission.

  18. Standardized Laboratory Feeding of Larval Aedes japonicus japonicus (Diptera: Culicidae).

    PubMed

    Bock, Friederike; Kuch, Ulrich; Pfenninger, Markus; Müller, Ruth

    2015-01-01

    The Asian bush mosquito (Aedes japonicus japonicus, Theobald 1901) is an invasive culicid species which originates in Asia but is nowadays present in northern America and Europe. It is a competent vector for several human disease pathogens. In addition to the public health threat, this invasive species may also be an ecological threat for native container-breeding mosquitoes which share a similar larval habitat. Therefore, it is of importance to gain knowledge on ecological and eco-toxicological features of the Asian bush mosquito. However, optimal laboratory feeding conditions have not yet been established. Standardized feeding methods will be needed in assessing the impact of insecticides or competitional strength of this species. To fill this gap, we performed experiments on food quality and quantity for Ae. j. japonicus larvae. We found out that the commercial fish food TetraMin (Tetra, Melle, Germany) in a dose of 10 mg per larva is the most suitable food tested. We also suggest a protocol with a feeding sequence of seven portions for all larval stages of this species.

  19. 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.

  20. Gliogenesis in the mushroom body of the carpenter ant, Camponotus japonicus.

    PubMed

    Nasu, Natsume; Hara, Kenji

    2012-12-01

    Mushroom bodies (MBs) are insect brain centers involved in multimodal sensory integration and memory formation. Advanced Hymenoptera, such as ants and bees, have particularly large and elaborately organized MBs, which are repeatedly implicated in complex behaviors. In this study, to address the developmental aspects of their MBs, gliogenesis of mushroom body neuroblasts (MB Nbs) was examined in the carpenter ant Camponotus japonicus. Reversed Polarity (REPO) is a paired-like homeodomain protein located exclusively in the nucleus of differentiating glial cells in the fruit fly Drosophila melanogaster. First, the molecular aspects of C. japonicus REPO (CjREPO) were identified. Then, the antibody (CjREPO-antibody) was raised against a peptide of CjREPO. Immunohistochemistry revealed that the strong labeling was located in the nucleus of glial cells in the developing brains, whereas no immunoreactivity was detectable in progeny derived from MB Nbs. These findings suggest that MB Nb in the ant is a neuronal precursor that does not produce glial cells.

  1. Expert systems identify fossils and manage large paleontological databases

    SciTech Connect

    Beightol, D.S. ); Conrad, M.A.

    1988-02-01

    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.

  2. Lotus japonicus ARPC1 is required for rhizobial infection.

    PubMed

    Hossain, Md Shakhawat; Liao, Jinqiu; James, Euan K; Sato, Shusei; Tabata, Satoshi; Jurkiewicz, Anna; Madsen, Lene H; Stougaard, Jens; Ross, Loretta; Szczyglowski, Krzysztof

    2012-10-01

    Remodeling of the plant cell cytoskeleton precedes symbiotic entry of nitrogen-fixing bacteria within the host plant roots. Here we identify a Lotus japonicus gene encoding a predicted ACTIN-RELATED PROTEIN COMPONENT1 (ARPC1) as essential for rhizobial infection but not for arbuscular mycorrhiza symbiosis. In other organisms ARPC1 constitutes a subunit of the ARP2/3 complex, the major nucleator of Y-branched actin filaments. The L. japonicus arpc1 mutant showed a distorted trichome phenotype and was defective in epidermal infection thread formation, producing mostly empty nodules. A few partially colonized nodules that did form in arpc1 contained abnormal infections. Together with previously described L. japonicus Nck-associated protein1 and 121F-specific p53 inducible RNA mutants, which are also impaired in the accommodation of rhizobia, our data indicate that ARPC1 and, by inference a suppressor of cAMP receptor/WASP-family verpolin homologous protein-ARP2/3 pathway, must have been coopted during evolution of nitrogen-fixing symbiosis to specifically mediate bacterial entry.

  3. Identifying the Crystal Graveyards Remaining After Large Silicic Eruptions

    NASA Astrophysics Data System (ADS)

    Gelman, S. E.; Deering, C. D.; Bachmann, O.; Huber, C.; Gutiérrez, F. J.

    2014-12-01

    The accumulation of voluminous crystal-poor rhyolites from an upper crustal mush environment inherently necessitates the complementary formation of unerupted silicic cumulates. However, identification of such frozen cumulates remains controversial. This has motivated us to develop of a new geochemical model aimed at better constraining the behavior of trace elements in a magma reservoir concurrently tracking crystallization and imperfect segregation of melt. We use a numerical method to solve our model equations rather than seek analytical solutions, thereby relieving overly simplistic assumptions for the dependencies between partition coefficient or melt segregation rate as functions of crystallinity. Our model allows partition coefficient to vary depending on the crystallinizing mineralogy at any particular stage in magma cooling, as well as the ability to test different rates and efficiencies of crystal-melt segregation. We apply our model first to the Searchlight Pluton as a well-constrained case study, which allows us to quantitatively test existing interpretations of that pluton. Building on this, we broaden our model to better understand the relationship between volcanic and plutonic rocks utilizing the NAVDAT database. Our results produce unambiguous fractionation signatures for segregated melts, while those signatures are muted for their cumulate counterparts. These models suggest that some large granitiods may represent accumulations of crystals, having lost melt in some cases to volcanic eruptions or to higher level evolved plutonic units, although the trace element signature of this process is expected to be subtle.

  4. 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.

  5. Detection of VM55599 and preparaherquamide from Aspergillus japonicus and Penicillium fellutanum: biosynthetic implications.

    PubMed

    Ding, Yousong; Gruschow, Sabine; Greshock, Thomas J; Finefield, Jennifer M; Sherman, David H; Williams, Robert M

    2008-09-01

    The secondary metabolites VM55599 (4) and preparaherquamide (5) have been identified by LC-MS(n) analysis as natural metabolites in cultures of Penicillium fellutanum, whereas preparaherquamide has been identified only in cultures of Aspergillus japonicus. In accord with a previous proposal, the identification of both metabolites, which have a diastereomeric relationship, provides indirect support for a unified biosynthetic scheme.

  6. In-Frame Deletions Allow Functional Characterization of Complex Cellulose Degradation Phenotypes in Cellvibrio japonicus.

    PubMed

    Nelson, Cassandra E; Gardner, Jeffrey G

    2015-09-01

    The depolymerization of the recalcitrant polysaccharides found in lignocellulose has become an area of intense interest due to the role of this process in global carbon cycling, human gut microbiome nutritional contributions, and bioenergy production. However, underdeveloped genetic tools have hampered study of bacterial lignocellulose degradation, especially outside model organisms. In this report, we describe an in-frame deletion strategy for the Gram-negative lignocellulose-degrading bacterium Cellvibrio japonicus. This method leverages optimized growth conditions for conjugation and sacB counterselection for the generation of markerless in-frame deletions. This method produces mutants in as few as 8 days and allows for the ability to make multiple gene deletions per strain. It is also possible to remove large sections of the genome, as shown in this report with the deletion of the nine-gene (9.4-kb) gsp operon in C. japonicus. We applied this system to study the complex phenotypes of cellulose degradation in C. japonicus. Our data indicated that a Δcel5B Δcel6A double mutant is crippled for cellulose utilization, more so than by either single mutation alone. Additionally, we deleted individual genes in the two-gene cbp2ED operon and showed that both genes contribute to cellulose degradation in C. japonicus. Overall, these described techniques substantially enhance the utility of C. japonicus as a model system to study lignocellulose degradation.

  7. 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.

  8. Does Autocthonous Primary Production Influence Oviposition by Aedes japonicus japonicus (Diptera: Culicidae) in Container Habitats?

    PubMed Central

    LORENZ, AMANDA R.; WALKER, EDWARD D.; KAUFMAN, MICHAEL G.

    2014-01-01

    Aedes (Finlaya) japonicus japonicus (Theobald) (Diptera: Culicidae) is recently invasive in North America and has expanded its range rapidly since 1998. Throughout its native and expanded range, Ae. j. japonicus larvae are commonly observed in many types of natural and artificial water-filled containers that vary in organic matter content and exposure to sunlight. Larvae are most often found in containers with decaying leaf material or algae, and we postulated that the added autocthonous primary production from algae could be both an important food source for larvae and an influential oviposition attractant to adult Ae. j. japonicus. We tested this hypothesis by placing plastic containers with varied levels of shading to manipulate algal density in the field, and then monitored oviposition by natural populations of Ae. j. japonicus. Over 99% of larvae hatching from eggs laid on the walls of our containers were Ae. j. japonicus, indicating that this species is a dominant colonizer of artificial containers in the study areas. Although full shading treatments effectively reduced algal biomass (significant reduction in chlorophyll a levels), at only one of three sites did this appear to affect Ae. j. japonicus oviposition. We conclude that algae in larval habitats are not a major factor in oviposition choices of adult Ae. j. japonicus females except when in situ primary production is high enough to substantially alter overall organic matter content cues. PMID:23427654

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  10. 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.

  11. Transcriptome Response Mediated by Cold Stress in Lotus japonicus

    PubMed Central

    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. PMID:27066029

  12. Petal Development in Lotus japonicus.

    PubMed

    Weng, Lin; Tian, Zhaoxia; Feng, Xianzhong; Li, Xin; Xu, Shilei; Hu, Xiaohe; Luo, Da; Yang, Jun

    2011-10-01

    Previous studies have demonstrated that petal shape and size in legume flowers are determined by two separate mechanisms, dorsoventral (DV) and organ internal (IN) asymmetric mechanisms, respectively. However, little is known about the molecular mechanisms controlling petal development in legumes. To address this question, we investigated petal development along the floral DV axis in Lotus japonicus with respect to cell and developmental biology by comparing wild-type legumes to mutants. Based on morphological markers, the entire course of petal development, from initiation to maturity, was grouped to define 3 phases or 13 stages. In terms of epidermal micromorphology from adaxial surface, mature petals were divided into several distinct domains, and characteristic epidermal cells of each petal differentiated at stage 9, while epidermal cells of all domains were observed until stage 12. TCP and MIXTA-like genes were found to be differentially expressed in various domains of petals at stages 9 and 12. Our results suggest that DV and IN mechanisms interplay at different stages of petal development, and their interaction at the cellular and molecular level guides the elaboration of domains within petals to achieve their ideal shape, and further suggest that TCP genes determine petal identity along the DV axis by regulating MIXTA-like gene expression.

  13. 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

  14. 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

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

    PubMed Central

    2014-01-01

    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

  16. Trissolcus japonicus (Ashmead) emerges in North America

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  17. Multiple components are integrated to determine leaf complexity in Lotus japonicus.

    PubMed

    Wang, Zhenhua; Chen, Jianghua; Weng, Lin; Li, Xin; Cao, Xianglin; Hu, Xiaohe; Luo, Da; Yang, Jun

    2013-05-01

    Transcription factors and phytohormones have been reported to play crucial roles to regulate leaf complexity among plant species. Using the compound-leafed species Lotus japonicus, a model legume plant with five visible leaflets, we characterized four independent mutants with reduced leaf complexity, proliferating floral meristem (pfm), proliferating floral organ-2 (pfo-2), fused leaflets1 (ful1) and umbrella leaflets (uml), which were further identified as loss-of-function mutants of Arabidopsis orthologs LEAFY (LFY), UNUSUAL FLORAL ORGANS (UFO), CUP-SHAPED COTYLEDON 2 (CUC2) and PIN-FORMED 1 (PIN1), respectively. Comparing the leaf development of wild-type and mutants by a scanning electron microscopy approach, leaflet initiation and/or dissection were found to be affected in these mutants. Expression and phenotype analysis indicated that PFM/LjLFY and PFO/LjUFO determined the basipetal leaflet initiation manner in L. japonicus. Genetic analysis of ful1 and uml mutants and their double mutants revealed that the CUC2-like gene and auxin pathway also participated in leaflet dissection in L. japonicus, and their functions might influence cytokinin biogenesis directly or indirectly. Our results here suggest that multiple genes were interplayed and played conserved functions in controlling leaf complexity during compound leaf development in L. japonicus.

  18. Using Clickers to Identify the Muddiest Points in Large Chemistry Classes

    ERIC Educational Resources Information Center

    King, Daniel B.

    2011-01-01

    One of the biggest challenges for instruction in large-enrollment introductory courses is identifying points of student confusion. One technique that is used to address this problem is the muddiest-point card. However, this technique is logistically difficult to implement in large classes. Personal response devices (or clickers) can be used to…

  19. Understanding the Heat Shock Response in the Sea Cucumber Apostichopus japonicus, Using iTRAQ-Based Proteomics.

    PubMed

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

    2016-02-04

    The sea cucumber Apostichopus japonicus is exploited as a commercial species owing to their high nutritive and medicinal value. Recent high summer temperatures have caused high mortality rates in A. japonicus. In this study, we applied the isobaric tag for relative and absolute quantitation (iTRAQ) technique to investigate the global protein expression profile under an acute short-term (48 h) heat stress. In total, 3432 proteins were identified, and 127 proteins showed significant heat stress responses, with 61 upregulated proteins and 66 downregulated proteins. Our results suggest that heat stress influenced the expression of proteins involved in various biological processes, such as tissue protection and detoxification, lipid and amino acid metabolism, energy production and usage, transcription and translation, cell apoptosis, and cell proliferation. These findings provide a better understanding about the response and thermo-tolerance mechanisms of A. japonicus under heat stress.

  20. Understanding the Heat Shock Response in the Sea Cucumber Apostichopus japonicus, Using iTRAQ-Based Proteomics

    PubMed Central

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

    2016-01-01

    The sea cucumber Apostichopus japonicus is exploited as a commercial species owing to their high nutritive and medicinal value. Recent high summer temperatures have caused high mortality rates in A. japonicus. In this study, we applied the isobaric tag for relative and absolute quantitation (iTRAQ) technique to investigate the global protein expression profile under an acute short-term (48 h) heat stress. In total, 3432 proteins were identified, and 127 proteins showed significant heat stress responses, with 61 upregulated proteins and 66 downregulated proteins. Our results suggest that heat stress influenced the expression of proteins involved in various biological processes, such as tissue protection and detoxification, lipid and amino acid metabolism, energy production and usage, transcription and translation, cell apoptosis, and cell proliferation. These findings provide a better understanding about the response and thermo-tolerance mechanisms of A. japonicus under heat stress. PMID:26861288

  1. Reassimilation of ammonium in Lotus japonicus.

    PubMed

    Betti, Marco; García-Calderón, Margarita; Pérez-Delgado, Carmen M; Credali, Alfredo; Pal'ove-Balang, Peter; Estivill, Guillermo; Repčák, Miroslav; Vega, José M; Galván, Francisco; Márquez, Antonio J

    2014-10-01

    This review summarizes the most recent results obtained in the analysis of two important metabolic pathways involved in the release of internal sources of ammonium in the model legume Lotus japonicus: photorespiratory metabolism and asparagine breakdown mediated by aparaginase (NSE). The use of photorespiratory mutants deficient in plastidic glutamine synthetase (GS2) enabled us to investigate the transcriptomics and metabolomic changes associated with photorespiratory ammonium accumulation in this plant. The results obtained indicate the existence of a coordinate regulation of genes involved in photorespiratory metabolism. Other types of evidence illustrate the multiple interconnections existing among the photorespiratory pathway and other processes such as intermediate metabolism, nodule function, and secondary metabolism in this plant, all of which are substantially affected in GS2-deficient mutants because of the impairment of the photorespiratory cycle. Finally, the importance of asparagine metabolism in L. japonicus is highlighted because of the fact that asparagine constitutes the vast majority of the reduced nitrogen translocated between different organs of this plant. The different types of NSE enzymes and genes which are present in L. japonicus are described. There is a particular focus on the most abundant K(+)-dependent LjNSE1 isoform and how TILLING mutants were used to demonstrate by reverse genetics the importance of this particular isoform in plant growth and seed production.

  2. Biosynthesis of the Nitrile Glucosides Rhodiocyanoside A and D and the Cyanogenic Glucosides Lotaustralin and Linamarin in Lotus japonicus1

    PubMed Central

    Forslund, Karin; Morant, Marc; Jørgensen, Bodil; Olsen, Carl Erik; Asamizu, Erika; Sato, Shusei; Tabata, Satoshi; Bak, Søren

    2004-01-01

    Lotus japonicus was shown to contain the two nitrile glucosides rhodiocyanoside A and rhodiocyanoside D as well as the cyanogenic glucosides linamarin and lotaustralin. The content of cyanogenic and nitrile glucosides in L. japonicus depends on plant developmental stage and tissue. The cyanide potential is highest in young seedlings and in apical leaves of mature plants. Roots and seeds are acyanogenic. Biosynthetic studies using radioisotopes demonstrated that lotaustralin, rhodiocyanoside A, and rhodiocyanoside D are derived from the amino acid l-Ile, whereas linamarin is derived from Val. In silico homology searches identified two cytochromes P450 designated CYP79D3 and CYP79D4 in L. japonicus. The two cytochromes P450 are 94% identical at the amino acid level and both catalyze the conversion of Val and Ile to the corresponding aldoximes in biosynthesis of cyanogenic glucosides and nitrile glucosides in L. japonicus. CYP79D3 and CYP79D4 are differentially expressed. CYP79D3 is exclusively expressed in aerial parts and CYP79D4 in roots. Recombinantly expressed CYP79D3 and CYP79D4 in yeast cells showed higher catalytic efficiency with l-Ile as substrate than with l-Val, in agreement with lotaustralin and rhodiocyanoside A and D being the major cyanogenic and nitrile glucosides in L. japonicus. Ectopic expression of CYP79D2 from cassava (Manihot esculenta Crantz.) in L. japonicus resulted in a 5- to 20-fold increase of linamarin content, whereas the relative amounts of lotaustralin and rhodiocyanoside A/D were unaltered. PMID:15122013

  3. 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

  4. Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation.

    PubMed

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

    2014-12-01

    Sea cucumbers, Apostichopus japonicus, experience seasonally high water temperatures during the summer months and enter aestivation to survive. Aestivation is characterized by strong metabolic rate depression which is supported by a series of strategies including reorganizing metabolic processes, suppressing cell functions, enhancing cytoprotective mechanisms, and altered gene expression. The respiratory tree tissue of the sea cucumber is an excellent material for studying aestivation, undergoing obvious atrophy during aestivation. The present study analyzed the global gene expression profile of respiratory tree tissue of A. japonicus during aestivation by constructing and screening three libraries representing key stages of aestivation: non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA) using RNA-seq. A total of 1240, 1184 and 303 differentially expressed genes (DEGs) were identified following the criteria of |log2 ratio|≥1 and FDR≤0.001 in comparisons of DA vs. NA, AA vs. NA and DA vs. AA. A set of respiratory tree specific DEGs was identified the first time and, in addition, common DEGs that were responsive to aestivation in both respiratory tree and intestine were identified. Functional analysis of DEGs was further performed by GO enrichment analysis and respiratory tree specific GO terms were screened out and provide interesting hints for further studies of the molecular regulation of aestivation in A. japonicus.

  5. 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.

  6. La Crosse Virus in Aedes japonicus japonicus mosquitoes in the Appalachian Region, United States.

    PubMed

    Harris, M Camille; Dotseth, Eric J; Jackson, Bryan T; Zink, Steven D; Marek, Paul E; Kramer, Laura D; Paulson, Sally L; Hawley, Dana M

    2015-04-01

    La Crosse virus (LACV), a leading cause of arboviral encephalitis in children in the United States, is emerging in Appalachia. For local arboviral surveillance, mosquitoes were tested. LACV RNA was detected and isolated from Aedes japonicus mosquitoes. These invasive mosquitoes may significantly affect LACV range expansion and dynamics.

  7. Neuropeptides and polypeptide hormones in echinoderms: new insights from analysis of the transcriptome of the sea cucumber Apostichopus japonicus.

    PubMed

    Rowe, Matthew L; Achhala, Sufyan; Elphick, Maurice R

    2014-02-01

    Echinoderms are of special interest for studies in comparative endocrinology because of their phylogenetic position in the animal kingdom as deuterostomian invertebrates. Furthermore, their pentaradial symmetry as adult animals provides a unique context for analysis of the physiological and behavioral roles of peptide signaling systems. Here we report the first extensive survey of neuropeptide and peptide hormone precursors in a species belonging to the class Holothuroidea. Transcriptome sequence data obtained from the sea cucumber Apostichopus japonicus were analyzed to identify homologs of precursor proteins that have recently been identified in the sea urchin Strongylocentrotus purpuratus (class Echinoidea). A total of 17 precursor proteins have been identified in A. japonicus, including precursors of peptides related to thyrotropin-releasing hormone, pedal peptide/orcokinin-type peptides, AN peptides/tachykinins, luqins, corticotropin-releasing hormone (CRH), GPA2-type glycoprotein hormone subunits and bursicon. In addition, an unusual finding was an A. japonicus calcitonin-type precursor protein (AjCTLPP), the first to be discovered that comprises two calcitonin-like peptides; this contrasts with the products of the alternatively-spliced calcitonin/CGRP gene in vertebrates, which comprise either calcitonin or CGRP. Collectively, the data obtained provide new insights on the evolution and diversity of neuropeptides and polypeptide hormones. Furthermore, because A. japonicus is one of several sea cucumber species that are used for human consumption, our findings may have practical and economic impact by providing a basis for neuroendocrine-based strategies to improve methods of aquaculture.

  8. Leojaponic acids A and B, two new homologous terpenoids, isolated from Leonurus japonicus.

    PubMed

    Wu, Han-Kui; Mao, Yan-Jun; Sun, Shan-Shan; Xu, Zhi-Yong; Ma, Ya; Cao, Jin-Xia; Qi, He; Wu, Zhi-Fu; Li, Gang; Yang, Wei-Hua

    2016-04-01

    The present study aimed at isolation and purification of the bioactive terpenoids from the herb of Leonurus japonicus by chromatographic separations such as silica gel, sephadex LH-20 and C18 reversed phase silica gel, as well as preparative HPLC. As a result, leojaponic acids A (1, C17H24O4) and B (2, C18H26O4), two homologous terpenoids, together with (-)-loliolide (3), 1-(3-ethylphenyl) ethane-1, 2-diol (4) and dibutyl phthalate (5), were isolated from the EtOH extract of L. japonicus. All the chemical structures of the isolates were elucidated on the basis of 1D and 2D NMR analyses. Compounds 1 and 2 were new terpenoids, and Compounds 3 and 4 were isolated and identified for the first time from this plant. In addition, the α-glucosidase and tyrosinase inhibitory activity of the new compounds were evaluated.

  9. Effective Boolean dynamics analysis to identify functionally important genes in large-scale signaling networks.

    PubMed

    Trinh, Hung-Cuong; Kwon, Yung-Keun

    2015-11-01

    Efficiently identifying functionally important genes in order to understand the minimal requirements of normal cellular development is challenging. To this end, a variety of structural measures have been proposed and their effectiveness has been investigated in recent literature; however, few studies have shown the effectiveness of dynamics-based measures. This led us to investigate a dynamic measure to identify functionally important genes, and the effectiveness of which was verified through application on two large-scale human signaling networks. We specifically consider Boolean sensitivity-based dynamics against an update-rule perturbation (BSU) as a dynamic measure. Through investigations on two large-scale human signaling networks, we found that genes with relatively high BSU values show slower evolutionary rate and higher proportions of essential genes and drug targets than other genes. Gene-ontology analysis showed clear differences between the former and latter groups of genes. Furthermore, we compare the identification accuracies of essential genes and drug targets via BSU and five well-known structural measures. Although BSU did not always show the best performance, it effectively identified the putative set of genes, which is significantly different from the results obtained via the structural measures. Most interestingly, BSU showed the highest synergy effect in identifying the functionally important genes in conjunction with other measures. Our results imply that Boolean-sensitive dynamics can be used as a measure to effectively identify functionally important genes in signaling networks.

  10. Male tarsi specific odorant-binding proteins in the diving beetle Cybister japonicus sharp

    PubMed Central

    Song, Li-Mei; Jiang, Xiang; Wang, Xue-Min; Li, Jin-Dong; Zhu, Fang; Tu, Xiong-Bing; Zhang, Ze-Hua; Ban, Li-Ping

    2016-01-01

    Odorant binding proteins (OBPs) play critical roles in chemical communication of insects, as they recognize and transport environmental chemical signals to receptors. The diving beetle Cybister japonicus Sharp shows a remarkable sexual dimorphism. The foreleg tarsi of males are equipped with large suction cups, believed to help holding the female during underwater courtship and mating. Here, we identified two OBPs highly and specifically expressed in male tarsi, suggesting important functions of these structures in chemical communication. The first protein, CjapOBP1, exhibits the 6 conserved cysteines motif of classic OBPs, while the second, CjapOBP2, contains only four cysteines and can be assigned to the sub-class of C-minus OBPs. Both proteins were expressed in a bacterial system and the purified recombinant proteins were used to for antibodies preparation. Western Blot analysis showed that CjapOBP1 is predominantly expressed in male tarsi and could be also detected in antennae and palpi of both sexes, while CjapOBP2, besides male tarsi, is also present in testis. Ligand-binding experiments showed a good binding affinity between CjapOBP1, CjapOBP2 and citral and coniferyl aldehyde, respectively. These results support a possible function of these two OBPs in the male foreleg tarsi of diving beetles in chemical communication. PMID:27545810

  11. Identifying early stage precipitation in large-scale atomistic simulations of superalloys

    NASA Astrophysics Data System (ADS)

    Schmidt, Eric; Bristowe, Paul D.

    2017-04-01

    A method for identifying and classifying ordered phases in large chemically and thermally disordered atomistic models is presented. The method uses Steinhardt parameters to represent local atomic configurations and develops probability density functions to classify individual atoms using naïve Bayes. The method is applied to large molecular dynamics simulations of supersaturated Ni-20 at% Al solid solutions in order to identify the formation of embryonic γ‧-Ni3Al. The composition and temperatures are chosen to promote precipitation, which is observed in the form of ordering and is found to occur more likely in regions with above average Al concentration producing ‘clusters’ of increasing size. The results are interpreted in terms of a precipitation mechanism in which the solid solution is unstable with respect to ordering and potentially followed by either spinodal decomposition or nucleation and growth.

  12. Controller design and parameter identifiability studies for a large space antenna

    NASA Technical Reports Server (NTRS)

    Joshi, S. M.

    1985-01-01

    The problem of control systems synthesis and parameter identifiability are considered for a large, space-based antenna. Two methods are considered for control system synthesis, the first of which uses torque actuators and collocated attitude and rate sensors, and the second method is based on the linear-quadratic-Gaussian (LQG) control theory. The predicted performance obtained by computing variances of pointing, surface and feed misalignment errors in the presence of sensor noise indicates that the LQG-based controller yields superior results. Since controller design requires the knowledge of the system parameters, the identifiability of the structural parameters is investigated by obtaining Cramer-Rao lower bounds. The modal frequencies are found to have the best identifiability, followed by damping ratios, and mode-slopes.

  13. Postembryonic development of the mushroom bodies in the ant, Camponotus japonicus.

    PubMed

    Ishii, Yuri; Kubota, Kanae; Hara, Kenji

    2005-07-01

    Mushroom bodies (MB) are insect brain centers involved in learning and other complex behaviors and they are particularly large in ants. We describe the larval and pupal development of the MB in the carpenter ant, Camponotus japonicus. Based on morphological cues, we characterized the stages of preimaginal development of worker ants. We then describe morphological changes and neurogenesis underlying the MB development. Kenyon cells are produced in a proliferation cluster formed by symmetrical division of MB neuroblasts. While the duration of larval instars shows great individual variation, MB neuroblasts increase in number in each successive larval instar. The number of neuroblasts increases further during prepupal stages and peaks during early pupal stages. It decreases rapidly, and then neurogenesis generally ceases during the mid pupal stage (P4). In contrast to the larval period, the MB development of individuals is highly synchronized with physical time throughout metamorphosis. We show that carpenter ants (C. japonicus) have approximately half as many MB neuroblasts than are found in the honey bee Apis mellifera. Mature MBs of carpenter ants and honey bees reportedly comprise almost the same number of neurons. We therefore suggest that the MB neuroblasts in C. japonicus divide more often in order to produce a final number of MB neurons similar to that of honey bees.

  14. Isolated history of the coastal plant Lathyrus japonicus (Leguminosae) in Lake Biwa, an ancient freshwater lake

    PubMed Central

    Ohtsuki, Tatsuo; Kaneko, Yuko; Setoguchi, Hiroaki

    2011-01-01

    Background and aims Lake Biwa is one of the world's few ancient lakes. Formed ∼4 million years ago, the lake harbours many coastal species that commonly inhabit seashores. The beach pea Lathyrus japonicus is a typical coastal species of this freshwater lake, but its inland populations are faced with the threat of extinction. Here, we investigated the phylogeographical and population structures of both inland and coastal populations of L. japonicus. We also elucidated the historical isolation of the Lake Biwa population. Methodology In total, 520 individuals from 50 L. japonicus populations were sampled throughout the species distribution in Japan. Chloroplast haplotyping using intergenic spacers psbA–trnH and atpI–atpH was performed to investigate the phylogeographical structure as well as the genetic diversity of L. japonicus. Six nuclear microsatellite markers were also used to analyse the population structure. Principal results Population structure analyses of chloroplast DNA (cpDNA) and nuclear DNA (nDNA) identified inland and coastal groups. Based on the genetic differentiation, inland populations exhibited a single cpDNA haplotype and significantly lower values of HS, AR and FIS than coastal populations. In addition to the presence of a bottleneck, the lack of gene flow among inland populations was supported by estimates of recent migration rates between subpopulations. Conclusions Our data revealed that inland populations have been isolated in Lake Biwa as ‘landlocked’ populations since the predecessor lake was isolated from sea. This was also seen in a previous study of Calystegia soldanella. However, the high genetic differentiation, accompanied by a lack of gene flow among the Lake Biwa populations (according to the BAYESASS+ analysis), contradicts the results with C. soldanella. We conclude that because of the presence of a bottleneck and low genetic diversity of the inland populations, self-sustaining population persistence may be difficult in

  15. New nodulation mutants responsible for infection thread development in Lotus japonicus.

    PubMed

    Yano, Koji; Tansengco, Myra L; Hio, Taihei; Higashi, Kuniko; Murooka, Yoshikatsu; Imaizumi-Anraku, Haruko; Kawaguchi, Masayoshi; Hayashi, Makoto

    2006-07-01

    Legume plants develop specialized root organs, the nodules, through a symbiotic interaction with rhizobia. The developmental process of nodulation is triggered by the bacterial microsymbiont but regulated systemically by the host legume plants. Using ethylmethane sulfonate mutagenesis as a tool to identify plant genes involved in symbiotic nodule development, we have isolated and analyzed five nodulation mutants, Ljsym74-3, Ljsym79-2, Ljsym79-3, Ljsym80, and Ljsym82, from the model legume Lotus japonicus. These mutants are defective in developing functional nodules and exhibit nitrogen starvation symptoms after inoculation with Mesorhizobium loti. Detailed observation revealed that infection thread development was aborted in these mutants and the nodules formed were devoid of infected cells. Mapping and complementation tests showed that Ljsym74-3, and Ljsym79-2 and Ljsym79-3, were allelic with reported mutants of L. japonicus, alb1 and crinkle, respectively. The Ljsym82 mutant is unique among the mutants because the infection thread was aborted early in its development. Ljsym74-3 and Ljsym80 were characterized as mutants with thick infection threads in short root hairs. Map-based cloning and molecular characterization of these genes will help us understand the genetic mechanism of infection thread development in L. japonicus.

  16. 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.

  17. 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.

  18. An interaction screen identifies headcase as a regulator of large-scale pruning

    PubMed Central

    Loncle, Nicolas; Williams, Darren W

    2012-01-01

    Large-scale pruning, the removal of long neuronal processes, is deployed widely within the developing nervous system and is essential for proper circuit formation. In Drosophila the dendrites of the class IV dendritic arborization sensory neuron ddaC undergo large-scale pruning by local degeneration controlled by the steroid hormone ecdysone. The molecular mechanisms that control such events are largely unknown. To identify new molecules that orchestrate this developmental degeneration we performed a genetic interaction screen. Our approach combines the strength of Drosophila forward genetics with detailed in vivo imaging of ddaC neurons. This screen allowed us to identify headcase (hdc) as a new gene involved in dendrite pruning. hdc is evolutionarily conserved, but the protein’s function is unknown. Here we show that hdc is expressed just prior to metamorphosis in sensory neurons that undergo remodeling. hdc is required in a cell autonomous manner to control dendrite severing, the first phase of pruning. Our epistasis experiments with known regulators of dendrite pruning reveal hdc as a founding member of a new pathway downstream of ecdysone signaling. PMID:23197702

  19. A Review of Methods Used for Identifying Structural Changes in a Large Protein Complex

    PubMed Central

    Nadeau, Owen W.; Carlson, Gerald M.

    2013-01-01

    This chapter explores the structural responses of a massive, hetero-oligomeric protein complex to a single allosteric activator as probed by a wide range of chemical, biochemical, and biophysical approaches. Some of the approaches used are amenable only to large protein targets, whereas others push the limits of their utility. Some of the techniques focus on individual subunits, or portions thereof, while others examine the complex as a whole. Despite the absence of crystallographic data for the complex, the diverse techniques identify and implicate a small region of its catalytic subunit as the master allosteric activation switch for the entire complex. PMID:22052488

  20. 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.

  1. 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

  2. A Large-Scale Functional Screen to Identify Epigenetic Repressors of Retrotransposon Expression.

    PubMed

    Ecco, Gabriela; Rowe, Helen M; Trono, Didier

    2016-01-01

    Deposition of epigenetic marks is an important layer of the transcriptional control of retrotransposons, especially during early embryogenesis. Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs) are one of the largest families of transcription factors, and collectively partake in this process by tethering to thousands of retroelement-containing genomic loci their cofactor KAP1, which acts as a scaffold for a heterochromatin-inducing machinery. However, while the sequence-specific DNA binding potential of the poly-zinc finger-containing KRAB-ZFPs is recognized, very few members of the family have been assigned specific targets. In this chapter, we describe a large-scale functional screen to identify the retroelements bound by individual murine KRAB-ZFPs. Our method is based on the automated transfection of a library of mouse KRAB-ZFP-containing vectors into 293T cells modified to express GFP from a PGK promoter harboring in its immediate vicinity a KAP1-recruiting retroelement-derived sequence. Analysis is then performed by plate reader and flow cytometry fluorescence readout. Such large-scale DNA-centered functional approach can not only help to identify the trans-acting factors responsible for silencing retrotransposons, but also serve as a model for dissecting the transcriptional networks influenced by retroelement-derived cis-acting sequences.

  3. Large-Scale RNA Interference Screening in Mammalian Cells Identifies Novel Regulators of Mutant Huntingtin Aggregation

    PubMed Central

    Tosaki, Asako; Bauer, Peter O.; Wada, Koji; Kurosawa, Masaru; Shimogori, Tomomi; Hattori, Nobutaka; Nukina, Nobuyuki

    2014-01-01

    In polyglutamine (polyQ) diseases including Huntington's disease (HD), mutant proteins containing expanded polyQ stretch form aggregates in neurons. Genetic or RNAi screenings in yeast, C. elegans or Drosophila have identified multiple genes modifying polyQ aggregation, a few of which are confirmed effective in mammals. However, the overall molecular mechanism underlying polyQ protein aggregation in mammalian cells still remains obscure. We here perform RNAi screening in mouse neuro2a cells to identify mammalian modifiers for aggregation of mutant huntingtin, a causative protein of HD. By systematic cell transfection and automated cell image analysis, we screen ∼12000 shRNA clones and identify 111 shRNAs that either suppress or enhance mutant huntingtin aggregation, without altering its gene expression. Classification of the shRNA-targets suggests that genes with various cellular functions such as gene transcription and protein phosphorylation are involved in modifying the aggregation. Subsequent analysis suggests that, in addition to the aggregation-modifiers sensitive to proteasome inhibition, some of them, such as a transcription factor Tcf20, and kinases Csnk1d and Pik3c2a, are insensitive to it. As for Tcf20, which contains polyQ stretches at N-terminus, its binding to mutant huntingtin aggregates is observed in neuro2a cells and in HD model mouse neurons. Notably, except Pik3c2a, the rest of the modifiers identified here are novel. Thus, our first large-scale RNAi screening in mammalian system identifies previously undescribed genetic players that regulate mutant huntingtin aggregation by several, possibly mammalian-specific mechanisms. PMID:24705917

  4. 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

  5. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus.

    PubMed

    Gardner, Jeffrey G

    2016-07-01

    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. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable 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.

  6. 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.

  7. 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

  8. Two new sesquiterpenes from Chloranthus japonicus Sieb.

    PubMed

    Lu, Qiang-Qiang; Shi, Xin-Wei; Zheng, Shao-Jun; Zhou, Jun-Hui; Cui, Xin-Ai; Gao, Jin-Ming

    2016-11-01

    Two new sesquiterpenes, namely, 1β,10β-dihydroxy-eremophil-7(11), 8-dien-12,8-olide (1) and 8,12-epoxy-1β-hydroxyeudesm-3,7,11-trien-9-one (2), together with three known sesquiterpenoids, shizukolidol (3), 4α-hydroxy-5α(H)-8β-methoxy-eudesm-7(11)-en-12,8-olide (4), and neolitacumone B (5), and two known monoterpenes, (3R,4S,6R)-p-menth-1-en-3,6-diol (6) and (R)-p-menth-1-en-4,7-diol (7), were isolated from the whole plant of Chloranthus japonicus Sieb. Their structures were elucidated on the basis of spectroscopic data analysis and comparison with those of related known compounds. Compounds 4-7 were isolated from this plant for the first time.

  9. Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.

    PubMed

    Burstein, David; Amaro, Francisco; Zusman, Tal; Lifshitz, Ziv; Cohen, Ofir; Gilbert, Jack A; Pupko, Tal; Shuman, Howard A; Segal, Gil

    2016-02-01

    Infection by the human pathogen Legionella pneumophila relies on the translocation of ∼ 300 virulence proteins, termed effectors, which manipulate host cell processes. However, almost no information exists regarding effectors in other Legionella pathogens. Here we sequenced, assembled and characterized the genomes of 38 Legionella species and predicted their effector repertoires using a previously validated machine learning approach. This analysis identified 5,885 predicted effectors. The effector repertoires of different Legionella species were found to be largely non-overlapping, and only seven core effectors were shared by all species studied. Species-specific effectors had atypically low GC content, suggesting exogenous acquisition, possibly from the natural protozoan hosts of these species. Furthermore, we detected numerous new conserved effector domains and discovered new domain combinations, which allowed the inference of as yet undescribed effector functions. The effector collection and network of domain architectures described here can serve as a roadmap for future studies of effector function and evolution.

  10. Large-Scale Gene-Centric Meta-analysis across 32 Studies Identifies Multiple Lipid Loci

    PubMed Central

    Asselbergs, Folkert W.; Guo, Yiran; van Iperen, Erik P.A.; Sivapalaratnam, Suthesh; Tragante, Vinicius; Lanktree, Matthew B.; Lange, Leslie A.; Almoguera, Berta; Appelman, Yolande E.; Barnard, John; Baumert, Jens; Beitelshees, Amber L.; Bhangale, Tushar R.; Chen, Yii-Der Ida; Gaunt, Tom R.; Gong, Yan; Hopewell, Jemma C.; Johnson, Toby; Kleber, Marcus E.; Langaee, Taimour Y.; Li, Mingyao; Li, Yun R.; Liu, Kiang; McDonough, Caitrin W.; Meijs, Matthijs F.L.; Middelberg, Rita P.S.; Musunuru, Kiran; Nelson, Christopher P.; O’Connell, Jeffery R.; Padmanabhan, Sandosh; Pankow, James S.; Pankratz, Nathan; Rafelt, Suzanne; Rajagopalan, Ramakrishnan; Romaine, Simon P.R.; Schork, Nicholas J.; Shaffer, Jonathan; Shen, Haiqing; Smith, Erin N.; Tischfield, Sam E.; van der Most, Peter J.; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Volcik, Kelly A.; Zhang, Li; Bailey, Kent R.; Bailey, Kristian M.; Bauer, Florianne; Boer, Jolanda M.A.; Braund, Peter S.; Burt, Amber; Burton, Paul R.; Buxbaum, Sarah G.; Chen, Wei; Cooper-DeHoff, Rhonda M.; Cupples, L. Adrienne; deJong, Jonas S.; Delles, Christian; Duggan, David; Fornage, Myriam; Furlong, Clement E.; Glazer, Nicole; Gums, John G.; Hastie, Claire; Holmes, Michael V.; Illig, Thomas; Kirkland, Susan A.; Kivimaki, Mika; Klein, Ronald; Klein, Barbara E.; Kooperberg, Charles; Kottke-Marchant, Kandice; Kumari, Meena; LaCroix, Andrea Z.; Mallela, Laya; Murugesan, Gurunathan; Ordovas, Jose; Ouwehand, Willem H.; Post, Wendy S.; Saxena, Richa; Scharnagl, Hubert; Schreiner, Pamela J.; Shah, Tina; Shields, Denis C.; Shimbo, Daichi; Srinivasan, Sathanur R.; Stolk, Ronald P.; Swerdlow, Daniel I.; Taylor, Herman A.; Topol, Eric J.; Toskala, Elina; van Pelt, Joost L.; van Setten, Jessica; Yusuf, Salim; Whittaker, John C.; Zwinderman, A.H.; Anand, Sonia S.; Balmforth, Anthony J.; Berenson, Gerald S.; Bezzina, Connie R.; Boehm, Bernhard O.; Boerwinkle, Eric; Casas, Juan P.; Caulfield, Mark J.; Clarke, Robert; Connell, John M.; Cruickshanks, Karen J.; Davidson, Karina W.; Day, Ian N.M.; de Bakker, Paul I.W.; Doevendans, Pieter A.; Dominiczak, Anna F.; Hall, Alistair S.; Hartman, Catharina A.; Hengstenberg, Christian; Hillege, Hans L.; Hofker, Marten H.; Humphries, Steve E.; Jarvik, Gail P.; Johnson, Julie A.; Kaess, Bernhard M.; Kathiresan, Sekar; Koenig, Wolfgang; Lawlor, Debbie A.; März, Winfried; Melander, Olle; Mitchell, Braxton D.; Montgomery, Grant W.; Munroe, Patricia B.; Murray, Sarah S.; Newhouse, Stephen J.; Onland-Moret, N. Charlotte; Poulter, Neil; Psaty, Bruce; Redline, Susan; Rich, Stephen S.; Rotter, Jerome I.; Schunkert, Heribert; Sever, Peter; Shuldiner, Alan R.; Silverstein, Roy L.; Stanton, Alice; Thorand, Barbara; Trip, Mieke D.; Tsai, Michael Y.; van der Harst, Pim; van der Schoot, Ellen; van der Schouw, Yvonne T.; Verschuren, W.M. Monique; Watkins, Hugh; Wilde, Arthur A.M.; Wolffenbuttel, Bruce H.R.; Whitfield, John B.; Hovingh, G. Kees; Ballantyne, Christie M.; Wijmenga, Cisca; Reilly, Muredach P.; Martin, Nicholas G.; Wilson, James G.; Rader, Daniel J.; Samani, Nilesh J.; Reiner, Alex P.; Hegele, Robert A.; Kastelein, John J.P.; Hingorani, Aroon D.; Talmud, Philippa J.; Hakonarson, Hakon; Elbers, Clara C.; Keating, Brendan J.; Drenos, Fotios

    2012-01-01

    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 cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) covering ∼2,000 candidate genes. SNP-lipid associations were replicated either in a cohort comprising an additional 24,736 samples or within the Global Lipid Genetic Consortium. We identified four, six, ten, and four unreported SNPs in established lipid genes for HDL-C, LDL-C, TC, and TGs, respectively. We also identified several lipid-related SNPs in previously unreported genes: DGAT2, HCAR2, GPIHBP1, PPARG, and FTO for HDL-C; SOCS3, APOH, SPTY2D1, BRCA2, and VLDLR for LDL-C; SOCS3, UGT1A1, BRCA2, UBE3B, FCGR2A, CHUK, and INSIG2 for TC; and SERPINF2, C4B, GCK, GATA4, INSR, and LPAL2 for TGs. The proportion of explained phenotypic variance in the subset of studies providing individual-level data was 9.9% for HDL-C, 9.5% for LDL-C, 10.3% for TC, and 8.0% for TGs. This large meta-analysis of lipid phenotypes with the use of a dense gene-centric approach identified multiple SNPs not previously described in established lipid genes and several previously unknown loci. The explained phenotypic variance from this approach was comparable to that from a meta-analysis of GWAS data, suggesting that a focused genotyping approach can further increase the understanding of heritability of plasma lipids. PMID:23063622

  11. Statistical Analyses of Scatterplots to Identify Important Factors in Large-Scale Simulations

    SciTech Connect

    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 considered 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.

  12. Large-Scale Evaluation of Candidate Genes Identifies Associations between VEGF Polymorphisms and Bladder Cancer Risk

    PubMed Central

    García-Closas, Montserrat; Malats, Núria; Real, Francisco X; Yeager, Meredith; Welch, Robert; Silverman, Debra; Kogevinas, Manolis; Dosemeci, Mustafa; Figueroa, Jonine; Chatterjee, Nilanjan; Tardón, Adonina; Serra, Consol; Carrato, Alfredo; García-Closas, Reina; Murta-Nascimento, Cristiane; Rothman, Nathaniel; Chanock, Stephen J

    2007-01-01

    Common genetic variation could alter the risk for developing bladder cancer. We conducted a large-scale evaluation of single nucleotide polymorphisms (SNPs) in candidate genes for cancer to identify common variants that influence bladder cancer risk. An Illumina GoldenGate assay was used to genotype 1,433 SNPs within or near 386 genes in 1,086 cases and 1,033 controls in Spain. The most significant finding was in the 5′ UTR of VEGF (rs25648, p for likelihood ratio test, 2 degrees of freedom = 1 × 10−5). To further investigate the region, we analyzed 29 additional SNPs in VEGF, selected to saturate the promoter and 5′ UTR and to tag common genetic variation in this gene. Three additional SNPs in the promoter region (rs833052, rs1109324, and rs1547651) were associated with increased risk for bladder cancer: odds ratio (95% confidence interval): 2.52 (1.06–5.97), 2.74 (1.26–5.98), and 3.02 (1.36–6.63), respectively; and a polymorphism in intron 2 (rs3024994) was associated with reduced risk: 0.65 (0.46–0.91). Two of the promoter SNPs and the intron 2 SNP showed linkage disequilibrium with rs25648. Haplotype analyses revealed three blocks of linkage disequilibrium with significant associations for two blocks including the promoter and 5′ UTR (global p = 0.02 and 0.009, respectively). These findings are biologically plausible since VEGF is critical in angiogenesis, which is important for tumor growth, its elevated expression in bladder tumors correlates with tumor progression, and specific 5′ UTR haplotypes have been shown to influence promoter activity. Associations between bladder cancer risk and other genes in this report were not robust based on false discovery rate calculations. In conclusion, this large-scale evaluation of candidate cancer genes has identified common genetic variants in the regulatory regions of VEGF that could be associated with bladder cancer risk. PMID:17319747

  13. 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

  14. Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma.

    PubMed

    Cerhan, James R; Berndt, Sonja I; Vijai, Joseph; Ghesquières, Hervé; McKay, James; Wang, Sophia S; Wang, Zhaoming; Yeager, Meredith; Conde, Lucia; de Bakker, Paul I W; Nieters, Alexandra; Cox, David; Burdett, Laurie; Monnereau, Alain; Flowers, Christopher R; De Roos, Anneclaire J; Brooks-Wilson, Angela R; Lan, Qing; Severi, Gianluca; Melbye, Mads; Gu, Jian; Jackson, Rebecca D; Kane, Eleanor; Teras, Lauren R; Purdue, Mark P; Vajdic, Claire M; Spinelli, John J; Giles, Graham G; Albanes, Demetrius; Kelly, Rachel S; Zucca, Mariagrazia; Bertrand, Kimberly A; Zeleniuch-Jacquotte, Anne; Lawrence, Charles; Hutchinson, Amy; Zhi, Degui; Habermann, Thomas M; Link, Brian K; Novak, Anne J; Dogan, Ahmet; Asmann, Yan W; Liebow, Mark; Thompson, Carrie A; Ansell, Stephen M; Witzig, Thomas E; Weiner, George J; Veron, Amelie S; Zelenika, Diana; Tilly, Hervé; Haioun, Corinne; Molina, Thierry Jo; Hjalgrim, Henrik; Glimelius, Bengt; Adami, Hans-Olov; Bracci, Paige M; Riby, Jacques; Smith, Martyn T; Holly, Elizabeth A; Cozen, Wendy; Hartge, Patricia; Morton, Lindsay M; Severson, Richard K; Tinker, Lesley F; North, Kari E; Becker, Nikolaus; Benavente, Yolanda; Boffetta, Paolo; Brennan, Paul; Foretova, Lenka; Maynadie, Marc; Staines, Anthony; Lightfoot, Tracy; Crouch, Simon; Smith, Alex; Roman, Eve; Diver, W Ryan; Offit, Kenneth; Zelenetz, Andrew; Klein, Robert J; Villano, Danylo J; Zheng, Tongzhang; Zhang, Yawei; Holford, Theodore R; Kricker, Anne; Turner, Jenny; Southey, Melissa C; Clavel, Jacqueline; Virtamo, Jarmo; Weinstein, Stephanie; Riboli, Elio; Vineis, Paolo; Kaaks, Rudolph; Trichopoulos, Dimitrios; Vermeulen, Roel C H; Boeing, Heiner; Tjonneland, Anne; Angelucci, Emanuele; Di Lollo, Simonetta; Rais, Marco; Birmann, Brenda M; Laden, Francine; Giovannucci, Edward; Kraft, Peter; Huang, Jinyan; Ma, Baoshan; Ye, Yuanqing; Chiu, Brian C H; Sampson, Joshua; Liang, Liming; Park, Ju-Hyun; Chung, Charles C; Weisenburger, Dennis D; Chatterjee, Nilanjan; Fraumeni, Joseph F; Slager, Susan L; Wu, Xifeng; de Sanjose, Silvia; Smedby, Karin E; Salles, Gilles; Skibola, Christine F; Rothman, Nathaniel; Chanock, Stephen J

    2014-11-01

    Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of European ancestry, with additional genotyping of 9 promising SNPs in 1,359 cases and 4,557 controls. In our multi-stage analysis, five independent SNPs in four loci achieved genome-wide significance marked by rs116446171 at 6p25.3 (EXOC2; P = 2.33 × 10(-21)), rs2523607 at 6p21.33 (HLA-B; P = 2.40 × 10(-10)), rs79480871 at 2p23.3 (NCOA1; P = 4.23 × 10(-8)) and two independent SNPs, rs13255292 and rs4733601, at 8q24.21 (PVT1; P = 9.98 × 10(-13) and 3.63 × 10(-11), respectively). These data provide substantial new evidence for genetic susceptibility to this B cell malignancy and point to pathways involved in immune recognition and immune function in the pathogenesis of DLBCL.

  15. Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing

    PubMed Central

    Nadeau, Nicola J.; Whibley, Annabel; Jones, Robert T.; Davey, John W.; Dasmahapatra, Kanchon K.; Baxter, Simon W.; Quail, Michael A.; Joron, Mathieu; ffrench-Constant, Richard H.; Blaxter, Mark L.; Mallet, James; Jiggins, Chris D.

    2012-01-01

    Heliconius butterflies represent a recent radiation of species, in which wing pattern divergence has been implicated in speciation. Several loci that control wing pattern phenotypes have been mapped and two were identified through sequencing. These same gene regions play a role in adaptation across the whole Heliconius radiation. Previous studies of population genetic patterns at these regions have sequenced small amplicons. Here, we use targeted next-generation sequence capture to survey patterns of divergence across these entire regions in divergent geographical races and species of Heliconius. This technique was successful both within and between species for obtaining high coverage of almost all coding regions and sufficient coverage of non-coding regions to perform population genetic analyses. We find major peaks of elevated population differentiation between races across hybrid zones, which indicate regions under strong divergent selection. These ‘islands’ of divergence appear to be more extensive between closely related species, but there is less clear evidence for such islands between more distantly related species at two further points along the ‘speciation continuum’. We also sequence fosmid clones across these regions in different Heliconius melpomene races. We find no major structural rearrangements but many relatively large (greater than 1 kb) insertion/deletion events (including gain/loss of transposable elements) that are variable between races. PMID:22201164

  16. 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

  17. Identifying Space Use at Foraging Arena Scale within the Home Ranges of Large Herbivores

    PubMed Central

    Owen-Smith, Norman; Martin, Jodie

    2015-01-01

    An intermediate spatiotemporal scale of food procurement by large herbivores is evident within annual or seasonal home ranges. It takes the form of settlement periods spanning several days or weeks during which foraging activity is confined to spatially discrete foraging arenas, separated by roaming interludes. Extended by areas occupied for other activities, these foraging arenas contribute towards generating the home range structure. We delineated and compared the foraging arenas exploited by two African large herbivores, sable antelope (a ruminant) and plains zebra (a non-ruminant), using GPS-derived movement data. We developed a novel approach to specifically delineate foraging arenas based on local change points in distance relative to adjoining clusters of locations, and compared its output with modifications of two published methods developed for home range estimation and residence time estimation respectively. We compared how these herbivore species responded to seasonal variation in food resources and how they differed in their spatial patterns of resource utilization. Sable antelope herds tended to concentrate their space use locally, while zebra herds moved more opportunistically over a wider set of foraging arenas. The amalgamated extent of the foraging arenas exploited by sable herds amounted to 12-30 km2, compared with 22-100 km2 for the zebra herds. Half-day displacement distances differed between settlement periods and roaming interludes, and zebra herds generally shifted further over 12h than sable herds. Foraging arenas of sable herds tended to be smaller than those of zebra, and were occupied for period twice as long, and hence exploited more intensively in days spent per unit area than the foraging arenas of zebra. For sable both the intensity of utilization of foraging arenas and proportion of days spent in foraging arenas relative to roaming interludes declined as food resources diminished seasonally, while zebra showed no seasonal variation

  18. Managing more than the mean: using quantile regression to identify factors related to large elk groups.

    PubMed

    Brennan, Angela; Cross, Paul C; Creel, Scott

    2015-12-01

    Animal group size distributions are often right-skewed, whereby most groups are small, but most individuals occur in larger groups that may also disproportionately affect ecology and policy. In this case, examining covariates associated with upper quantiles of the group size distribution could facilitate better understanding and management of large animal groups.We studied wintering elk groups in Wyoming, where group sizes span several orders of magnitude, and issues of disease, predation and property damage are affected by larger group sizes. We used quantile regression to evaluate relationships between the group size distribution and variables of land use, habitat, elk density and wolf abundance to identify conditions important to larger elk groups.We recorded 1263 groups ranging from 1 to 1952 elk and found that across all quantiles of group size, group sizes were larger in open habitat and on private land, but the largest effect occurred between irrigated and non-irrigated land [e.g. the 90th quantile group size increased by 135 elk (95% CI = 42, 227) on irrigation].Only upper quantile group sizes were positively related to broad-scale measures of elk density and wolf abundance. For wolf abundance, this effect was greater on elk groups found in open habitats and private land than those in closed habitats or public land. If we had limited our analysis to mean or median group sizes, we would not have detected these effects. Synthesis and applications. Our analysis of elk group size distributions using quantile regression suggests that private land, irrigation, open habitat, elk density and wolf abundance can affect large elk group sizes. Thus, to manage larger groups by removal or dispersal of individuals, we recommend incentivizing hunting on private land (particularly if irrigated) during the regular and late hunting seasons, promoting tolerance of wolves on private land (if elk aggregate in these areas to avoid wolves) and creating more winter range and

  19. Identifying Space Use at Foraging Arena Scale within the Home Ranges of Large Herbivores.

    PubMed

    Owen-Smith, Norman; Martin, Jodie

    2015-01-01

    An intermediate spatiotemporal scale of food procurement by large herbivores is evident within annual or seasonal home ranges. It takes the form of settlement periods spanning several days or weeks during which foraging activity is confined to spatially discrete foraging arenas, separated by roaming interludes. Extended by areas occupied for other activities, these foraging arenas contribute towards generating the home range structure. We delineated and compared the foraging arenas exploited by two African large herbivores, sable antelope (a ruminant) and plains zebra (a non-ruminant), using GPS-derived movement data. We developed a novel approach to specifically delineate foraging arenas based on local change points in distance relative to adjoining clusters of locations, and compared its output with modifications of two published methods developed for home range estimation and residence time estimation respectively. We compared how these herbivore species responded to seasonal variation in food resources and how they differed in their spatial patterns of resource utilization. Sable antelope herds tended to concentrate their space use locally, while zebra herds moved more opportunistically over a wider set of foraging arenas. The amalgamated extent of the foraging arenas exploited by sable herds amounted to 12-30 km2, compared with 22-100 km2 for the zebra herds. Half-day displacement distances differed between settlement periods and roaming interludes, and zebra herds generally shifted further over 12h than sable herds. Foraging arenas of sable herds tended to be smaller than those of zebra, and were occupied for period twice as long, and hence exploited more intensively in days spent per unit area than the foraging arenas of zebra. For sable both the intensity of utilization of foraging arenas and proportion of days spent in foraging arenas relative to roaming interludes declined as food resources diminished seasonally, while zebra showed no seasonal variation

  20. Improvement of red color development on the surface of kuruma prawn Marsupenaeus japonicus under various conditions.

    PubMed

    Ando, Masashi; Fukai, Takamitsu; Kawasaki, Ken-Ichi; Itoh, Tomohiro; Tsukamasa, Yasuyuki

    2014-02-01

    The degree of red color development on the surface of prawns by cooking is an important index for food quality. In this study, we tested several factors that are thought to influence the red color development to identify possible correlations with various conditions. Live kuruma prawns, Marsupenaeus japonicus, (15.4 cm, 25.2 g on average) were used in this study. In case of cooking at 100 °C for 1 min after 24 h of storage at 0 °C, 5 °C, and 20 °C, the red color development rate of prawns stored at 5 °C and 20 °C was significantly lower than that of prawns cooked just after killing. In case of cooking at 100 °C, 80 °C, and 60 °C after storage for 24 h at 0 °C, there was no color development at 60 °C and significantly less color development at 80 °C compared to cooking just after killing. Preparation using 1% sodium carbonate before cooking at 80 °C could compensate for the lack of red color development. Short exposure of live kuruma prawns to low-oxygen conditions had no influence on the color development, but putting the prawns in freshwater for 3 h significantly reduced the red color development rate. In conclusion, the storage time has little influence on the red color development when the cooking temperature is sufficiently high. However, in case a large amount of prawns is cooked followed by lowering the cooking temperature and/or prawns are exposed to serious stresses before cooking, an alkaline preparation could compensate for the lack of red color development.

  1. Large-Scale Screening of a Targeted Enterococcus faecalis Mutant Library Identifies Envelope Fitness Factors

    PubMed Central

    Rigottier-Gois, Lionel; Alberti, Adriana; Houel, Armel; Taly, Jean-François; Palcy, Philippe; Manson, Janet; Pinto, Daniela; Matos, Renata C.; Carrilero, Laura; Montero, Natalia; Tariq, Muhammad; Karsens, Harma; Repp, Christian; Kropec, Andrea; Budin-Verneuil, Aurélie; Benachour, Abdellah; Sauvageot, Nicolas; Bizzini, Alain; Gilmore, Michael S.; Bessières, Philippe; Kok, Jan; Huebner, Johannes; Lopes, Fatima; Gonzalez-Zorn, Bruno; Hartke, Axel; Serror, Pascale

    2011-01-01

    Spread of antibiotic resistance among bacteria responsible for nosocomial and community-acquired infections urges for novel therapeutic or prophylactic targets and for innovative pathogen-specific antibacterial compounds. Major challenges are posed by opportunistic pathogens belonging to the low GC% Gram-positive bacteria. Among those, Enterococcus faecalis is a leading cause of hospital-acquired infections associated with life-threatening issues and increased hospital costs. To better understand the molecular properties of enterococci that may be required for virulence, and that may explain the emergence of these bacteria in nosocomial infections, we performed the first large-scale functional analysis of E. faecalis V583, the first vancomycin-resistant isolate from a human bloodstream infection. E. faecalis V583 is within the high-risk clonal complex 2 group, which comprises mostly isolates derived from hospital infections worldwide. We conducted broad-range screenings of candidate genes likely involved in host adaptation (e.g., colonization and/or virulence). For this purpose, a library was constructed of targeted insertion mutations in 177 genes encoding putative surface or stress-response factors. Individual mutants were subsequently tested for their i) resistance to oxidative stress, ii) antibiotic resistance, iii) resistance to opsonophagocytosis, iv) adherence to the human colon carcinoma Caco-2 epithelial cells and v) virulence in a surrogate insect model. Our results identified a number of factors that are involved in the interaction between enterococci and their host environments. Their predicted functions highlight the importance of cell envelope glycopolymers in E. faecalis host adaptation. This study provides a valuable genetic database for understanding the steps leading E. faecalis to opportunistic virulence. PMID:22194979

  2. Identification of xenobiotic biodegradation and metabolism-related genes in the copepod Tigriopus japonicus whole transcriptome analysis.

    PubMed

    Kim, Hui-Su; Lee, Bo-Young; Won, Eun-Ji; Han, Jeonghoon; Hwang, Dae-Sik; Park, Heum Gi; Lee, Jae-Seong

    2015-12-01

    In this study, the whole transcriptome of Tigriopus japonicus was sequenced using next generation sequencing technology. De novo assembly was performed using Trinity, which assembled 140,130 contigs. Transdecoder found 54,761 candidate coding contigs, 39,507 of which showed homology to other species covering 15,310 genes by BLAST analysis. Functional gene annotation was performed by Gene Ontology, InterProScan, and KEGG pathway analyses. In addition to various metabolism-related pathways, xenobiotic biodegradation and metabolism were other interesting pathways in T. japonicus. Transcripts encoding various enzymes (e.g. superoxide dismutase, heat shock protein, and peroxidases) in response to a variety of stimuli were identified, which might be useful candidate biomarkers for ecotoxicology studies.

  3. The K+-dependent asparaginase, NSE1, is crucial for plant growth and seed production in Lotus japonicus.

    PubMed

    Credali, Alfredo; García-Calderón, Margarita; Dam, Svend; Perry, Jillian; Díaz-Quintana, Antonio; Parniske, Martin; Wang, Trevor L; Stougaard, Jens; Vega, José M; Márquez, Antonio J

    2013-01-01

    The physiological role of K(+)-dependent and K(+)-independent asparaginases in plants remains unclear, and the contribution from individual isoforms during development is poorly understood. We have used reverse genetics to assess the phenotypes produced by the deficiency of K(+)-dependent NSE1 asparaginase in the model legume Lotus japonicus. For this purpose, four different mutants were identified by TILLING and characterized, two of which affected the structure and function of the asparaginase molecule and caused asparagine accumulation. Plant growth and total seed weight of mature mutant seeds as well as the level of both legumin and convicilin seed storage proteins were affected in the mutants. The mutants isolated in the present work are the first of their type in legumes and have enabled us to demonstrate the importance of asparagine and K(+)-dependent NSE1 asparaginase for nitrogen remobilization and seed production in L. japonicus plants.

  4. Identification and functional characterisation of 5-HT4 receptor in sea cucumber Apostichopus japonicus (Selenka)

    PubMed Central

    Wang, Tianming; Yang, Zhen; Zhou, Naiming; Sun, Lina; Lv, Zhenming; Wu, Changwen

    2017-01-01

    Serotonin (5-HT) is an important neurotransmitter and neuromodulator that controls a variety of sensory and motor functions through 5-HT receptors (5-HTRs). The 5-HT4R subfamily is linked to Gs proteins, which activate adenylyl cyclases (ACs), and is involved in many responses in peripheral organs. In this study, the 5-HT4R from Apostichopus japonicus (Aj5-HT4R) was identified and characterised. The cloned full-length Aj5-HT4R cDNA is 1,544 bp long and contains an open reading frame 1,011 bp in length encoding 336 amino acid proteins. Bioinformatics analysis of the Aj5-HT4R protein indicated this receptor was a member of class A G protein coupled receptor (GPCR) family. Further experiments using Aj5-HT4R-transfected HEK293 cells demonstrated that treatment with 5-HT triggered a significant increase in intracellular cAMP level in a dose-dependent manner and induced a rapid internalisation of Aj5-HT4R fused with enhanced green fluorescent protein (Aj5-HT4R-EGFP) from the cell surface into the cytoplasm. In addition, the transcriptional profiles of Aj5-HT4R in aestivating A. japonicas and phosphofructokinase (AjPFK) in 5-HT administrated A. japonicus have been analysed by real-time PCR assays. Results have led to a basic understanding of Aj5-HT4R in A. japonicus, and provide a foundation for further exploration of the cell signaling and regulatory functions of this receptor. PMID:28059140

  5. Two distinct EIN2 genes cooperatively regulate ethylene signaling in Lotus japonicus.

    PubMed

    Miyata, Kana; Kawaguchi, Masayoshi; Nakagawa, Tomomi

    2013-09-01

    Leguminous plants establish a mutualistic symbiosis with bacteria, collectively referred to as rhizobia. Host plants positively and negatively regulate the symbiotic processes to keep the symbiosis at an appropriate level. Although the plant hormone ethylene is known as a negative regulator of symbiotic processes, the molecular mechanisms of ethylene signaling remain unresolved, especially in the model plant Lotus japonicus. Here, we identified two genes, LjEIN2-1 and LjEIN2-2, from L. japonicus. These genes share moderate similarity in their amino acid sequences, are located on different chromosomes and are composed of different numbers of exons. Suppression of either LjEIN2-1 or LjEIN2-2 expression significantly promoted the root growth of transformed plants on plates containing 1-amino-cyclopropane-carboxylic acid (ACC), the biosynthetic precursor of ethylene. Simultaneous suppression of both LjEIN2-1 and LjEIN2-2 markedly increased the ethylene insensitivity of transgenic roots and resulted in an increased nodulation phenotype. These results indicate that LjEIN2-1 and LjEIN2-2 concertedly regulate ethylene signaling in L. japonicus. We also observed that Nod factor (NF) induced the expression of the ethylene-responsive gene LjACO2, and simultaneous treatment with NF and ACC markedly increases its transcript level compared with either NF or ACC alone. Because LjACO2 encodes ACC oxidase, which is a key enzyme in ethylene biosynthesis, this result suggests the existence of an NF-triggered negative feedback mechanism through ethylene signaling.

  6. Synchronous activation of cell division by light or temperature stimuli in the dimorphic yeast Schizosaccharomyces japonicus.

    PubMed

    Okamoto, Sho; Furuya, Kanji; Nozaki, Shingo; Aoki, Keita; Niki, Hironori

    2013-09-01

    Many fungi respond to light and regulate fungal development and behavior. A blue light-activated complex has been identified in Neurospora crassa as the product of the wc-1 and wc-2 genes. Orthologs of WC-1 and WC-2 have hitherto been found only in filamentous fungi and not in yeast, with the exception of the basidiomycete pathogenic yeast Cryptococcus. Here, we report that the fission yeast Schizosaccharomyces japonicus responds to blue light depending on Wcs1 and Wcs2, orthologs of components of the WC complex. Surprisingly, those of ascomycete S. japonicus are more closely related to those of the basidiomycete. S. japonicus reversibly changes from yeast to hyphae in response to environmental stresses. After incubation at 30°C, a colony of yeast was formed, and then hyphal cells extended from the periphery of the colony. When light cycles were applied, distinct dark- and bright-colored hyphal cell stripes were formed because the growing hyphal cells had synchronously activated cytokinesis. In addition, temperature cycles of 30°C for 12 h and 35°C for 12 h or of 25°C for 12 h and 30°C for 12 h during incubation in the dark induced a response in the hyphal cells similar to that of light. The stripe formation of the temperature cycles was independent of the wcs genes. Both light and temperature, which are daily external cues, have the same effect on growing hyphal cells. A dual sensing mechanism of external cues allows organisms to adapt to daily changes of environmental alteration.

  7. 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

  8. 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.

  9. 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.

  10. Characterisation of inorganic elements and volatile organic compounds in the dried sea cucumber Stichopus japonicus.

    PubMed

    Lee, Hae-Won; Lim, Na-Lae; Cho, Kichul; Yang, Hye Young; Yim, Kyung June; Kim, Mi-Ju; Lee, Myunglip; Kim, Dong Hyeun; Koh, Hyoung Bum; Jung, Won-Kyo; Roh, Seong Woon; Kim, Daekyung

    2014-03-15

    The sea cucumber Stichopus japonicus lives in a variety of marine habitats and is an important cultivated edible aquatic species in East Asia. In this study, S. japonicus, collected from the sea near Jeju Island of Korea, was lyophilised or vacuum-dried and then analysed by gas chromatography-mass spectrometry (GC-MS) or inductively coupled plasma mass spectrometry (ICP-MS). The GC-MS profiles of vacuum-dried and lyophilised samples differed. Based on direct injection and static headspace analysis, 37 volatile organic compounds (VOCs) were identified in vacuum-dried samples and 33 VOCs were identified in lyophilised samples. Therefore, the odour of vacuum-dried sea cucumber is thought to be due to the presence of various VOCs that are absent in lyophilised sea cucumber. According to ICP-MS analysis, the levels of 15 inorganic elements were slightly higher in lyophilised samples than in vacuum-dried samples. The results of the inorganic and organic chemical analyses provide information about the composition of dried sea cucumber.

  11. 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

  12. 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

  13. Overexpression of the Starch Phosphorylase-Like Gene (PHO3) in Lotus japonicus has a Profound Effect on the Growth of Plants and Reduction of Transitory Starch Accumulation

    PubMed Central

    Qin, Shanshan; Tang, Yuehui; Chen, Yaping; Wu, Pingzhi; Li, Meiru; Wu, Guojiang; Jiang, Huawu

    2016-01-01

    Two isoforms of starch phosphorylase (PHO; EC 2.4.1.1), plastidic PHO1 and cytosolic PHO2, have been found in all plants studied to date. Another starch phosphorylase-like gene, PHO3, which is an ortholog of Chlamydomonas PHOB, has been detected in some plant lineages. In this study, we identified three PHO isoform (LjPHO) genes in the Lotus japonicus genome. Expression of the LjPHO3 gene was observed in all tissues tested in L. japonicus, and the LjPHO3 protein was located in the chloroplast. Overexpression of LjPHO3 in L. japonicus resulted in a drastic decline in starch granule sizes and starch content in leaves. The LjPHO3 overexpression transgenic seedlings were smaller, and showed decreased pollen fertility and seed set rate. Our results suggest that LjPHO3 may participate in transitory starch metabolism in L. japonicus leaves, but its catalytic properties remain to be studied. PMID:27630651

  14. Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  15. 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.

  16. 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

  17. A Large-Scale Quantitative Proteomic Approach To Identifying Sulfur Mustard-Induced Protein Phosphorylation Cascades

    DTIC Science & Technology

    2009-07-31

    with immobilized metal affinity chromatography to study the large-scale protein phosphorylation changes resulting from SM exposure in a human...medium, resulting in isotopically “light” and “ heavy ” cell populations, respectively. Protein samples collected from control (light-labeled) and...experimental ( heavy -labeled) cells can then be mixed in equal ratios, digested with trypsin, and analyzed by high-resolution mass spectrometry. The

  18. Mechanism of resistance to fenoxaprop in Japanese foxtail (Alopecurus japonicus) from China.

    PubMed

    Xu, Hongle; Zhu, Xudong; Wang, Hongchun; Li, Jun; Dong, Liyao

    2013-09-01

    Japanese foxtail is one of the most common and troublesome weeds infesting cereal and oilseed rape fields in China. Repeated use during the last three decades of the ACCase-inhibiting herbicide fenoxaprop-P-ethyl to control this weed has resulted in the occurrence of resistance. Dose-response tests established that a population (AHFD-1) from eastern China had evolved high-level resistance to fenoxaprop-P-ethyl. Based on the resistance index, this resistant population of A. japonicus is 60.31-fold resistant to fenoxaprop-P-ethyl. Subsequently, only a tryptophan to cysteine substitution was identified to confer resistance to fenoxaprop-P-ethyl in this resistant population. ACCase activity tests further confirmed this substitution was linked to resistance. This is the first report of the occurrence of Trp-2027-Cys substitution of ACCase in A. japonicus. From whole-plant pot dose-response tests, we confirmed that this population conferred resistance to other APP herbicides, including clodinafop-propargyl, fluazifop-P-butyl, quizalofop-P-ethyl, haloxyfop-R-methyl, cyhalofop-butyl, metamifop, DEN herbicide pinoxaden, but not to CHD herbicides clethodim, sethoxydim. There was also no resistance observed to ALS-inhibiting herbicides sulfosulfuron, mesosulfuron-methyl, flucarbazone-sodium, pyroxsulam, Triazine herbicide prometryne and glyphosate. However, this resistant population was likely to confer slightly (or no) resistant to Urea herbicides chlortoluron and isoproturon.

  19. Nodule-specific regulation of phosphatidylinositol transfer protein expression in Lotus japonicus.

    PubMed

    Kapranov, P; Routt, S M; Bankaitis, V A; de Bruijn, F J; Szczyglowski, K

    2001-06-01

    Phosphatidylinositol transfer proteins (PITPs) modulate signal transduction pathways and membrane-trafficking functions in eukaryotes. Here, we describe the characterization of a gene family from Lotus japonicus that encodes a novel class of plant PITP-like proteins (LjPLPs) and that is regulated in an unusual nodule-specific manner. Members of this gene family were identified based on their nucleotide sequence homology with a previously described cDNA, LjNOD16, which encodes the L. japonicus late nodulin Nlj16. Nlj16 or highly related amino acid sequences are shown to constitute C-terminal domains of LjPLPs and are suggested to function as specific plasma membrane targeting modules. The expression patterns of one member of this gene family (LjPLP-IV) revealed that LjNOD16 mRNA synthesis in nodules is the result of the transcriptional activity of a nodule-specific promoter located in an intron of the LjPLP-IV gene. This intron-borne bidirectional promoter also generates nodule-specific antisense transcripts derived from the N-terminal PITP domain coding region of the LjPLP-IV gene. We propose that Nlj16 protein synthesis and LjPLP-IV antisense transcript generation are components of an elaborate mechanism designed to control LjPLP synthesis and/or functioning in nodules.

  20. Novel, highly expressed late nodulin gene (LjNOD16) from Lotus japonicus

    SciTech Connect

    Kapranov, P.; Bruijn, F.J. de; Szczyglowski, K.

    1997-04-01

    We have isolated a Lotus japonicus cDNA corresponding to a highly abundant, late nodule-specific RNA species that encodes a polypeptide with a predicted molecular mass of 15.6 kD. The protein and its corresponding gene were designated NIj16 and LjNOD16, respectively. LjNOD16 was found to be expressed only in the infected cells of L. japonicus nodules. Related DNA sequences could be identified in the genomes of both Glycine max and Medicago sativa. In the latter, a homologous mRNA species was detected in the nodules. Unlike LiNOD16, its alfalfa homologs appear to represent low-abundance mRNA species. However, the proteins corresponding to the LjNOD16 and its alfalfa homolog could be detected at similar levels in nodules but not in roots of both legume species. The predicted amino acid sequence analysis of nodulin NIj16 revealed the presence of a long {alpha}-helical region and a positively charged C terminus. The former domain has a very high propensity to form a coiled-coil type structure, indicating that nodulin NIj16 may interact with an as-yet-unidentified protein target(s) in the nodule-infected cells. Homology searches revealed no significant similarities to any known sequences in the databases, with the exception of two related, anonymous Arabidopsis expressed sequence tags.

  1. Identifying the Root Causes of Wait States in Large-Scale Parallel Applications

    SciTech Connect

    Böhme, David; Geimer, Markus; Arnold, Lukas; Voigtlaender, Felix; Wolf, Felix

    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 a 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.

  2. Identifying functional connectivity in large-scale neural ensemble recordings: a multiscale data mining approach.

    PubMed

    Eldawlatly, Seif; Jin, Rong; Oweiss, Karim G

    2009-02-01

    Identifying functional connectivity between neuronal elements is an essential first step toward understanding how the brain orchestrates information processing at the single-cell and population levels to carry out biological computations. This letter suggests a new approach to identify functional connectivity between neuronal elements from their simultaneously recorded spike trains. In particular, we identify clusters of neurons that exhibit functional interdependency over variable spatial and temporal patterns of interaction. We represent neurons as objects in a graph and connect them using arbitrarily defined similarity measures calculated across multiple timescales. We then use a probabilistic spectral clustering algorithm to cluster the neurons in the graph by solving a minimum graph cut optimization problem. Using point process theory to model population activity, we demonstrate the robustness of the approach in tracking a broad spectrum of neuronal interaction, from synchrony to rate co-modulation, by systematically varying the length of the firing history interval and the strength of the connecting synapses that govern the discharge pattern of each neuron. We also demonstrate how activity-dependent plasticity can be tracked and quantified in multiple network topologies built to mimic distinct behavioral contexts. We compare the performance to classical approaches to illustrate the substantial gain in performance.

  3. Differences in MITF gene expression and histology between albino and normal sea cucumbers ( Apostichopus japonicus Selenka)

    NASA Astrophysics Data System (ADS)

    Zhao, Heling; Yang, Hongsheng; Zhao, Huan; Liu, Shilin; Wang, Tianming

    2012-01-01

    Albino Apostichopus japonicus occur both in the wild and in captivity. The offspring of albino A. japonicus also suffer from albinism. The formation of melanin in the melanocytes is dependant on microphthalmia-associated transcription factor (MITF). To investigate the role of MITF in controlling albinism, we cloned the full-length MITF cDNA from A. japonicus and compared MITF mRNA expression in albino and normal A. japonicus. In addition, we used light and electron microscopy to compare histological samples of normal and albino A. japonicus. The body wall of albino adults was characterized by significantly lower levels of MITF expression and lower numbers of epidermal melanocytes, which also contained less melanin. In albino juvenile offspring, MITF expression levels were significantly lower 32 d after fertilization and there were fewer, and less developed, epidermal melanocytes. Thus, we conclude that albino A. japonicus have fewer melanocytes and a reduced ability to synthesize melanin, likely because of lower expression of MITF.

  4. 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

  5. Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules.

    PubMed

    Shively, Christian A; Kweon, Hye Kyong; Norman, Kaitlyn L; Mellacheruvu, Dattatreya; Xu, Tao; Sheidy, Daniel T; Dobry, Craig J; Sabath, Ivan; Cosky, Eric E P; Tran, Elizabeth J; Nesvizhskii, Alexey; Andrews, Philip C; Kumar, Anuj

    2015-10-01

    Yeast pseudohyphal filamentation is a stress-responsive growth transition relevant to processes required for virulence in pathogenic fungi. Pseudohyphal growth is controlled through a regulatory network encompassing conserved MAPK (Ste20p, Ste11p, Ste7p, Kss1p, and Fus3p), protein kinase A (Tpk2p), Elm1p, and Snf1p kinase pathways; however, the scope of these pathways is not fully understood. Here, we implemented quantitative phosphoproteomics to identify each of these signaling networks, generating a kinase-dead mutant in filamentous S. cerevisiae and surveying for differential phosphorylation. By this approach, we identified 439 phosphoproteins dependent upon pseudohyphal growth kinases. We report novel phosphorylation sites in 543 peptides, including phosphorylated residues in Ras2p and Flo8p required for wild-type filamentous growth. Phosphoproteins in these kinase signaling networks were enriched for ribonucleoprotein (RNP) granule components, and we observe co-localization of Kss1p, Fus3p, Ste20p, and Tpk2p with the RNP component Igo1p. These kinases localize in puncta with GFP-visualized mRNA, and KSS1 is required for wild-type levels of mRNA localization in RNPs. Kss1p pathway activity is reduced in lsm1Δ/Δ and pat1Δ/Δ strains, and these genes encoding P-body proteins are epistatic to STE7. The P-body protein Dhh1p is also required for hyphal development in Candida albicans. Collectively, this study presents a wealth of data identifying the yeast phosphoproteome in pseudohyphal growth and regulatory interrelationships between pseudohyphal growth kinases and RNPs.

  6. Identifying gene-environment interactions in schizophrenia: contemporary challenges for integrated, large-scale investigations.

    PubMed

    van Os, Jim; Rutten, Bart P; Myin-Germeys, Inez; Delespaul, Philippe; Viechtbauer, Wolfgang; van Zelst, Catherine; Bruggeman, Richard; Reininghaus, Ulrich; Morgan, Craig; Murray, Robin M; Di Forti, Marta; McGuire, Philip; Valmaggia, Lucia R; Kempton, Matthew J; Gayer-Anderson, Charlotte; Hubbard, Kathryn; Beards, Stephanie; Stilo, Simona A; Onyejiaka, Adanna; Bourque, Francois; Modinos, Gemma; Tognin, Stefania; Calem, Maria; O'Donovan, Michael C; Owen, Michael J; Holmans, Peter; Williams, Nigel; Craddock, Nicholas; Richards, Alexander; Humphreys, Isla; Meyer-Lindenberg, Andreas; Leweke, F Markus; Tost, Heike; Akdeniz, Ceren; Rohleder, Cathrin; Bumb, J Malte; Schwarz, Emanuel; Alptekin, Köksal; Üçok, Alp; Saka, Meram Can; Atbaşoğlu, E Cem; Gülöksüz, Sinan; Gumus-Akay, Guvem; Cihan, Burçin; Karadağ, Hasan; Soygür, Haldan; Cankurtaran, Eylem Şahin; Ulusoy, Semra; Akdede, Berna; Binbay, Tolga; Ayer, Ahmet; Noyan, Handan; Karadayı, Gülşah; Akturan, Elçin; Ulaş, Halis; Arango, Celso; Parellada, Mara; Bernardo, Miguel; Sanjuán, Julio; Bobes, Julio; Arrojo, Manuel; Santos, Jose Luis; Cuadrado, Pedro; Rodríguez Solano, José Juan; Carracedo, Angel; García Bernardo, Enrique; Roldán, Laura; López, Gonzalo; Cabrera, Bibiana; Cruz, Sabrina; Díaz Mesa, Eva Ma; Pouso, María; Jiménez, Estela; Sánchez, Teresa; Rapado, Marta; González, Emiliano; Martínez, Covadonga; Sánchez, Emilio; Olmeda, Ma Soledad; de Haan, Lieuwe; Velthorst, Eva; van der Gaag, Mark; Selten, Jean-Paul; van Dam, Daniella; van der Ven, Elsje; van der Meer, Floor; Messchaert, Elles; Kraan, Tamar; Burger, Nadine; Leboyer, Marion; Szoke, Andrei; Schürhoff, Franck; Llorca, Pierre-Michel; Jamain, Stéphane; Tortelli, Andrea; Frijda, Flora; Vilain, Jeanne; Galliot, Anne-Marie; Baudin, Grégoire; Ferchiou, Aziz; Richard, Jean-Romain; Bulzacka, Ewa; Charpeaud, Thomas; Tronche, Anne-Marie; De Hert, Marc; van Winkel, Ruud; Decoster, Jeroen; Derom, Catherine; Thiery, Evert; Stefanis, Nikos C; Sachs, Gabriele; Aschauer, Harald; Lasser, Iris; Winklbaur, Bernadette; Schlögelhofer, Monika; Riecher-Rössler, Anita; Borgwardt, Stefan; Walter, Anna; Harrisberger, Fabienne; Smieskova, Renata; Rapp, Charlotte; Ittig, Sarah; Soguel-dit-Piquard, Fabienne; Studerus, Erich; Klosterkötter, Joachim; Ruhrmann, Stephan; Paruch, Julia; Julkowski, Dominika; Hilboll, Desiree; Sham, Pak C; Cherny, Stacey S; Chen, Eric Y H; Campbell, Desmond D; Li, Miaoxin; Romeo-Casabona, Carlos María; Emaldi Cirión, Aitziber; Urruela Mora, Asier; Jones, Peter; Kirkbride, James; Cannon, Mary; Rujescu, Dan; Tarricone, Ilaria; Berardi, Domenico; Bonora, Elena; Seri, Marco; Marcacci, Thomas; Chiri, Luigi; Chierzi, Federico; Storbini, Viviana; Braca, Mauro; Minenna, Maria Gabriella; Donegani, Ivonne; Fioritti, Angelo; La Barbera, Daniele; La Cascia, Caterina Erika; Mulè, Alice; Sideli, Lucia; Sartorio, Rachele; Ferraro, Laura; Tripoli, Giada; Seminerio, Fabio; Marinaro, Anna Maria; McGorry, Patrick; Nelson, Barnaby; Amminger, G Paul; Pantelis, Christos; Menezes, Paulo R; Del-Ben, Cristina M; Gallo Tenan, Silvia H; Shuhama, Rosana; Ruggeri, Mirella; Tosato, Sarah; Lasalvia, Antonio; Bonetto, Chiara; Ira, Elisa; Nordentoft, Merete; Krebs, Marie-Odile; Barrantes-Vidal, Neus; Cristóbal, Paula; Kwapil, Thomas R; Brietzke, Elisa; Bressan, Rodrigo A; Gadelha, Ary; Maric, Nadja P; Andric, Sanja; Mihaljevic, Marina; Mirjanic, Tijana

    2014-07-01

    Recent years have seen considerable progress in epidemiological and molecular genetic research into environmental and genetic factors in schizophrenia, but methodological uncertainties remain with regard to validating environmental exposures, and the population risk conferred by individual molecular genetic variants is small. There are now also a limited number of studies that have investigated molecular genetic candidate gene-environment interactions (G × E), however, so far, thorough replication of findings is rare and G × E research still faces several conceptual and methodological challenges. In this article, we aim to review these recent developments and illustrate how integrated, large-scale investigations may overcome contemporary challenges in G × E research, drawing on the example of a large, international, multi-center study into the identification and translational application of G × E in schizophrenia. While such investigations are now well underway, new challenges emerge for G × E research from late-breaking evidence that genetic variation and environmental exposures are, to a significant degree, shared across a range of psychiatric disorders, with potential overlap in phenotype.

  7. Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution.

    PubMed

    Clarke, Thomas H; Garb, Jessica E; Hayashi, Cheryl Y; Arensburger, Peter; Ayoub, Nadia A

    2015-06-08

    The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae).

  8. Identifying Gene-Environment Interactions in Schizophrenia: Contemporary Challenges for Integrated, Large-scale Investigations

    PubMed Central

    2014-01-01

    Recent years have seen considerable progress in epidemiological and molecular genetic research into environmental and genetic factors in schizophrenia, but methodological uncertainties remain with regard to validating environmental exposures, and the population risk conferred by individual molecular genetic variants is small. There are now also a limited number of studies that have investigated molecular genetic candidate gene-environment interactions (G × E), however, so far, thorough replication of findings is rare and G × E research still faces several conceptual and methodological challenges. In this article, we aim to review these recent developments and illustrate how integrated, large-scale investigations may overcome contemporary challenges in G × E research, drawing on the example of a large, international, multi–center study into the identification and translational application of G × E in schizophrenia. While such investigations are now well underway, new challenges emerge for G × E research from late-breaking evidence that genetic variation and environmental exposures are, to a significant degree, shared across a range of psychiatric disorders, with potential overlap in phenotype. PMID:24860087

  9. Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution

    PubMed Central

    Clarke, Thomas H.; Garb, Jessica E.; Hayashi, Cheryl Y.; Arensburger, Peter; Ayoub, Nadia A.

    2015-01-01

    The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). PMID:26058392

  10. Identifying anomalously early spring onsets in the CESM large ensemble project

    NASA Astrophysics Data System (ADS)

    Labe, Zachary; Ault, Toby; Zurita-Milla, Raul

    2016-08-01

    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.

  11. 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

  12. Identifying large-scale patterns of unpredictability and response to insolation in atmospheric data

    PubMed Central

    Arizmendi, Fernando; Barreiro, Marcelo; Masoller, Cristina

    2017-01-01

    Understanding the complex dynamics of the atmosphere is of paramount interest due to its impact in the entire climate system and in human society. Here we focus on identifying, from data, the geographical regions which have similar atmospheric properties. We study surface air temperature (SAT) time series with monthly resolution, recorded at a regular grid covering the Earth surface. We consider two datasets: NCEP CDAS1 and ERA Interim reanalysis. We show that two surprisingly simple measures are able to extract meaningful information: i) the distance between the lagged SAT and the incoming solar radiation and ii) the Shannon entropy of SAT and SAT anomalies. The distance uncovers well-defined spatial patterns formed by regions with similar SAT response to solar forcing while the entropy uncovers regions with similar degree of SAT unpredictability. The entropy analysis also allows identifying regions in which SAT has extreme values. Importantly, we uncover differences between the two datasets which are due to the presence of extreme values in one dataset but not in the other. Our results indicate that the distance and entropy measures can be valuable tools for the study of other climatological variables, for anomaly detection and for performing model inter-comparisons. PMID:28358355

  13. 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

  14. 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

  15. Unexpected Patterns of Admixture in German Populations of Aedes japonicus japonicus (Diptera: Culicidae) Underscore the Importance of Human Intervention

    PubMed Central

    Zielke, Dorothee E.; Werner, Doreen; Schaffner, Francis; Kampen, Helge; Fonseca, Dina M.

    2014-01-01

    The mosquito Aedes japonicus japonicus, originally restricted to temperate East Asia, is now widespread in North America and more recently has become established in Europe. To ascertain the putative number of separate introductions to Europe and examine patterns of expansion we analyzed the genetic makeup of Ae. j. japonicus populations from five cemeteries in North Rhine-Westphalia and Rhineland-Palatinate, two western German federal states, as well as of specimens from populations in Belgium, Switzerland, and Austria/Slovenia. To do so, we genotyped individual specimens at seven pre-existing polymorphic microsatellite loci and sequenced part of the nad4 mitochondrial locus. We found evidence of two different genotypic signatures associated with different nad4 mitochondrial haplotypes, indicating at least two genetically differentiated populations of Ae. j. japonicus in Europe (i.e. two distinct genotypes). Belgian, Swiss, and Austrian/Slovenian populations all share the same genotypic signature although they have become differentiated since isolation. Contrary to expectations, the German Ae. j. japonicus are not closely related to those in Belgium which are geographically nearest but are also highly inbred. German populations have a unique genotype but also evidence of mixing between the two genotypes. Also unexpectedly, the populations closest to the center of the German infestation had the highest levels of admixture indicating that separate introductions did not expand and merge but instead their expansion was driven by punctuated human-mediated transport. Critically, the resulting admixed populations have higher genetic diversity and appear invasive as indicated by their increased abundance and recent spread across western Germany. PMID:24992470

  16. Managing more than the mean: Using quantile regression to identify factors related to large elk groups

    USGS Publications Warehouse

    Brennan, Angela K.; Cross, Paul C.; Creely, Scott

    2015-01-01

    Synthesis and applications. Our analysis of elk group size distributions using quantile regression suggests that private land, irrigation, open habitat, elk density and wolf abundance can affect large elk group sizes. Thus, to manage larger groups by removal or dispersal of individuals, we recommend incentivizing hunting on private land (particularly if irrigated) during the regular and late hunting seasons, promoting tolerance of wolves on private land (if elk aggregate in these areas to avoid wolves) and creating more winter range and varied habitats. Relationships to the variables of interest also differed by quantile, highlighting the importance of using quantile regression to examine response variables more completely to uncover relationships important to conservation and management.

  17. Large area stress distribution in crystalline materials calculated from lattice deformation identified by electron backscatter diffraction.

    PubMed

    Shao, Yongliang; Zhang, Lei; Hao, Xiaopeng; Wu, Yongzhong; Dai, Yuanbin; Tian, Yuan; Huo, Qin

    2014-08-05

    We report a method to obtain the stress of crystalline materials directly from lattice deformation by Hooke's law. The lattice deformation was calculated using the crystallographic orientations obtained from electron backscatter diffraction (EBSD) technology. The stress distribution over a large area was obtained efficiently and accurately using this method. Wurtzite structure gallium nitride (GaN) crystal was used as the example of a hexagonal crystal system. With this method, the stress distribution of a GaN crystal was obtained. Raman spectroscopy was used to verify the stress distribution. The cause of the stress distribution found in the GaN crystal was discussed from theoretical analysis and EBSD data. Other properties related to lattice deformation, such as piezoelectricity, can also be analyzed by this novel approach based on EBSD data.

  18. Use of laser microdissection for the construction of Humulus japonicus Siebold et Zuccarini, 1846 (Cannabaceae) sex chromosome-specific DNA library and cytogenetics analysis

    PubMed Central

    Yakovin, Nickolay A.; Divashuk, Mikhail G.; Razumova, Olga V.; Soloviev, Alexander A.; Karlov, Gennady I.

    2014-01-01

    Abstract Dioecy is relatively rare among plant species, and distinguishable sex chromosomes have been reported in few dioecious species. The multiple sex chromosome system (XX/XY1Y2) of Humulus japonicus Siebold et Zuccarini, 1846 differs from that of other members of the family Cannabaceae, in which the XX/XY chromosome system is present. Sex chromosomes of Humulus japonicus were isolated from meiotic chromosome spreads of males by laser microdissection with the P.A.L.M. MicroLaser system. The chromosomal DNA was directly amplified by degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR). Fast fluorescence in situ hybridization (FAST-FISH) using a labeled, chromosome-specific DOP-PCR product as a probe showed preferential hybridization to sex chromosomes. In addition, the DOP-PCR product was used to construct a short-insert, Humulus japonicus sex chromosomes-specific DNA library. The randomly sequenced clones showed that about 12% of them have significant homology to Humulus lupulus and 88% to Cannabis sativa Linnaeus, 1753 sequences from GenBank database. Forty-four percent of the sequences show homology to plant retroelements. It was concluded that laser microdissection is a useful tool for isolating the DNA of sex chromosomes of Humulus japonicus and for the construction of chromosome-specific DNA libraries for the study of the structure and evolution of sex chromosomes. The results provide the potential for identifying unique or sex chromosome-specific sequence elements in Humulus japonicus and could aid in the identification of sex chromosome-specific repeat and coding regions through chromosome isolation and genome complexity reduction. PMID:25610546

  19. 26 CFR 301.6867-1 - Presumptions where owner of large amount of cash is not identified.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... cash is not identified. 301.6867-1 Section 301.6867-1 Internal Revenue INTERNAL REVENUE SERVICE..., Bankruptcy, and Receiverships Jeopardy § 301.6867-1 Presumptions where owner of large amount of cash is not... 6861 (relating to jeopardy assessments), if cash in excess of $10,000 is found in the...

  20. An in vitro polysome display system for identifying ligands from very large peptide libraries.

    PubMed Central

    Mattheakis, L C; Bhatt, R R; Dower, W J

    1994-01-01

    We have used an in vitro protein synthesis system to construct a very large library of peptides displayed on polysomes. A pool of DNA sequences encoding 10(12) random decapeptides was incubated in an Escherichia coli S30 coupled transcription/translation system. Polysomes were isolated and screened by affinity selection of the nascent peptides on an immobilized monoclonal antibody specific for the peptide dynorphin B. The mRNA from the enriched pool of polysomes was recovered, copied into cDNA, and amplified by the polymerase chain reaction (PCR) to produce template for the next round of in vitro synthesis and selection. A portion of the amplified template from each round was cloned into a filamentous phagemid vector to determine the specificity of peptide binding by phage ELISA and to sequence the DNA. After four rounds of affinity selection, the majority of clones encoded peptides that bound specifically to the antibody and contained a consensus sequence that is similar to the known epitope for the antibody. Synthetic peptides corresponding to several of these sequences have binding affinities ranging from 7 to 140 nM. The in vitro system described here has the potential to screen peptide libraries that are three to six orders of magnitude larger than current biological peptide display systems. Images PMID:7522328

  1. Prospective Large-Scale Field Study Generates Predictive Model Identifying Major Contributors to Colony Losses

    PubMed Central

    Kielmanowicz, Merav Gleit; Inberg, Alex; Lerner, Inbar Maayan; Golani, Yael; Brown, Nicholas; Turner, Catherine Louise; Hayes, Gerald J. R.; Ballam, Joan M.

    2015-01-01

    Over the last decade, unusually high losses of colonies have been reported by beekeepers across the USA. Multiple factors such as Varroa destructor, bee viruses, Nosema ceranae, weather, beekeeping practices, nutrition, and pesticides have been shown to contribute to colony losses. Here we describe a large-scale controlled trial, in which different bee pathogens, bee population, and weather conditions across winter were monitored at three locations across the USA. In order to minimize influence of various known contributing factors and their interaction, the hives in the study were not treated with antibiotics or miticides. Additionally, the hives were kept at one location and were not exposed to potential stress factors associated with migration. Our results show that a linear association between load of viruses (DWV or IAPV) in Varroa and bees is present at high Varroa infestation levels (>3 mites per 100 bees). The collection of comprehensive data allowed us to draw a predictive model of colony losses and to show that Varroa destructor, along with bee viruses, mainly DWV replication, contributes to approximately 70% of colony losses. This correlation further supports the claim that insufficient control of the virus-vectoring Varroa mite would result in increased hive loss. The predictive model also indicates that a single factor may not be sufficient to trigger colony losses, whereas a combination of stressors appears to impact hive health. PMID:25875764

  2. Prospective large-scale field study generates predictive model identifying major contributors to colony losses.

    PubMed

    Kielmanowicz, Merav Gleit; Inberg, Alex; Lerner, Inbar Maayan; Golani, Yael; Brown, Nicholas; Turner, Catherine Louise; Hayes, Gerald J R; Ballam, Joan M

    2015-04-01

    Over the last decade, unusually high losses of colonies have been reported by beekeepers across the USA. Multiple factors such as Varroa destructor, bee viruses, Nosema ceranae, weather, beekeeping practices, nutrition, and pesticides have been shown to contribute to colony losses. Here we describe a large-scale controlled trial, in which different bee pathogens, bee population, and weather conditions across winter were monitored at three locations across the USA. In order to minimize influence of various known contributing factors and their interaction, the hives in the study were not treated with antibiotics or miticides. Additionally, the hives were kept at one location and were not exposed to potential stress factors associated with migration. Our results show that a linear association between load of viruses (DWV or IAPV) in Varroa and bees is present at high Varroa infestation levels (>3 mites per 100 bees). The collection of comprehensive data allowed us to draw a predictive model of colony losses and to show that Varroa destructor, along with bee viruses, mainly DWV replication, contributes to approximately 70% of colony losses. This correlation further supports the claim that insufficient control of the virus-vectoring Varroa mite would result in increased hive loss. The predictive model also indicates that a single factor may not be sufficient to trigger colony losses, whereas a combination of stressors appears to impact hive health.

  3. Effect of intestinal autochthonous probiotics isolated from the gut of sea cucumber (Apostichopus japonicus) on immune response and growth of A. japonicus.

    PubMed

    Chi, Cheng; Liu, Jia-Yan; Fei, Shi-Zhou; Zhang, Chao; Chang, Ya-Qing; Liu, Xiao-Lin; Wang, Gao-Xue

    2014-06-01

    The study isolated 224 bacteria from the intestine of Apostichopus japonicus, then selected and identified three of the bacteria (HS1, HS7, and HS10) which demonstrated amylase, lipase, and protease production capacity as candidate probiotics for sea cucumbers. The three potential probiotics showed no pathogenicity both in hemolytic assays on sheep blood agar plates and after immersing sea cucumbers in a suspension of the bacteria. To reveal the effects of these three potential probiotics on the innate immunity of sea cucumbers, total coelomocyte counts, respiratory burst activity, superoxide dismutase activity, lysozyme activity, acid phosphatase activity, and phagocytic activity by coelomocytes were examined after feeding with four different diets for up to 28 days. Also the specific growth rate and survival rate were investigated after a 60-day feeding trial. Sea cucumbers were fed with 4 diets: one control, three diets supplemented with 1 × 10(9) cell g(-1) of HS1, HS7, and HS10 for 28-60 days. Results showed that sea cucumbers fed diets containing HS1, HS7, and HS10 had led to an enhanced cellular and humoral immune response, notably higher total coelomocytes counts, respiratory burst activity, lysozyme activity, acid phosphatase activity, and phagocytic activity, as recorded during the four weeks of probiotics administration. On the other hand, the survival rate among dietary treatments ranged from 90.71 to 97.97% with significant improvement (P < 0.05) compared to that of the control; and the growth rate observed in the sea cucumbers fed HS1 and HS7 showed sharp increases after 60 days feeding. The present study confirmed the potential beneficial effects of Pseudoalteromonas elyakovii HS1, Shewanella japonica HS7, and Vibrio tasmaniensis HS10 as dietary probiotics in A. japonicus.

  4. Large-scale neurochemical metabolomics analysis identifies multiple compounds associated with methamphetamine exposure

    PubMed Central

    Adkins, Daniel E.; Vunck, Sarah A.; Batman, Angela M.; Vann, Robert E.; Clark, Shaunna L.; Beardsley, Patrick M.; van den Oord, Edwin J. C. G.

    2012-01-01

    Methamphetamine (MA) is an illegal stimulant drug of abuse with serious negative health consequences. The neurochemical effects of MA have been partially characterized, with a traditional focus on classical neurotransmitter systems. However, these directions have not yet led to novel drug treatments for MA abuse or toxicity. As an alternative approach, we describe here the first application of metabolomics to investigate the neurochemical consequences of MA exposure in the rodent brain. We examined single exposures at 3 mg/kg and repeated exposures at 3 mg/kg over 5 days in eight common inbred mouse strains. Brain tissue samples were assayed using high-throughput gas and liquid chromatography mass spectrometry, yielding quantitative data on >300 unique metabolites. Association testing and false discovery rate control yielded several metabolome-wide significant associations with acute MA exposure, including compounds such as lactate (p = 4.4 × 10−5, q = 0.013), tryptophan (p = 7.0 × 10−4, q = 0.035) and 2-hydroxyglutarate (p = 1.1 × 10−4, q = 0.022). Secondary analyses of MA-induced increase in locomotor activity showed associations with energy metabolites such as succinate (p = 3.8 × 10−7). Associations specific to repeated (5 day) MA exposure included phosphocholine (p = 4.0 × 10−4, q = 0.087) and ergothioneine (p = 3.0 × 10−4, q = 0.087). Our data appear to confirm and extend existing models of MA action in the brain, whereby an initial increase in energy metabolism, coupled with an increase in behavioral locomotion, gives way to disruption of mitochondria and phospholipid pathways and increased endogenous antioxidant response. Our study demonstrates the power of comprehensive MS-based metabolomics to identify drug-induced changes to brain metabolism and to develop neurochemical models of drug effects. PMID:23554582

  5. High-resolution sulfur isotopes in ice cores identify large stratospheric volcanic eruptions

    NASA Astrophysics Data System (ADS)

    Burke, Andrea; Sigl, Michael; Adkins, Jess; Paris, Guillaume; McConnell, Joe

    2016-04-01

    The record of the volcanic forcing of climate over the past 2500 years is reconstructed primarily from sulfate concentrations in ice cores. Of particular interest are stratospheric eruptions, as these afford sulfate aerosols the longest residence time and largest dispersion in the atmosphere, and thus the greatest impact on radiative forcing. Identification of stratospheric eruptions currently relies on the successful matching of the same volcanic sulphate peak in ice cores from both the Northern and Southern hemispheres (a "bipolar event"). These are interpreted to reflect the global distribution of sulfur aerosols by the stratospheric winds. Despite its recent success, this method relies on precise and accurate dating of ice cores, in order to distinguish between a true 'bipolar event' and two separate eruptions that occurred in close temporal succession. Sulfur isotopes can been used to distinguish between these two scenarios since stratospheric sulfur aerosols are exposed to UV radiation which imparts a mass independent fractionation (Baroni et al., 2007). Mass independent fractionation of sulfate in ice cores thus offers a novel method of fingerprinting stratospheric eruptions, and thus refining the historic record of explosive volcanism and its forcing of climate. Here we present new high-resolution (sub-annual) sulfur isotope data from the Tunu Ice core in Greenland over seven eruptions. Sulfur isotopes were measured by MC-ICP-MS, which substantially reduces sample size requirements and allows high temporal resolution from a single ice core. We demonstrate the efficacy of the method on recent, well-known eruptions (including Pinatubo and Katmai/Novarupta), and then apply it to unidentified sulfate peaks, allowing us to identify new stratospheric eruptions. Baroni, M., Thiemens, M. H., Delmas, R. J., & Savarino, J. (2007). Mass-independent sulfur isotopic compositions in stratospheric volcanic eruptions. Science, 315(5808), 84-87. http://doi.org/10

  6. Large-Scale Transposition Mutagenesis of Streptomyces coelicolor Identifies Hundreds of Genes Influencing Antibiotic Biosynthesis.

    PubMed

    Xu, Zhong; Wang, Yemin; Chater, Keith F; Ou, Hong-Yu; Xu, H Howard; Deng, Zixin; Tao, Meifeng

    2017-03-15

    Gram-positive Streptomyces bacteria produce thousands of bioactive secondary metabolites, including antibiotics. To systematically investigate genes affecting secondary metabolism, we developed a hyperactive transposase-based Tn5 transposition system and employed it to mutagenize the model species Streptomyces coelicolor, leading to the identification of 51,443 transposition insertions. These insertions were distributed randomly along the chromosome except for some preferred regions associated with relatively low GC content in the chromosomal core. The base composition of the insertion site and its flanking sequences compiled from the 51,443 insertions implied a 19-bp expanded target site surrounding the insertion site, with a slight nucleic acid base preference in some positions, suggesting a relative randomness of Tn5 transposition targeting in the high-GC Streptomyces genome. From the mutagenesis library, 724 mutants involving 365 genes had altered levels of production of the tripyrrole antibiotic undecylprodigiosin (RED), including 17 genes in the RED biosynthetic gene cluster. Genetic complementation revealed that most of the insertions (more than two-thirds) were responsible for the changed antibiotic production. Genes associated with branched-chain amino acid biosynthesis, DNA metabolism, and protein modification affected RED production, and genes involved in signaling, stress, and transcriptional regulation were overrepresented. Some insertions caused dramatic changes in RED production, identifying future targets for strain improvement.IMPORTANCE High-GC Gram-positive streptomycetes and related actinomycetes have provided more than 100 clinical drugs used as antibiotics, immunosuppressants, and antitumor drugs. Their genomes harbor biosynthetic genes for many more unknown compounds with potential as future drugs. Here we developed a useful genome-wide mutagenesis tool based on the transposon Tn5 for the study of secondary metabolism and its regulation

  7. Expanded polystyrene (EPS) floats for surveillance of Ochlerotatus japonicus.

    PubMed

    Scott, Jamesina J; Crans, Wayne J

    2003-12-01

    Blocks of expanded polystyrene (EPS) were placed in a variety of habitats to investigate their potential as an egg-collection device for container-dwelling Aedes and Ochlerotatus species. Eggs from Ochlerotatus japonicus, Oc. triseriatus, Oc. hendersoni, and Aedes albopictus were collected with EPS floats. The float provides an inexpensive, low-maintenance alternative to the Centers for Disease Control ovitrap for sampling container-dwelling mosquito species that are important vectors of disease. Eggs collected on the floats have many potential applications, including use in routine population surveillance; detection of Oc. japonicus, Ae. albopictus, and other container-dwelling species in new areas; species distribution studies; natural transovarial transmission studies; ovipositional studies; collection of local field populations for insecticide resistance assays; assessment of adulticiding efficacy; and establishment of new laboratory colonies.

  8. Petasites japonicus Stimulates the Proliferation of Mouse Spermatogonial Stem Cells

    PubMed Central

    Kim, Yong-Hee; Lee, Dong Gu; Kim, Bang-Jin; Kim, Ki-Jung; Kim, Byung-Gak; Oh, Myeong-Geun; Han, Chan Kyu; Lee, Sanghyun; Ryu, Buom-Yong

    2015-01-01

    Oriental natural plants have been used as medical herbs for the treatment of various diseases for over 2,000 years. In this study, we evaluated the effect of several natural plants on the preservation of male fertility by assessing the ability of plant extracts to stimulate spermatogonial stem cell (SSC) proliferation by using a serum-free culture method. In vitro assays showed that Petasites japonicus extracts, especially the butanol fraction, have a significant effect on germ cells proliferation including SSCs. The activity of SSCs cultured in the presence of the Petasites japonicus butanol fraction was confirmed by normal colony formation and spermatogenesis following germ cell transplantation of the treated SSCs. Our findings could lead to the discovery of novel factors that activate SSCs and could be useful for the development of technologies for the prevention of male infertility. PMID:26207817

  9. Phyllosticta ophiopogonis sp. nov. from Ophiopogon japonicus (Liliaceae)

    PubMed Central

    Wikee, S.; Wulandari, N.F.; McKenzie, E.H.C.; Hyde, K.D.

    2011-01-01

    A leaf spotting disease of an ornamental variety of Ophiopogon japonicus was discovered at several locations in northern Thailand. In all cases a species of Phyllosticta was associated with the lesions. Phyllosticta ophiopogonis sp. nov. is distinguished from Phyllosticta species from Liliaceae in conidia size, mucilaginous sheath and appendage thus the species is introduced as new in this paper. The new species which causes unsightly lesions on this ornamental plant is described, illustrated and compared with other similar Phyllosticta species. PMID:23961156

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

    PubMed Central

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

    2016-01-01

    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. PMID:26905381

  11. 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.

  12. Automated NMR fragment based screening identified a novel interface blocker to the LARG/RhoA complex.

    PubMed

    Gao, Jia; Ma, Rongsheng; Wang, Wei; Wang, Na; Sasaki, Ryan; Snyderman, David; Wu, Jihui; Ruan, Ke

    2014-01-01

    The small GTPase cycles between the inactive GDP form and the activated GTP form, catalyzed by the upstream guanine exchange factors. The modulation of such process by small molecules has been proven to be a fruitful route for therapeutic intervention to prevent the over-activation of the small GTPase. The fragment based approach emerging in the past decade has demonstrated its paramount potential in the discovery of inhibitors targeting such novel and challenging protein-protein interactions. The details regarding the procedure of NMR fragment screening from scratch have been rarely disclosed comprehensively, thus restricts its wider applications. To achieve a consistent screening applicable to a number of targets, we developed a highly automated protocol to cover every aspect of NMR fragment screening as possible, including the construction of small but diverse libray, determination of the aqueous solubility by NMR, grouping compounds with mutual dispersity to a cocktail, and the automated processing and visualization of the ligand based screening spectra. We exemplified our streamlined screening in RhoA alone and the complex of the small GTPase RhoA and its upstream guanine exchange factor LARG. Two hits were confirmed from the primary screening in cocktail and secondary screening over individual hits for LARG/RhoA complex, while one of them was also identified from the screening for RhoA alone. HSQC titration of the two hits over RhoA and LARG alone, respectively, identified one compound binding to RhoA.GDP at a 0.11 mM affinity, and perturbed the residues at the switch II region of RhoA. This hit blocked the formation of the LARG/RhoA complex, validated by the native gel electrophoresis, and the titration of RhoA to ¹⁵N labeled LARG in the absence and presence the compound, respectively. It therefore provides us a starting point toward a more potent inhibitor to RhoA activation catalyzed by LARG.

  13. Automated NMR Fragment Based Screening Identified a Novel Interface Blocker to the LARG/RhoA Complex

    PubMed Central

    Gao, Jia; Ma, Rongsheng; Wang, Wei; Wang, Na; Sasaki, Ryan; Snyderman, David; Wu, Jihui; Ruan, Ke

    2014-01-01

    The small GTPase cycles between the inactive GDP form and the activated GTP form, catalyzed by the upstream guanine exchange factors. The modulation of such process by small molecules has been proven to be a fruitful route for therapeutic intervention to prevent the over-activation of the small GTPase. The fragment based approach emerging in the past decade has demonstrated its paramount potential in the discovery of inhibitors targeting such novel and challenging protein-protein interactions. The details regarding the procedure of NMR fragment screening from scratch have been rarely disclosed comprehensively, thus restricts its wider applications. To achieve a consistent screening applicable to a number of targets, we developed a highly automated protocol to cover every aspect of NMR fragment screening as possible, including the construction of small but diverse libray, determination of the aqueous solubility by NMR, grouping compounds with mutual dispersity to a cocktail, and the automated processing and visualization of the ligand based screening spectra. We exemplified our streamlined screening in RhoA alone and the complex of the small GTPase RhoA and its upstream guanine exchange factor LARG. Two hits were confirmed from the primary screening in cocktail and secondary screening over individual hits for LARG/RhoA complex, while one of them was also identified from the screening for RhoA alone. HSQC titration of the two hits over RhoA and LARG alone, respectively, identified one compound binding to RhoA.GDP at a 0.11 mM affinity, and perturbed the residues at the switch II region of RhoA. This hit blocked the formation of the LARG/RhoA complex, validated by the native gel electrophoresis, and the titration of RhoA to 15N labeled LARG in the absence and presence the compound, respectively. It therefore provides us a starting point toward a more potent inhibitor to RhoA activation catalyzed by LARG. PMID:24505392

  14. 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.

  15. RNA-seq dependent transcriptional analysis unveils gene expression profile in the intestine of sea cucumber Apostichopus japonicus during aestivation.

    PubMed

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

    2014-06-01

    The seasonal marine, the sea cucumber Apostichopus japonicus (Selenka, 1867), cycles annually between periods of torpor when water temperature is above about 25°C in summer and active life when temperature is below about 18°C. This species is a good candidate model organism for studies of environmentally-induced aestivation in marine invertebrates. Previous studies have examined various aspects of aestivation of A. japonicus, however, knowledge of the molecular regulation underpinning these events is still fragmentary. In the present study, we constructed a global gene expression profile of the intestine tissue of A. japonicus using RNA-seq to identify transcriptional responses associated with transitions between different states: non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA). The analysis identified 1245 differentially expressed genes (DEGs) between DA vs. NA states, 1338 DEGs between AA vs. DA, and 1321 DEGs between AA vs. NA using the criteria |Log2Ratio|≥1 and FDR≤0.001. Of these, 25 of the most significant DEGs were verified by real-time PCR, showing trends in expression patterns that were almost in full concordance between the two techniques. GO analysis revealed that for DA vs. NA, 24 metabolic associated processes were highly enriched (corrected p value<0.05) whereas for AA vs. NA, 12 transport and metabolism associated processes were significantly enriched (corrected p value<0.05). Pathways associated with aestivation were also mined, and indicated that most DEGs were enriched in metabolic and signal transduction pathways in the deep aestivation stage. Two up pathways were significantly enriched at the arousal stage (ribosome and metabolism of xenobiotics by cytochrome P450 pathway). A set of key DEGs was identified that may play vital roles in aestivation; these involved metabolism, detoxification and tissue protection, and energy-expensive processes. Our work presents an overview of dynamic gene expression in torpor

  16. An Unusual Intrinsically Disordered Protein from the Model Legume Lotus japonicus Stabilizes Proteins in Vitro*

    PubMed Central

    Haaning, Svend; Radutoiu, Simona; Hoffmann, Søren V.; Dittmer, Jens; Giehm, Lise; Otzen, Daniel E.; Stougaard, Jens

    2008-01-01

    Intrinsic structural disorder is a prevalent feature of proteins with chaperone activity. Using a complementary set of techniques, we have structurally characterized LjIDP1 (intrinsically disordered protein 1) from the model legume Lotus japonicus, and our results provide the first structural characterization of a member of the Lea5 protein family (PF03242). Contrary to in silico predictions, we show that LjIDP1 is intrinsically disordered and probably exists as an ensemble of conformations with limited residual β-sheet, turn/loop, and polyproline II secondary structure. Furthermore, we show that LjIDP1 has an inherent propensity to undergo a large conformational shift, adopting a largely α-helical structure when it is dehydrated and in the presence of different detergents and alcohols. This is consistent with an overrepresentation of order-promoting residues in LjIDP1 compared with the average of intrinsically disordered proteins. In line with functioning as a chaperone, we show that LjIDP1 effectively prevents inactivation of two model enzymes under conditions that promote protein misfolding and aggregation. The LjIdp1 gene is expressed in all L. japonicus tissues tested. A higher expression level was found in the root tip proximal zone, in roots inoculated with compatible endosymbiotic M. loti, and in functional nitrogen-fixing root nodules. We suggest that the ability of LjIDP1 to prevent protein misfolding and aggregation may play a significant role in tissues, such as symbiotic root nodules, which are characterized by high metabolic activity. PMID:18779323

  17. 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.

  18. ROP6 is involved in root hair deformation induced by Nod factors in Lotus japonicus.

    PubMed

    Ke, Danxia; Li, Xiangyong; Han, Yapeng; Cheng, Lin; Yuan, Hongyu; Wang, Lei

    2016-11-01

    Roots of leguminous plants perceive Nod factor signals, and then root hair deformation responses such as swelling and curling are activated. However, very little is known about the molecular mechanisms of such root hair deformation. We have previously shown that LjROP6, a member of the Rho family of small GTPases, was identified as an NFR5 (Nod Factor Receptor 5)-interacting protein and participated in symbiotic nodulation in Lotus japonicus. In this study, we identified ten LjROP GTPases including LjROP6, and they were distributed into groups II, III, IV but not group I by phylogenetic analysis. The expression profiles of ten LjROP genes during nodulation were examined. LjROP6 belonged to group IV and interacted with NFR5 in a GTP-dependent manner. Overexpression of either wild-type ROP6 or a constitutively active mutant (ROP6-CA) generated root hair tip growth depolarization, while overexpression of a dominant negative mutant (ROP6-DN) exhibited normal root hair growth. After inoculating with Mesorhizobium loti or adding Nod factors to hairy roots, overexpression of ROP6 and ROP6-CA exhibited extensive root hair deformation, while overexpression of ROP6-DN inhibited root hair deformation. The infection event and nodule number were increased in ROP6 and ROP6-CA overexpressing transgenic plants; but decreased in ROP6-DN overexpressing transgenic plants. These studies provide strong evidence that ROP6 GTPase, which binds NFR5 in a GTP-dependent manner, is involved in root hair development as well as root hair deformation responses induced by NFs in the early stage of symbiotic interaction in L. japonicus.

  19. Status of Aedes japonicus in the Metropolitan Mosquito Control District, Minnesota.

    PubMed

    Johnson, Kirk A; Brogren, Sandra J; Crane, Diann M; Lamere, Carey A

    2010-09-01

    ABSTRACT. The Asian exotic mosquito Aedes japonicus was 1st collected in Minnesota in 2007 and was well established in parts of the Metropolitan Mosquito Control District (MMCD) by 2008. Surveillance strategies were devised for 2009 to track the expansion of its range through MMCD and to direct control efforts. Sampling of larvae from container and tire habitats was the primary method used to document Ae. japonicus presence, but larvae were found in other habitats as well. Adult Ae. japonicus were collected by vacuum aspirator, gravid trap, and New Jersey trap but not by CO2-baited Centers for Disease Control and Prevention light trap. Aedes japonicus were collected from each of the 7 counties surveyed; in 5 of the counties for the 1st time in 2009. Preliminary findings suggest that a control strategy involving intensive source reduction can reduce Ae. japonicus populations.

  20. Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families.

    PubMed

    Seidl, Michael F; Van den Ackerveken, Guido; Govers, Francine; Snel, Berend

    2012-01-01

    The taxonomic class of oomycetes contains numerous pathogens of plants and animals but is related to nonpathogenic diatoms and brown algae. Oomycetes have flexible genomes comprising large gene families that play roles in pathogenicity. The evolutionary processes that shaped the gene content have not yet been studied by applying systematic tree reconciliation of the phylome of these species. We analyzed evolutionary dynamics of ten Stramenopiles. Gene gains, duplications, and losses were inferred by tree reconciliation of 18,459 gene trees constituting the phylome with a highly supported species phylogeny. We reconstructed a strikingly large last common ancestor of the Stramenopiles that contained ~10,000 genes. Throughout evolution, the genomes of pathogenic oomycetes have constantly gained and lost genes, though gene gains through duplications outnumber the losses. The branch leading to the plant pathogenic Phytophthora genus was identified as a major transition point characterized by increased frequency of duplication events that has likely driven the speciation within this genus. Large gene families encoding different classes of enzymes associated with pathogenicity such as glycoside hydrolases are formed by complex and distinct patterns of duplications and losses leading to their expansion in extant oomycetes. This study unveils the large-scale evolutionary dynamics that shaped the genomes of pathogenic oomycetes. By the application of phylogenetic based analyses methods, it provides additional insights that shed light on the complex history of oomycete genome evolution and the emergence of large gene families characteristic for this important class of pathogens.

  1. Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

    NASA Astrophysics Data System (ADS)

    Lu, Xia; Luan, Sheng; Kong, Jie; Hu, Longyang; Mao, Yong; Zhong, Shengping

    2017-01-01

    The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplified with specific products and 24 (80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.

  2. Large-scale chemical similarity networks for target profiling of compounds identified in cell-based chemical screens.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Li, Chien-Ming; Hu, Qiyang; Huang, Yong; Damoiseaux, Robert; Torres, Jorge Z

    2015-03-01

    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/).

  3. Release method and anatomical hook location: effects on short-term mortality of angler-caught Acanthopagrus australis and Argyrosomus japonicus.

    PubMed

    Butcher, Paul A; Broadhurst, Matt K; Reynolds, Darren; Reid, Dennis D; Gray, Charles A

    2007-02-08

    One field and 3 aquaria experiments were done to quantify the short-term mortality of yellowfin bream Acanthopagrus australis and mulloway Argyrosomus japonicus after being angled and subjected to 3 general handling treatments. Anglers were supplied with identical J-type hooks and asked to handle hooked fish by either (1) physically removing the hook or (2) cutting the line (5 cm from the mouth of the fish) and leaving the hook in. Some hooked A. japonicus were subjected to a third handling treatment where the line was cut underwater without exposing the fish to air. Technical and biological data were collected before all fish were released into sea cages and monitored for 5 d. Control fish were seined and similarly caged and monitored. Concentrations of plasma glucose and cortisol were collected from a sample of fish on the first and last day of the experiments. Significant predictors of mortality for both species involved the presence of blood at the mouth and an interaction between anatomical hook location and hook removal. A. australis and A. japonicus that had their ingested hooks removed experienced the greatest mortalities (87.5 and 72.7%, respectively). Typically, these fish suffered damage to their oesophagus, stomach wall and vital organs. Mortality rates of A. australis and A. japonicus were significantly decreased to 1.7 and 16%, respectively, when they were released with their lines cut, with some of these fish free of hooks after 5 d. In contrast, few mortalities occurred in either species when the hooks were removed or the lines cut on mouth-hooked fish or in A. japonicus when it was released with no air exposure. For A. australis, the field- and aquaria-based experiments provided comparable results in terms of identifying treatment-specific effects, but there were potential biases in rates of hook ingestion. Irrespective of the treatment of fish, all experiments caused physiological changes measured as elevations in either plasma cortisol or glucose

  4. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression

    PubMed Central

    Rhodes, Daniel R.; Yu, Jianjun; Shanker, K.; Deshpande, Nandan; Varambally, Radhika; Ghosh, Debashis; Barrette, Terrence; Pandey, Akhilesh; Chinnaiyan, Arul M.

    2004-01-01

    Many studies have used DNA microarrays to identify the gene expression signatures of human cancer, yet the critical features of these often unmanageably large signatures remain elusive. To address this, we developed a statistical method, comparative metaprofiling, which identifies and assesses the intersection of multiple gene expression signatures from a diverse collection of microarray data sets. We collected and analyzed 40 published cancer microarray data sets, comprising 38 million gene expression measurements from >3,700 cancer samples. From this, we characterized a common transcriptional profile that is universally activated in most cancer types relative to the normal tissues from which they arose, likely reflecting essential transcriptional features of neoplastic transformation. In addition, we characterized a transcriptional profile that is commonly activated in various types of undifferentiated cancer, suggesting common molecular mechanisms by which cancer cells progress and avoid differentiation. Finally, we validated these transcriptional profiles on independent data sets. PMID:15184677

  5. Statistical Analyses of Scatterplots to Identify Important Factors in Large-Scale Simulations, 2. Robustness of Techniques

    SciTech Connect

    Helton, J.C.; Kleijnen, J.P.C.

    1999-03-24

    Procedures for identifying patterns in scatterplots generated in Monte Carlo sensitivity analyses are described and illustrated. These procedures attempt to detect increasingly complex patterns in scatterplots and involve the identification of (i) linear relationships with correlation coefficients, (ii) monotonic relationships with rank correlation coefficients, (iii) trends in central tendency as defined by means, medians and the Kruskal-Wallis statistic, (iv) trends in variability as defined by variances and interquartile ranges, and (v) deviations from randomness as defined by the chi-square statistic. A sequence of example analyses with a large model for two-phase fluid flow illustrates how the individual procedures can differ in the variables that they identify as having effects on particular model outcomes. The example analyses indicate that the use of a sequence of procedures is a good analysis strategy and provides some assurance that an important effect is not overlooked.

  6. A novel common large genomic deletion and two new missense mutations identified in the Romanian phenylketonuria population.

    PubMed

    Gemperle-Britschgi, Corinne; Iorgulescu, Daniela; Mager, Monica Alina; Anton-Paduraru, Dana; Vulturar, Romana; Thöny, Beat

    2016-01-15

    The mutation spectrum for the phenylalanine hydroxylase (PAH) gene was investigated in a cohort of 84 hyperphenylalaninemia (HPA) patients from Romania identified through newborn screening or neurometabolic investigations. Differential diagnosis identified 81 patients with classic PAH deficiency while 3 had tetrahydropterin-cofactor deficiency and/or remained uncertain due to insufficient specimen. PAH-genetic analysis included a combination of Sanger sequencing of exons and exon–intron boundaries, MLPA and NGS with genomic DNA, and cDNA analysis from immortalized lymphoblasts. A diagnostic efficiency of 99.4% was achieved, as for one allele (out of a total of 162 alleles) no mutation could be identified. The most prevalent mutation was p.Arg408Trp which was found in ~ 38% of all PKU alleles. Three novel mutations were identified, including the two missense mutations p.Gln226Lys and p.Tyr268Cys that were both disease causing by prediction algorithms, and the large genomic deletion EX6del7831 (c.509 + 4140_706 + 510del7831) that resulted in skipping of exon 6 based on PAH-cDNA analysis in immortalized lymphocytes. The genomic deletion was present in a heterozygous state in 12 patients, i.e. in ~ 8% of all the analyzed PKU alleles, and might have originated from a Romanian founder.

  7. Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries

    PubMed Central

    Inglese, James; Auld, Douglas S.; Jadhav, Ajit; Johnson, Ronald L.; Simeonov, Anton; Yasgar, Adam; Zheng, Wei; Austin, Christopher P.

    2006-01-01

    High-throughput screening (HTS) of chemical compounds to identify modulators of molecular targets is a mainstay of pharmaceutical development. Increasingly, HTS is being used to identify chemical probes of gene, pathway, and cell functions, with the ultimate goal of comprehensively delineating relationships between chemical structures and biological activities. Achieving this goal will require methodologies that efficiently generate pharmacological data from the primary screen and reliably profile the range of biological activities associated with large chemical libraries. Traditional HTS, which tests compounds at a single concentration, is not suited to this task, because HTS is burdened by frequent false positives and false negatives and requires extensive follow-up testing. We have developed a paradigm, quantitative HTS (qHTS), tested with the enzyme pyruvate kinase, to generate concentration–response curves for >60,000 compounds in a single experiment. We show that this method is precise, refractory to variations in sample preparation, and identifies compounds with a wide range of activities. Concentration–response curves were classified to rapidly identify pyruvate kinase activators and inhibitors with a variety of potencies and efficacies and elucidate structure–activity relationships directly from the primary screen. Comparison of qHTS with traditional single-concentration HTS revealed a high prevalence of false negatives in the single-point screen. This study demonstrates the feasibility of qHTS for accurately profiling every compound in large chemical libraries (>105 compounds). qHTS produces rich data sets that can be immediately mined for reliable biological activities, thereby providing a platform for chemical genomics and accelerating the identification of leads for drug discovery. PMID:16864780

  8. 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.

  9. Molecular cloning and characterization of four caspases members in Apostichopus japonicus.

    PubMed

    Shao, Yina; Li, Chenghua; Zhang, Weiwei; Duan, Xuemei; Li, Ye; Jin, Chunhua; Xiong, Jinbo; Qiu, Qiongfen

    2016-08-01

    The caspase family representing aspartate-specific cysteine proteases have been demonstrated to possess key roles in apoptosis and immune response. We previously demonstrated that LPS challenged Apostichopus japonicus coelomocyte could significantly induced apoptosis in vitro. However, apoptosis related molecules were scarcely investigated in this economic species. In the present work, we cloned and characterized four members caspase family from A. japonicus (designated as Ajcaspase-2, Ajcaspase-3, Ajcaspase-6, and Ajcaspase-8, respectively) by RACE. Multiple sequence alignment and structural analysis revealed that all Ajcaspases contained the conservative CASC domain at C terminal, in which some unique features for each Ajcaspase made them different from each other. These specific domains together with phylogenetic analysis supported that all these four identified proteins belonged to novel members of apoptotic signaling pathway in sea cucumber. Tissue distribution analysis revealed that four Ajcaspase genes were constitutively expressed in all examined tissues. The expression of Ajcaspase-2 was tightly correlated with that of Ajcaspase-8 in each detected tissues. Ajcaspase-3 and Ajcaspase-6 transcripts were both highly expressed in immune tissue of coelomocytes. Furthermore, the Vibrio splendidus challenged sea cucumber coelomocytes could significantly up-regulate the mRNA expressions of four genes. The expression levels of Ajcaspase-2 and Ajcaspase-8 were relative earlier than those of Ajcaspase-6 and Ajcaspase-3, respectively, which could be inferred that Ajcapase-2 might directly modulate Ajcaspase-6, and Ajcaspase-8 initiate the expression of Ajcaspase-3. The induce expressions differed among each Ajcaspase depending upon their roles such as initiator or effector caspase. All our results demonstrated that four Ajcaspases present diversified functions in apoptotic cascade signaling pathway of sea cucumber under immune response.

  10. The Cloning and Characterization of the Enolase2 Gene of Gekko japonicus and Its Polyclonal Antibody Preparation

    PubMed Central

    Li, Jing; Wu, Ronghua; Chen, Haijiao; Zhou, Youlang; Li, Yan; Wang, Yongjun; Liu, Yan; Liu, Mei

    2013-01-01

    The enolase2 gene is usually expressed in mature neurons and also named neuron specific enolase (NSE). In the present study, we first obtained the NSE gene cDNA sequence by using the RACE method based on the expressed sequence tag (EST) fragment from the cDNA library of Gekko japonicus and identified one transcript of about 2.2 kb in central nervous system of Gekko japonicus by Northern blotting. The open reading frame of NSE is 1305 bp, which encodes a 435 amino-acid protein. We further investigated the multi-tissue expression pattern of NSE by RT-PCR and found that the expression of NSE mRNA was very high in brain, spinal cord and low in heart, while it was not detectable in other tissues. The real-time quantitative PCR was used to investigate the time-dependent change in the expression of the NSE mRNA level after gecko spinal cord transection and found it significantly increased at one day, reaching its highest level three days post-injury and then decreasing at the seventh day of the experiment. The recombinant plasmid of pET-32a-NSE was constructed and induced to express His fused NSE protein. The purified NSE protein was used to immunize rabbits to generate polyclonal antisera. The titer of the antiserum was more than 1:65536 determined by ELISA. Western blotting showed that the prepared antibody could specifically recognize the recombinant and endogenous NSE protein. The result of immunohistochemistry revealed that positive signals were present in neurons of the brain and the spinal cord. This study provided the tools of cDNA and polyclonal antibody for studying NSE function in Gekko japonicus. PMID:23615470

  11. 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.

  12. 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

  13. 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

  14. [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.

  15. Optimization of the fermentation conditions of Rhizopus japonicus M193 for the production of chitin deacetylase and chitosan.

    PubMed

    Zhang, Hongcai; Yang, Shoufeng; Fang, Jiyang; Deng, Yun; Wang, Danfeng; Zhao, Yanyun

    2014-01-30

    To improve the production of chitin deacetylase (CDA) for the bioconversion of chitin to chitosan with desirable functionality, the effect of the nutritional requirement on the CDA production from Rhizopus japonicus M193 fermentation was investigated under submerged conditions. Nutritional elements including glucose (g/L), inoculum level (%), and MgSO4·7H2O (g/L), as well as culture time (d) were identified as the most critical factors for the CDA production based on the results from Plackett-Burman design (PBD). Taguchi design with orthogonal array was further employed to optimize R. japonicus M193 fermentation conditions based on the results from PBD, in which 2.5% chitin, 5 g/L glucose, 5% inoculum level, 0.6g/L MgSO4·7H2O, and 5d culture time were identified as the optimal fermentation conditions. Under this condition, the maximum CDA production, DDA and MM of produced chitosan were 547.38 ± 12.06 U/L, 78.85 ± 1.68%, and 125.63 ± 3.74 kDa, respectively. Obtained chitosan displayed similar physicochemical and structural properties to those of commercial chitosan extracted using chemical method based on the results from Fourier transform infrared spectrometer (FT-IR), thermogravimetric analysis (TGA)-differential scanning calorimetry (DSC), and nuclear magnetic resonance (NMR) assays, while the use of chemical reagents was significantly reduced.

  16. Applying MetaMap to Medline for identifying novel associations in a large clinical dataset: a feasibility analysis

    PubMed Central

    Hanauer, David A; Saeed, Mohammed; Zheng, Kai; Mei, Qiaozhu; Shedden, Kerby; Aronson, Alan R; Ramakrishnan, Naren

    2014-01-01

    Objective We describe experiments designed to determine the feasibility of distinguishing known from novel associations based on a clinical dataset comprised of International Classification of Disease, V.9 (ICD-9) codes from 1.6 million patients by comparing them to associations of ICD-9 codes derived from 20.5 million Medline citations processed using MetaMap. Associations appearing only in the clinical dataset, but not in Medline citations, are potentially novel. Methods Pairwise associations of ICD-9 codes were independently identified in both the clinical and Medline datasets, which were then compared to quantify their degree of overlap. We also performed a manual review of a subset of the associations to validate how well MetaMap performed in identifying diagnoses mentioned in Medline citations that formed the basis of the Medline associations. Results The overlap of associations based on ICD-9 codes in the clinical and Medline datasets was low: only 6.6% of the 3.1 million associations found in the clinical dataset were also present in the Medline dataset. Further, a manual review of a subset of the associations that appeared in both datasets revealed that co-occurring diagnoses from Medline citations do not always represent clinically meaningful associations. Discussion Identifying novel associations derived from large clinical datasets remains challenging. Medline as a sole data source for existing knowledge may not be adequate to filter out widely known associations. Conclusions In this study, novel associations were not readily identified. Further improvements in accuracy and relevance for tools such as MetaMap are needed to realize their expected utility. PMID:24928177

  17. Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci.

    PubMed

    Saxena, Richa; Elbers, Clara C; Guo, Yiran; Peter, Inga; Gaunt, Tom R; Mega, Jessica L; Lanktree, Matthew B; Tare, Archana; Castillo, Berta Almoguera; Li, Yun R; Johnson, Toby; Bruinenberg, Marcel; Gilbert-Diamond, Diane; Rajagopalan, Ramakrishnan; Voight, Benjamin F; Balasubramanyam, Ashok; Barnard, John; Bauer, Florianne; Baumert, Jens; Bhangale, Tushar; Böhm, Bernhard O; Braund, Peter S; Burton, Paul R; Chandrupatla, Hareesh R; Clarke, Robert; Cooper-DeHoff, Rhonda M; Crook, Errol D; Davey-Smith, George; Day, Ian N; de Boer, Anthonius; de Groot, Mark C H; Drenos, Fotios; Ferguson, Jane; Fox, Caroline S; Furlong, Clement E; Gibson, Quince; Gieger, Christian; Gilhuijs-Pederson, Lisa A; Glessner, Joseph T; Goel, Anuj; Gong, Yan; Grant, Struan F A; Grobbee, Diederick E; Hastie, Claire; Humphries, Steve E; Kim, Cecilia E; Kivimaki, Mika; Kleber, Marcus; Meisinger, Christa; Kumari, Meena; Langaee, Taimour Y; Lawlor, Debbie A; Li, Mingyao; Lobmeyer, Maximilian T; Maitland-van der Zee, Anke-Hilse; Meijs, Matthijs F L; Molony, Cliona M; Morrow, David A; Murugesan, Gurunathan; Musani, Solomon K; Nelson, Christopher P; Newhouse, Stephen J; O'Connell, Jeffery R; Padmanabhan, Sandosh; Palmen, Jutta; Patel, Sanjey R; Pepine, Carl J; Pettinger, Mary; Price, Thomas S; Rafelt, Suzanne; Ranchalis, Jane; Rasheed, Asif; Rosenthal, Elisabeth; Ruczinski, Ingo; Shah, Sonia; Shen, Haiqing; Silbernagel, Günther; Smith, Erin N; Spijkerman, Annemieke W M; Stanton, Alice; Steffes, Michael W; Thorand, Barbara; Trip, Mieke; van der Harst, Pim; van der A, Daphne L; van Iperen, Erik P A; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V; Verweij, Niek; Wolffenbuttel, Bruce H R; Young, Taylor; Zafarmand, M Hadi; Zmuda, Joseph M; Boehnke, Michael; Altshuler, David; McCarthy, Mark; Kao, W H Linda; Pankow, James S; Cappola, Thomas P; Sever, Peter; Poulter, Neil; Caulfield, Mark; Dominiczak, Anna; Shields, Denis C; Bhatt, Deepak L; Bhatt, Deepak; Zhang, Li; Curtis, Sean P; Danesh, John; Casas, Juan P; van der Schouw, Yvonne T; Onland-Moret, N Charlotte; Doevendans, Pieter A; Dorn, Gerald W; Farrall, Martin; FitzGerald, Garret A; Hamsten, Anders; Hegele, Robert; Hingorani, Aroon D; Hofker, Marten H; Huggins, Gordon S; Illig, Thomas; Jarvik, Gail P; Johnson, Julie A; Klungel, Olaf H; Knowler, William C; Koenig, Wolfgang; März, Winfried; Meigs, James B; Melander, Olle; Munroe, Patricia B; Mitchell, Braxton D; Bielinski, Susan J; Rader, Daniel J; Reilly, Muredach P; Rich, Stephen S; Rotter, Jerome I; Saleheen, Danish; Samani, Nilesh J; Schadt, Eric E; Shuldiner, Alan R; Silverstein, Roy; Kottke-Marchant, Kandice; Talmud, Philippa J; Watkins, Hugh; Asselbergs, Folkert W; Asselbergs, Folkert; de Bakker, Paul I W; McCaffery, Jeanne; Wijmenga, Cisca; Sabatine, Marc S; Wilson, James G; Reiner, Alex; Bowden, Donald W; Hakonarson, Hakon; Siscovick, David S; Keating, Brendan J

    2012-03-09

    To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with ∼2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and clinical trials totaling 17,418 cases and 70,298 controls. First, meta-analysis of 25 studies comprising 14,073 cases and 57,489 controls of European descent confirmed eight established T2D loci at genome-wide significance. In silico follow-up analysis of putative association signals found in independent genome-wide association studies (including 8,130 cases and 38,987 controls) performed by the DIAGRAM consortium identified a T2D locus at genome-wide significance (GATAD2A/CILP2/PBX4; p = 5.7 × 10(-9)) and two loci exceeding study-wide significance (SREBF1, and TH/INS; p < 2.4 × 10(-6)). Second, meta-analyses of 1,986 cases and 7,695 controls from eight African-American studies identified study-wide-significant (p = 2.4 × 10(-7)) variants in HMGA2 and replicated variants in TCF7L2 (p = 5.1 × 10(-15)). Third, conditional analysis revealed multiple known and novel independent signals within five T2D-associated genes in samples of European ancestry and within HMGA2 in African-American samples. Fourth, a multiethnic meta-analysis of all 39 studies identified T2D-associated variants in BCL2 (p = 2.1 × 10(-8)). Finally, a composite genetic score of SNPs from new and established T2D signals was significantly associated with increased risk of diabetes in African-American, Hispanic, and Asian populations. In summary, large-scale meta-analysis involving a dense gene-centric approach has uncovered additional loci and variants that contribute to T2D risk and suggests substantial overlap of T2D association signals across multiple ethnic groups.

  18. Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci

    PubMed Central

    Saxena, Richa; Elbers, Clara C.; Guo, Yiran; Peter, Inga; Gaunt, Tom R.; Mega, Jessica L.; Lanktree, Matthew B.; Tare, Archana; Castillo, Berta Almoguera; Li, Yun R.; Johnson, Toby; Bruinenberg, Marcel; Gilbert-Diamond, Diane; Rajagopalan, Ramakrishnan; Voight, Benjamin F.; Balasubramanyam, Ashok; Barnard, John; Bauer, Florianne; Baumert, Jens; Bhangale, Tushar; Böhm, Bernhard O.; Braund, Peter S.; Burton, Paul R.; Chandrupatla, Hareesh R.; Clarke, Robert; Cooper-DeHoff, Rhonda M.; Crook, Errol D.; Davey-Smith, George; Day, Ian N.; de Boer, Anthonius; de Groot, Mark C.H.; Drenos, Fotios; Ferguson, Jane; Fox, Caroline S.; Furlong, Clement E.; Gibson, Quince; Gieger, Christian; Gilhuijs-Pederson, Lisa A.; Glessner, Joseph T.; Goel, Anuj; Gong, Yan; Grant, Struan F.A.; Grobbee, Diederick E.; Hastie, Claire; Humphries, Steve E.; Kim, Cecilia E.; Kivimaki, Mika; Kleber, Marcus; Meisinger, Christa; Kumari, Meena; Langaee, Taimour Y.; Lawlor, Debbie A.; Li, Mingyao; Lobmeyer, Maximilian T.; Maitland-van der Zee, Anke-Hilse; Meijs, Matthijs F.L.; Molony, Cliona M.; Morrow, David A.; Murugesan, Gurunathan; Musani, Solomon K.; Nelson, Christopher P.; Newhouse, Stephen J.; O'Connell, Jeffery R.; Padmanabhan, Sandosh; Palmen, Jutta; Patel, Sanjey R.; Pepine, Carl J.; Pettinger, Mary; Price, Thomas S.; Rafelt, Suzanne; Ranchalis, Jane; Rasheed, Asif; Rosenthal, Elisabeth; Ruczinski, Ingo; Shah, Sonia; Shen, Haiqing; Silbernagel, Günther; Smith, Erin N.; Spijkerman, Annemieke W.M.; Stanton, Alice; Steffes, Michael W.; Thorand, Barbara; Trip, Mieke; van der Harst, Pim; van der A, Daphne L.; van Iperen, Erik P.A.; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Wolffenbuttel, Bruce H.R.; Young, Taylor; Zafarmand, M. Hadi; Zmuda, Joseph M.; Boehnke, Michael; Altshuler, David; McCarthy, Mark; Kao, W.H. Linda; Pankow, James S.; Cappola, Thomas P.; Sever, Peter; Poulter, Neil; Caulfield, Mark; Dominiczak, Anna; Shields, Denis C.; Bhatt, Deepak L.; Zhang, Li; Curtis, Sean P.; Danesh, John; Casas, Juan P.; van der Schouw, Yvonne T.; Onland-Moret, N. Charlotte; Doevendans, Pieter A.; Dorn, Gerald W.; Farrall, Martin; FitzGerald, Garret A.; Hamsten, Anders; Hegele, Robert; Hingorani, Aroon D.; Hofker, Marten H.; Huggins, Gordon S.; Illig, Thomas; Jarvik, Gail P.; Johnson, Julie A.; Klungel, Olaf H.; Knowler, William C.; Koenig, Wolfgang; März, Winfried; Meigs, James B.; Melander, Olle; Munroe, Patricia B.; Mitchell, Braxton D.; Bielinski, Susan J.; Rader, Daniel J.; Reilly, Muredach P.; Rich, Stephen S.; Rotter, Jerome I.; Saleheen, Danish; Samani, Nilesh J.; Schadt, Eric E.; Shuldiner, Alan R.; Silverstein, Roy; Kottke-Marchant, Kandice; Talmud, Philippa J.; Watkins, Hugh; Asselbergs, Folkert W.; de Bakker, Paul I.W.; McCaffery, Jeanne; Wijmenga, Cisca; Sabatine, Marc S.; Wilson, James G.; Reiner, Alex; Bowden, Donald W.; Hakonarson, Hakon; Siscovick, David S.; Keating, Brendan J.

    2012-01-01

    To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with ∼2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and clinical trials totaling 17,418 cases and 70,298 controls. First, meta-analysis of 25 studies comprising 14,073 cases and 57,489 controls of European descent confirmed eight established T2D loci at genome-wide significance. In silico follow-up analysis of putative association signals found in independent genome-wide association studies (including 8,130 cases and 38,987 controls) performed by the DIAGRAM consortium identified a T2D locus at genome-wide significance (GATAD2A/CILP2/PBX4; p = 5.7 × 10−9) and two loci exceeding study-wide significance (SREBF1, and TH/INS; p < 2.4 × 10−6). Second, meta-analyses of 1,986 cases and 7,695 controls from eight African-American studies identified study-wide-significant (p = 2.4 × 10−7) variants in HMGA2 and replicated variants in TCF7L2 (p = 5.1 × 10−15). Third, conditional analysis revealed multiple known and novel independent signals within five T2D-associated genes in samples of European ancestry and within HMGA2 in African-American samples. Fourth, a multiethnic meta-analysis of all 39 studies identified T2D-associated variants in BCL2 (p = 2.1 × 10−8). Finally, a composite genetic score of SNPs from new and established T2D signals was significantly associated with increased risk of diabetes in African-American, Hispanic, and Asian populations. In summary, large-scale meta-analysis involving a dense gene-centric approach has uncovered additional loci and variants that contribute to T2D risk and suggests substantial overlap of T2D association signals across multiple ethnic groups. PMID:22325160

  19. 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.

  20. Statistical Analyses of Scatterplots to Identify Important Factors in Large-Scale Simulations, 1: Review and Comparison of Techniques

    SciTech Connect

    Kleijnen, J.P.C.; Helton, J.C.

    1999-03-24

    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 (i) linear relationships with correlation coefficients, (ii) monotonic relationships with rank correlation coefficients, (iii) trends in central tendency as defined by means, medians and the Kruskal-Wallis statistic, (iv) trends in variability as defined by variances and interquartile ranges, and (v) deviations from randomness as defined by the chi-square statistic. The following two topics related to the robustness of these procedures are considered 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: (i) Type I errors are unavoidable, (ii) Type 11errors can occur when inappropriate analysis procedures are used, (iii) physical explanations should always be sought for why statistical procedures identify variables as being important, and (iv) the identification of important variables tends to be stable for independent Latin hypercube samples.

  1. Chemical communication during mating of the harpacticoid Tigriopus japonicus

    PubMed Central

    Kelly, L. S.

    1998-01-01

    The importance of contact and diffusible pheromones in the reproductive biology of the harpacticoid Tigriopus japonicus was studied. When given a choice, males preferred developmentally advanced conspecific female partners over less mature or congeneric females. Males judged female attractiveness on a relative scale, based on the locally available females. The attractiveness of a female copepodid was reduced with non-fatal proteolytic treatment, but only if normal females were also present. To sample the available females, males repeatedly grabbed the caudal rami and terminal urosome segment of potential partners before committing themselves to guarding one female. Males occasionally dropped their copepodid partners. Releases increased in frequency in water conditioned from virgin adult females and adult males, decreased in mated-female conditioned water and were unaffected by copepodids or their treated water. The waning attractiveness of a recently mated female was tracked over 16 h. Relationships between Tigriopus japonicus adults appeared to involve both contact and diffusible pheromones. No evidence of a diffusible copepodid pheromone was uncovered.

  2. 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

  3. 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.

  4. An apposition-like compound eye with a layered rhabdom in the small diving beetle Agabus japonicus (Coleoptera, Dytiscidae).

    PubMed

    Jia, Lei-Po; Liang, Ai-Ping

    2014-11-01

    The fine structure of the compound eyes of the adult diving beetle Agabus japonicus is described with light, scanning, and transmission electron microscopy. The eye of A. japonicus is mango-shaped and consists of about 985 ommatidia. Each ommatidium is composed of a corneal facet lens, an eucone type of crystalline cone, a fused layered rhabdom with a basal rhabdomere, seven retinula cells (including six distal cells and one basal cell), two primary pigment cells and an undetermined number of secondary pigment cells that are restricted to the distalmost region of the eye. A clear-zone, separating dioptric apparatus from photoreceptive structures, is not developed and the eye thus resembles an apposition eye. The cross-sectional areas of the rhabdoms are relatively large indicative of enhanced light-sensitivity. The distal and central region of the rhabdom is layered with interdigitating microvilli suggesting polarization sensitivity. According to the features mentioned above, we suggest that 1) the eye, seemingly of the apposition type, occurs in a taxon for which the clear-zone (superposition) eye is characteristic; 2) the eye possesses adaptations to function in a dim-light environment; 3) the eye may be sensitive to underwater polarized light or linearly water-reflected polarized light.

  5. Systems analysis in Cellvibrio japonicus resolves predicted redundancy of β-glucosidases and determines essential physiological functions

    DOE PAGES

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

    2017-01-24

    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

  6. 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.

  7. Identification of nutrient and physical seed trait QTL in the model legume Lotus japonicus.

    PubMed

    Klein, Melinda A; Grusak, Michael A

    2009-08-01

    Legume seeds have the potential to provide a significant portion of essential micronutrients to the human diet. To identify the genetic basis for seed nutrient density, quantitative trait locus (QTL) analysis was conducted with the Miyakojima MG-20 x Gifu B-129 recombinant inbred population from the model legume Lotus japonicus. This population was grown to seed under greenhouse conditions in 2006 and 2007. Phenotypic data were collected for seed calcium (Ca), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P), sulfur (S), and zinc (Zn) concentrations and content. Data for physical seed traits (average seed mass and seed-pod allocation values) were also collected. Based on these phenotypic data, QTL analyses identified 103 QTL linked to 55 different molecular markers. Transgressive segregation, identified within this recombinant inbred population for both seed nutrient and physical traits, suggests new allelic combinations are available for agronomic trait improvement. QTL co-localization was also seen, suggesting that common transport processes might contribute to seed nutrient loading. Identification of loci involved in seed mineral density can be an important first step in identifying the genetic factors and, consequently, the physiological processes involved in mineral distribution to developing seeds. Longer term research efforts will focus on facilitating agronomic breeding efforts through ortholog identification in related crop legumes.

  8. CAROTENOID CLEAVAGE DIOXYGENASE 7 modulates plant growth, reproduction, senescence, and determinate nodulation in the model legume Lotus japonicus

    PubMed Central

    Liu, Junwei; Novero, Mara; Charnikhova, Tatsiana; Ferrandino, Alessandra; Schubert, Andrea; Ruyter-Spira, Carolien; Bonfante, Paola; Lovisolo, Claudio; Bouwmeester, Harro J.; Cardinale, Francesca

    2013-01-01

    Strigolactones (SLs) are newly identified hormones that regulate multiple aspects of plant development, infection by parasitic weeds, and mutualistic symbiosis in the roots. In this study, the role of SLs was studied for the first time in the model plant Lotus japonicus using transgenic lines silenced for CAROTENOID CLEAVAGE DIOXYGENASE 7 (LjCCD7), the orthologue of Arabidopsis More Axillary Growth 3. Transgenic LjCCD7-silenced plants displayed reduced height due to shorter internodes, and more branched shoots and roots than the controls, and an increase in total plant biomass, while their root:shoot ratio remained unchanged. Moreover, these lines had longer primary roots, delayed senescence, and reduced flower/pod numbers from the third round of flower and pod setting onwards. Only a mild reduction in determinate nodule numbers and hardly any impact on the colonization by arbuscular mycorrhizal fungi were observed. The results show that the impairment of CCD7 activity in L. japonicus leads to a phenotype linked to SL functions, but with specific features possibly due to the peculiar developmental pattern of this plant species. It is believed that the data also link determinate nodulation, plant reproduction, and senescence to CCD7 function for the first time. PMID:23567864

  9. 16S rRNA gene phylogenesis of culturable predominant bacteria from diseased Apostichopus japonicus (Holothuroidea, Echinodermata)

    NASA Astrophysics Data System (ADS)

    Ma, Haiyan; Jiang, Guoliang; Wu, Zhiqiang; Wang, Xin

    2009-06-01

    Cultured Apostichopus japonicus in China suffers from a kind of skin ulceration disease that has caused severe economic loss in recent years. The disease, pathogens of which are supposed to be bacteria by most researchers, is highly infectious and can often cause all individuals in the same culture pool to die in a very short time. The 16S rRNA gene phylogenesis of the culturable bacteria from the lesions of diseased individuals was conducted to study the biodiversity of the bacterial communities in the lesions and to identify probable pathogen(s) associated with this kind of disease. S. japonica samples were selected from a hatchery located in the eastern part of Qingdao, China. Bacterial universal primers GM5F and DS907R were used to amplify the 16S rRNA gene of bacteria colonies, and touchdown PCR was performed to amplify the target sequences. The results suggest that γ- proteobacteria (Alteromonadales and Vibrionales) of CFB group, many strains of which have been also determined as pathogens in other marine species, are the predominant bacterial genera of the diseased Apostichopus japonicus individuals.

  10. Network of GRAS Transcription Factors Involved in the Control of Arbuscule Development in Lotus japonicus1[OPEN

    PubMed Central

    Xue, Li; Cui, Haitao; Buer, Benjamin; Vijayakumar, Vinod; Delaux, Pierre-Marc; Junkermann, Stefanie; Bucher, Marcel

    2015-01-01

    Arbuscular mycorrhizal (AM) fungi, in symbiosis with plants, facilitate acquisition of nutrients from the soil to their host. After penetration, intracellular hyphae form fine-branched structures in cortical cells termed arbuscules, representing the major site where bidirectional nutrient exchange takes place between the host plant and fungus. Transcriptional mechanisms underlying this cellular reprogramming are still poorly understood. GRAS proteins are an important family of transcriptional regulators in plants, named after the first three members: GIBBERELLIC ACID-INSENSITIVE, REPRESSOR of GAI, and SCARECROW. Here, we show that among 45 transcription factors up-regulated in mycorrhizal roots of the legume Lotus japonicus, expression of a unique GRAS protein particularly increases in arbuscule-containing cells under low phosphate conditions and displays a phylogenetic pattern characteristic of symbiotic genes. Allelic rad1 mutants display a strongly reduced number of arbuscules, which undergo accelerated degeneration. In further studies, two RAD1-interacting proteins were identified. One of them is the closest homolog of Medicago truncatula, REDUCED ARBUSCULAR MYCORRHIZATION1 (RAM1), which was reported to regulate a glycerol-3-phosphate acyl transferase that promotes cutin biosynthesis to enhance hyphopodia formation. As in M. truncatula, the L. japonicus ram1 mutant lines show compromised AM colonization and stunted arbuscules. Our findings provide, to our knowledge, new insight into the transcriptional program underlying the host’s response to AM colonization and propose a function of GRAS transcription factors including RAD1 and RAM1 during arbuscule development. PMID:25560877

  11. Identification and functional characterization of a sulfate transporter induced by both sulfur starvation and mycorrhiza formation in Lotus japonicus.

    PubMed

    Giovannetti, Marco; Tolosano, Matteo; Volpe, Veronica; Kopriva, Stanislav; Bonfante, Paola

    2014-11-01

    Arbuscular mycorrhizas (AMs) are one of the most widespread symbioses in the world. They allow plants to receive mineral nutrients from the symbiotic fungus which in turn gets back up to 20% of plant carbon and completes its life cycle. Especially in low-nutrient conditions, AM fungi are capable of significantly improving plant phosphate and nitrogen acquisition, but fewer data are available about sulfur (S) nutrition. We focused on S metabolism in Lotus japonicus upon mycorrhizal colonization under sulfur starvation or repletion. We investigated both tissue sulfate concentrations and S-related gene expression, at cell-type or whole-organ level. Gene expression and sulfate tissue concentration showed that Rhizophagus irregularis colonization can improve plant S nutritional status under S starvation. A group 1 sulfate transporter, LjSultr1;2, induced by both S starvation and mycorrhiza formation, was identified. Its transcript was localized in arbuscule-containing cells, which was confirmed with a promoter-GUS assay, and its function was verified through phenotyping of TILLING mutants in nonmycorrhizal seedlings. LjSultr1;2 thus appears to encode a key protein involved in plant sulfate uptake. In contrast to phosphate transporters, a single gene, LjSultr1;2, seems to mediate both direct and symbiotic pathways of S uptake in L. japonicus.

  12. Weak larval competition between the invasive mosquito Aedes japonicus japonicus (Diptera: Culicidae) and three resident container-inhabiting mosquitoes in the laboratory.

    PubMed

    Hardstone, Melissa C; Andreadis, Theodore G

    2012-03-01

    The spread of exotic mosquito species into new environments can introduce shifts in mosquito populations and potentially alter public health risks to mosquito-borne diseases. The successful establishment of exotic species may occur due to their competitive advantage over other cohabitating species. We hypothesized that the recently introduced exotic mosquito Aedes japonicus japonicus (Theobald) would be a more effective competitor than Aedes atropalpus (Coquillett) and Aedes triseriatus (Say), and an equal competitor to Culex pipiens (L.) based on larval abundance data within tire habitats. Impacts of competition were measured using the larval developmental rate and survival of larvae, adult mortality, wing length, and sex ratio. We found that intraspecific competition acted strongest against Ae. japonicus versus the other three resident mosquito species by delaying larval development and increasing adult mortality. Interspecific competition was generally weak and significant main effects were only detected for species and density. Overall, our results show that larval competition between Ae. japonicus and the three resident species was weak when present, indicating that other ecological or behavioral factors may be influencing the invasion success for Ae. japonicus in North America.

  13. 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

  14. 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

  15. A large-scale functional screen identifies Nova1 and Ncoa3 as regulators of neuronal miRNA function.

    PubMed

    Störchel, Peter H; Thümmler, Juliane; Siegel, Gabriele; Aksoy-Aksel, Ayla; Zampa, Federico; Sumer, Simon; Schratt, Gerhard

    2015-09-02

    MicroRNAs (miRNAs) are important regulators of neuronal development, network connectivity, and synaptic plasticity. While many neuronal miRNAs were previously shown to modulate neuronal morphogenesis, little is known regarding the regulation of miRNA function. In a large-scale functional screen, we identified two novel regulators of neuronal miRNA function, Nova1 and Ncoa3. Both proteins are expressed in the nucleus and the cytoplasm of developing hippocampal neurons. We found that Nova1 and Ncoa3 stimulate miRNA function by different mechanisms that converge on Argonaute (Ago) proteins, core components of the miRNA-induced silencing complex (miRISC). While Nova1 physically interacts with Ago proteins, Ncoa3 selectively promotes the expression of Ago2 at the transcriptional level. We further show that Ncoa3 regulates dendritic complexity and dendritic spine maturation of hippocampal neurons in a miRNA-dependent fashion. Importantly, both the loss of miRNA activity and increased dendrite complexity upon Ncoa3 knockdown were rescued by Ago2 overexpression. Together, we uncovered two novel factors that control neuronal miRISC function at the level of Ago proteins, with possible implications for the regulation of synapse development and plasticity.

  16. Large-scale genotyping identifies a new locus at 22q13.2 associated with female breast size

    PubMed Central

    Li, Jingmei; Foo, Jia Nee; Schoof, Nils; Varghese, Jajini S.; Fernandez-Navarro, Pablo; Gierach, Gretchen L.; Quek, Swee Tian; Hartman, Mikael; Nord, Silje; Kristensen, Vessela N.; Pollán, Marina; Figueroa, Jonine D.; Thompson, Deborah J.; Li, Yi; Khor, Chiea Chuen; Humphreys, Keith; Liu, Jianjun; Czene, Kamila; Hall, Per

    2014-01-01

    Background Individual differences in breast size are a conspicuous feature of variation in human females and have been associated with fecundity and advantage in selection of mates. To identify common variants that are associated with breast size, we conducted a large-scale genotyping association meta-analysis in 7,169 women of European descent across 3 independent sample collections with digital or screen film mammograms. Methods The samples consisted of the Swedish KARMA, LIBRO-1 and SASBAC studies genotyped on iCOGS, a custom illumina iSelect genotyping array comprising of 211,155 single nucleotide polymorphisms (SNPs) designed for replication and fine mapping of common and rare variants with relevance to breast, ovary and prostate cancer. Breast size of each subject was ascertained by measuring total breast area (mm2) on a mammogram. Results We confirm genome-wide significant associations at 8p11.23 (rs10086016, P = 1.3 × 10−14) and report a new locus at 22q13 (rs5995871, P = 3.2 × 10−8). The latter region contains the MKL1 gene, which has been shown to impact endogenous estrogen-receptor α transcriptional activity and is recruited on estradiol-sensitive genes. We also replicated previous GWAS findings for breast size at four other loci. Conclusion A new locus at 22q13 may be associated with female breast size. PMID:23825393

  17. 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).

  18. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    SciTech Connect

    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 remarkable 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.

  19. Germination rate of Phyllospadix japonicus seeds relative to storage methods and periods

    NASA Astrophysics Data System (ADS)

    Park, Jung-Im; Lee, Kun-Seop; Son, Min Ho

    2014-03-01

    To determine the optimal storage method and longest possible storage period of Phyllospadix japonicus seeds, we examined post-storage germination rates using different storage methods and periods for P. japonicus seeds harvested in Korean coastal waters. P. japonicus seeds are classified as recalcitrant seeds with an average moisture content of 45.4%. Germination rates of P. japonicus seeds stored in seawater at 4 °C, seawater at room temperature with air supply, and an aquarium with continuous seawater circulation ranged from 35.0% to 43.5%, whereas seeds stored in seawater at 30°C, a refrigerator at -20°C, and a desiccator at room temperature did not germinate. Seeds stored at 4°C maintained germination rates of 72.5˜73.0% until 30 days of storage, but showed rapidly decreasing germination rates after 60 days and no germination after 180 days. Since few studies have investigated seed storage of P. japonicus, these results will serve as useful data for seed-based P. japonicus habitat restoration.

  20. 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

  1. 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 Central

    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

  2. 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

  3. Quantitative trait locus analysis of symbiotic nitrogen fixation activity in the model legume Lotus japonicus.

    PubMed

    Tominaga, Akiyoshi; Gondo, Takahiro; Akashi, Ryo; Zheng, Shao-Hui; Arima, Susumu; Suzuki, Akihiro

    2012-05-01

    Many legumes form nitrogen-fixing root nodules. An elevation of nitrogen fixation in such legumes would have significant implications for plant growth and biomass production in agriculture. To identify the genetic basis for the regulation of nitrogen fixation, quantitative trait locus (QTL) analysis was conducted with recombinant inbred lines derived from the cross Miyakojima MG-20 × Gifu B-129 in the model legume Lotus japonicus. This population was inoculated with Mesorhizobium loti MAFF303099 and grown for 14 days in pods containing vermiculite. Phenotypic data were collected for acetylene reduction activity (ARA) per plant (ARA/P), ARA per nodule weight (ARA/NW), ARA per nodule number (ARA/NN), NN per plant, NW per plant, stem length (SL), SL without inoculation (SLbac-), shoot dry weight without inoculation (SWbac-), root length without inoculation (RLbac-), and root dry weight (RWbac-), and finally 34 QTLs were identified. ARA/P, ARA/NN, NW, and SL showed strong correlations and QTL co-localization, suggesting that several plant characteristics important for symbiotic nitrogen fixation are controlled by the same locus. QTLs for ARA/P, ARA/NN, NW, and SL, co-localized around marker TM0832 on chromosome 4, were also co-localized with previously reported QTLs for seed mass. This is the first report of QTL analysis for symbiotic nitrogen fixation activity traits.

  4. 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.

  5. Reactions of Lotus japonicus ecotypes and mutants to root parasitic plants.

    PubMed

    Kubo, Mie; Ueda, Hiroaki; Park, Pyoyun; Kawaguchi, Masayoshi; Sugimoto, Yukihiro

    2009-03-01

    Witchweeds (Striga spp.) and broomrapes (Orobanche spp.) are obligate root parasitic plants on economically important field and horticultural crops. The parasites' seeds are induced to germinate by root-derived chemical signals. The radicular end is transformed into a haustorium which attaches, penetrates the host root and establishes connection with the vascular system of the host. Reactions of Lotus japonicus, a model legume for functional genomics, were studied for furthering the understanding of host-parasite interactions. Lotus japonicus was compatible with Orobanche aegyptiaca, but not with Orobanche minor, Striga hermonthica and Striga gesnerioides. Orobanche minor successfully penetrated Lotus japonicus roots, but failed to establish connections with the vascular system. Haustoria in Striga hermonthica attached to the roots, but penetration and subsequent growth of the endophyte in the cortex were restricted. Striga gesnerioides did not parasitize Lotus japonicus. Among seven mutants of Lotus japonicus (castor-5, har1-5, alb1-1, ccamk-3, nup85-3, nfr1-3 and nsp2-1) with altered characteristics in relation to rhizobial nodulation and mycorrhizal colonization, castor-5 and har1-5 were parasitized by Orobanche aegyptiaca with higher frequency than the wild type. In contrast, Orobanche aegyptiaca tubercle development was delayed on the mutants nup85-3, nfr1-3 and nsp2-1. These results suggest that nodulation, mycorrhizal colonization and infection by root parasitic plants in Lotus japonicus may be modulated by similar mechanisms and that Lotus japonicus is a potential model legume for studying plant-plant parasitism.

  6. Occurrence of anisakid nematode larvae in chub mackerel (Scomber japonicus) caught off Korea.

    PubMed

    Bak, Tae-Jong; Jeon, Chan-Hyeok; Kim, Jeong-Ho

    2014-11-17

    Chub mackerel (Scomber japonicus) is a pelagic fish species widely distributing in the Indo-Pacific and a commercially important fish species in Korea. It is known to harbor anisakid nematodes larvae, and ingesting the raw or undercooked fish can accidentally cause human infection. In this study, we isolated the nematode larvae in 417 chub mackerel caught from 7 sampling locations around the Korean Peninsula in 2011 and 2012, and identified them by PCR-RFLP of the ITS (internal transcribed spacer) of ribosomal DNA and the direct sequencing of the mitochondrial DNA cox2 gene. The prevalence of infection was 55.4% (231/417) and the mean intensity was 7.0 (1628/231). Most of the nematodes (1523/1628; 93.6%) were found in the body cavity, while 5.5% (89/1628) were found in the gastrointestinal tract. Four different species were identified by PCR-RFLP and direct sequencing. Most of the nematodes (1535/1628; 94.3%) were identified as Anisakis pegreffii, and 2.8% (46/1628) were identified as Hysterothylacium sp. A hybrid genotype (Anisakis simplex sensu stricto×A. pegreffii) and A. simplex sensu stricto were 2.5% (41/1628) and 0.4% (6/1628) of the identified nematodes, respectively. The anisakid nematode assemblage of chub mackerel in Korea was similar to that of chub mackerel from the Tsushima Current stock in Japan, in that A. pegreffii was the dominant species. Since most of the anisakid nematodes were found in the body cavity and most of them were identified as A. pegreffii or Hysterothylacium sp. by PCR-RFLP and direct sequencing, chub mackerel may not greatly contribute to human anisakidosis in Korea. Alternately, A. pegreffii may be responsible for human anisakidosis in Korea, in addition to A. simplex sensu stricto. Further studies, such as the molecular diagnosis of human anisakidosis, are necessary for assessing the epidemiological role of chub mackerel in Korea.

  7. Supplemental effects and metabolic fate of crystalline arginine in juvenile shrimp Marsupenaeus japonicus.

    PubMed

    Teshima, Shin-ichi; Ishikawa, Manabu; Shah Alam, Md; Koshio, Shunsuke; Michael, Fady Raafat

    2004-02-01

    Feeding experiments with juvenile kuruma shrimp (Marsupenaeus japonicus) were conducted to understand the effects of supplemental levels of crystalline arginine hydrochloride on the growth and assimilation of arginine. In experiment 1 the juvenile shrimp were maintained on diets with and without arginine supplements. The addition of 3.0% arginine to a casein-based diet was slightly effective in improving the growth of the juveniles. In experiment 2, tracer experiments using [14C] arginine were conducted to clarify the ingestion and assimilation of arginine, 9 and 24 h after feeding, at different levels of supplemental arginine. Tracer experiments showed that the leaching rate of arginine 1 h after feeding ranged from 16 to 26% in the diets with different levels (0, 0.1, 1.5, 3.0 and 6.0%) of supplemental arginine; that is, 74-84% of the given arginine was actually ingested by the shrimp fed the diets. However, with increasing levels of supplemental arginine the incorporation rate of arginine into the whole body decreased and the utilization of absorbed arginine for body protein synthesis was reduced, whereas the excretion of absorbed arginine was increased. Thus, the absorbed arginine was not effectively utilized for body protein synthesis when large amounts of arginine were supplemented to the diets.

  8. 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%.

  9. Identification and characterization a novel transcription factor activator protein-1 in the sea cucumber Apostichopus japonicus.

    PubMed

    Yang, Limeng; Li, Chenghua; Chang, Yaqing; Gao, Yinxue; Wang, Yi; Wei, Jing; Song, Jian; Sun, Ping

    2015-08-01

    The transcription factor activator protein-1 (AP-1) is an important gene expression regulator with typical Jun and region-leucine zipper (bZIP) domains and can respond to a plethora of physiological and pathological stimulus. In this study, we identified a novel AP-1 gene in Apostichopus japonicus by transcriptome sequencing and RACE approaches (designated as AjAP-1). The full-length of AjAP-1 was of 2944 bp including a 5' untranslated region (UTR) of 201 bp, a 3' UTR of 1753 bp and a putative open reading frame of 990 bp encoding a polypeptide of 329 amino acid residues. Two representative domains of Jun and bZIP as well as two nuclear localization signals (NLSs) were also detected in deduced amino acid of AjAP-1. Spatial distribution expression indicated that AjAP-1 was ubiquitously expressed in all examined tissues with predominant expression in the body wall, moderate in the tube feet, respiratory tree and colemocytes and slightly weak in the intestine and longitudinal muscle. Time-course expression analysis in intestine and coelomocytes revealed that AjAP-1 both reached its peak expression at 4 h after Vibrio splendidus challenge with a 2.6 and 8.2-fold increase compared to their control groups, respectively. Taken together, all these results suggested that AjAP-1 was a novel immune factor and might be involved in the processes of anti-bacteria response in sea cucumber.

  10. 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.

  11. Purification and characterization of bioactive peptides RYamide and CCHamide in the kuruma shrimp Marsupenaeus japonicus.

    PubMed

    Mekata, Tohru; Kono, Tomoya; Satoh, Jun; Yoshida, Morikatsu; Mori, Kenji; Sato, Takahiro; Miyazato, Mikiya; Ida, Takanori

    2017-01-04

    To understand the regulation systems of appetite, bioactive peptides from the kuruma shrimp Marsupenaeus japonicus (Mj) were isolated and purified by reverse pharmacological assays using CHO cells expressing the Drosophila melanogaster G-protein-coupled receptors (GPCRs) CG5811 (a RYamide receptor) or CG14593 (a CCHamide-2 receptor). Four peptides having binding activity to GPCRs were obtained and named Mj RYamide-1, Mj RYamide-2, Mj RYamide-3, and Mj CCHamide. Genes encoding the prepropeptides of these peptides were identified using kuruma shrimp transcriptome databases. The Mj prepro-RYamide gene encodes a 130-amino acid polypeptide containing Mj RYamide-1, Mj RYamide-2, and Mj RYamide-3, whereas the Mj prepro-CCHamide gene encodes a 119-amino acid polypeptide containing a single Mj CCHamide peptide. The expression of these genes was confirmed in various neuronal organs including the brain and ventral nerve cord. In addition, prepro-RYamide gene expression is significantly reduced in the brain after starvation. RYamides may thus be associated with regulation of feeding or digestion. Changes in kayak (the c-fos ortholog in invertebrates) gene expression after administration of synthetic peptides were also investigated. Mj kayak expression levels are upregulated in hepatopancreas after treatment with Mj RYamide-3 or CCHamide. Thus, the peptides isolated in this study may have some regulatory effect on cellular metabolism in aquacultured invertebrates.

  12. Down-regulated Lotus japonicus GCR1 plants exhibit nodulation signalling pathways alteration.

    PubMed

    Rogato, Alessandra; Valkov, Vladimir Totev; Alves, Ludovico Martins; Apone, Fabio; Colucci, Gabriella; Chiurazzi, Maurizio

    2016-06-01

    G Protein Coupled Receptor (GPCRs) are integral membrane proteins involved in various signalling pathways by perceiving many extracellular signals and transducing them to heterotrimeric G proteins, which further transduce these signals to intracellular downstream effectors. GCR1 is the only reliable plant candidate as a member of the GPCRs superfamily. In the legume/rhizobia symbiotic interaction, G proteins are involved in signalling pathways controlling different steps of the nodulation program. In order to investigate the putative hierarchic role played by GCR1 in these symbiotic pathways we identified and characterized the Lotus japonicus gene encoding the seven transmembrane GCR1 protein. The detailed molecular and topological analyses of LjGCR1 expression patterns that are presented suggest a possible involvement in the early steps of nodule organogenesis. Furthermore, phenotypic analyses of independent transgenic RNAi lines, showing a significant LjGCR1 expression down regulation, suggest an epistatic action in the control of molecular markers of nodulation pathways, although no macroscopic symbiotic phenotypes could be revealed.

  13. Polymorphisms of E1 and GIGANTEA in wild populations of Lotus japonicus.

    PubMed

    Wakabayashi, Tomomi; Oh, Hana; Kawaguchi, Masayoshi; Harada, Kyuya; Sato, Shusei; Ikeda, Hajime; Setoguchi, Hiroaki; Hiroaki, Setoguchi

    2014-11-01

    In plants, timing of flowering is an essential factor that controls the survival rates of descendants. The circadian clock genes E1 and GIGANTEA (GI) play a central role in transmitting signals to flowering locus T (FT) in leguminous plants. Lotus japonicus is a wild Japanese species that ranges from northern Hokkaido to the southern Ryukyus and exhibits a wide range in terms of the time between seeding and first flowering. In this study, we first identified LjGI and analyzed polymorphisms of LjE1 and LjGI among wild populations covering the entire distribution range of this species in Japan. LjGI had a coding sequence (CDS) length of 3495 bp and included 14 exons. The homologies of DNA and amino acid sequences between LjGI and GmGI were 89 and 88% (positive rate was 92%), respectively. LjE1 harbored five nucleic acid changes in a 552 bp CDS, all of which were nonsynonymous; four of the changes were located in the core function area. LjE1 alleles exhibited partial north-south differentiation and non-neutrality. In contrast, the LjGI harbored one synonymous and one nonsynonymous change. Thus, our study suggests that LjE1 may be involved in the control of flowering times, whereas LjGI may be under strong purifying selection.

  14. Effect of season on heavy metal contents and chemical compositions of chub mackerel (Scomber japonicus) muscle.

    PubMed

    Bae, J H; Lim, S Y

    2012-02-01

    Seasonal variations of heavy metals concentrations and overall chemical compositions were determined in chub mackerel caught in the Southern Sea of Korea. The average mercury and lead content varied between 0.04 and 0.08 mg/kg and between 0.01 and 0.02 mg/kg, respectively. Seasonal variations were not detected in lead, but mercury displayed maximal values in winter (P < 0.05). A distinct seasonal pattern was found in crude fat content with maximal values in December and minimal values in April. Fatty acid composition showed that monounsaturated fatty acids levels were the highest in August, while polyunsaturated fatty acids (PUFA) levels were the highest in April. The major contributing factors to the seasonal variation of PUFA amounted to 20:5n-3 and 22:6n-3. The total amino acids content varied from 180.6 to 187.7 mg/g. There were no significant seasonal variations in total amounts of amino acids. Practical Application:  Mackerel (Scomber japonicus) is one of the most important fishing resources in Korea. The effects of polyunsaturated fatty acids (PUFA) on the human body have been identified, and consequently, the intake of fish lipids has steadily increased among the human population. There have been few studies on safety and alterations in chemical composition of mackerel attributed to seasonal fluctuations. Therefore, the results presented in this study could be used to improve the safety and nutrition information available to consumers.

  15. 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.

  16. 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.

  17. Chemical composition and antimicrobial activity of the essential oils from Chloranthus japonicus Sieb. and Chloranthus multistachys Pei.

    PubMed

    Kang, Jie-fang; Zhang, Yuan; Du, Yong-liang; Wang, Zhe-zhi

    2010-01-01

    We examined the composition and antimicrobial activity of two essential oils from Chloranthus japonicus Sieb. and Chloranthus multistachys Pei. GC-FID and GC-MS analyses identified 48 and 39 compounds, which represented 95.56% and 94.58%, respectively, of all components in these oils. Of these, 28 compounds were common to both, with a relatively high amount of oxygenated monoterpenes (50.95% and 39.97%). Antimicrobial properties were evaluated in vitro via disc diffusion and microbroth dilution assays. Activities were strong against most tested microorganisms, with inhibition zones ranging from 8.1 to 22.2 mm. For both species, minimum values for inhibitory and bactericidal concentrations were 0.39 to 12.50 mg/mL and 0.78 to 50.00 mg/mL, respectively. These results suggest that these essential oils are potent natural sources of antimicrobial agents for the medicinal and pharmaceutical industries.

  18. 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.

  19. 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.

  20. Phylogenetic differentiation between Atlantic Scomber colias and Pacific Scomber japonicus based on nuclear DNA sequences.

    PubMed

    Infante, Carlos; Blanco, Enrique; Zuasti, Eugenia; Crespo, Aniela; Manchado, Manuel

    2007-05-01

    In the classical taxonomy, three Scomber species are distinguished: S. scombrus, S. australasicus, and S. japonicus. Yet, some fish taxonomists have recently recognized Scomber colias, inhabiting the Atlantic Ocean, as a separate species from S. japonicus, distributed in the Pacific Ocean. Such proposal was based on significant mitochondrial DNA divergence as well as great phenotypic variation among individuals from these two ocean basins. However, in the absence of nuclear DNA data this issue remains still controversial. In this study, a phylogenetic analysis of nuclear 5S rDNA sequences was performed. A total of 30 individuals of S. colias collected in the Atlantic and 34 specimens of S. japonicus from the Pacific were characterized. Moreover, nine individuals of Pacific S. australasicus and eight of Atlantic S. scombrus were included. Maximum likelihood, maximum parsimony, and neighbor-joining analyses revealed the presence of two well-supported distinct clades corresponding to S. colias and S. japonicus, respectively. Altogether, morphologic and genetic data are in agreement with the recognition of two different species, S. colias in the Atlantic, and S. japonicus in the Pacific.

  1. An effective seeding method for restoring the surfgrass Phyllospadix japonicus using an aartificial reef

    NASA Astrophysics Data System (ADS)

    Park, Jung-Im; Son, Min Ho; Kim, Jeong Bae; Lee, Kun-Seop

    2014-12-01

    Phyllospadix japonicus is an abundant surfgrass that thrives mainly along the exposed rocky shores of Northeastern Asia. On the eastern coast of Korea, surfgrass populations have been adversely affected by increasing human pressures. We developed a seeding method using an artificial reef for the restoration of P. japonicus. In January 2005, we planted P. japonicus seeds on the lower part of coarse hemp-plant brush that was embedded densely on the concave surface on the top of artificial reefs. The reefs were then installed on an exposed rocky shore. To evaluate the feasibility of this seed-based surfgrass restoration technique, we monitored the seedling/shoot density and morphological characteristics of the shoots over a 2-year period. Seedlings began to emerge within the first month after seeding, reaching densities of up to 275.0 shoots m-2 by April 2005. After an initial decline, shoot density increased through the production of lateral shoots, and densities of up to 997.1 shoots m-2 were observed by the end of the experiment. Shoot height, the number of leaves, and leaf width rapidly increased during the first year after seeding, whereas the number of rhizome internodes and rhizome length rapidly increased during the second year. The P. japonicus shoots exhibited approximately 63.4 mm of rhizome elongation during the study period. Because seeded P. japonicus on the artificial reefs were successfully established at the study site, this seeding method using an artificial reef may offer an effective approach to restoring surfgrass habitat.

  2. 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

  3. Using Exploratory and Confirmatory Methods to Identify the Cognitive Dimensions in a Large-Scale Science Assessment

    ERIC Educational Resources Information Center

    Leighton, Jacqueline P.; Gokiert, Rebecca J.; Cui, Ying

    2007-01-01

    Studies of test dimensionality indicate that many large-scale science assessments measure multiple dimensions. These findings have reinforced the perspective that science achievement is an inherently dynamic process and that there is benefit in reporting subscores in science. A limitation with some of these studies is that they fail to indicate…

  4. SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function.

    PubMed

    Li, Man; Li, Yong; Weeks, Olivia; Mijatovic, Vladan; Teumer, Alexander; Huffman, Jennifer E; Tromp, Gerard; Fuchsberger, Christian; Gorski, Mathias; Lyytikäinen, Leo-Pekka; Nutile, Teresa; Sedaghat, Sanaz; Sorice, Rossella; Tin, Adrienne; Yang, Qiong; Ahluwalia, Tarunveer S; Arking, Dan E; Bihlmeyer, Nathan A; Böger, Carsten A; Carroll, Robert J; Chasman, Daniel I; Cornelis, Marilyn C; Dehghan, Abbas; Faul, Jessica D; Feitosa, Mary F; Gambaro, Giovanni; Gasparini, Paolo; Giulianini, Franco; Heid, Iris; Huang, Jinyan; Imboden, Medea; Jackson, Anne U; Jeff, Janina; Jhun, Min A; Katz, Ronit; Kifley, Annette; Kilpeläinen, Tuomas O; Kumar, Ashish; Laakso, Markku; Li-Gao, Ruifang; Lohman, Kurt; Lu, Yingchang; Mägi, Reedik; Malerba, Giovanni; Mihailov, Evelin; Mohlke, Karen L; Mook-Kanamori, Dennis O; Robino, Antonietta; Ruderfer, Douglas; Salvi, Erika; Schick, Ursula M; Schulz, Christina-Alexandra; Smith, Albert V; Smith, Jennifer A; Traglia, Michela; Yerges-Armstrong, Laura M; Zhao, Wei; Goodarzi, Mark O; Kraja, Aldi T; Liu, Chunyu; Wessel, Jennifer; Boerwinkle, Eric; Borecki, Ingrid B; Bork-Jensen, Jette; Bottinger, Erwin P; Braga, Daniele; Brandslund, Ivan; Brody, Jennifer A; Campbell, Archie; Carey, David J; Christensen, Cramer; Coresh, Josef; Crook, Errol; Curhan, Gary C; Cusi, Daniele; de Boer, Ian H; de Vries, Aiko P J; Denny, Joshua C; Devuyst, Olivier; Dreisbach, Albert W; Endlich, Karlhans; Esko, Tõnu; Franco, Oscar H; Fulop, Tibor; Gerhard, Glenn S; Glümer, Charlotte; Gottesman, Omri; Grarup, Niels; Gudnason, Vilmundur; Hansen, Torben; Harris, Tamara B; Hayward, Caroline; Hocking, Lynne; Hofman, Albert; Hu, Frank B; Husemoen, Lise Lotte N; Jackson, Rebecca D; Jørgensen, Torben; Jørgensen, Marit E; Kähönen, Mika; Kardia, Sharon L R; König, Wolfgang; Kooperberg, Charles; Kriebel, Jennifer; Launer, Lenore J; Lauritzen, Torsten; Lehtimäki, Terho; Levy, Daniel; Linksted, Pamela; Linneberg, Allan; Liu, Yongmei; Loos, Ruth J F; Lupo, Antonio; Meisinger, Christine; Melander, Olle; Metspalu, Andres; Mitchell, Paul; Nauck, Matthias; Nürnberg, Peter; Orho-Melander, Marju; Parsa, Afshin; Pedersen, Oluf; Peters, Annette; Peters, Ulrike; Polasek, Ozren; Porteous, David; Probst-Hensch, Nicole M; Psaty, Bruce M; Qi, Lu; Raitakari, Olli T; Reiner, Alex P; Rettig, Rainer; Ridker, Paul M; Rivadeneira, Fernando; Rossouw, Jacques E; Schmidt, Frank; Siscovick, David; Soranzo, Nicole; Strauch, Konstantin; Toniolo, Daniela; Turner, Stephen T; Uitterlinden, André G; Ulivi, Sheila; Velayutham, Dinesh; Völker, Uwe; Völzke, Henry; Waldenberger, Melanie; Wang, Jie Jin; Weir, David R; Witte, Daniel; Kuivaniemi, Helena; Fox, Caroline S; Franceschini, Nora; Goessling, Wolfram; Köttgen, Anna; Chu, Audrey Y

    2017-03-01

    Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L; PStage1<3.7×10(-7)), of which most were common and annotated as nonsynonymous variants. Gene-based analysis identified associations of functional rare variants in three genes with eGFRcrea, including a novel association with the SOS Ras/Rho guanine nucleotide exchange factor 2 gene, SOS2 (P=5.4×10(-8) by sequence kernel association test). Experimental follow-up in zebrafish embryos revealed changes in glomerular gene expression and renal tubule morphology in the embryonic kidney of acp1- and sos2-knockdowns. These developmental abnormalities associated with altered blood clearance rate and heightened prevalence of edema. This study expands the number of loci associated with kidney function and identifies novel genes with potential roles in kidney formation.

  5. A Novel Interaction between CCaMK and a Protein Containing the Scythe_N Ubiquitin-Like Domain in Lotus japonicus1[C][W][OA

    PubMed Central

    Kang, Heng; Zhu, Hui; Chu, Xiaojie; Yang, Zhenzhen; Yuan, Songli; Yu, Dunqiang; Wang, Chao; Hong, Zonglie; Zhang, Zhongming

    2011-01-01

    In the Rhizobium-legume symbiosis, calcium/calmodulin-dependent protein kinase (CCaMK) is a key regulator for both rhizobial infection and nodule organogenesis. Deregulation of CCaMK by either a point mutation in the autophosphorylation site or the deletion of the carboxyl-terminal regulatory domain results in spontaneous nodule formation without rhizobia. However, the underlying biochemical mechanisms are poorly understood. Here, using the kinase domain of CCaMK as a bait in yeast two-hybrid screening, we identify a novel protein, CIP73 (for CCaMK-interacting protein of approximately 73 kD), that interacts with CCaMK. CIP73 contains a Scythe_N ubiquitin-like domain and belongs to the large ubiquitin superfamily. Deletion and mutagenesis analysis demonstrate that CIP73 could only interact with CCaMK when the calmodulin-binding domain and three EF-hand motifs are removed from the kinase domain. The amino-terminal 80 amino acid residues (80–160) of CCaMK are required for interacting with CIP73 in yeast cells. On the other hand, protein pull-down assay and bimolecular fluorescence complementation assay in Nicotiana benthamiana show that the full-length CCaMK could interact with CIP73 in vitro and in planta. Importantly, CCaMK phosphorylates the amino terminus of CIP73 in a Ca2+/calmodulin-dependent manner in vitro. CIP73 transcripts are preferentially expressed in roots, and very low expression is detected in leaves, stems, and nodules. The expression in roots is significantly decreased after inoculation of Mesorhizobium loti. RNA interference knockdown of CIP73 expression by hairy root transformation in Lotus japonicus led to decreased nodule formation, suggesting that CIP73 performed an essential role in nodulation. PMID:21209278

  6. 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.

  7. The research progress of antitumorous effectiveness of Stichopus japonicus acid mucopolysaccharide in north of China.

    PubMed

    Lu, Yun; Wang, Bao-Lei

    2009-03-01

    The sea cucumbers growing in the estuary of the Pohai of northern China are called Stichopus japonicus and are the orthodox holothurians in traditional Chinese medicine. There are multiple biological active ingredients in S. japonicus, and S. japonicus acid mucopolysaccharide (SJAMP) is one of the important ingredients. SJAMP has multiple pharmacologic actions, such as antitumor, immunologic regulation, anticoagulated blood, and antivirus. The research on antitumor has been carried out by way of animal experiments aiming at studying internal tumor-inhibiting effect of SJAMP, and the route of administration is usually peritoneal or intragastric. Additionally, sea cucumbers have been widely recognized and applied as medicated food or therapeutic prescriptions during and after the treatment of some tumors.

  8. Large-Scale Computational Screening Identifies First in Class Multitarget Inhibitor of EGFR Kinase and BRD4

    PubMed Central

    Allen, Bryce K.; Mehta, Saurabh; Ember, Stewart W. J.; Schonbrunn, Ernst; Ayad, Nagi; Schürer, Stephan C.

    2015-01-01

    Inhibition of cancer-promoting kinases is an established therapeutic strategy for the treatment of many cancers, although resistance to kinase inhibitors is common. One way to overcome resistance is to target orthogonal cancer-promoting pathways. Bromo and Extra-Terminal (BET) domain proteins, which belong to the family of epigenetic readers, have recently emerged as promising therapeutic targets in multiple cancers. The development of multitarget drugs that inhibit kinase and BET proteins therefore may be a promising strategy to overcome tumor resistance and prolong therapeutic efficacy in the clinic. We developed a general computational screening approach to identify novel dual kinase/bromodomain inhibitors from millions of commercially available small molecules. Our method integrated machine learning using big datasets of kinase inhibitors and structure-based drug design. Here we describe the computational methodology, including validation and characterization of our models and their application and integration into a scalable virtual screening pipeline. We screened over 6 million commercially available compounds and selected 24 for testing in BRD4 and EGFR biochemical assays. We identified several novel BRD4 inhibitors, among them a first in class dual EGFR-BRD4 inhibitor. Our studies suggest that this computational screening approach may be broadly applicable for identifying dual kinase/BET inhibitors with potential for treating various cancers. PMID:26596901

  9. Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease.

    PubMed

    Nalls, Mike A; Pankratz, Nathan; Lill, Christina M; Do, Chuong B; Hernandez, Dena G; Saad, Mohamad; DeStefano, Anita L; Kara, Eleanna; Bras, Jose; Sharma, Manu; Schulte, Claudia; Keller, Margaux F; Arepalli, Sampath; Letson, Christopher; Edsall, Connor; Stefansson, Hreinn; Liu, Xinmin; Pliner, Hannah; Lee, Joseph H; Cheng, Rong; Ikram, M Arfan; Ioannidis, John P A; Hadjigeorgiou, Georgios M; Bis, Joshua C; Martinez, Maria; Perlmutter, Joel S; Goate, Alison; Marder, Karen; Fiske, Brian; Sutherland, Margaret; Xiromerisiou, Georgia; Myers, Richard H; Clark, Lorraine N; Stefansson, Kari; Hardy, John A; Heutink, Peter; Chen, Honglei; Wood, Nicholas W; Houlden, Henry; Payami, Haydeh; Brice, Alexis; Scott, William K; Gasser, Thomas; Bertram, Lars; Eriksson, Nicholas; Foroud, Tatiana; Singleton, Andrew B

    2014-09-01

    We conducted a meta-analysis of Parkinson's disease genome-wide association studies using a common set of 7,893,274 variants across 13,708 cases and 95,282 controls. Twenty-six loci were identified as having genome-wide significant association; these and 6 additional previously reported loci were then tested in an independent set of 5,353 cases and 5,551 controls. Of the 32 tested SNPs, 24 replicated, including 6 newly identified loci. Conditional analyses within loci showed that four loci, including GBA, GAK-DGKQ, SNCA and the HLA region, contain a secondary independent risk variant. In total, we identified and replicated 28 independent risk variants for Parkinson's disease across 24 loci. Although the effect of each individual locus was small, risk profile analysis showed substantial cumulative risk in a comparison of the highest and lowest quintiles of genetic risk (odds ratio (OR) = 3.31, 95% confidence interval (CI) = 2.55-4.30; P = 2 × 10(-16)). We also show six risk loci associated with proximal gene expression or DNA methylation.

  10. A large-scale genome-wide association and meta-analysis identified four novel susceptibility loci for leprosy

    PubMed Central

    Wang, Zhenzhen; Sun, Yonghu; Fu, Xi'an; Yu, Gongqi; Wang, Chuan; Bao, Fangfang; Yue, Zhenhua; Li, Jianke; Sun, Lele; Irwanto, Astrid; Yu, Yongxiang; Chen, Mingfei; Mi, Zihao; Wang, Honglei; Huai, Pengcheng; Li, Yi; Du, Tiantian; Yu, Wenjun; Xia, Yang; Xiao, Hailu; You, Jiabao; Li, Jinghui; Yang, Qing; Wang, Na; Shang, Panpan; Niu, Guiye; Chi, Xiaojun; Wang, Xiuhuan; Cao, Jing; Cheng, Xiujun; Liu, Hong; Liu, Jianjun; Zhang, Furen

    2016-01-01

    Leprosy, a chronic infectious disease, results from the uncultivable pathogen Mycobacterium leprae (M. leprae), and usually progresses to peripheral neuropathy and permanent progressive deformity if not treated. Previously published genetic studies have identified 18 gene/loci significantly associated with leprosy at the genome-wide significant level. However as a complex disease, only a small proportion of leprosy risk could be explained by those gene/loci. To further identify more susceptibility gene/loci, we hereby performed a three-stage GWAS comprising 8,156 leprosy patients and 15,610 controls of Chinese ancestry. Four novel loci were identified including rs6807915 on 3p25.2 (P=1.94 × 10−8, OR=0.89), rs4720118 on 7p14.3 (P=3.85 × 10−10, OR=1.16), rs55894533 on 8p23.1 (P=5.07 × 10−11, OR=1.15) and rs10100465 on 8q24.11 (P=2.85 × 10−11, OR=0.85). Altogether, these findings have provided new insight and significantly expanded our understanding of the genetic basis of leprosy. PMID:27976721

  11. Reactive Oxygen Species (ROS)-Activated ATM-Dependent Phosphorylation of Cytoplasmic Substrates Identified by Large-Scale Phosphoproteomics Screen.

    PubMed

    Kozlov, Sergei V; Waardenberg, Ashley J; Engholm-Keller, Kasper; Arthur, Jonathan W; Graham, Mark E; Lavin, Martin

    2016-03-01

    Ataxia-telangiectasia, mutated (ATM) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signaling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle checkpoints, initiating DNA repair, and regulating gene expression. ATM kinase can be activated by a variety of stimuli, including oxidative stress. Here, we confirmed activation of cytoplasmic ATM by autophosphorylation at multiple sites. Then we employed a global quantitative phosphoproteomics approach to identify cytoplasmic proteins altered in their phosphorylation state in control and ataxia-telangiectasia (A-T) cells in response to oxidative damage. We demonstrated that ATM was activated by oxidative damage in the cytoplasm as well as in the nucleus and identified a total of 9,833 phosphorylation sites, including 6,686 high-confidence sites mapping to 2,536 unique proteins. A total of 62 differentially phosphorylated peptides were identified; of these, 43 were phosphorylated in control but not in A-T cells, and 19 varied in their level of phosphorylation. Motif enrichment analysis of phosphopeptides revealed that consensus ATM serine glutamine sites were overrepresented. When considering phosphorylation events, only observed in control cells (not observed in A-T cells), with predicted ATM sites phosphoSerine/phosphoThreonine glutamine, we narrowed this list to 11 candidate ATM-dependent cytoplasmic proteins. Two of these 11 were previously described as ATM substrates (HMGA1 and UIMCI/RAP80), another five were identified in a whole cell extract phosphoproteomic screens, and the remaining four proteins had not been identified previously in DNA damage response screens. We validated the phosphorylation of three of these proteins (oxidative stress responsive 1 (OSR1), HDGF, and ccdc82) as ATM dependent after H2O2 exposure, and another protein (S100A11) demonstrated ATM

  12. 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.

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

    PubMed Central

    Kong, Derong; Sun, He; Gu, Chenlei; Wang, Hongdi; Qiu, Xuemei; Chang, Yaqing; Liu, Zhanjiang

    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. PMID:26989617

  14. Experimental transmission of eastern equine encephalitis virus by Ochlerotatus j. japonicus (Diptera: Culicidae).

    PubMed

    Sardelis, Michael R; Dohm, David J; Pagac, Benedict; Andre, Richard G; Turell, Michael J

    2002-05-01

    We evaluated the potential for Ochlerotatus j. japonicus (Theobald), a newly recognized invasive mosquito species in the United States, to transmit eastern equine encephalitis (EEE) virus. Aedes albopictus (Skuse) and Culex pipiens (L.) were similarly tested for comparison. Ochlerotatus j. japonicus and Ae. albopictus became infected and transmitted EEE virus by bite after feeding on young chickens 1 d after they had been inoculated with EEE virus (viremias ranging from 10(7.0-8.7) plaque-forming units [PFU]/ml of blood). No Cx. pipiens (n = 20) had detectable levels of virus 14 d after feeding on an EEE-virus infected chicken with a viremia of 10(8.1) PFU per ml of blood. Depending on the viral titer in the donor chicken, infection rates ranged from 55-100% for Oc. j. japonicus and 93-100% for Ae. albopictus. In these two species, dissemination rates were identical to or nearly identical to infection rates. Depending on the viral titer in the blood meal, estimated transmission rates ranged from 15 to 25% for Oc. j. japonicus and 59-63% for Ae. albopictus. Studies of replication of EEE virus in Oc. j. japonicus showed that there was an "eclipse phase" in the first 4 d after an infectious blood meal, that viral titers peak by day 7 at around 10(5.7) per mosquito, and that virus escaped the mid-gut as soon as 3 d after the infectious blood meal. These data, combined with the opportunistic feeding behavior of Oc. j. japonicus in Asia and the reported expansion of its range in the eastern United States, indicate that it could function as a bridge vector for EEE virus between the enzootic Culiseta melanura (Coquillett)-avian cycle and susceptible mammalian hosts.

  15. 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.

  16. Calnexin functions in antibacterial immunity of Marsupenaeus japonicus.

    PubMed

    Zhang, Qing; Wang, Xiu-Qing; Jiang, Hai-Shan; Jia, Wen-Ming; Zhao, Xiao-Fan; Wang, Jin-Xing

    2014-10-01

    Calnexin (Cnx) is an endoplasmic reticulum membrane-bound lectin chaperone that comprises a dedicated maturation system with another lectin chaperone calreticulin (Crt). This maturation system is known as the Cnx/Crt cycle. The main functions of Cnx are Ca(2+) storage, glycoprotein folding, and quality control of synthesis. Recent studies have shown that Cnx is important in phagocytosis and in optimizing dendritic cell immunity. However, the functions of Cnx in invertebrate innate immunity remain unclear. In this research, we characterized Cnx in the kuruma shrimp Marsupenaeus japonicus (designated as MjCnx) and detected its function in shrimp immunity. The expression of MjCnx was upregulated in several tissues challenged with Vibrio anguillarum. Recombinant MjCnx could bind to bacteria by binding polysaccharides. MjCnx protein existed in the cytoplasm and on the membrane of hemocytes and was upregulated by bacterial challenge. The recombinant MjCnx enhanced the clearance of V. anguillarum in vivo, and the clearance effects were impaired after silencing MjCnx with RNA interference assay. Recombinant MjCnx promoted phagocytosis efficiency of hemocytes. These results suggest that MjCnx functions as one of the pattern recognition receptors and has crucial functions in shrimp antibacterial immunity.

  17. 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.

  18. 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.

  19. 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.

  20. Identifying sensitive areas of adaptive observations for prediction of the Kuroshio large meander using a shallow-water model

    NASA Astrophysics Data System (ADS)

    Zou, Guang'an; Wang, Qiang; Mu, Mu

    2016-09-01

    Sensitive areas for prediction of the Kuroshio large meander using a 1.5-layer, shallow-water ocean model were investigated using the conditional nonlinear optimal perturbation (CNOP) and first singular vector (FSV) methods. A series of sensitivity experiments were designed to test the sensitivity of sensitive areas within the numerical model. The following results were obtained: (1) the eff ect of initial CNOP and FSV patterns in their sensitive areas is greater than that of the same patterns in randomly selected areas, with the eff ect of the initial CNOP patterns in CNOP sensitive areas being the greatest; (2) both CNOP- and FSV-type initial errors grow more quickly than random errors; (3) the eff ect of random errors superimposed on the sensitive areas is greater than that of random errors introduced into randomly selected areas, and initial errors in the CNOP sensitive areas have greater eff ects on final forecasts. These results reveal that the sensitive areas determined using the CNOP are more sensitive than those of FSV and other randomly selected areas. In addition, ideal hindcasting experiments were conducted to examine the validity of the sensitive areas. The results indicate that reduction (or elimination) of CNOP-type errors in CNOP sensitive areas at the initial time has a greater forecast benefit than the reduction (or elimination) of FSV-type errors in FSV sensitive areas. These results suggest that the CNOP method is suitable for determining sensitive areas in the prediction of the Kuroshio large-meander path.

  1. The first large duplication of the RSK2 gene identified in a Coffin-Lowry syndrome patient.

    PubMed

    Marques Pereira, Patricia; Heron, Delphine; Hanauer, André

    2007-12-01

    Heterogeneous mutations in the X-linked gene RPS6KA3, encoding the protein kinase RSK2, are responsible for Coffin-Lowry Syndrome. Here we have further studied a male patient with a highly suggestive clinical diagnosis of CLS but in whom no mutation was found by exon sequencing. Western blot analysis revealed a protein much larger than the normal expected size. Sequencing of the RSK2 cDNA, showed the presence of an in-frame tandem duplication of exons 17-20. The mutated RSK2 protein was found to be inactive in an in-vitro kinase assay. This event, which was the result of a homologous unequal recombination between Alu sequences, is the first reported large duplication of the RPS6KA3 gene. Our finding provides further evidence that immunoblot analysis, or a molecular assay capable to detect large genomic mutational events, is essential for patients with a highly suggestive CLS clinical diagnosis but remaining without mutation after exon sequencing.

  2. Identifying sources of groundwater nitrate contamination in a large alluvial groundwater basin with highly diversified intensive agricultural production.

    PubMed

    Lockhart, K M; King, A M; Harter, T

    2013-08-01

    Groundwater quality is a concern in alluvial aquifers underlying agricultural areas worldwide. Nitrate from land applied fertilizers or from animal waste can leach to groundwater and contaminate drinking water resources. The San Joaquin Valley, California, is an example of an agricultural landscape with a large diversity of field, vegetable, tree, nut, and citrus crops, but also confined animal feeding operations (CAFOs, here mostly dairies) that generate, store, and land apply large amounts of liquid manure. As in other such regions around the world, the rural population in the San Joaquin Valley relies almost exclusively on shallow domestic wells (≤150 m deep), of which many have been affected by nitrate. Variability in crops, soil type, and depth to groundwater contribute to large variability in nitrate occurrence across the underlying aquifer system. The role of these factors in controlling groundwater nitrate contamination levels is examined. Two hundred domestic wells were sampled in two sub-regions of the San Joaquin Valley, Stanislaus and Merced (Stan/Mer) and Tulare and Kings (Tul/Kings) Counties. Forty six percent of well water samples in Tul/Kings and 42% of well water samples in Stan/Mer exceeded the MCL for nitrate (10mg/L NO3-N). For statistical analysis of nitrate contamination, 78 crop and landuse types were considered by grouping them into ten categories (CAFO, citrus, deciduous fruits and nuts, field crops, forage, native, pasture, truck crops, urban, and vineyards). Vadose zone thickness, soil type, well construction information, well proximity to dairies, and dominant landuse near the well were considered. In the Stan/Mer area, elevated nitrate levels in domestic wells most strongly correlate with the combination of very shallow (≤21 m) water table and the presence of either CAFO derived animal waste applications or deciduous fruit and nut crops (synthetic fertilizer applications). In Tulare County, statistical data indicate that elevated

  3. Identifying sources of groundwater nitrate contamination in a large alluvial groundwater basin with highly diversified intensive agricultural production

    NASA Astrophysics Data System (ADS)

    Lockhart, K. M.; King, A. M.; Harter, T.

    2013-08-01

    Groundwater quality is a concern in alluvial aquifers underlying agricultural areas worldwide. Nitrate from land applied fertilizers or from animal waste can leach to groundwater and contaminate drinking water resources. The San Joaquin Valley, California, is an example of an agricultural landscape with a large diversity of field, vegetable, tree, nut, and citrus crops, but also confined animal feeding operations (CAFOs, here mostly dairies) that generate, store, and land apply large amounts of liquid manure. As in other such regions around the world, the rural population in the San Joaquin Valley relies almost exclusively on shallow domestic wells (≤ 150 m deep), of which many have been affected by nitrate. Variability in crops, soil type, and depth to groundwater contribute to large variability in nitrate occurrence across the underlying aquifer system. The role of these factors in controlling groundwater nitrate contamination levels is examined. Two hundred domestic wells were sampled in two sub-regions of the San Joaquin Valley, Stanislaus and Merced (Stan/Mer) and Tulare and Kings (Tul/Kings) Counties. Forty six percent of well water samples in Tul/Kings and 42% of well water samples in Stan/Mer exceeded the MCL for nitrate (10 mg/L NO3-N). For statistical analysis of nitrate contamination, 78 crop and landuse types were considered by grouping them into ten categories (CAFO, citrus, deciduous fruits and nuts, field crops, forage, native, pasture, truck crops, urban, and vineyards). Vadose zone thickness, soil type, well construction information, well proximity to dairies, and dominant landuse near the well were considered. In the Stan/Mer area, elevated nitrate levels in domestic wells most strongly correlate with the combination of very shallow (≤ 21 m) water table and the presence of either CAFO derived animal waste applications or deciduous fruit and nut crops (synthetic fertilizer applications). In Tulare County, statistical data indicate that elevated

  4. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways.

    PubMed

    Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian'an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O'Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tõnu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

    2012-09-01

    Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control.

  5. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.

    PubMed

    Soler Artigas, María; Loth, Daan W; Wain, Louise V; Gharib, Sina A; Obeidat, Ma'en; Tang, Wenbo; Zhai, Guangju; Zhao, Jing Hua; Smith, Albert Vernon; Huffman, Jennifer E; Albrecht, Eva; Jackson, Catherine M; Evans, David M; Cadby, Gemma; Fornage, Myriam; Manichaikul, Ani; Lopez, Lorna M; Johnson, Toby; Aldrich, Melinda C; Aspelund, Thor; Barroso, Inês; Campbell, Harry; Cassano, Patricia A; Couper, David J; Eiriksdottir, Gudny; Franceschini, Nora; Garcia, Melissa; Gieger, Christian; Gislason, Gauti Kjartan; Grkovic, Ivica; Hammond, Christopher J; Hancock, Dana B; Harris, Tamara B; Ramasamy, Adaikalavan; Heckbert, Susan R; Heliövaara, Markku; Homuth, Georg; Hysi, Pirro G; James, Alan L; Jankovic, Stipan; Joubert, Bonnie R; Karrasch, Stefan; Klopp, Norman; Koch, Beate; Kritchevsky, Stephen B; Launer, Lenore J; Liu, Yongmei; Loehr, Laura R; Lohman, Kurt; Loos, Ruth J F; Lumley, Thomas; Al Balushi, Khalid A; Ang, Wei Q; Barr, R Graham; Beilby, John; Blakey, John D; Boban, Mladen; Boraska, Vesna; Brisman, Jonas; Britton, John R; Brusselle, Guy G; Cooper, Cyrus; Curjuric, Ivan; Dahgam, Santosh; Deary, Ian J; Ebrahim, Shah; Eijgelsheim, Mark; Francks, Clyde; Gaysina, Darya; Granell, Raquel; Gu, Xiangjun; Hankinson, John L; Hardy, Rebecca; Harris, Sarah E; Henderson, John; Henry, Amanda; Hingorani, Aroon D; Hofman, Albert; Holt, Patrick G; Hui, Jennie; Hunter, Michael L; Imboden, Medea; Jameson, Karen A; Kerr, Shona M; Kolcic, Ivana; Kronenberg, Florian; Liu, Jason Z; Marchini, Jonathan; McKeever, Tricia; Morris, Andrew D; Olin, Anna-Carin; Porteous, David J; Postma, Dirkje S; Rich, Stephen S; Ring, Susan M; Rivadeneira, Fernando; Rochat, Thierry; Sayer, Avan Aihie; Sayers, Ian; Sly, Peter D; Smith, George Davey; Sood, Akshay; Starr, John M; Uitterlinden, André G; Vonk, Judith M; Wannamethee, S Goya; Whincup, Peter H; Wijmenga, Cisca; Williams, O Dale; Wong, Andrew; Mangino, Massimo; Marciante, Kristin D; McArdle, Wendy L; Meibohm, Bernd; Morrison, Alanna C; North, Kari E; Omenaas, Ernst; Palmer, Lyle J; Pietiläinen, Kirsi H; Pin, Isabelle; Pola Sbreve Ek, Ozren; Pouta, Anneli; Psaty, Bruce M; Hartikainen, Anna-Liisa; Rantanen, Taina; Ripatti, Samuli; Rotter, Jerome I; Rudan, Igor; Rudnicka, Alicja R; Schulz, Holger; Shin, So-Youn; Spector, Tim D; Surakka, Ida; Vitart, Veronique; Völzke, Henry; Wareham, Nicholas J; Warrington, Nicole M; Wichmann, H-Erich; Wild, Sarah H; Wilk, Jemma B; Wjst, Matthias; Wright, Alan F; Zgaga, Lina; Zemunik, Tatijana; Pennell, Craig E; Nyberg, Fredrik; Kuh, Diana; Holloway, John W; Boezen, H Marike; Lawlor, Debbie A; Morris, Richard W; Probst-Hensch, Nicole; Kaprio, Jaakko; Wilson, James F; Hayward, Caroline; Kähönen, Mika; Heinrich, Joachim; Musk, Arthur W; Jarvis, Deborah L; Gläser, Sven; Järvelin, Marjo-Riitta; Ch Stricker, Bruno H; Elliott, Paul; O'Connor, George T; Strachan, David P; London, Stephanie J; Hall, Ian P; Gudnason, Vilmundur; Tobin, Martin D

    2011-09-25

    Pulmonary function measures reflect respiratory health and are used in the diagnosis of chronic obstructive pulmonary disease. We tested genome-wide association with forced expiratory volume in 1 second and the ratio of forced expiratory volume in 1 second to forced vital capacity in 48,201 individuals of European ancestry with follow up of the top associations in up to an additional 46,411 individuals. We identified new regions showing association (combined P < 5 × 10(-8)) with pulmonary function in or near MFAP2, TGFB2, HDAC4, RARB, MECOM (also known as EVI1), SPATA9, ARMC2, NCR3, ZKSCAN3, CDC123, C10orf11, LRP1, CCDC38, MMP15, CFDP1 and KCNE2. Identification of these 16 new loci may provide insight into the molecular mechanisms regulating pulmonary function and into molecular targets for future therapy to alleviate reduced lung function.

  6. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

    PubMed Central

    Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian’an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O’Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tönu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

    2012-01-01

    Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have raised the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional follow-up of these newly discovered loci will further improve our understanding of glycemic control. PMID:22885924

  7. Genome-wide association and large scale follow-up identifies 16 new loci influencing lung function

    PubMed Central

    Artigas, María Soler; Loth, Daan W; Wain, Louise V; Gharib, Sina A; Obeidat, Ma’en; Tang, Wenbo; Zhai, Guangju; Zhao, Jing Hua; Smith, Albert Vernon; Huffman, Jennifer E; Albrecht, Eva; Jackson, Catherine M; Evans, David M; Cadby, Gemma; Fornage, Myriam; Manichaikul, Ani; Lopez, Lorna M; Johnson, Toby; Aldrich, Melinda C; Aspelund, Thor; Barroso, Inês; Campbell, Harry; Cassano, Patricia A; Couper, David J; Eiriksdottir, Gudny; Franceschini, Nora; Garcia, Melissa; Gieger, Christian; Gislason, Gauti Kjartan; Grkovic, Ivica; Hammond, Christopher J; Hancock, Dana B; Harris, Tamara B; Ramasamy, Adaikalavan; Heckbert, Susan R; Heliövaara, Markku; Homuth, Georg; Hysi, Pirro G; James, Alan L; Jankovic, Stipan; Joubert, Bonnie R; Karrasch, Stefan; Klopp, Norman; Koch, Beate; Kritchevsky, Stephen B; Launer, Lenore J; Liu, Yongmei; Loehr, Laura R; Lohman, Kurt; Loos, Ruth JF; Lumley, Thomas; Al Balushi, Khalid A; Ang, Wei Q; Barr, R Graham; Beilby, John; Blakey, John D; Boban, Mladen; Boraska, Vesna; Brisman, Jonas; Britton, John R; Brusselle, Guy G; Cooper, Cyrus; Curjuric, Ivan; Dahgam, Santosh; Deary, Ian J; Ebrahim, Shah; Eijgelsheim, Mark; Francks, Clyde; Gaysina, Darya; Granell, Raquel; Gu, Xiangjun; Hankinson, John L; Hardy, Rebecca; Harris, Sarah E; Henderson, John; Henry, Amanda; Hingorani, Aroon D; Hofman, Albert; Holt, Patrick G; Hui, Jennie; Hunter, Michael L; Imboden, Medea; Jameson, Karen A; Kerr, Shona M; Kolcic, Ivana; Kronenberg, Florian; Liu, Jason Z; Marchini, Jonathan; McKeever, Tricia; Morris, Andrew D; Olin, Anna-Carin; Porteous, David J; Postma, Dirkje S; Rich, Stephen S; Ring, Susan M; Rivadeneira, Fernando; Rochat, Thierry; Sayer, Avan Aihie; Sayers, Ian; Sly, Peter D; Smith, George Davey; Sood, Akshay; Starr, John M; Uitterlinden, André G; Vonk, Judith M; Wannamethee, S Goya; Whincup, Peter H; Wijmenga, Cisca; Williams, O Dale; Wong, Andrew; Mangino, Massimo; Marciante, Kristin D; McArdle, Wendy L; Meibohm, Bernd; Morrison, Alanna C; North, Kari E; Omenaas, Ernst; Palmer, Lyle J; Pietiläinen, Kirsi H; Pin, Isabelle; Polašek, Ozren; Pouta, Anneli; Psaty, Bruce M; Hartikainen, Anna-Liisa; Rantanen, Taina; Ripatti, Samuli; Rotter, Jerome I; Rudan, Igor; Rudnicka, Alicja R; Schulz, Holger; Shin, So-Youn; Spector, Tim D; Surakka, Ida; Vitart, Veronique; Völzke, Henry; Wareham, Nicholas J; Warrington, Nicole M; Wichmann, H-Erich; Wild, Sarah H; Wilk, Jemma B; Wjst, Matthias; Wright, Alan F; Zgaga, Lina; Zemunik, Tatijana; Pennell, Craig E; Nyberg, Fredrik; Kuh, Diana; Holloway, John W; Boezen, H Marike; Lawlor, Debbie A; Morris, Richard W; Probst-Hensch, Nicole; Kaprio, Jaakko; Wilson, James F; Hayward, Caroline; Kähönen, Mika; Heinrich, Joachim; Musk, Arthur W; Jarvis, Deborah L; Gläser, Sven; Järvelin, Marjo-Riitta; Stricker, Bruno H Ch; Elliott, Paul; O’Connor, George T; Strachan, David P; London, Stephanie J; Hall, Ian P; Gudnason, Vilmundur; Tobin, Martin D

    2011-01-01

    Pulmonary function measures reflect respiratory health and predict mortality, and are used in the diagnosis of chronic obstructive pulmonary disease (COPD). We tested genome-wide association with the forced expiratory volume in 1 second (FEV1) and the ratio of FEV1 to forced vital capacity (FVC) in 48,201 individuals of European ancestry, with follow-up of top associations in up to an additional 46,411 individuals. We identified new regions showing association (combined P<5×10−8) with pulmonary function, in or near MFAP2, TGFB2, HDAC4, RARB, MECOM (EVI1), SPATA9, ARMC2, NCR3, ZKSCAN3, CDC123, C10orf11, LRP1, CCDC38, MMP15, CFDP1, and KCNE2. Identification of these 16 new loci may provide insight into the molecular mechanisms regulating pulmonary function and into molecular targets for future therapy to alleviate reduced lung function. PMID:21946350

  8. Genotypic and phenotypic diversity of rhizobia isolated from Lathyrus japonicus indigenous to Japan.

    PubMed

    Aoki, Seishiro; Kondo, Tetsuya; Prévost, Danielle; Nakata, Sayuri; Kajita, Tadashi; Ito, Motomi

    2010-11-01

    Sixty-one rhizobial strains from Lathyrus japonicus nodules growing on the seashore in Japan were characterized and compared to two strains from Canada. The PCR-based method was used to identify test strains with novel taxonomic markers that were designed to discriminate between all known Lathyrus rhizobia. Three genomic groups (I, II, and III) were finally identified using RAPD, RFLP, and phylogenetic analyses. Strains in genomic group I (related to Rhizobium leguminosarum) were divided into two subgroups (Ia and Ib) and subgroup Ia was related to biovar viciae. Strains in subgroup Ib, which were all isolated from Japanese sea pea, belonged to a distinct group from other rhizobial groups in the recA phylogeny and PCR-based grouping, and were more tolerant to salt than the isolate from an inland legume. Test strains in genomic groups II and III belonged to a single clade with the reference strains of R. pisi, R. etli, and R. phaseoli in the 16S rRNA phylogeny. The PCR-based method and phylogenetic analysis of recA revealed that genomic group II was related to R. pisi. The analyses also showed that genomic group III harbored a mixed chromosomal sequence of different genomic groups, suggesting a recent horizontal gene transfer between diverse rhizobia. Although two Canadian strains belonged to subgroup Ia, molecular and physiological analyses showed the divergence between Canadian and Japanese strains. Phylogenetic analysis of nod genes divided the rhizobial strains into several groups that reflected the host range of rhizobia. Symbiosis between dispersing legumes and rhizobia at seashore is discussed.

  9. The proteome of seed development in the model legume Lotus japonicus.

    PubMed

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

    2009-03-01

    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.

  10. 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.

  11. Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network.

    PubMed

    Kim, Taehyong; Dreher, Kate; Nilo-Poyanco, Ricardo; Lee, Insuk; Fiehn, Oliver; Lange, Bernd Markus; Nikolau, Basil J; Sumner, Lloyd; Welti, Ruth; Wurtele, Eve S; Rhee, Seung Y

    2015-04-01

    Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.

  12. Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk

    PubMed Central

    Zhang, Ben; Jia, Wei-Hua; Matsuda, Koichi; Kweon, Sun-Seog; Matsuo, Keitaro; Xiang, Yong-Bing; Shin, Aesun; Jee, Sun Ha; Kim, Dong-Hyun; Cai, Qiuyin; Long, Jirong; Shi, Jiajun; Wen, Wanqing; Yang, Gong; Zhang, Yanfeng; Li, Chun; Li, Bingshan; Guo, Yan; Ren, Zefang; Ji, Bu-Tian; Pan, Zhi-Zhong; Takahashi, Atsushi; Shin, Min-Ho; Matsuda, Fumihiko; Gao, Yu-Tang; Oh, Jae Hwan; Kim, Soriul; Ahn, Yoon-Ok; Chan, Andrew T; Chang-Claude, Jenny; Slattery, Martha L.; Gruber, Stephen B.; Schumacher, Fredrick R.; Stenzel, Stephanie L.; Casey, Graham; Kim, Hyeong-Rok; Jeong, Jin-Young; Park, Ji Won; Li, Hong-Lan; Hosono, Satoyo; Cho, Sang-Hee; Kubo, Michiaki; Shu, Xiao-Ou; Zeng, Yi-Xin; Zheng, Wei

    2014-01-01

    Known genetic loci explain only a small proportion of the familial relative risk of colorectal cancer (CRC). We conducted the largest genome-wide association study in East Asians with 14,963 CRC cases and 31,945 controls and identified six new loci associated with CRC risk (P = 3.42 × 10−8 to 9.22 × 10−21) at 10q22.3, 10q25.2, 11q12.2, 12p13.31, 17p13.3 and 19q13.2. Two of these loci map to genes (TCF7L2 and TGFB1) with established roles in colorectal tumorigenesis. Four other loci are located in or near genes involved in transcription regulation (ZMIZ1), genome maintenance (FEN1), fatty acid metabolism (FADS1 and FADS2), cancer cell motility and metastasis (CD9) and cell growth and differentiation (NXN). We also found suggestive evidence for three additional loci associated with CRC risk near genome-wide significance at 8q24.11, 10q21.1 and 10q24.2. Furthermore, we replicated 22 previously reported CRC loci. Our study provides insights into the genetic basis of CRC and suggests new biological pathways. PMID:24836286

  13. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.

    PubMed

    Rivadeneira, Fernando; Styrkársdottir, Unnur; Estrada, Karol; Halldórsson, Bjarni V; Hsu, Yi-Hsiang; Richards, J Brent; Zillikens, M Carola; Kavvoura, Fotini K; Amin, Najaf; Aulchenko, Yurii S; Cupples, L Adrienne; Deloukas, Panagiotis; Demissie, Serkalem; Grundberg, Elin; Hofman, Albert; Kong, Augustine; Karasik, David; van Meurs, Joyce B; Oostra, Ben; Pastinen, Tomi; Pols, Huibert A P; Sigurdsson, Gunnar; Soranzo, Nicole; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Williams, Frances M K; Wilson, Scott G; Zhou, Yanhua; Ralston, Stuart H; van Duijn, Cornelia M; Spector, Timothy; Kiel, Douglas P; Stefansson, Kari; Ioannidis, John P A; Uitterlinden, André G

    2009-11-01

    Bone mineral density (BMD) is a heritable complex trait used in the clinical diagnosis of osteoporosis and the assessment of fracture risk. We performed meta-analysis of five genome-wide association studies of femoral neck and lumbar spine BMD in 19,195 subjects of Northern European descent. We identified 20 BMD loci that reached genome-wide significance (GWS; P < 5 x 10(-8)), of which 13 map to regions not previously associated with this trait: 1p31.3 (GPR177), 2p21 (SPTBN1), 3p22 (CTNNB1), 4q21.1 (MEPE), 5q14 (MEF2C), 7p14 (STARD3NL), 7q21.3 (FLJ42280), 11p11.2 (LRP4, ARHGAP1, F2), 11p14.1 (DCDC5), 11p15 (SOX6), 16q24 (FOXL1), 17q21 (HDAC5) and 17q12 (CRHR1). The meta-analysis also confirmed at GWS level seven known BMD loci on 1p36 (ZBTB40), 6q25 (ESR1), 8q24 (TNFRSF11B), 11q13.4 (LRP5), 12q13 (SP7), 13q14 (TNFSF11) and 18q21 (TNFRSF11A). The many SNPs associated with BMD map to genes in signaling pathways with relevance to bone metabolism and highlight the complex genetic architecture that underlies osteoporosis and variation in BMD.

  14. Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.

    PubMed

    Mann, Rachel A; Smits, Theo H M; Bühlmann, Andreas; Blom, Jochen; Goesmann, Alexander; Frey, Jürg E; Plummer, Kim M; Beer, Steven V; Luck, Joanne; Duffy, Brion; Rodoni, Brendan

    2013-01-01

    The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus) and strains infecting Rubus (raspberries and blackberries). Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains), the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1(Ea) and a putative secondary metabolite pathway only present in Rubus-infecting strains.

  15. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4

    PubMed Central

    Sklar, Pamela; Ripke, Stephan; Scott, Laura J.; Andreassen, Ole A.; Cichon, Sven; Craddock, Nick; Edenberg, Howard J.; Nurnberger, John I.; Rietschel, Marcella; Blackwood, Douglas; Corvin, Aiden; Flickinger, Matthew; Guan, Weihua; Mattingsdal, Morten; Mcquillin, Andrew; Kwan, Phoenix; Wienker, Thomas F.; Daly, Mark; Dudbridge, Frank; Holmans, Peter A.; Lin, Danyu; Burmeister, Margit; Greenwood, Tiffany A.; Hamshere, Marian L.; Muglia, Pierandrea; Smith, Erin N.; Zandi, Peter P.; Nievergelt, Caroline M.; Mckinney, Rebecca; Shilling, Paul D.; Schork, Nicholas J.; Bloss, Cinnamon S.; Foroud, Tatiana; Koller, Daniel L.; Gershon, Elliot S.; Liu, Chunyu; Badner, Judith A.; Scheftner, William A.; Lawson, William B.; Nwulia, Evaristus A.; Hipolito, Maria; Coryell, William; Rice, John P.; Byerley, William; McMahon, Francis J.; Schulze, Thomas G.; Berrettini, Wade; Lohoff, Falk W.; Potash, James B.; Mahon, Pamela B.; Mcinnis, Melvin G.; Zöllner, Sebastian; Zhang, Peng; Craig, David W.; Szelinger, Szabocls; Barrett, Thomas B.; Breuer, René; Meier, Sandra; Strohmaier, Jana; Witt, Stephanie H.; Tozzi, Federica; Farmer, Anne; McGuffin, Peter; Strauss, John; Xu, Wei; Kennedy, James L.; Vincent, John B.; Matthews, Keith; Day, Richard; Ferreira, Manuel D.C.; O'Dushlaine, Colm; Perlis, Roy; Raychaudhuri, Soumya; Ruderfer, Douglas; Hyoun, Phil L.; Smoller, Jordan W.; Li, Jun; Absher, Devin; Thompson, Robert C.; Meng, Fan Guo; Schatzberg, Alan F.; Bunney, William E.; Barchas, Jack D.; Jones, Edward G.; Watson, Stanley J.; Myers, Richard M.; Akil, Huda; Boehnke, Michael; Chambert, Kim; Moran, Jennifer; Scolnick, Ed; Djurovic, Srdjan; Melle, Ingrid; Morken, Gunnar; Gill, Michael; Morris, Derek; Quinn, Emma; Mühleisen, Thomas W.; Degenhardt, Franziska A.; Mattheisen, Manuel; Schumacher, Johannes; Maier, Wolfgang; Steffens, Michael; Propping, Peter; Nöthen, Markus M.; Anjorin, Adebayo; Bass, Nick; Gurling, Hugh; Kandaswamy, Radhika; Lawrence, Jacob; Mcghee, Kevin; Mcintosh, Andrew; Mclean, Alan W.; Muir, Walter J.; Pickard, Benjamin S.; Breen, Gerome; St Clair, David; Caesar, Sian; Gordon-Smith, Katherine; Jones, Lisa; Fraser, Christine; Green, Elaine K.; Grozeva, Detelina; Jones, Ian R.; Kirov, George; Moskvina, Valentina; Nikolov, Ivan; O'Donovan, Michael C.; Owen, Michael J.; Collier, David A.; Elkin, Amanda; Williamson, Richard; Young, Allan H.; Ferrier, I Nicol; Stefansson, Kari; Stefansson, Hreinn; Porgeirsson, Porgeir; Steinberg, Stacy; Gustafsson, Omar; Bergen, Sarah E.; Nimgaonkar, Vishwajit; hultman, Christina; Landén, Mikael; Lichtenstein, Paul; Sullivan, Patrick; Schalling, Martin; Osby, Urban; Backlund, Lena; Frisén, Louise; Langstrom, Niklas; Jamain, Stéphane; Leboyer, Marion; Etain, Bruno; Bellivier, Frank; Petursson, Hannes; Sigur Sson, Engilbert; Müller-Mysok, Bertram; Lucae, Susanne; Schwarz, Markus; Schofield, Peter R.; Martin, Nick; Montgomery, Grant W.; Lathrop, Mark; Oskarsson, Högni; Bauer, Michael; Wright, Adam; Mitchell, Philip B.; Hautzinger, Martin; Reif, Andreas; Kelsoe, John R.; Purcell, Shaun M.

    2011-01-01

    We conducted a combined genome-wide association (GWAS) analysis of 7,481 individuals affected with bipolar disorder and 9,250 control individuals within the Psychiatric Genomewide Association Study Consortium Bipolar Disorder group (PGC-BD). We performed a replication study in which we tested 34 independent SNPs in 4,493 independent bipolar disorder cases and 42,542 independent controls and found strong evidence for replication. In the replication sample, 18 of 34 SNPs had P value < 0.05, and 31 of 34 SNPs had signals with the same direction of effect (P = 3.8 × 10−7). In the combined analysis of all 63,766 subjects (11,974 cases and 51,792 controls), genome-wide significant evidence for association was confirmed for CACNA1C and found for a novel gene ODZ4. In a combined analysis of non-overlapping schizophrenia and bipolar GWAS samples we observed strong evidence for association with SNPs in CACNA1C and in the region of NEK4/ITIH1,3,4. Pathway analysis identified a pathway comprised of subunits of calcium channels enriched in the bipolar disorder association intervals. The strength of the replication data implies that increasing samples sizes in bipolar disorder will confirm many additional loci. PMID:21926972

  16. Identifying, monitoring and implementing "sustainable" agricultural practices for smallholder farmers over large geographic areas in India and Vietnam

    NASA Astrophysics Data System (ADS)

    Kritee, K.; Ahuja, R.; Nair, D.; Esteves, T.; Rudek, J.; Thu Ha, T.

    2015-12-01

    Industrial agriculture systems, mostly in developed and some emerging economies, are far different from the small-holder farms (size <1 acre) in Asia and Africa. Along with our partners from non-governmental, corporate, academic and government sectors and tens of thousands of farming families, we have worked actively in five states in India and two provinces in Vietnam for the last five years to understand how sustainable and climate smart farming practices can be monitored at small-holder farms. Here, any approach to monitor farming must begin by accounting for the tremendous management variability from farm to farm and also the current inability to ground-truth remote sensing data due to lack of relaible basic parameters (e.g., yields, N use, farm boundaries) which are necessary for calibrating empirical/biogeochemical models. While we continue to learn from new research, we have found that it is crucial to follow some steps if sustainable farming programs are to succeed at small-holder farms Demographic data collection and GPS plot demarcation to establish farm size and ownership Baseline nutrient, water & energy use and crop yield determination via surveys and self-reporting which are verifiable through farmer networks given the importance of peer to peer learning in the dissemination of new techniques in such landscapes "Sustainable" practice determination in consultation with local universities/NGO experts Measurements on representative plots for 3-4 years to help calibrate biogeochemical models and/or empirical equations and establish which practices are truly "sustainable" (e.g., GHG emission reduction varies from 0-7 tCO2e/acre for different sustainable practices). Propagation of sustainable practices across the landscape via local NGOs/governments after analyzing the replicability of identified farming practices in the light of local financial, cultural or socio-political barriers. We will present results from representative plots (including soil and

  17. Geospatial analysis of invasion of the Asian tiger mosquito Aedes albopictus: competition with Aedes japonicus japonicus in its northern limit area in Japan.

    PubMed

    Nihei, Naoko; Komagata, Osamu; Mochizuki, Kan-ichiro; Kobayashi, Mutsuo

    2014-05-01

    The mosquito Aedes albopictus, indigenous to Southeast Asia and nearby islands, has spread almost worldwide during recent decades. We confirm the invasion of this mosquito, first reported in Yamagata city in northeast Honshu, Japan in 2000. Previously, only Ae. japonicus japonicus had been collected in this place, but 2 years later, the population of Ae. albopictus had increased, so more than 80% of the total number of larval colonies there consisted of this species. In contrast to Yamagata's new residential area, now infested by Ae. albopictus, the original mosquito remains in the city but its habitats are generally closer to the surrounding mountains, where the normalized difference vegetation index is higher. The factors affecting the distribution of both species in Yamagata city were studied using geographical information systems (GIS) based on data derived from field surveys, aerial photographs, satellite images and digital maps. The range of Aedes mosquito habitats was estimated and visualised on polygon maps and no significant differences were noted when the polygon area was calculated by GIS software in comparison with the satellite images. Although Ae. j. japonicus was expected to be rapidly overrun by Ae. albopictus, this did not happen. Currently, both species coexist; not only in separate sites, but also simultaneously in various water bodies, where larvae from both species have frequently been seen. However, the competitive relationship between these two Aedes species within a warming environment is an issue that should be closely monitored.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  19. The introduced Asian parasitic copepod Neoergasilus japonicus (Harada) (Cyclopoida: Ergasilidae) from endangered cichlid teleosts in Mexico.

    PubMed

    Suárez-Morales, Eduardo; Paredes-Trujillo, Amelia; González-Solís, David

    2010-11-01

    The cyclopoid copepod Neoergasilus japonicus ( Harada, 1930 ) is recorded from three endangered or threatened fish species from southeast Mexico: the tailbar cichlid Vieja hartwegi (Taylor and Miller, 1980); the Angostura cichlid V. breidohri (Werner and Stawikowski, 1987); and the sieve cichlid C. grammodes (Taylor and Miller, 1980). This ectoparasitic copepod is considered, together with most other members of Neoergasilus, an Eastern Asian form. N. japonicus is one of the most widespread parasitic Asian copepods, as it has rapidly invaded Europe and North America, including Mexico. We estimated the prevalence, mean abundance, and intensity of infection of N. japonicus in these cichlid teleosts; our data agree with previous works stating the high prevalence of this ectoparasite. This copepod has a wide range of hosts among freshwater fish taxa, but this is only the second published report from cichlids in the Neotropical region. The three cichlids surveyed, V. hartwegi, V. breidohri, and C. grammodes, are new hosts of this copepod. Its occurrence in Mexico is attributed to different events of introduction by human agency. This is the southernmost record of N. japonicus in continental America. It is a matter of concern that this copepod is parasitizing endangered or threatened endemic cichlids in the Neotropical region. Because its high infective efficiency and ability to shift hosts, this Asian parasite is expected to spread farther southwards into Central and South America.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  1. Syntenin is involved in the bacteria clearance response of kuruma shrimp (Marsupenaeus japonicus).

    PubMed

    Liu, Qian; Chen, Xiao-wei; Che, Chun-jing; Ding, Ding; Kang, Cui-jie

    2015-06-01

    Syntenin is a multifunctional cytosolic adaptor protein that contributes to cell migration, proliferation, attachment, and apoptosis, as well as immune response to virus, in vertebrates. However, the functions of syntenin in the antibacterial response of invertebrates remain unclear. In this study, we identified a syntenin-like gene (MjSyn) from the kuruma shrimp (Marsupenaeus japonicus) and detected its function in the antibacterial immunity of shrimp. The full-length MjSyn was 1223 bp with a 963 bp open reading frame that encodes 320 amino acids. The deduced MjSyn proteins contained two atypical PDZ domains (sequence repeat that was first reported in the postsynaptic density protein or PSD-95, DlgA, and ZO-1 protein), an N-terminal domain, and a C-terminal domain. Reverse transcription (RT)-PCR results showed that MjSyn was expressed in all tested tissues. Quantitative real-time PCR analysis revealed that MjSyn transcripts in the hemocyte, gill, and intestine were significantly induced at various time points after infection with Staphylococcus aureus and Vibrio anguillarum. The knockdown of the expression of MjSyn by RNA interference resulted in a significant decrease in the phagocytic ability and increased bacteria number in vivo of shrimp. Moreover, the expression of MjCnx, a cytoplasma and membrane location lectin chaperone protein, was inhibited in the MjSyn-knocked down shrimp, which indicated a possible calnexin-related way. Thus, the MjSyn participates in the bacterial clearance response of kuruma shrimp, thereby providing new insight into the function of this kind of important adaptor protein.

  2. 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.

  3. 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

  4. 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.

  5. Enzymatic elucidation of haemocyanin from Kuruma shrimp Marsupenaeus japonicus and its molecular recognition mechanism towards pathogens.

    PubMed

    Sivakamavalli, Jeyachandran; Vaseeharan, Baskaralingam

    2015-01-01

    Haemocyanin is an important non-specific immune protein present in the hemolymph of invertebrates, which have the ability to recognize the microbial pathogens and trigger the innate immune system. In this study, we isolated and purified the haemocyanin using gel filtration chromatography and investigated its microbial recognition mechanism against the invading pathogens. Kuruma shrimp Marsupenaeus japonicus haemocyanin showed the single band with a molecular weight of 76 kDa on SDS-PAGE and its molecular mass was analysed through the MALDI. Pathogen recognition mechanism of M. japonicus haemocyanin was detected through bacterial agglutination, agglutination inhibition and prophenoloxidase activity. M. japonicus haemocyanin agglutinate all human blood RBC types and showed the bacterial agglutination against all tested Gram positive Staphylococcus aureus, Enterococcus faecalis and Bacillus subtilis and Gram negative Pseudomonas aeruginosa, Proteus vulgaris and Vibrio parahaemolyticus at the concentrations ranging from 30 to 50 μg/ml. Agglutination was inhibited by 50-200 mM of N-acetylneuraminic acid, a-D-glucose, D-galactose and D-xylose. Our results suggest that, 76 kDa subunit of M. japonicus haemocyanin recognize the pathogenic surface proteins which are present on the outer membrane of the bacteria and mediates the bacterial agglutination through haemocytes. This bacterial agglutination was visualized through Confocal Laser Scanning Microscopy (CLSM). This present study would be helpful to explore the importance of haemocyanin in innate immune response of M. japonicus and its eliciting pathogen recognition mechanism leads to the development of innate immunity in crustaceans.

  6. Purification, characterization, cDNA cloning and in vitro expression of a serine proteinase from the intestinal tract of sea cucumber (Stichopus japonicus) with collagen degradation activity.

    PubMed

    Yan, Long-Jie; Zhan, Chun-Lan; Cai, Qiu-Feng; Weng, Ling; Du, Cui-Hong; Liu, Guang-Ming; Su, Wen-Jin; Cao, Min-Jie

    2014-05-21

    Sea cucumber (Stichopus japonicus) autolysis during transportation and processing is a major problem and the specific proteinases responsible for autolysis have not yet been identified. In the present study, a 34 kDa serine proteinase (SP) was isolated to high purity from sea cucumber intestinal tract by a series of column chromatographies. Peptide mass fingerprinting revealed that six peptide fragments were identical to a proprotein convertase subtilisin/kexin type 9 preproprotein from sea cucumber A. japonicus. The enzyme hydrolyzed gelatin effectively at pH 6.0-9.0 and 35-40 °C, and the enzyme activity was strongly inhibited by SP inhibitors. Sea cucumber collagen was hydrolyzed significantly by purified SP at 37 °C and more gradually at 4 °C, suggesting that SP may be involved in autolysis. In addition, the SP gene that codes for 377 amino acid residues was cloned into an E. coli expression vector and expressed in vitro. A polyclonal antibody against rSP was prepared and found to react specifically against both rSP and endogenous SP, which may prove useful for future studies on the physiological functions of SP.

  7. 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.

  8. Whole genome sequencing identifies ANXA3 and MTHFR mutations in a large family with an unknown equinus deformity associated genetic disorder.

    PubMed

    Zhang, Zhiqun; Kong, Zhuqing; Zhu, Miao; Lu, Wenxiang; Ni, Lei; Bai, Yunfei; Lou, Yue

    2016-10-01

    The aim of this study was to characterize a previously uncharacterized genetic disorder associated with equinus deformity in a large Chinese family at the genetic level. Blood samples were obtained and whole genome sequencing was performed. Differential gene variants were identified and potential impacts on protein structure were predicted. Based on the control sample, several diseases associated variants were identified and selected for further validation. One of the potential variants identified was a ANXA3 gene [chr4, c.C820T(p.R274*)] variant. Further bioinformatic analysis showed that the observed mutation could lead to a three-dimensional conformational change. Moreover, a MTHFR variant that is different from variants associated with clubfoot was also identified. Bioinformatic analysis showed that this mutation could alter the protein binding region. These findings imply that this uncharacterized genetic disorder is not clubfoot, despite sharing some similar symptoms. Furthermore, specific CNV profiles were identified in association with the diseased samples, thus further speaking to the complexity of this multigenerational disorder. This study examined a previously uncharacterized genetic disorder appearing similar to clubfoot and yet having distinct features. Following whole genome sequencing and comparative analysis, several differential gene variants were identified to enable a further distinction from clubfoot. It is hoped that these findings will provide further insight into this disorder and other similar disorders.

  9. A genetic linkage map of the sea cucumber, Apostichopus japonicus (Selenka), based on AFLP and microsatellite markers.

    PubMed

    Li, Q; Chen, L; Kong, L

    2009-10-01

    We present the first genetic maps of the sea cucumber (Apostichopus japonicus), constructed with an F(1) pseudo-testcross strategy. The 37 amplified fragment length polymorphism (AFLP) primer combinations chosen identified 484 polymorphic markers. Of the 21 microsatellite primer pairs tested, 16 identified heterozygous loci in one or other parent, and six were fully informative, as they segregated in both parents. The female map comprised 163 loci, spread over 20 linkage groups (which equals the haploid chromosome number), and spanned 1522.0 cM, with a mean marker density of 9.3 cM. The equivalent figures for the male map were 162 loci, 21 linkage groups, 1276.9 and 7.9 cM. About 2.5% of the AFLP markers displayed segregation distortion and were not used for map construction. The estimated coverage of the genome was 84.8% for the female map and 83.4% for the male map. The maps generated will serve as a basis for the construction of a high-resolution genetic map and mapping of the functional genes and quantitative trait loci, which will then open the way for the application of a marker-assisted selection breeding strategy in this species.

  10. Scanning the effects of ethyl methanesulfonate on the whole genome of Lotus japonicus using second-generation sequencing analysis.

    PubMed

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

    2015-02-06

    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.

  11. 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.

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

    PubMed Central

    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. PMID:26244987

  13. 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

  14. Microsatellite DNA polymorphisms and the relation with body weight in sea cucumber Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Wang, Xiuli; Shan, Xue; Qiu, Xuemei; Meng, Xiangying; Chang, Yaqing

    2009-05-01

    The relationship between microsatellite polymorphism and body weight of captive bred Chinese sea cucumber Apostichopus japonicus was investigated in two local populations in Dalian. Among ten loci discovered, nine show changes except for AJ07 loci. Seven loci were found highly polymorphic in both populations. For each locus in two populations, the average number of alleles is 6.428 6 and 6.285 7, the average observed heterozygosity at 0.225 7 and 0.245 9, the expected heterozygosity at 0.776 8 and 0.748 8, the polymorphism information content (PIC) at 0.709 2 and 0.674 6, respectively. Further analysis show significant correlation between A. japonicus body weight and occurrence markers AJ02 and AJ04. The findings of the relation may be helpful for molecular breeding, as well as the marker-assisted selection of sea cucumbers.

  15. 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.

  16. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes

    PubMed Central

    Zeggini, Eleftheria; Scott, Laura J.; Saxena, Richa; Voight, Benjamin F.; Marchini, Jonathan L; Hu, Tainle; de Bakker, Paul IW; Abecasis, Gonçalo R; Almgren, Peter; Andersen, Gitte; Ardlie, Kristin; Boström, Kristina Bengtsson; Bergman, Richard N; Bonnycastle, Lori L; Borch-Johnsen, Knut; Burtt, Noël P; Chen, Hong; Chines, Peter S; Daly, Mark J; Deodhar, Parimal; Ding, Charles; Doney, Alex S F; Duren, William L; Elliott, Katherine S; Erdos, Michael R; Frayling, Timothy M; Freathy, Rachel M; Gianniny, Lauren; Grallert, Harald; Grarup, Niels; Groves, Christopher J; Guiducci, Candace; Hansen, Torben; Herder, Christian; Hitman, Graham A; Hughes, Thomas E; Isomaa, Bo; Jackson, Anne U; Jørgensen, Torben; Kong, Augustine; Kubalanza, Kari; Kuruvilla, Finny G; Kuusisto, Johanna; Langenberg, Claudia; Lango, Hana; Lauritzen, Torsten; Li, Yun; Lindgren, Cecilia M; Lyssenko, Valeriya; Marvelle, Amanda F; Meisinger, Christa; Midthjell, Kristian; Mohlke, Karen L; Morken, Mario A; Morris, Andrew D; Narisu, Narisu; Nilsson, Peter; Owen, Katharine R; Palmer, Colin NA; Payne, Felicity; Perry, John RB; Pettersen, Elin; Platou, Carl; Prokopenko, Inga; Qi, Lu; Qin, Li; Rayner, Nigel W; Rees, Matthew; Roix, Jeffrey J; Sandbæk, Anelli; Shields, Beverley; Sjögren, Marketa; Steinthorsdottir, Valgerdur; Stringham, Heather M; Swift, Amy J; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Timpson, Nicholas J; Tuomi, Tiinamaija; Tuomilehto, Jaakko; Walker, Mark; Watanabe, Richard M; Weedon, Michael N; Willer, Cristen J; Illig, Thomas; Hveem, Kristian; Hu, Frank B; Laakso, Markku; Stefansson, Kari; Pedersen, Oluf; Wareham, Nicholas J; Barroso, Inês; Hattersley, Andrew T; Collins, Francis S; Groop, Leif; McCarthy, Mark I; Boehnke, Michael; Altshuler, David

    2009-01-01

    Genome-wide association (GWA) studies have identified multiple new genomic loci at which common variants modestly but reproducibly influence risk of type 2 diabetes (T2D)1-11. Established associations to common and rare variants explain only a small proportion of the heritability of T2D. As previously published analyses had limited power to discover loci at which common alleles have modest effects, we performed meta-analysis of three T2D GWA scans encompassing 10,128 individuals of European-descent and ~2.2 million SNPs (directly genotyped and imputed). Replication testing was performed in an independent sample with an effective sample size of up to 53,975. At least six new loci with robust evidence for association were detected, including the JAZF1 (p=5.0×10−14), CDC123/CAMK1D (p=1.2×10−10), TSPAN8/LGR5 (p=1.1×10−9), THADA (p=1.1×10−9), ADAMTS9 (p=1.2×10−8), and NOTCH2 (p=4.1×10−8) gene regions. The large number of loci with relatively small effects indicates the value of large discovery and follow-up samples in identifying additional clues about the inherited basis of T2D. PMID:18372903

  17. Larval Mosquito Habitat Utilization and Community Dynamics of Aedes albopictus and Aedes japonicus (Diptera: Culicidae)

    DTIC Science & Technology

    2012-01-01

    along with buckets, trash cans, and plant receptacles. Although slightly less abundant, Ae. japonicus prefers similar habitats. Our data collec...midgeMetriocnemius knabi, and their carnivorous host Sarracenia purpurea, pp. 161Ð 189. In J. H. Frank and L. P. Lounibos (eds.), Phyto- telmata...Terrestrial Plants as Hosts for Aquatic Insect Communities. Plexus Publishing Inc., Medford, NJ. Campos, R. E., and L. P. Lounibos. 2000. Life tables of

  18. Comparative analysis of immunocompetence between females and males in the sea cucumber Apostichopus japonicus.

    PubMed

    Jiang, Jingwei; Zhou, Zunchun; Dong, Ying; Gao, Shan; Sun, Hongjuan; Chen, Zhong; Yang, Aifu; Su, Hesheng

    2017-04-01

    In order to preliminarily understand the immune difference between females and males in the sea cucumber Apostichopus japonicus, the activities assay of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), phenoloxidase (PO), acid phosphatase (ACP) and alkaline phosphatase (ALP) with biochemical methods, the detection of PO isozymes with native-PAGE and catechol staining, and the test of antibacterial activities with bacterial growth curve determination method were performed in this study using cell-free coelomic fluid (CCF) and coelomocyte lysate supernatant (CLS) from females and males as the samples. The PO activities were not detected in the CLS and showed no significant difference between the CCF from females and males. However, totally five PO isozyme bands were detected in the CLS of females while only four were detected in the CLS of males after zymogram analysis. These results implied that the PO isozymes in the coelomocytes of viripotent A. japonicus were inactive under natural condition and may be activated by some certain treatments during native-PAGE, and PO might play different immune and physiological roles between females and males. In addition, the activities of SOD, CAT, POD and ALP in the CCF and the activities of CAT, POD, ACP and ALP in the CLS from males were all significantly higher than those from females. The results collectively suggested that in viripotent A. japonicus, the gender had a remarkable effect on the immunity, and the immunocompetence of males might have an advantage over that of females. Furthermore, the activities of all determined enzymes except PO and the number of detected PO isozymes showed higher values in CLS than in CCF, implying that in viripotent A. japonicus, the coelomocytes might take more immune responsibility in comparison with CCF.

  19. 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.

  20. Identification of the retinoblastoma (Rb) gene and expression in response to environmental stressors in the intertidal copepod Tigriopus japonicus.

    PubMed

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

    2015-12-01

    There have been no reports thus far on the structure or molecular characterization of the retinoblastoma (Rb) gene of aquatic animals. Herein we describe the identification of the Rb gene of the intertidal copepod Tigriopus japonicus. In silico analyses revealed the conserved Rb domains of T. japonicus with those of protostomes. Phylogenetic analysis revealed that orthologs of Rb gene were evolved by an ancient split event in deuterostomes, while only a single Rb gene was conserved in protostomes except for Drosophila. The transcription of the T. japonicus Rb gene continuously increased across the molting transition from nauplius to the copepodid and adult stages, suggesting that it may play a developmental role in the molting process of T. japonicus. Information on Rb's response to environmental stressors, including toxin exposure, is lacking in copepods. To examine the transcriptional response to stressful conditions in laboratory culture conditions, copepods were exposed to UV-B radiation and different concentrations of metals, environmental toxins, and biocides. Transcription of the T. japonicus Rb gene was upregulated in response to about half of the 96 h-LD50 of UV-B radiation (12 kJ/m(2)) for 48 h, while the approximate 96 h-LD50 value (24 kJ/m(2)) of UV-B and relatively high concentrations of several toxins and biocides induced the downregulation of T. japonicus Rb mRNA expression. Taken together, our findings suggest that the T. japonicus Rb gene is sensitive to environmentally unfavorable conditions that can induce cell cycle alteration.

  1. Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis

    PubMed Central

    Haase, Nicholas J.; Beissinger, Timothy; Hirsch, Candice N.; Vaillancourt, Brieanne; Deshpande, Shweta; Barry, Kerrie; Buell, C. Robin; Kaeppler, Shawn M.; de Leon, Natalia

    2015-01-01

    Delayed transition from the vegetative stage to the reproductive stage of development and increased plant height have been shown to increase biomass productivity in grasses. The goal of this project was to detect quantitative trait loci using extremes from a large synthetic population, as well as a related recombinant inbred line mapping population for these two traits. Ten thousand individuals from a B73 × Mo17 noninbred population intermated for 14 generations (IBM Syn14) were grown at a density of approximately 16,500 plants ha−1. Flowering time and plant height were measured within this population. DNA was pooled from the 46 most extreme individuals from each distributional tail for each of the traits measured and used in bulk segregant analysis (BSA) sequencing. Allelic divergence at each of the ∼1.1 million SNP loci was estimated as the difference in allele frequencies between the selected extremes. Additionally, 224 intermated B73 × Mo17 recombinant inbred lines were concomitantly grown at a similar density adjacent to the large synthetic population and were assessed for flowering time and plant height. Using the BSA sequencing method, 14 and 13 genomic regions were identified for flowering time and plant height, respectively. Linkage mapping with the RIL population identified eight and three regions for flowering time and plant height, respectively. Of the regions identified, three colocalized between the two populations for flowering time and two colocalized for plant height. This study demonstrates the utility of using BSA sequencing for the dissection of complex quantitative traits important for production of lignocellulosic ethanol. PMID:26038364

  2. 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.

  3. 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.

  4. 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

  5. Modulation of phenolic metabolism under stress conditions in a Lotus japonicus mutant lacking plastidic glutamine synthetase.

    PubMed

    García-Calderón, Margarita; Pons-Ferrer, Teresa; Mrázova, Anna; Pal'ove-Balang, Peter; Vilková, Mária; Pérez-Delgado, Carmen M; Vega, José M; Eliášová, Adriana; Repčák, Miroslav; Márquez, Antonio J; Betti, Marco

    2015-01-01

    This paper was aimed to investigate the possible implications of the lack of plastidic glutamine synthetase (GS2) in phenolic metabolism during stress responses in the model legume Lotus japonicus. Important changes in the transcriptome were detected in a GS2 mutant called Ljgln2-2, compared to the wild type, in response to two separate stress conditions, such as drought or the result of the impairment of the photorespiratory cycle. Detailed transcriptomic analysis showed that the biosynthesis of phenolic compounds was affected in the mutant plants in these two different types of stress situations. For this reason, the genes and metabolites related to this metabolic route were further investigated using a combined approach of gene expression analysis and metabolite profiling. A high induction of the expression of several genes for the biosynthesis of different branches of the phenolic biosynthetic pathway was detected by qRT-PCR. The extent of induction was always higher in Ljgln2-2, probably reflecting the higher stress levels present in this genotype. This was paralleled by accumulation of several kaempferol and quercetine glycosides, some of them described for the first time in L. japonicus, and of high levels of the isoflavonoid vestitol. The results obtained indicate that the absence of GS2 affects different aspects of phenolic metabolism in L. japonicus plants in response to stress.

  6. Variations in otolith patterns, sizes and body morphometrics of jack mackerel Trachurus japonicus juveniles.

    PubMed

    Kanaji, Y; Kishida, M; Watanabe, Y; Kawamura, T; Xie, S; Yamashita, Y; Sassa, C; Tsukamoto, Y

    2010-10-01

    Variations in otolith patterns, sizes and body morphometrics of jack mackerel Trachurus japonicus juveniles were investigated. Under transmitted light, translucent (W(t)) and opaque otoliths (W(o)) were detected in juveniles collected from Wakasa Bay between July 2005 and April 2006, whereas only opaque otoliths (G(o)) were detected in Goto-nada Sea individuals between May and June 2006. Three groups of juveniles were distinguished based on differences in hatch season, otolith size and growth history, and body morphometrics. As T. japonicus has different spawning seasons according to spawning grounds, each group was estimated to hatch in different waters. Juveniles with W(t) otoliths were considered to have stayed in coastal habitat longer, as the hatch area was estimated to be near Wakasa Bay. Juveniles with W(o) and G(o) otoliths appear to recruit to coastal waters at larger size, since their hatch areas were estimated to be far from each collection area. Larger otoliths of W(t) were attributed to otolith accretion after the second growth flexion, which was observed only for W(t) . Standard length of W(t) fish at the second otolith growth flexion was estimated to correspond to recruitment size to coastal rocky reefs in Wakasa Bay. Body morphometrics were correlated with otolith size after removing body size effect, suggesting that morphological variations of T. japonicus juveniles were also associated with the timing of recruitment to coastal habitat.

  7. Lotus japonicus CASTOR and POLLUX are ion channels essential for perinuclear calcium spiking in legume root endosymbiosis.

    PubMed

    Charpentier, Myriam; Bredemeier, Rolf; Wanner, Gerhard; Takeda, Naoya; Schleiff, Enrico; Parniske, Martin

    2008-12-01

    The mechanism underlying perinuclear calcium spiking induced during legume root endosymbioses is largely unknown. Lotus japonicus symbiosis-defective castor and pollux mutants are impaired in perinuclear calcium spiking. Homology modeling suggested that the related proteins CASTOR and POLLUX might be ion channels. Here, we show that CASTOR and POLLUX form two independent homocomplexes in planta. CASTOR reconstituted in planar lipid bilayers exhibited ion channel activity, and the channel characteristics were altered in a symbiosis-defective mutant carrying an amino acid replacement close to the selectivity filter. Permeability ratio determination and competition experiments reveled a weak preference of CASTOR for cations such as potassium over anions. POLLUX has an identical selectivity filter region and complemented a potassium transport-deficient yeast mutant, suggesting that POLLUX is also a potassium-permeable channel. Immunogold labeling localized the endogenous CASTOR protein to the nuclear envelope of Lotus root cells. Our data are consistent with a role of CASTOR and POLLUX in modulating the nuclear envelope membrane potential. They could either trigger the opening of calcium release channels or compensate the charge release during the calcium efflux as counter ion channels.

  8. Genome-wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in Lotus japonicus.

    PubMed

    Guether, Mike; Balestrini, Raffaella; Hannah, Matthew; He, Ji; Udvardi, Michael K; Bonfante, Paola

    2009-01-01

    * Arbuscular mycorrhizas (AMs) contribute significantly to soil nutrient uptake in plants. As a consequence of the fungal colonization and of the deep reorganization shown by arbusculated cells, important impacts on root transcriptome are expected. * An Affymetrix GeneChip with 50,000 probe-sets and real-time RT-PCR allowed us to detect transcriptional changes triggered in Lotus japonicus by the AM fungus Gigaspora margarita, when arbuscules are at their maximum (28 d postinoculation (dpi)). An early time (4 dpi) was selected to differentiate genes potentially involved in signaling and/or in colonization of outer tissues. * A large number (75 out of 558) of mycorrhiza-induced genes code for proteins involved in protein turnover, membrane dynamics and cell wall synthesis, while many others are involved in transport (47) or transcription (24). Induction of a subset (24 genes) of these was tested and confirmed by qRT-PCR, and transcript location in arbusculated cells was demonstrated for seven genes using laser-dissected cells. * When compared with previously published papers, the transcript profiles indicate the presence of a core set of responsive genes (25) that seem to be conserved irrespective of the symbiotic partner identity.

  9. Characterization and expression analysis of microRNAs in the tube foot of sea cucumber Apostichopus japonicus.

    PubMed

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

    2014-01-01

    MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA with average length of 22 nucleotides, participating in the post-transcriptional regulation of gene expression. In this study, we report the identification and characterization of miRNAs in the tube foot of sea cucumber (Apostichopus japonicus) by next generation sequencing with Illumina HiSeq 2000 platform. Through the bioinformatic analysis, we identified 260 conserved miRNAs and six novel miRNAs from the tube foot small RNA transcriptome. Quantitative realtime PCR (qRT-PCR) was performed to characterize the specific expression in the tube foot. The results indicated that four miRNAs, including miR-29a, miR-29b, miR-2005 and miR-278-3p, were significantly up-regulated in the tube foot. The target genes of the four specifically expressed miRNAs were predicted in silico and validated by performing qRT-PCR. Gene ontology (GO) and KEGG pathway analyses with the target genes of these four miRNAs were conducted to further understand the regulatory function in the tube foot. This is the first study to profile the miRNA transcriptome of the tube foot in sea cucumber. This work will provide valuable genomic resources to understand the mechanisms of gene regulation in the tube foot, and will be useful to assist the molecular breeding in sea cucumber.

  10. A Galectin from the Kuruma Shrimp (Marsupenaeus japonicus) Functions as an Opsonin and Promotes Bacterial Clearance from Hemolymph

    PubMed Central

    Xu, Sen; Zhang, Xiao-Wen; Zhao, Xiao-Fan; Vasta, Gerardo Raul; Wang, Jin-Xing

    2014-01-01

    Galectins are a lectin family characterized by a conserved sequence motif in the carbohydrate recognition domain, which preferential binds to galactosyl moieties. However, few studies about the biological roles of galectins in invertebrates have been reported except for the galectin (CvGal1) from the eastern oyster Crassostrea virginica. Furthermore, galectins have been described in only a few crustacean species, and no functional studies have been reported so far. In this study, we identified and functionally characterized a galectin from the kuruma shrimp Marsupenaeus japonicus, which we designated MjGal. Upon Vibrio anguillarum challenge, expression of MjGal was up-regulated mostly in hemocytes and hepatopancreas, and the protein bound to both Gram-positive and Gram-negative bacteria through the recognition of lipoteichoic acid (LTA) or lipopolysaccharide (LPS), respectively. By also binding to the shrimp hemocyte surface, MjGal functions as an opsonin for microbial pathogens, promoting their phagocytosis. Further, as shown by RNA interference, MjGal participates in clearance of bacteria from circulation, and thereby contributes to the shrimp’s immune defense against infectious challenge. Elucidation of functional and mechanistic aspects of shrimp immunity will enable the development of novel strategies for intervention in infectious diseases currently affecting the shrimp farming industry worldwide. PMID:24618590

  11. A galectin from the kuruma shrimp (Marsupenaeus japonicus) functions as an opsonin and promotes bacterial clearance from hemolymph.

    PubMed

    Shi, Xiu-Zhen; Wang, Lei; Xu, Sen; Zhang, Xiao-Wen; Zhao, Xiao-Fan; Vasta, Gerardo Raul; Wang, Jin-Xing

    2014-01-01

    Galectins are a lectin family characterized by a conserved sequence motif in the carbohydrate recognition domain, which preferential binds to galactosyl moieties. However, few studies about the biological roles of galectins in invertebrates have been reported except for the galectin (CvGal1) from the eastern oyster Crassostrea virginica. Furthermore, galectins have been described in only a few crustacean species, and no functional studies have been reported so far. In this study, we identified and functionally characterized a galectin from the kuruma shrimp Marsupenaeus japonicus, which we designated MjGal. Upon Vibrio anguillarum challenge, expression of MjGal was up-regulated mostly in hemocytes and hepatopancreas, and the protein bound to both Gram-positive and Gram-negative bacteria through the recognition of lipoteichoic acid (LTA) or lipopolysaccharide (LPS), respectively. By also binding to the shrimp hemocyte surface, MjGal functions as an opsonin for microbial pathogens, promoting their phagocytosis. Further, as shown by RNA interference, MjGal participates in clearance of bacteria from circulation, and thereby contributes to the shrimp's immune defense against infectious challenge. Elucidation of functional and mechanistic aspects of shrimp immunity will enable the development of novel strategies for intervention in infectious diseases currently affecting the shrimp farming industry worldwide.

  12. Phenotypic and genetic characterization of bacteria isolated from diseased cultured sea cucumber Apostichopus japonicus in northeastern China.

    PubMed

    Li, Hua; Qiao, Guo; Gu, Jie-Quan; Zhou, Wei; Li, Qiang; Woo, Sung-Ho; Xu, De-Hai; Park, Soo-Il

    2010-09-17

    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 bacterial samples were isolated from diseased sea cucumbers and identified through biochemical tests, 16S rRNA gene sequence analysis and PCR amplification, followed by pathogenicity determination. The results showed that the 31 isolates belonged to the genera Vibrio (64.5%), Shewanella (12.9%), Serratia (12.9%), Pseudoalteromonas (6.4%) and Flavobacterium (3.2 %). The 3 prominent strains were Vibrio splendidus (41.9%), Shewanella (12.9%) and Serratia odorifera biogroup I (12.9%). Pathogenicity tests demonstrated that 13 out of 31 isolates were pathogenic, including 8 strains of V splendidus, 3 strains of Shewanella sp. and 2 strains of Pseudoalteromonas tetraodonis. The pathogenic V splendidus showed the highest frequency of appearance. Median lethal dose (LD50) values (14 d) of V splendidus, Shewanella sp. and P. tetraodonis were 1.74 x 10(7), 7.76 x 10(6), 7.24 x 10(7) CFU g(-1) body weight of sea cucumber, respectively. The virulences differed by species: Shewanella sp. > V splendidus> P. tetraodonis. This is the first report of Shewanella sp. virulence in sea cucumber.

  13. The first description of complete invertebrate arginine metabolism pathways implies dose-dependent pathogen regulation in Apostichopus japonicus

    PubMed Central

    Yina, Shao; Chenghua, Li; Weiwei, Zhang; Zhenhui, Wang; Zhimeng, Lv

    2016-01-01

    In this study, three typical members representative of different arginine metabolic pathways were firstly identified from Apostichopus japonicus, including nitric oxide synthase (NOS), arginase, and agmatinase. Spatial expression analysis revealed that the AjNOS transcript presented negative expression patterns relative to those of Ajarginase or Ajagmatinase in most detected tissues. Furthermore, Vibrio splendidus-challenged coelomocytes and intestine, and LPS-exposed primary coelomocytes could significantly induce AjNOS expression, followed by obviously inhibited Arginase and AjAgmatinase transcripts at the most detected time points. Silencing the three members with two specific siRNAs in vivo and in vitro collectively indicated that AjNOS not only compete with Ajarginase but also with Ajagmatinase in arginine metabolism. Interestingly, Ajarginase and Ajagmatinase displayed cooperative expression profiles in arginine utilization. More importantly, live pathogens of V. splendidus and Vibrio parahaemolyticus co-incubated with primary cells also induced NO production and suppressed arginase activity in a time-dependent at an appropriate multiplicity of infection (MOI) of 10, without non-pathogen Escherichia coli. When increasing the pathogen dose (MOI = 100), arginase activity was significantly elevated, and NO production was depressed, with a larger magnitude in V. splendidus co-incubation. The present study expands our understanding of the connection between arginine’s metabolic and immune responses in non-model invertebrates. PMID:27032691

  14. Leucine-rich repeats containing protein functions in the antibacterial immune reaction in stomach of kuruma shrimp Marsupenaeus japonicus.

    PubMed

    Shi, Xiu-Zhen; Feng, Xiao-Wu; Sun, Jie-Jie; Zhao, Xiao-Fan; Wang, Jin-Xing

    2017-02-01

    Leucine rich repeat (LRR) motif exists in many immune receptors of animals and plants. Most LRR containing (LRRC) proteins are involved in protein-ligand and protein-protein interaction, but the exact functions of most LRRC proteins were not well-studied. In this study, an LRRC protein was identified from kuruma shrimp Marsupenaeus japonicus, and named as MjLRRC1. MjLRRC1 was consistently expressed in different tissues of normal shrimp with higher expression in gills and stomach. At the transcriptional level, there were no significant changes of MjLRRC1 after injection of Vibrio anguillarum or Staphylococcus aureus in gills and hepatopancreas. While in V. anguillarum oral infection, MjLRRC1 was upregulated in stomach but not in intestine. The recombinant MjLRRC1 protein could bind to Gram-positive and Gram-negative bacteria, bacterial cell wall components including peptidoglycan, lipoteichoic acid, and lipopolysaccharide. MjLRRC1 regulated the expression of some antimicrobial peptide (AMP) genes and participated in bacteria clearance of stomach. All these results suggested that MjLRRC1 might play important roles in antibacterial immune response of kuruma shrimp.

  15. 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.

  16. PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp. on intestinal microbial diversity in kuruma shrimp ( Marsupenaeus japonicus)

    NASA Astrophysics Data System (ADS)

    Liu, Huaide; Liu, Mei; Wang, Baojie; Jiang, Keyong; Jiang, Shan); Sun, Shujuan; Wang, Lei

    2010-07-01

    In this study, the intestinal microbiota of kuruma shrimp ( Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp. on intestinal microbial diversity. Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp. amended feed. PCR and denaturing gradient gel electrophoresis (DGGE) analyses were then performed on DNA extracted directly from the guts. Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons, and distinct bands in the gels were sequenced. The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp. and uncultured gamma proteobacterium. Overall, the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.

  17. Antioxidative-related genes expression following perfluorooctane sulfonate (PFOS) exposure in the intertidal mud crab, Macrophthalmus japonicus

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    Perfluorooctane sulfonate (PFOS) is a persistent environmental contaminant that is used as a surfactant in various industries and consumer products. The intertidal mud crab, Macrophthalmus japonicus, is one of the most abundant macrobenthic creatures. In this study, we have investigated the effect of PFOS on the molecular transcription of antioxidant and detoxification signaling in M. japonicus crab. The selected stress response genes were superoxide dismutases (CuZnSOD and MnSOD), catalase (CAT), glutathione peroxidase (GPx), phospholipid hydroperoxide glutathione peroxidase (PHGPx), peroxiredoxin (Prx), and thioredoxin reductase (TrxR). Significant up-regulation of SODs and CAT was observed after 24 and 96 h exposure to PFOS at different concentrations. The gene expression levels of GPx, PHGPx, and TrXR were significantly up-regulated after exposure to PFOS for 96 h. The transcript levels of CAT and PHGPx were induced in dose- and time-dependent manners after PFOS treatments. However, Prx gene expression was significantly up-regulated in M. japonicus crabs exposed to 10 and 30 μg L-1 PFOS for 96 h. Additionally, PFOS toxicity in M. japonicus induced reduced survival rates at relatively high concentrations of PFOS exposure. Our findings support the contention that exposures to PFOS induced the response of genes related to oxidative stress and detoxification in M. japonicus crabs.

  18. 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.

  19. 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.

  20. Suppressor of cytokine signaling 2 (SOCS2) negatively regulates the expression of antimicrobial peptides by affecting the Stat transcriptional activity in shrimp Marsupenaeus japonicus.

    PubMed

    Sun, Jie-Jie; Lan, Jiang-Feng; Xu, Ji-Dong; Niu, Guo-Juan; Wang, Jin-Xing

    2016-09-01

    The suppressor of cytokine signaling (SOCS) family is a kind of negative regulators in the Janus kinase/signal transducer and activator of transcription (Jak/Stat) pathway in mammals and Drosophila. In kuruma shrimp, Marsupenaeus japonicus, SOCS2 is identified and its expression can be stimulated by peptidoglycan and polycytidylic acid. However, if SOCS2 participates in regulating Jak/Stat pathway in shrimp still needs further study. In this study, SOCS2 with Src homology 2 domain and SOCS box was identified in kuruma shrimp, M. japonicus. SOCS2 existed in hemocytes, heart, hepatopancreas, gills, stomach, and intestine, the expression of SOCS2 was upregulated significantly in the hemocytes and intestine of shrimp challenged with Vibrio anguillarum at 6 h. To analyze SOCS2 function in shrimp immunity, bacterial clearance and survival rate were analyzed after knockdown of SOCS2 in shrimp challenged with V. anguillarum. Results showed that bacterial clearance increased, and the survival rate improved significantly comparing with controls. The SOCS2 was expressed in Escherichia coli and the recombinant SOCS2 was injected into shrimp, and Stat phosphorylation and translocation were analyzed. The result showed that "overexpression" of SOCS2 declined Stat phosphorylation level and inhibited Stat translocation into the nucleus. After knockdown of SOCS2 in shrimp prior to V. anguillarum infection, the expression level of antimicrobial peptides, including anti-lipopolysaccharide factors C1, C2 and D1, and Crustin I was upregulated significantly, and the expression of the AMPs was declined after recombinant SOCS2 injection. The SOCS2 expression was also decreased in Stat-knockdown shrimp challenged by V. anguillarum at 6 and 12 h. Therefore, SOCS2 negatively regulates the AMP expression by inhibiting Stat phosphorylation and translocation into nucleus in shrimp, meanwhile, SOCS2 expression was also regulated by Jak/Stat pathway.

  1. 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.

  2. The challenge of monitoring elusive large carnivores: An accurate and cost-effective tool to identify and sex pumas (Puma concolor) from footprints

    PubMed Central

    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. PMID:28273159

  3. Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice

    PubMed Central

    Vaz, Candida; Tanavde, Vivek M.; Maurer-Stroh, Sebastian; Zauscher, Stefan; Gonzalez, Pedro; Young, Terri L.

    2016-01-01

    Development of myopia is associated with large-scale changes in ocular tissue gene expression. Although differential expression of coding genes underlying development of myopia has been a subject of intense investigation, the role of non-coding genes such as microRNAs in the development of myopia is largely unknown. In this study, we explored myopia-associated miRNA expression profiles in the retina and sclera of C57Bl/6J mice with experimentally induced myopia using microarray technology. We found a total of 53 differentially expressed miRNAs in the retina and no differences in miRNA expression in the sclera of C57BL/6J mice after 10 days of visual form deprivation, which induced -6.93 ± 2.44 D (p < 0.000001, n = 12) of myopia. We also identified their putative mRNA targets among mRNAs found to be differentially expressed in myopic retina and potential signaling pathways involved in the development of form-deprivation myopia using miRNA-mRNA interaction network analysis. Analysis of myopia-associated signaling pathways revealed that myopic response to visual form deprivation in the retina is regulated by a small number of highly integrated signaling pathways. Our findings highlighted that changes in microRNA expression are involved in the regulation of refractive eye development and predicted how they may be involved in the development of myopia by regulating retinal gene expression. PMID:27622715

  4. 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.

  5. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.

    PubMed

    Zeggini, Eleftheria; Scott, Laura J; Saxena, Richa; Voight, Benjamin F; Marchini, Jonathan L; Hu, Tianle; de Bakker, Paul I W; Abecasis, Gonçalo R; Almgren, Peter; Andersen, Gitte; Ardlie, Kristin; Boström, Kristina Bengtsson; Bergman, Richard N; Bonnycastle, Lori L; Borch-Johnsen, Knut; Burtt, Noël P; Chen, Hong; Chines, Peter S; Daly, Mark J; Deodhar, Parimal; Ding, Chia-Jen; Doney, Alex S F; Duren, William L; Elliott, Katherine S; Erdos, Michael R; Frayling, Timothy M; Freathy, Rachel M; Gianniny, Lauren; Grallert, Harald; Grarup, Niels; Groves, Christopher J; Guiducci, Candace; Hansen, Torben; Herder, Christian; Hitman, Graham A; Hughes, Thomas E; Isomaa, Bo; Jackson, Anne U; Jørgensen, Torben; Kong, Augustine; Kubalanza, Kari; Kuruvilla, Finny G; Kuusisto, Johanna; Langenberg, Claudia; Lango, Hana; Lauritzen, Torsten; Li, Yun; Lindgren, Cecilia M; Lyssenko, Valeriya; Marvelle, Amanda F; Meisinger, Christa; Midthjell, Kristian; Mohlke, Karen L; Morken, Mario A; Morris, Andrew D; Narisu, Narisu; Nilsson, Peter; Owen, Katharine R; Palmer, Colin N A; Payne, Felicity; Perry, John R B; Pettersen, Elin; Platou, Carl; Prokopenko, Inga; Qi, Lu; Qin, Li; Rayner, Nigel W; Rees, Matthew; Roix, Jeffrey J; Sandbaek, Anelli; Shields, Beverley; Sjögren, Marketa; Steinthorsdottir, Valgerdur; Stringham, Heather M; Swift, Amy J; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Timpson, Nicholas J; Tuomi, Tiinamaija; Tuomilehto, Jaakko; Walker, Mark; Watanabe, Richard M; Weedon, Michael N; Willer, Cristen J; Illig, Thomas; Hveem, Kristian; Hu, Frank B; Laakso, Markku; Stefansson, Kari; Pedersen, Oluf; Wareham, Nicholas J; Barroso, Inês; Hattersley, Andrew T; Collins, Francis S; Groop, Leif; McCarthy, Mark I; Boehnke, Michael; Altshuler, David

    2008-05-01

    Genome-wide association (GWA) studies have identified multiple loci at which common variants modestly but reproducibly influence risk of type 2 diabetes (T2D). Established associations to common and rare variants explain only a small proportion of the heritability of T2D. As previously published analyses had limited power to identify variants with modest effects, we carried out meta-analysis of three T2D GWA scans comprising 10,128 individuals of European descent and approximately 2.2 million SNPs (directly genotyped and imputed), followed by replication testing in an independent sample with an effective sample size of up to 53,975. We detected at least six previously unknown loci with robust evidence for association, including the JAZF1 (P = 5.0 x 10(-14)), CDC123-CAMK1D (P = 1.2 x 10(-10)), TSPAN8-LGR5 (P = 1.1 x 10(-9)), THADA (P = 1.1 x 10(-9)), ADAMTS9 (P = 1.2 x 10(-8)) and NOTCH2 (P = 4.1 x 10(-8)) gene regions. Our results illustrate the value of large discovery and follow-up samples for gaining further insights into the inherited basis of T2D.

  6. 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

  7. 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.

  8. A large-scale survey of the novel 15q24 microdeletion syndrome in autism spectrum disorders identifies an atypical deletion that narrows the critical region

    PubMed Central

    2010-01-01

    Background The 15q24 microdeletion syndrome has been recently described as a recurrent, submicroscopic genomic imbalance found in individuals with intellectual disability, typical facial appearance, hypotonia, and digital and genital abnormalities. Gene dosage abnormalities, including copy number variations (CNVs), have been identified in a significant fraction of individuals with autism spectrum disorders (ASDs). In this study we surveyed two ASD cohorts for 15q24 abnormalities to assess the frequency of genomic imbalances in this interval. Methods We screened 173 unrelated subjects with ASD from the Central Valley of Costa Rica and 1336 subjects with ASD from 785 independent families registered with the Autism Genetic Resource Exchange (AGRE) for CNVs across 15q24 using oligonucleotide arrays. Rearrangements were confirmed by array comparative genomic hybridization and quantitative PCR. Results Among the patients from Costa Rica, an atypical de novo deletion of 3.06 Mb in 15q23-q24.1 was detected in a boy with autism sharing many features with the other 13 subjects with the 15q24 microdeletion syndrome described to date. He exhibited intellectual disability, constant smiling, characteristic facial features (high anterior hairline, broad medial eyebrows, epicanthal folds, hypertelorism, full lower lip and protuberant, posteriorly rotated ears), single palmar crease, toe syndactyly and congenital nystagmus. The deletion breakpoints are atypical and lie outside previously characterized low copy repeats (69,838-72,897 Mb). Genotyping data revealed that the deletion had occurred in the paternal chromosome. Among the AGRE families, no large 15q24 deletions were observed. Conclusions From the current and previous studies, deletions in the 15q24 region represent rare causes of ASDs with an estimated frequency of 0.1 to 0.2% in individuals ascertained for ASDs, although the proportion might be higher in sporadic cases. These rates compare with a frequency of about 0.3% in

  9. Identification and expression patterns of extracellular matrix-associated genes fibropellin-ia and tenascin involved in regeneration of sea cucumber Apostichopus japonicus.

    PubMed

    Ba, Huazhong; Yao, Feng; Yang, Lei; Qin, Tong; Luan, Hong; Li, Zhengmin; Zou, Xiangyang; Hou, Lin

    2015-07-01

    Sea cucumbers have a strong regenerative capacity. Many important genes involved in the molecular mechanism of regeneration and associated with intercellular signaling pathways of regeneration have been identified. The product of the fibropellin-ia gene forms a layer known as the apical lamina that surrounds the sea cucumber embryo throughout development. Meanwhile, the tenascin gene displays highly restricted and dynamic patterns of expression in the embryo and is expressed in the adult during normal processes such as wound healing, nerve regeneration and tissue involution. In this study, we cloned for the first time full-length cDNAs of fibropellin-ia (1390 bp, encoding a 199 amino acid protein) and tenascin (1366 bp, encoding a 179 amino acid protein) from Apostichopus japonicus (designated Aj-fnia and Aj-tenascin, respectively) using rapid amplification of cDNA ends. The structures and characteristics of these two genes were analyzed bioinformatically, and their expression patterns associated with extracellular matrix remodeling in regeneration of A. japonicus were investigated by real-time PCR and in situ hybridization (ISH). Expression levels of Aj-fnia and Aj-tenascin in the regeneration tissues were higher than those in normal tissues. The highest expression levels of Aj-fnia and Aj-tenascin were shown in the intestine and respiratory tree on the 15th and 20th days after sea cucumbers were eviscerated. In the body wall, the highest expression levels of Aj-fnia and Aj-tenascin occurred at 35 and 45 min during early regeneration and then emerged between 5 and 7 days again during late regeneration after the body wall was injured. ISH analysis revealed expression of these genes in the body wall, longitudinal muscle, intestine and respiratory tree. These findings suggest that Aj-fnia and Aj-tenascin are crucial genes that play important roles in the regeneration of the sea cucumber.

  10. Variant translocation partners of the anaplastic lymphoma kinase (ALK) gene in two cases of anaplastic large cell lymphoma, identified by inverse cDNA polymerase chain reaction.

    PubMed

    Takeoka, Kayo; Okumura, Atsuko; Honjo, Gen; Ohno, Hitoshi

    2014-01-01

    In anaplastic large cell lymphoma (ALCL), the anaplastic lymphoma kinase (ALK) gene is rearranged with diverse partners due to variant translocations/inversions. Case 1 was a 39-year-old man who developed multiple tumors in the mediastinum, psoas muscle, lung, and lymph nodes. A biopsy specimen of the inguinal node was effaced by large tumor cells expressing CD30, epithelial membrane antigen, and cytoplasmic ALK, which led to a diagnosis of ALK(+) ALCL. Case 2 was a 51-year-old man who was initially diagnosed with undifferentiated carcinoma. He developed multiple skin tumors eight years after his initial presentation, and was finally diagnosed with ALK(+) ALCL. He died of therapy-related acute myeloid leukemia. G-banding and fluorescence in situ hybridization using an ALK break-apart probe revealed the rearrangement of ALK and suggested variant translocation in both cases. We applied an inverse cDNA polymerase chain reaction (PCR) strategy to identify the partner of ALK. Nucleotide sequencing of the PCR products and a database search revealed that the sequences of ATIC in case 1 and TRAF1 in case 2 appeared to follow those of ALK. We subsequently confirmed ATIC-ALK and TRAF1-ALK fusions by reverse transcriptase PCR and nucleotide sequencing. We successfully determined the partner gene of ALK in two cases of ALK(+) ALCL. ATIC is the second most common partner of variant ALK rearrangements, while the TRAF1-ALK fusion gene was first reported in 2013, and this is the second reported case of ALK(+) ALCL carrying TRAF1-ALK.

  11. UCH-L1 is induced in germinal center B cells and identifies patients with aggressive germinal center diffuse large B-cell lymphoma.

    PubMed

    Bedekovics, Tibor; Hussain, Sajjad; Feldman, Andrew L; Galardy, Paul J

    2016-03-24

    Gene expression profiling has identified 2 major subclasses of diffuse large B-cell lymphoma (DLBCL). Cases resembling germinal center (GC) B cells (GCB-DLBCL) generally occur in younger patients, have a distinct molecular pathophysiology, and have improved outcomes compared with those similar to activated post-GC cells (activated B-cell DLBCL). We previously found that the ubiquitin hydrolase UCH-L1 is frequently overexpressed in mature B-cell malignancies and is a potent oncogene in mice. The cause for its overexpression in lymphoma, and whether it impacts the outcome of patients with DLBCL is unknown. Here, we show that UCH-L1 reflects GC lineage in lymphoma and is an oncogenic biomarker of aggressive GCB-DLBCL. We find that UCH-L1 is specifically induced in GC B cells in mice and humans, and that its expression correlates highly with the GCB subtype in DLBCL. We also find that UCH-L1 cooperates with BCL6 in a mouse model of GC B-cell lymphoma, but not with the development of multiple myeloma derived from post-GC cells. Despite the typically good outcomes of GCB-DLBCL, increased UCHL1 identifies a subgroup with early relapses independent of MYC expression, suggesting biological diversity in this subset of disease. Consistent with this, forced Uchl1 overexpression had a substantial impact on gene expression in GC B cells including pathways of cell cycle progression, cell death and proliferation, and DNA replication. These data demonstrate a novel role for UCH-L1 outside of the nervous system and suggest its potential use as a biomarker and therapeutic target in DLBCL.

  12. Identification of cDNAs encoding pterocarpan reductase involved in isoflavan phytoalexin biosynthesis in Lotus japonicus by EST mining.

    PubMed

    Akashi, Tomoyoshi; Koshimizu, Shoko; Aoki, Toshio; Ayabe, Shin-Ichi

    2006-10-16

    Isoflavans and pterocarpans are the major biosynthetically connected phytoalexins in legumes. A search of the expressed sequence tag library of a model legume Lotus japonicus, which produces an (-)-isoflavan, for homologs of phenylcoumaran benzylic ether reductase catalyzing the reductive cleavage of dihydrofurans, yielded seven full-length cDNAs, and the encoded proteins were analyzed in vitro. Four of them cleaved the dihydrofuran of a pterocarpan medicarpin to yield an isoflavan (-)-vestitol and were designated pterocarpan reductase (PTR). Two PTRs displayed enantiospecificity to (-)-medicarpin, representing genuine L. japonicus PTRs, while the other two lacked enantiospecificity and were presumed to be evolutionarily primitive types.

  13. Paired geochemical tracing and load monitoring analysis for identifying sediment sources in a large catchment draining into the Great Barrier Reef Lagoon

    NASA Astrophysics Data System (ADS)

    Furuichi, Takahisa; Olley, Jon; Wilkinson, Scott; Lewis, Stephen; Bainbridge, Zoe; Burton, Joanne

    2016-08-01

    While sediment tracing has been typically applied to identify sediment sources that are difficult to measure by gauging (monitoring), it can also be useful in estimating relative sediment yields from gauged river catchments. The major and trace element composition of river sediments from eleven locations in the 130000 km2 Burdekin River catchment, northeastern Australia was analysed to examine relative contributions from upstream source areas in the 2011/12 water year. Sediment tracing results are compared against estimates derived from sediment load monitoring at three locations. Comparisons show that there is good agreement between tracing results and monitoring data at one of the tributary confluences. At the second site, notable contrasts were found between the load estimates from the monitoring and tracing data. At this site a large impoundment occurs between the upstream sampling/gauging sites for source sediments and the downstream sampling/gauging sites for target sediments. The contrast is likely caused by temporal variations in particle size distributions of suspended sediment from each river and differential trapping efficiencies in the impoundment for sediment derived from the different tributaries. In the absence of the detailed particle size data and trapping efficiency estimates, sediment tracing provides the unique opportunity to elucidate source contributions of the finer fractions of suspended sediment. At a third site, where there were recognised measurement gaps in the monitoring data during large discharge events, the relative load estimates from the tracing data provided a means of constraining the recognized uncertainty of monitored load estimates. We conclude that sediment tracing can be used as a valuable adjunct to monitoring data particularly in remote, large and data-sparse catchments. Both tracing results and monitoring data show that the Upper Burdekin River and Bowen-Bogie Rivers were the dominant source of the < 10 μm sediments

  14. Large-Scale Functional RNAi Screen in C. elegans Identifies TGF-β and Notch Signaling Pathways as Modifiers of CACNA1A

    PubMed Central

    Pereira, Maria da Conceição; Morais, Sara; Sequeiros, Jorge

    2016-01-01

    Variants in CACNA1A that encodes the pore-forming α1-subunit of human voltage-gated Cav2.1 (P/Q-type) Ca2+ channels cause several autosomal-dominant neurologic disorders, including familial hemiplegic migraine type 1, episodic ataxia type 2, and spinocerebellar ataxia type 6. To identify modifiers of incoordination in movement disorders, we performed a large-scale functional RNAi screen, using the Caenorhabditis elegans strain CB55, which carries a truncating mutation in the unc-2 gene, the worm ortholog for the human CACNA1A. The screen was carried out by the feeding method in 96-well liquid culture format, using the ORFeome v1.1 feeding library, and time-lapse imaging of worms in liquid culture was used to assess changes in thrashing behavior. We looked for genes that, when silenced, either ameliorated the slow and uncoordinated phenotype of unc-2, or interacted to produce a more severe phenotype. Of the 350 putative hits from the primary screen, 37 genes consistently showed reproducible results. At least 75% of these are specifically expressed in the C. elegans neurons. Functional network analysis and gene ontology revealed overrepresentation of genes involved in development, growth, locomotion, signal transduction, and vesicle-mediated transport. We have expanded the functional network of genes involved in neurodegeneration leading to cerebellar ataxia related to unc-2/CACNA1A, further confirming the involvement of the transforming growth factor β pathway and adding a novel signaling cascade, the Notch pathway. PMID:27005779

  15. Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies.

    PubMed

    Willemsen, Marjolein H; de Leeuw, Nicole; de Brouwer, Arjan P M; Pfundt, Rolph; Hehir-Kwa, Jayne Y; Yntema, Helger G; Nillesen, Willy M; de Vries, Bert B A; van Bokhoven, Hans; Kleefstra, Tjitske

    2012-11-01

    Genome-wide array studies are now routinely being used in the evaluation of patients with cognitive disorders (CD) and/or congenital anomalies (CA). Therefore, inevitably each clinician is confronted with the challenging task of the interpretation of copy number variations detected by genome-wide array platforms in a diagnostic setting. Clinical interpretation of autosomal copy number variations is already challenging, but assessment of the clinical relevance of copy number variations of the X-chromosome is even more complex. This study provides an overview of the X-Chromosome copy number variations that we have identified by genome-wide array analysis in a large cohort of 4407 male and female patients. We have made an interpretation of the clinical relevance of each of these copy number variations based on well-defined criteria and previous reports in literature and databases. The prevalence of X-chromosome copy number variations in this cohort was 57/4407 (∼1.3%), of which 15 (0.3%) were interpreted as (likely) pathogenic.

  16. 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.

  17. Effects of acute temperature or salinity stress on the immune response in sea cucumber, Apostichopus japonicus.

    PubMed

    Wang, Fangyu; Yang, Hongsheng; Gao, Fei; Liu, Guangbin

    2008-12-01

    Invertebrates are increasingly raised in mariculture, where it is important to monitor immune function and to minimize stresses that could suppress immunity. The activities of phagocytosis, superoxide dismutase (SOD), catalase (CAT), myeloperoxidase (MPO), and lysozyme (LSZ) were measured to evaluate the immune capacities of the sea cucumber, Apostichopus japonicus, to acute temperature changes (from 12 degrees C to 0 degrees C, 8 degrees C, 16 degrees C, 24 degrees C, and 32 degrees C for 72 h) and salinity changes (from 30 per thousand to 20 per thousand, 25 per thousand, and 35 per thousand for 72 h) in the laboratory. Phagocytosis was significantly affected by temperature increases in 3 h, and by salinity (25 per thousand and 35 per thousand) changes in 1 h. SOD activities decreased significantly in 0.5 h to 6 h samples at 24 degrees C. At 32 degrees C, SOD activities decreased significantly in 0.5 h and 1 h exposures, and obviously increased for 12 h exposure. CAT activities decreased significantly at 24 degrees C for 0.5 h exposure, and increased significantly at 32 degrees C in 3 h to 12 h exposures. Activities of MPO increased significantly at 0 degrees C in 0.5 h to 6 h exposures and at 8 degrees C for 1 h. By contrast, activities of MPO decreased significantly in 24 degrees C and 32 degrees C treatments. In elevated-temperature treatments, activities of LSZ increased significantly except at 32 degrees C for 6 h to 12 h exposures. SOD activity was significantly affected by salinity change. CAT activity decreased significantly after only 1 h exposure to salinity of 20 per thousand. Activities of MPO and LSZ showed that A. japonicus tolerates limited salinity stress. High-temperature stress had a much greater effect on the immune capacities of A. japonicus than did low-temperature and salinity stresses.

  18. A putative molybdate transporter LjMOT1 is required for molybdenum transport in Lotus japonicus.

    PubMed

    Gao, Jun-Shan; Wu, Fei-Fei; Shen, Zhi-Lin; Meng, Yan; Cai, Yong-Ping; Lin, Yi

    2016-11-01

    Molybdenum (Mo) is an essential micronutrient that is required for plant growth and development, and it affects the formation of root nodules and nitrogen fixation in legumes. In this study, Lotus japonicus was grown on MS solid media containing 0 nmol l(-1) (-Mo), 103 nmol l(-1) (+Mo) and 1030 nmol l(-1) (10 × Mo) of Mo. The phenotypes of plants growing on the three different media showed no obvious differences after 15 days, but the plants growing on -Mo for 45 days presented typical symptoms of Mo depletion, such as a short taproot, few lateral roots and yellowing leaves. A Mo transporter gene, LjMOT1, was isolated from L. japonicus. It encoded 468 amino acids, including two conserved motifs, and was predicted to locate to chromosome 3 of the L. japonicus genome. A homology comparison indicated that LjMOT1 had high similarities to other MOT1 proteins and was closely related to GmMOT1. Subcellular localization indicated that LjMOT1 is localized to the plasma membrane. qRT-PCR analyses showed that increasing Mo concentrations regulated the relative expression level of LjMOT1. Moreover, the Mo concentration in shoots was positively correlated to the expression of LjMOT1, but there was no such evident correlation in the roots. In addition, changes in the nitrate reductase activity were coincident with changes in the Mo concentration. These results suggest that LjMOT1 may be involved in the transport of Mo and provide a theoretical basis for further understanding of the mechanism of Mo transport in higher plants.

  19. Isolation and phenotypic characterization of Lotus japonicus mutants specifically defective in arbuscular mycorrhizal formation.

    PubMed

    Kojima, Tomoko; Saito, Katsuharu; Oba, Hirosuke; Yoshida, Yuma; Terasawa, Junya; Umehara, Yosuke; Suganuma, Norio; Kawaguchi, Masayoshi; Ohtomo, Ryo

    2014-05-01

    Several symbiotic mutants of legume plants defective in nodulation have also been shown to be mutants related to arbuscular mycorrhizal (AM) symbiosis. The origin of the AM symbiosis can be traced back to the early land plants. It has therefore been postulated that the older system of AM symbiosis was partially incorporated into the newer system of legume-rhizobium symbiosis. To unravel the genetic basis of the establishment of AM symbiosis, we screened about 34,000 plants derived from ethyl methanesulfonate (EMS)-mutagenized Lotus japonicus seeds by microscopic observation. As a result, three lines (ME778, ME966 and ME2329) were isolated as AM-specific mutants that exhibit clear AM-defective phenotypes but form normal effective root nodules with rhizobial infection. In the ME2329 mutant, AM fungi spread their hyphae into the intercellular space of the cortex and formed trunk hyphae in the cortical cells, but the development of fine branches in the arbuscules was arrested. The ME2329 mutant carried a nonsense mutation in the STR-homolog gene, implying that the line may be an str mutant in L. japonicus. On the ME778 and ME966 mutant roots, the entry of AM fungal hyphae was blocked between two adjacent epidermal cells. Occasionally, hyphal colonization accompanied by arbuscules was observed in the two mutants. The genes responsible for the ME778 and ME966 mutants were independently located on chromosome 2. These results suggest that the ME778 and ME966 lines are symbiotic mutants involved in the early stage of AM formation in L. japonicus.

  20. Functional Sperm of the Yellowtail (Seriola quinqueradiata) Were Produced in the Small-Bodied Surrogate, Jack Mackerel (Trachurus japonicus).

    PubMed

    Morita, Tetsuro; Morishima, Kagayaki; Miwa, Misako; Kumakura, Naoki; Kudo, Satomi; Ichida, Kensuke; Mitsuboshi, Toru; Takeuchi, Yutaka; Yoshizaki, Goro

    2015-10-01

    Production of xenogeneic gametes from large-bodied, commercially important marine species in closely related smaller surrogates with short generation times may enable rapid domestication of the targeted species. In this study, we aimed to produce gametes of Japanese yellowtail (Seriola quinqueradiata) using jack mackerel (Trachurus japonicus) as a surrogate with a smaller body size and shorter maturation period. Donor spermatogonia were collected from the testes of yellowtail males and transferred into the peritoneal cavity of 10- and 12-day-old jack mackerel larvae. Twenty days later, 59.5% of the recipients survived of which 88.2% had donor-derived germ cells in their gonads. One year later, genomic DNA templates were prepared from the semen of 96 male recipients and subjected to polymerase chain reaction (PCR) analyses using primers specific for the yellowtail vasa sequence, resulting in the detection of positive signals in semen from two recipients. The milt collected from the recipients was used for fertilization with yellowtail eggs. Of eight hatchlings obtained from the crosses, two were confirmed to be derived from donor yellowtail by DNA markers, although the others were gynogenetic diploids. These findings indicate that it is possible to produce donor-derived sperm in xenogeneic recipients with a smaller body size and shorter generation time by transplanting spermatogonia. Thus, the xenogeneic transplantation of spermatogonia might be a potential tool to produce gametes of large-bodied, commercially important fish, although the efficiency of the method requires further improvement. This is the first report demonstrating that donor-derived sperm could be produced in xenogeneic recipient via spermatogonial transplantation in carangid fishes.

  1. 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.

  2. 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

  3. Annual changes in serum leptin concentration in the adult female Japanese black bear (Ursus thibetanus japonicus).

    PubMed

    Tsubota, Toshio; Sato, Miho; Okano, Tsukasa; Nakamura, Sachiko; Asano, Makoto; Komatsu, Takeshi; Shibata, Haruki; Saito, Masayuki

    2008-12-01

    In the present study, assay of the serum leptin concentration of the Japanese black bear (Ursus thibetanus japonicus) was attempted using a canine-leptin-specific sandwich enzyme-linked immunosorbent assay (ELISA). The dose-response curve of the bear serum was linear and parallel to the canine leptin standard curve. In mated and unmated bears, the serum leptin concentration was stable at low levels from May to August or September, gradually increased from September or October, and then remarkably increased in late November. We conclude that this method may be useful for measuring bear serum leptin concentration and that the serum leptin concentration changes annually with a peak in late November.

  4. 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.

  5. Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset

    PubMed Central

    Tittarelli, Andrés; Santiago, Margarita; Morales, Andrea; Meisel, Lee A; Silva, Herman

    2009-01-01

    Background Cold acclimation is the process by which plants adapt to the low, non freezing temperatures that naturally occur during late autumn or early winter. This process enables the plants to resist the freezing temperatures of winter. Temperatures similar to those associated with cold acclimation are also used by the fruit industry to delay fruit ripening in peaches. However, peaches that are subjected to long periods of cold storage may develop chilling injury symptoms (woolliness and internal breakdown). In order to better understand the relationship between cold acclimation and chilling injury in peaches, we isolated and functionally characterized cold-regulated promoters from cold-inducible genes identified by digitally analyzing a large EST dataset. Results Digital expression analyses of EST datasets, revealed 164 cold-induced peach genes, several of which show similarities to genes associated with cold acclimation and cold stress responses. The promoters of three of these cold-inducible genes (Ppbec1, Ppxero2 and Pptha1) were fused to the GUS reporter gene and characterized for cold-inducibility using both transient transformation assays in peach fruits (in fruta) and stable transformation in Arabidopsis thaliana. These assays demonstrate that the promoter Pptha1 is not cold-inducible, whereas the Ppbec1 and Ppxero2 promoter constructs are cold-inducible. Conclusion This work demonstrates that during cold storage, peach fruits differentially express genes that are associated with cold acclimation. Functional characterization of these promoters in transient transformation assays in fruta as well as stable transformation in Arabidopsis, demonstrate that the isolated Ppbec1 and Ppxero2 promoters are cold-inducible promoters, whereas the isolated Pptha1 promoter is not cold-inducible. Additionally, the cold-inducible activity of the Ppbec1 and Ppxero2 promoters suggest that there is a conserved heterologous cold-inducible regulation of these promoters in

  6. Accuracy of Electronic Health Record Data for Identifying Stroke Cases in Large-Scale Epidemiological Studies: A Systematic Review from the UK Biobank Stroke Outcomes Group

    PubMed Central

    Woodfield, Rebecca; Grant, Ian; Sudlow, Cathie L. M.

    2015-01-01

    Objective Long-term follow-up of population-based prospective studies is often achieved through linkages to coded regional or national health care data. Our knowledge of the accuracy of such data is incomplete. To inform methods for identifying stroke cases in UK Biobank (a prospective study of 503,000 UK adults recruited in middle-age), we systematically evaluated the accuracy of these data for stroke and its main pathological types (ischaemic stroke, intracerebral haemorrhage, subarachnoid haemorrhage), determining the optimum codes for case identification. Methods We sought studies published from 1990-November 2013, which compared coded data from death certificates, hospital admissions or primary care with a reference standard for stroke or its pathological types. We extracted information on a range of study characteristics and assessed study quality with the Quality Assessment of Diagnostic Studies tool (QUADAS-2). To assess accuracy, we extracted data on positive predictive values (PPV) and—where available—on sensitivity, specificity, and negative predictive values (NPV). Results 37 of 39 eligible studies assessed accuracy of International Classification of Diseases (ICD)-coded hospital or death certificate data. They varied widely in their settings, methods, reporting, quality, and in the choice and accuracy of codes. Although PPVs for stroke and its pathological types ranged from 6–97%, appropriately selected, stroke-specific codes (rather than broad cerebrovascular codes) consistently produced PPVs >70%, and in several studies >90%. The few studies with data on sensitivity, specificity and NPV showed higher sensitivity of hospital versus death certificate data for stroke, with specificity and NPV consistently >96%. Few studies assessed either primary care data or combinations of data sources. Conclusions Particular stroke-specific codes can yield high PPVs (>90%) for stroke/stroke types. Inclusion of primary care data and combining data sources should

  7. Systematic large-scale meta-analysis identifies a panel of two mRNAs as blood biomarkers for colorectal cancer detection

    PubMed Central

    Rodia, Maria Teresa; Ugolini, Giampaolo; Mattei, Gabriella; Montroni, Isacco; Zattoni, Davide; Ghignone, Federico; Veronese, Giacomo; Marisi, Giorgia; Lauriola, Mattia; Strippoli, Pierluigi; Solmi, Rossella

    2016-01-01

    Colorectal cancer (CRC) is the third most common cancer in the world. A significant survival rate is achieved if it is detected at an early stage. A whole blood screening test, without any attempt to isolate blood fractions, could be an important tool to improve early detection of colorectal cancer. We searched for candidate markers with a novel approach based on the Transcriptome Mapper (TRAM), aimed at identifying specific RNAs with the highest differential expression ratio between colorectal cancer tissue and normal blood samples. This tool permits a large-scale systematic meta-analysis of all available data obtained by microarray experiments. The targeting of RNA took into consideration that tumour phenotypic variation is associated with changes in the mRNA levels of genes regulating or affecting this variation. A real time quantitative reverse transcription polymerase chain reaction (qRT- PCR) was applied to the validation of candidate markers in the blood of 67 patients and 67 healthy controls. The expression of genes: TSPAN8, LGALS4, COL1A2 and CEACAM6 resulted as being statistically different. In particular ROC curves attested for TSPAN8 an AUC of 0.751 with a sensitivity of 83.6% and a specificity of 58.2% at a cut off of 10.85, while the panel of the two best genes showed an AUC of 0.861 and a sensitivity of 92.5% with a specificity of 67.2%. Our preliminary study on a total of 134 subjects showed promising results for a blood screening test to be validated in a larger cohort with the staging stratification and in patients with other gastrointestinal diseases. PMID:26993598

  8. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  10. Complete Genome Sequence of a Fish Nervous Necrosis Virus Isolated from Sea Perch (Lateolabrax japonicus) in China

    PubMed Central

    Jia, Peng

    2015-01-01

    We sequenced and analyzed the complete genome of a fish nervous necrosis virus isolated from diseased sea perch (Lateolabrax japonicus) in Guangdong Province, China. The virus genome contains RNA1 (3,103 bp) and RNA2 (1,433 bp). Phylogenetic analysis shows that the virus belongs to the redspotted grouper nervous necrosis virus genotype of betanodavirus. PMID:26044411

  11. 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

  12. Changes in the expression of pituitary gonadotropin subunits during reproductive cycle of multiple spawning female chub mackerel Scomber japonicus.

    PubMed

    Nyuji, Mitsuo; Selvaraj, Sethu; Kitano, Hajime; Ohga, Hirofumi; Yoneda, Michio; Shimizu, Akio; Kaneko, Kensuke; Yamaguchi, Akihiko; Matsuyama, Michiya

    2012-06-01

    The endocrine regulation of reproduction in a multiple spawning fish with an asynchronous-type ovary remains largely unknown. The objectives of this study were to monitor changes in the mRNA expression of three gonadotropin (GtH) subunits (GPα, FSHβ, and LHβ) during the reproductive cycle of the female chub mackerel Scomber japonicus. Cloning and subsequent sequence analysis revealed that the cDNAs of chub mackerel GPα, FSHβ, and LHβ were 658, 535, and 599 nucleotides in length and encoded 117, 115, and 147 amino acids, respectively. We applied a quantitative real-time PCR assay to quantify the mRNA expression levels of these GtH subunits. During the seasonal reproductive cycle, FSHβ mRNA levels remained high during the vitellogenic stages, while GPα and LHβ mRNA levels peaked at the end of vitellogenesis. The expression of all three GtH subunits decreased during the post-spawning period. These results suggest that follicle-stimulating hormone (FSH) is involved in vitellogenesis, while luteinizing hormone (LH) functions during final oocyte maturation (FOM). Both GPα and FSHβ mRNA levels remained high during the FOM stages of the spawning cycle and increased further just after spawning. Thus, FSH synthesis may be strongly activated just after spawning to accelerate vitellogenesis in preparation for the next spawning. Alternatively, LHβ mRNA levels declined during hydration and then increased after ovulation. This study demonstrates that chub mackerel are a good model for investigating GtH functions in multiple spawning fish.

  13. 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.

  14. Histochemical localization and characterization of AKP, ACP, NSE, and POD from cultured Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Li, Jiye; Sun, Xiuqin; Zheng, Fengrong; Sun, Hushan

    2009-09-01

    We investigated the distribution of four enzymes involved in the immune response of Apostichopus japonicus. We collected samples of the tentacles, papillate podium, integument, respiratory tree, and digestive tract and stained them for acid phosphatase (ACP), alkaline phosphatase (AKP), non-specific esterase (NSE) and peroxidase (POD) activity. The distribution and content of ACP, AKP, NSE, and POD differed among the tissues. The coelomic epithelium of the tentacle, papillate podium, and integument and the mucous layer of respiratory tree were positive for ACP activity. The coelomic epithelium and cuticular layer of the tentacle, papillate podium, and integument and the mucous layer and tunica externa of the respiratory tree and digestive tract stained positive or weakly positive for AKP activity. Almost all the epithelial tissues stained positive, strongly positive, or very strongly positive for NSE activity. The cuticular layer of the tentacle and integument and the mucous layer, tunica submucosa, and tunica externa of the respiratory tree and digestive tract stained positive for POD activity. We hypothesize that these enzymes play a role in the immune response in A. japonicus.

  15. Molecular Characterization of LjABCG1, an ATP-Binding Cassette Protein in Lotus japonicus

    PubMed Central

    Sugiyama, Akifumi; Fukuda, Shoju; Takanashi, Kojiro; Yoshioka, Miki; Yoshioka, Hirofumi; Narusaka, Yoshihiro; Narusaka, Mari; Kojima, Mikiko; Sakakibara, Hitoshi; Shitan, Nobukazu; Sato, Shusei; Tabata, Satoshi; Kawaguchi, Masayoshi; Yazaki, Kazufumi

    2015-01-01

    LjABCG1, a full-size ABCG subfamily of ATP-binding cassette proteins of a model legume, Lotus japonicus, was reported as a gene highly expressed during the early stages of nodulation, but have not been characterized in detail. In this study we showed that the induction of LjABCG1 expression was remarkable by methyl jasmonate treatment, and reporter gene experiments indicated that LjABCG1 was strongly expressed in the nodule parenchyma and cell layers adjacent to the root vascular tissue toward the nodule. LjABCG1 was suggested to be localized at the plasma membrane based on the fractionation of microsomal membranes as well as separation via aqueous two-phase partitioning. The physiological functions of LjABCG1 in symbiosis and pathogenesis were analyzed in homologous and heterologous systems. LjABCG1 knock-down L. japonicus plants did not show clear phenotypic differences in nodule formation, and not in defense against Pseudomonas syringae, either. In contrast, when LjABCG1 was expressed in the Arabidopsis pdr8-1 mutant, the penetration frequency of Phytophthora infestans, a potato late blight pathogen, was significantly reduced in LjABCG1/pdr8-1 than in pdr8-1 plants. This finding indicated that LjABCG1, at least partially, complemented the phenotype of pdr8 in Arabidopsis, suggesting the multiple roles of this protein in plant-microbe interactions. PMID:26418593

  16. 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.

  17. 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.

  18. 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.

  19. A complex gene locus enables xyloglucan utilization in the model saprophyte Cellvibrio japonicus

    PubMed Central

    Larsbrink, Johan; Thompson, Andrew J; Lundqvist, Magnus; Gardner, Jeffrey G; Davies, Gideon J; Brumer, Harry

    2014-01-01

    The degradation of plant biomass by saprophytes is an ecologically important part of the global carbon cycle, which has also inspired a vast diversity of industrial enzyme applications. The xyloglucans (XyGs) constitute a family of ubiquitous and abundant plant cell wall polysaccharides, yet the enzymology of XyG saccharification is poorly studied. Here, we present the identification and molecular characterization of a complex genetic locus that is required for xyloglucan utilization by the model saprophyte Cellvibrio japonicus. In harness, transcriptomics, reverse genetics, enzyme kinetics, and structural biology indicate that the encoded cohort of an α-xylosidase, a β-galactosidase, and an α-l-fucosidase is specifically adapted for efficient, concerted saccharification of dicot (fucogalacto)xyloglucan oligosaccharides following import into the periplasm via an associated TonB-dependent receptor. The data support a biological model of xyloglucan degradation by C. japonicus with striking similarities – and notable differences – to the complex polysaccharide utilization loci of the Bacteroidetes. PMID:25171165

  20. Effect of 17beta-estradiol on the immunocompetence of Japanese sea bass (Lateolabrax japonicus).

    PubMed

    Thilagam, Harikrishnan; Gopalakrishnan, Singaram; Bo, Jun; Wang, Ke-Jian

    2009-08-01

    Environmental contaminants can interfere with hormonal regulation in both vertebrates and invertebrates, and these contaminants may disrupt the endocrine system of human and other organisms. Evidence is growing that contaminants may be partly responsible for the observed increase of disease in marine organisms by adversely affecting their immunity. Fish are commonly used as sentinel organisms in vertebrate immunotoxicology; however, to date, studies have been undertaken only on a single size group of fish (juvenile/adult) and for acute exposure. In the present study, Lateolabrax japonicus fingerlings and juveniles were exposed to two sublethal concentrations (200 and 2,000 ng/L) of 17beta-estradiol (E2) for 30 d under laboratory conditions, and alterations in immune parameters comprising differential leukocyte count, respiratory burst, myeloperoxidase, immunoglobulin levels, serum lysozyme, and bactericidal activity were investigated to establish whether estrogen produced immunomodulation and to understand the effects of long-term exposure on these immune parameters in fish fingerlings and juveniles. The results revealed a significant elevation of respiratory burst activity, myeloperoxidase, immunoglobulin levels, and differential leukocyte counts of the fish exposed to estrogen compared to the control. The remaining parameters were significantly reduced in the experimental groups when compared to the control. The results indicated that sublethal E(2) exposure induced immunomodulation in both fingerling and juvenile L. japonicus, and the changes caused by estrogen might affect the function of immune system in fish.

  1. miR-137 modulates coelomocyte apoptosis by targeting 14-3-3ζ in the sea cucumber Apostichopus japonicus.

    PubMed

    Lv, Miao; Chen, Huahui; Shao, Yina; Li, Chenghua; Xu, Wei; Zhang, Weiwei; Zhao, Xuelin; Duan, Xuemei

    2017-02-01

    MicroRNAs (miRNAs) have emerged as key regulators in the host immune response and play a pivotal role in host-pathogen interactions by suppressing the transcriptional and post-transcriptional expression of target genes. miR-137, a well-documented tumor repressor, was previously found by high-throughput sequencing to be differentially expressed in diseased specimens of the sea cucumber Apostichopus japonicus. In this study, we identified 14-3-3ζ protein (Aj14-3-3ζ) as a novel target of miR-137 using isobaric tags for relative and absolute quantification (iTRAQ) and transcriptome screening. Expression analysis indicated that consistently depressed expression profiles of miR-137 and Aj14-3-3ζ were detected in both LPS-exposed primary coelomocytes and Vibrio splendidus-challenged sea cucumbers, suggesting a positive regulatory interaction. Consistently, miR-137 overexpression or inhibition in vitro and in vivo showed no effect on Aj14-3-3ζ mRNA levels, but the concentration of Aj14-3-3ζ protein was induced or repressed, respectively. Moreover, siRNA-mediated Aj14-3-3ζ knockdown in vivo decreased both mRNA and protein expression levels of Aj14-3-3ζ and significantly promoted coelomocyte apoptosis as assessed by flow cytometry, consistent with miR-137 inhibition. Overall, these results enhance our understanding of miR-137 regulatory roles in sea cucumber pathogenesis.

  2. Role of Marsupenaeus japonicus crustin-like peptide against Vibrio penaeicida and white spot syndrome virus infection.

    PubMed

    Hipolito, Sheryll Grospe; Shitara, Aiko; Kondo, Hidehiro; Hirono, Ikuo

    2014-10-01

    Crustins are important AMP that has been identified in crustaceans. In this study, the role of Marsupenaeus japonicus crustin-like peptide (MjCRS) was examined in vivo by RNA interference (RNAi) using double-stranded RNA (dsRNA). Tissue expression analysis revealed that MjCRS transcripts are expressed in different tissues tested with the highest expression observed in hemocytes. Treatment with double-stranded RNA specific to MjCRS led to a significant reduction of MjCRS transcripts within the hemocytes. When MjCRS was silenced and subsequently infected with Vibrio penaeicida final mortality was significantly higher compared with PBS and dsGFP treated groups. On the other hand, final mortalities of MjCRS silenced and PBS injected groups were not significantly different after infection with white spot virus, however, both are significantly higher compared with dsGFP treated group. V. penaeicida infection significantly decreased MjCRS expression at 3, 6, 12 and 24h followed by significant increase at 48 h post-infection. On the contrary, white spot infection significantly increased MjCRS expression at 6 and 12h and decreased at 48 h post-infection. dsRNA treatment alone decreased total hemocyte counts (THCs) and subsequent V. penaeicida or white spot virus infection further decreased THCs. VP28 gene expression was both similarly increased in PBS injected group and MjCRS silenced group at 24 and 48 h-post infection. Results suggest that MjCRS is involved in antibacterial defense and might not have critical function against viral infection.

  3. 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

  4. Isolation and characterization of chitinase-producing Bacillus and Paenibacillus strains from salted and fermented shrimp, Acetes japonicus.

    PubMed

    Han, Kook-Il; Patnaik, Bharat Bhusan; Kim, Yong Hyun; Kwon, Hyun-Jung; Han, Yeon Soo; Han, Man-Deuk

    2014-04-01

    Chitinases catalyze the conversion of chitin and are produced by a wide range of bacteria. The biological applications of these enzymes have been exploited in food and pharmaceutical industries. We isolated 2 halophilic chitinase-producing novel strains of bacteria-SCH-1 and SCH-2 from Saeu-jeot, a traditional Korean salted and fermented food made with shrimp (Acetes japonicus). The isolated strains- SCH-1 and SCH-2 were Gram-positive, rod-shaped, endospore-forming facultative anaerobes, with strain SCH-2 showing peritrichous flagella. Molecular characterization of the 16S rRNA gene identified the strains SCH-1 and SCH-2 as Bacillus sp. and Paenibacillus sp. respectively. Basic Local Alignment Search Tool and subsequent phylogenetic analysis of strain SCH-1 showed an identity of 97.83% with Bacillus cereus ATCC 14579 (NR_074540), whereas strain SCH-2 showed an identity of 99.16% with Paenibacillus lautus JCM 9073 (NR_040882). Furthermore, the SCH-1 strain could use glucose, N-acetyl glucosamine, esculin, and maltose as carbon source substrates. Cellular fatty acid analysis showed that iso-C15:0 and anteiso-C15:0 are the major acids in strain SCH-1 and SCH-2, respectively. The SCH-1 strain showed a higher chitinase activity at 15.71 unit/mg protein compared with SCH-2 strain. Chitinase isozymes of Bacillus sp. SCH-1was expressed as 2 bands having sizes of 41 and 50 kDa, and as 4 bands with sizes of 30, 37, 45.7, and 50 kDa in Paenibacillus sp. SCH-2. The rich chitinase activity with the isozyme profiles of the isolated Bacillus and Paenibacillus strains provide advancement in the study of fermentation and may play putative functions in the chitin bioconversion of sea crustacean foods.

  5. 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.

  6. Structural analysis of a Lotus japonicus genome. III. Sequence features and mapping of sixty-two TAC clones which cover the 6.7 Mb regions of the genome.

    PubMed

    Kaneko, Takakazu; Asamizu, Erika; Kato, Tomohiko; Sato, Shusei; Nakamura, Yasukazu; Tabata, Satoshi

    2003-02-28

    A total of sixty-two clones were selected from a TAC (transformation-competent artificial chromosome) genomic library of the Lotus japonicus accession MG-20 based on the sequence information of expressed sequence tags (ESTs), cDNA and gene information, and their nucleotide sequences were determined. The length of the sequenced regions in this study is 6,682,189 bp, and the total length of the regions sequenced so far is 18,711,484 bp together with the nucleotide sequences of 121 TAC clones previously reported. By comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling, a total of 573 potential protein-coding genes with known or predicted functions, 91 gene segments and 272 pseudogenes were identified in the newly sequenced regions. Each of the sequenced clones was localized onto the linkage map of two accessions of L. japonicus, Gifu B-129 and Miyakojima MG-20, using simple sequence repeat length polymorphism (SSLP) or derived cleaved amplified polymorphic sequence (dCAPS) markers generated based on the nucleotide sequences of the clones. The sequence data, gene information and mapping information are available through the World Wide Web at http://www.kazusa.or.jp/lotus/.

  7. Monitoring and estimating scale-dependent hierarchical relationships between Sicyopterus japonicus density and stream habitat features in different seasons in northern Taiwan.

    PubMed

    Yu, Hsiao-Hsuan; Lin, Yu-Pin; Wang, Cheng-Long

    2011-11-01

    Biological and physical processes operate collaboratively through spatial or temporal scales to form ecological patterns, which are considered as a key element for understanding the natural liens within an ecosystem. Given the importance of scaling in ecological inference, this study elucidates how physical and biological variables under or within scales interact with each other. Density of Sicyopterus japonicus and environmental variables are examined and quantified at 70 stream sections distributed among 14 reaches in the Datuan stream catchment of northern Taiwan during the fall and winter of 2007, as well as the spring and summer of 2008. Hierarchical linear regression analysis indicates that S. japonicus density and habitat features are related on two levels, i.e., sections within reaches and reaches within streams throughout the year. Moreover, parameter uncertainty is represented by the confidence interval, which is calculated by the variance-covariance matrix of hierarchical linear model (HLM) parameters. According to HLM results, environmental variables at the section level (water depth and current velocity) and the reach level (stream width, water temperature, stream slope, soil erosion index) influence S. japonicus density. Although S. japonicus density varies significantly among reaches and sections within reaches, cross-level interaction may not always influence the distribution, processes and activities of S. japonicus throughout the year. The HLMs of S. japonicus density associated with stream features describe thoroughly multiple processes and the activities of S. japonicus across scales and within scales during different seasons. The annual HLM results represent the overall biological and physical patterns of the Datuan stream annually, explaining why they do not reflect seasonal associations or explain S. japonicus-related activities and environmental features of the stream.

  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. 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

  10. 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.

  11. [Characterization of the Gut Bacterial Community of the Japanese Sea Cucumber Apostichopus japonicus].

    PubMed

    Bogatyrenko, E A; Buzoleva, L S

    2016-01-01

    Comparative analysis of the composition and abundance of the gut bacterial community of the Japanese sea cucumber (trepang) Apostichopus japonicus and the soil from its habitat was carried out. In spite of the presence of strictly aerobic bacteria in the soil, gut microflora of this holothurian was shown to be formed by facultative anaerobes from the environment. Irrespective of the geographical location of the habitat, the sea cucmber gut community had a constant composition considered its normal microflora. Capacity of bactreia isolated from the Japanese sea cucumber for decomposition of starch, sodium alginate, chitin, chondroitin sulfate, Tweens, olive oil, casein, and gelatin was studied. Various degrees of enzymatic activity were shown for 33% of the studied bacterial strains, which indicates a considerable role of the trepang gut microflora in processing and assimilation of organic matter arriving with food.

  12. 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.

  13. 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.

  14. Bioactive Isopimarane Diterpenes from the Fungus, Epicoccum sp. HS-1, Associated with Apostichopus japonicus

    PubMed Central

    Xia, Xuekui; Qi, Jun; Liu, Yayue; Jia, Airong; Zhang, Yonggang; Liu, Changheng; Gao, Cuiling; She, Zhigang

    2015-01-01

    One new isopimarane diterpene (1), together with two known compounds, 11-deoxydiaporthein A (2) and iso-pimara-8(14),15-diene (3) were isolated from the culture of Epicoccum sp., which was associated with Apostichopus japonicus. Their structures were determined by the analysis of 1D and 2D NMR, as well as mass spectroscopic data. The absolute configuration of Compound 1 was deduced by a single-crystal X-ray diffraction experiment using CuKα radiation. In the bioactivity assay, both Compounds 1 and 2 exhibited α-glucosidase inhibitory activity with IC50 values of 4.6 ± 0.1 and 11.9 ± 0.4 μM, respectively. This was the first report on isopimarane diterpenes with α-glucosidase inhibitory activity. PMID:25738327

  15. 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.

  16. Spectral sensitivity of juvenile chub mackerel (Scomber japonicus) in visible and ultraviolet light.

    PubMed

    Matsumoto, Taro; Ihara, Hiroshi; Ishida, Yoshinari; Yamamoto, Shinji; Murata, Osamu; Ishibashi, Yasunori

    2010-03-01

    Although chub mackerel (Scomber japonicus) is widely distributed all over the world, the relevance of its visual sensitivity to its ecology is not yet fully understood. We investigated spectral sensitivity in juvenile chub mackerel in the range of ultraviolet (UV) to visible light (369-652 nm) by electroretinogram (ERG) using light-emitting diodes (LEDs). Sensitivity peaked at a wavelength of approximately 482 nm in dark-adapted fish and 525 nm in light-adapted fish. A secondary sensitivity peak in the UV range at approximately 382 nm was found in both dark- and light-adapted fish. The UV sensitivity of chub mackerel may be attributable to UV transmissibility of the optical media and to the presence of a beta-band of visible light-sensitive visual pigments, and not to an alpha-band of UV visual pigments. This UV sensitivity may be useful for feeding or communication with other fishes.

  17. Generation of 7137 non-redundant expressed sequence tags from a legume, Lotus japonicus.

    PubMed

    Asamizu, E; Nakamura, Y; Sato, S; Tabata, S

    2000-04-28

    For comprehensive analysis of genes expressed in a model legume, Lotus japonicus, a total of 22,983 5' end expressed sequence tags (ESTs) were accumulated from normalized and size-selected cDNA libraries constructed from young (2 weeks old) plants. The EST sequences were clustered into 7137 non-redundant groups. Similarity search against public non-redundant protein database indicated that 3302 groups showed similarity to genes of known function, 1143 groups to hypothetical genes, and 2692 were novel sequences. Homologues of 5 nodule-specific genes which have been reported in other legume species were contained in the collected ESTs, suggesting that the EST source generated in this study will become a useful tool for identification of genes related to legume-specific biological processes. The sequence data of individual ESTs are available at the web site: http://www.kazusa.or.jp/en/plant/lotus/EST/.

  18. The cloning of growth associated protein 43 of Gekko japonicus and its effect on cell morphology.

    PubMed

    Feng, Xiao; Zhou, Youlang; Liu, Mei; Gu, Xingxing; Wang, Yongjun; Ding, Fei; Gu, Xiaosong; Liu, Yan

    2012-07-01

    The growth-associated protein 43 (GAP-43) gene of Gekko japonicus was obtained from a brain and spinal cord cDNA library. The results of northern blot analysis showed the gecko GAP-43 gene transcript is 1.7 kb in length, and it was abundantly expressed in tissues of brain, spinal cord and ovary. Gecko GAP-43 promoted the outgrowth of Gsn3 cells and PC12 cell in vitro, and phosphorylation at serine 42 modulated the effect of GAP-43 on cell spreading and morphology. The change in GAP-43 expression in the spinal cord after tail amputation was examined by reverse transcription polymerase chain reaction (RT-PCR). The level of GAP-43 in the spinal cord was increased during the time course we examined, indicating a possible correlation between GAP-43 expression and the spinal cord injury and regeneration.

  19. Efficient Inactivation of Symbiotic Nitrogen Fixation Related Genes in Lotus japonicus Using CRISPR-Cas9

    PubMed Central

    Wang, Longxiang; Wang, Longlong; Tan, Qian; Fan, Qiuling; Zhu, Hui; Hong, Zonglie; Zhang, Zhongming; Duanmu, Deqiang

    2016-01-01

    The targeted genome editing technique, CRISPR/Cas9 system, has been widely used to modify genes of interest in a predictable and precise manner. In this study, we describe the CRISPR/Cas9-mediated efficient editing of representative SNF (symbiotic nitrogen fixation) related genes in the model legume Lotus japonicus via Agrobacterium-mediated stable or hairy root transformation. We first predicted nine endogenous U6 genes in Lotus and then demonstrated the efficacy of the LjU6-1 gene promoter in driving expression of single guide RNAs (sgRNAs) by using a split yellow fluorescence protein (YFP) reporter system to restore the fluorescence in Arabidopsis protoplasts. Next, we chose a customized sgRNA targeting SYMRK (symbiosis receptor-like kinase) loci and achieved ~35% mutagenic efficiency in 20 T0 transgenic plants, two of them containing biallelic homozygous mutations with a 2-bp deletion near the PAM region. We further designed two sgRNAs targeting three homologous leghemoglobin loci (LjLb1, LjLb2, LjLb3) for testing the possibility of generating multi-gene knockouts. 20 out of 70 hairy root transgenic plants exhibited white nodules, with at least two LjLbs disrupted in each plant. Compared with the constitutively active CaMV 35S promoter, the nodule-specific LjLb2 promoter was also effective in gene editing in nodules by hairy root transformation. Triple mutant knockout of LjLbs was also obtained by stable transformation using two sgRNAs. Collectively, these studies demonstrate that the CRISPR/Cas9 system should greatly facilitate functional analyses of SNF related genes in Lotus japonicus. PMID:27630657

  20. 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

  1. 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.

  2. Characterization of the genetic environment of blaESBL genes, integrons and toxin-antitoxin systems identified on large transferrable plasmids in multi-drug resistant Escherichia coli

    PubMed Central

    Wang, Juan; Stephan, Roger; Zurfluh, Katrin; Hächler, Herbert; Fanning, Séamus

    2015-01-01

    Objectives: Previously 14 conjugative plasmids from multi-drug resistant (MDR) Escherichia coli from healthy humans and food-producing animals in Switzerland were sequenced. The aim of this study was to extend the genetic characterization of these plasmids with a focus on blaESBL genes including blaCTX-M-1 and blaTEM, class 1 integrons and toxin-antitoxin (TA) systems contained therein. Methods: The nucleotide sequences and subsequent annotation therein of 14 conjugative plasmids were previously determined from their corresponding transconjugants. The TA loci were confirmed by RASTA-Bacteria. Results: Eight of the conjugative plasmids identified were found to encode genes expressing ESBLs. Structural heterogeneity was noted in the regions flanking both the blaCTX-M-1 and blaTEM genes. The blaCTX-M-1 genes were associated with the common insertion sequences ISEcp1 and IS26, and uniquely with an IS5 element in one case; while blaTEM genes were found to be associated with IS26 and Tn2. A new blaTEM-210 gene was identified. Seven class 1 integrons were also identified and assigned into 3 groups, denoted as In54, In369 and In501. Sixteen TA loci belonging to 4 of the TA gene families (relBE, vapBC, ccd and mazEF) were identified on 11 of these plasmids. Conclusions: Comparative sequence analysis of these plasmids provided data on the structures likely to contribute to sequence diversity associated with these accessory genes, including IS26, ISEcp1 and Tn2. All of them contribute to the dissemination of the corresponding resistance genes located on the different plasmids. There appears to be no association between β-lactam encoding genes and TA systems. PMID:25610429

  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. Diverse Small Molecule Inhibitors of Human Apurinic/Apyrimidinic Endonuclease APE1 Identified from a Screen of a Large Public Collection

    PubMed Central

    Dorjsuren, Dorjbal; Kim, Daemyung; Vyjayanti, Vaddadi N.; Maloney, David J.; Jadhav, Ajit; Wilson, David M.; Simeonov, Anton

    2012-01-01

    The major human apurinic/apyrimidinic endonuclease APE1 plays a pivotal role in the repair of base damage via participation in the DNA base excision repair (BER) pathway. Increased activity of APE1, often observed in tumor cells, is thought to contribute to resistance to various anticancer drugs, whereas down-regulation of APE1 sensitizes cells to DNA damaging agents. Thus, inhibiting APE1 repair endonuclease function in cancer cells is considered a promising strategy to overcome therapeutic agent resistance. Despite ongoing efforts, inhibitors of APE1 with adequate drug-like properties have yet to be discovered. Using a kinetic fluorescence assay, we conducted a fully-automated high-throughput screen (HTS) of the NIH Molecular Libraries Small Molecule Repository (MLSMR), as well as additional public collections, with each compound tested as a 7-concentration series in a 4 µL reaction volume. Actives identified from the screen were subjected to a panel of confirmatory and counterscreen tests. Several active molecules were identified that inhibited APE1 in two independent assay formats and exhibited potentiation of the genotoxic effect of methyl methanesulfonate with a concomitant increase in AP sites, a hallmark of intracellular APE1 inhibition; a number of these chemotypes could be good starting points for further medicinal chemistry optimization. To our knowledge, this represents the largest-scale HTS to identify inhibitors of APE1, and provides a key first step in the development of novel agents targeting BER for cancer treatment. PMID:23110144

  5. Identifying the “demon whale-biter”: Patterns of scarring on large whales attributed to a cookie-cutter shark Isistius sp

    PubMed Central

    Photopoulou, Theoni

    2016-01-01

    The presence of crater-like wounds on cetaceans and other large marine vertebrates and invertebrates has been attributed to various organisms. We review the evidence for the identity of the biting agent responsible for crater wounds on large whales, using data collected from sei (Balaenoptera borealis), fin (B. physalus), inshore and offshore Bryde’s (B. brydeii sp) and sperm whales (Physeter macrocephalus) examined at the Donkergat whaling station, Saldanha Bay, South Africa between March and October 1963. We then analyse the intensity and trends in its predation on large whales. Despite the scarcity of local records, we conclude that a cookie-cutter shark Isistius sp is the most likely candidate. We make inferences about the trends in (1) total counts of unhealed bitemarks, and (2) the proportion of unhealed bitemarks that were recent. We use day of the year; reproductive class, social grouping or sex; depth interval and body length as candidate covariates. The models with highest support for total counts of unhealed bitemarks involve the day of the year in all species. Depth was an important predictor in all species except offshore Bryde’s whales. Models for the proportion of recent bites were only informative for sei and fin whales. We conclude that temporal scarring patterns support what is currently hypothesized about the distribution and movements of these whale species, given that Isistius does not occur in the Antarctic and has an oceanic habitat. The incidence of fresh bites confirms the presence of Isistius in the region. The lower numbers of unhealed bites on medium-sized sperm whales suggests that this group spends more time outside the area in which bites are incurred, providing a clue to one of the biggest gaps in our understanding of the movements of mature and maturing sperm males. PMID:27055057

  6. Identifying the "demon whale-biter": Patterns of scarring on large whales attributed to a cookie-cutter shark Isistius sp.

    PubMed

    Best, Peter B; Photopoulou, Theoni

    2016-01-01

    The presence of crater-like wounds on cetaceans and other large marine vertebrates and invertebrates has been attributed to various organisms. We review the evidence for the identity of the biting agent responsible for crater wounds on large whales, using data collected from sei (Balaenoptera borealis), fin (B. physalus), inshore and offshore Bryde's (B. brydeii sp) and sperm whales (Physeter macrocephalus) examined at the Donkergat whaling station, Saldanha Bay, South Africa between March and October 1963. We then analyse the intensity and trends in its predation on large whales. Despite the scarcity of local records, we conclude that a cookie-cutter shark Isistius sp is the most likely candidate. We make inferences about the trends in (1) total counts of unhealed bitemarks, and (2) the proportion of unhealed bitemarks that were recent. We use day of the year; reproductive class, social grouping or sex; depth interval and body length as candidate covariates. The models with highest support for total counts of unhealed bitemarks involve the day of the year in all species. Depth was an important predictor in all species except offshore Bryde's whales. Models for the proportion of recent bites were only informative for sei and fin whales. We conclude that temporal scarring patterns support what is currently hypothesized about the distribution and movements of these whale species, given that Isistius does not occur in the Antarctic and has an oceanic habitat. The incidence of fresh bites confirms the presence of Isistius in the region. The lower numbers of unhealed bites on medium-sized sperm whales suggests that this group spends more time outside the area in which bites are incurred, providing a clue to one of the biggest gaps in our understanding of the movements of mature and maturing sperm males.

  7. 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.

  8. Optimal conditions for mycelial growth of Schizosaccharomyces japonicus cells in liquid medium: it enables the molecular investigation of dimorphism.

    PubMed

    Papp, László; Sipiczki, Matthias; Holb, Imre J; Miklós, Ida

    2014-12-01

    The non-pathogenic dimorphic fission yeast, Schizosaccharomyces japonicus, could be a suitable model organism for investigation of the genetic background of mycelial growth, as it has a haploid chromosome set and its genome is sequenced. Since earlier results have suggested that its morphological transition required solid substrates, but molecular biological experiments would require hyphae production in a liquid medium, we wanted to find circumstances which would enable hyphae production in liquid media. Several external conditions were investigated, but the strongest inducer was fetal bovine serum (FBS). Its positive effect could be hampered by heat and was dependent on pH, temperature and concentration of the serum. Other protein-containing compounds, such as peptone and bovine serum albumin or amino acids, proved to be ineffective or weak. Generally, the uninduced and induced mycelial growth of Sz. japonicus could be improved by lower external pH and higher temperature.

  9. Glutamine synthetase I-deficiency in Mesorhizobium loti differentially affects nodule development and activity in Lotus japonicus.

    PubMed

    Chungopast, Sirinapa; Thapanapongworakul, Pilunthana; Matsuura, Hiroyuki; Van Dao, Tan; Asahi, Toshimasa; Tada, Kuninao; Tajima, Shigeyuki; Nomura, Mika

    2014-03-01

    In this study, we focused on the effect of glutamine synthetase (GSI) activity in Mesorhizobium loti on the symbiosis between the host plant, Lotus japonicus, and the bacteroids. We used a signature-tagged mutant of M. loti (STM30) with a transposon inserted into the GSI (mll0343) gene. The L. japonicus plants inoculated with STM30 had significantly more nodules, and the occurrence of senesced nodules was much higher than in plants inoculated with the wild-type. The acetylene reduction activity (ARA) per nodule inoculated with STM30 was lowered compared to the control. Also, the concentration of chlorophyll, glutamine, and asparagine in leaves of STM30-infected plants was found to be reduced. Taken together, these data demonstrate that a GSI deficiency in M. loti differentially affects legume-rhizobia symbiosis by modifying nodule development and metabolic processes.

  10. Identifying a large landslide with small displacements in a zone of coseismic tectonic deformation; the Villa Del Monte landslide triggered by the 1989 Loma Prieta, California, earthquake

    USGS Publications Warehouse

    Keefer, David K.; Harp, Edwin L.; Griggs, Gary B.; Evans, Stephen G.; DeGraff, Jerome V.

    2002-01-01

    The Villa Del Monte landslide was one of 20 large and complex landslides triggered by the 1989 LomaPrieta, California, earthquake in a zone of pervasive coseismicground cracking near the fault rupture. The landslide was approximately 980 m long, 870 m wide, and encompassed an area of approximately 68 ha. Drilling data suggested that movement may have extended to depths as great as 85 m below the ground surface. Even though the landslide moved <1 m, it caused substantial damage to numerous dwellings and other structures, primarily as a result of differential displacements and internal Assuring. Surface cracks, scarps, and compression features delineating the Villa Del Monte landslide were discontinuous, probably because coseismic displacements were small; such discontinuous features were also characteristic of the other large, coseismic landslides in the area, which also moved only short distances during the earthquake. Because features marking landslide boundaries were discontinuous and because other types of coseismic ground cracks were widespread in the area, identification of the landslides required detailed mapping and analysis. Recognition that landslides such as that at Villa Del Monte may occur near earthquake-generating fault ruptures should aid in future hazard evaluations of areas along active faults.

  11. Wide mutation spectrum and frequent variant Ala27Thr of FBN1 identified in a large cohort of Chinese patients with sporadic TAAD

    PubMed Central

    Guo, Jun; Cai, Lun; Jia, Lixin; Li, Xiaoyan; Xi, Xin; Zheng, Shuai; Liu, Xuxia; Piao, Chunmei; Liu, Tingting; Sun, Zhongsheng; Cai, Tao; Du, Jie

    2015-01-01

    Genetic etiology in majority of patients with sporadic thoracic aortic aneurysm and dissections (STAAD) remains unknown. Recent GWAS study suggested common variant(s) in FBN1 is associated with STAAD. The present study aims to test this hypothesis and to identify mutation spectrum by targeted exome sequencing of the FBN1 gene in 146 unrelated patients with STAAD. Totally, 15.75% of FBN1 variants in STAAD were identified, including 5 disruptive and 18 missense mutations. Most of the variants were novel. Genotype-phenotype correlation analysis suggested that the maximum aortic diameter in the disruptive mutation group was significantly larger than that in the non-Cys missense mutation group. Interestingly, the variant Ala27Thr at −1 position, which is predicted to change the cleavage site of the signal peptidase of fibrillin-1, was detected in two unrelated patients. Furthermore, genotyping analysis of this variant detected 10 heterozygous Ala27Thr from additional 666 unrelated patients (1.50%), versus 7 from 1500 controls (0.47%), indicating a significant association of this variant with STAAD. Collectively, the identification of the variant Ala27Thr may represent a relatively common genetic predisposition and a novel pathogenetic mechanism for STAAD. Also, expansion of the mutation spectrum in FBN1 will be helpful in genetic counselling for Chinese patients with STAAD. PMID:26272055

  12. 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

  13. Anopheles lindesayi japonicus Yamada (Diptera: Culicidae) in Korea: comprehensive review, new collection records, and description of larval habitats

    DTIC Science & Technology

    2007-09-01

    3North Carolina Department ofEnvironment and Natural Resources. 585 Waughtown St.• Winston-Salem. NC 27107, U.S.A. fKorea Center for Disease Control ...Seou~ Korea Received 13 September 2007; Accepted 29 December 2007 ABSTRACf: Anopheles lindesayi japonicus Yamada is an uncommonly collected mosquito ...in Korea. and its presence is based upon limited collection data and anecdotal reports in Korean mosquito literature: 45 specimens collected from 15

  14. Functional characterization of P-glycoprotein in the intertidal copepod Tigriopus japonicus and its potential role in remediating metal pollution.

    PubMed

    Jeong, Chang-Bum; Kim, Bo-Mi; Kim, Rae-Kwon; Park, Heum Gi; Lee, Su-Jae; Shin, Kyung-Hoon; Leung, Kenneth Mei Yee; Rhee, Jae-Sung; Lee, Jae-Seong

    2014-11-01

    The intertidal copepod Tigriopus japonicus has been widely used in aquatic toxicity testing for diverse environmental pollutants including metals. Despite relatively well-characterized in vivo physiological modulations in response to aquatic pollutants, the molecular mechanisms due to toxicity and detoxification are still unclear. To better understand the mechanisms of metal transport and further detoxification, T. japonicus P-glycoprotein (TJ-P-gp) with conserved motifs/domains was cloned and measured for protein activity against the transcript and protein expression profiles in response to metal exposure. Specifically, we characterized the preliminary efflux activity and membrane topology of TJ-P-gp protein that supports a transport function for chemicals. To uncover whether the efflux activity of TJ-P-gp protein would be modulated by metal treatment, copepods were exposed to three metals (Cd, Cu, and Zn), and were observed for both dose- and time-dependency on the efflux activity of TJ-P-gp protein with or without 10μM of P-gp-specific inhibitors verapamil and zosuquidar (LY335979) for 24h over a wide range of metal concentrations. In particular, treatment with zosuquidar induced metal accumulation in the inner body of T. japonicus. In addition, three metals significantly induced the transporting activity of TJ-P-gp in a concentration-dependent manner in both transcript and protein levels within 24h. Together these data indicate that T. japonicus has a conserved P-gp-mediated metal defense system through the induction of transcriptional up-regulation of TJ-P-gp gene and TJ-P-gp protein activity. This finding provides further understanding of the molecular defense mechanisms involved in P-glycoprotein-mediated metal detoxification in copepods.

  15. 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 combined data set. MP analysis was performed in PAUP* 4.0b10 (Swofford 2000) by using a heuristic search with tree bisection reconnection (TBR...geology and tectonics of Japan and surrounding regions (Taira 2001). A split into northern and southern lines, that independently colonized the...japonicus, in the United States these include Ae. atropalpus and Ae. triseriatus two endemic mosquito species that colonize the same habitats. The assay

  16. 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.

  17. PERMANENT GENETIC RESOURCES: Isolation and characterization of nine microsatellite loci from the chub mackerel, Scomber japonicus (Perciformes, Scombridae).

    PubMed

    Yagishita, N; Kobayashi, T

    2008-03-01

    The stock abundance of the chub mackerel Scomber japonicus - a very important species for fisheries, particularly in Japan - in the Pacific Ocean off Japan has remained at a low level. For studying the population genetics of the chub mackerel, we isolated nine polymorphic microsatellite loci (12-31 alleles/locus; expected heterozygosity, 0.762-0.983) from this species. Cross-species amplification indicated that eight of the nine microsatellite loci in the blue mackerel S. australasicus were polymorphic and functional.

  18. A collaborative approach to identifying effective incentives for mental health clinicians to improve depression care in a large managed behavioral healthcare organization.

    PubMed

    Meredith, Lisa S; Branstrom, Robert B; Azocar, Francisca; Fikes, Ruth; Ettner, Susan L

    2011-05-01

    This descriptive study used stakeholder input to prioritize evidence-based strategies for improving depression care and to select incentives for mental health clinicians to adopt those strategies, and to conduct a feasibility test of an incentive-based program in a managed behavioral healthcare organization (MBHO). In two rounds of interviews and a stakeholder meeting, MBHO administrators and clinicians selected increasing combination treatment (antidepressant plus psychotherapy) rates as the program goal; and paying a bonus for case reviews, clinician feedback, and clinician education as incentives. We assessed program feasibility with case review and clinician surveys from a large independent practice association that contracts with the MBHO. Findings suggest that providing incentives for mental health clinicians is feasible and the incentive program did increase awareness. However, adoption may be challenging because of administrative barriers and limited clinical data available to MBHOs.

  19. Exploiting RNA-sequencing data from the porcine testes to identify the key genes involved in spermatogenesis in Large White pigs.

    PubMed

    Song, Huibin; Zhu, Lihua; Li, Yan; Ma, Changping; Guan, Kaifeng; Xia, Xuanyan; Li, Fenge

    2015-12-01

    Mammalian testis development and spermatogenesis play critical roles in male fertility. However, little genomic information is available for porcine sexually mature and immature testis. Presently, we detected approximately 76% of previously annotated genes that were expressed in the porcine testes by RNA sequencing. Taking an FDR of 0.001 and a |log2Ratio| of 1 as cutoffs, 10,095 genes were significantly differentially expressed between two stages, including 242 spermatogenesis-associated genes. These genes were significantly enriched to GO BP terms concerning spermatogenesis, male gamete generation, developmental process and sexual reproduction; to the KEEG pathways, including focal adhesion, ECM-receptor interaction, and phagosome. 186 extended transcripts, 1273 alternative splicing events and 2846 SNPs were detected in spermatogenesis-associated DEGs. Two PIWIL4 SNPs were successfully validated and suggested to be the potential molecular markers for semen quality. This study will help identify the specific genes and isoforms that are active in porcine spermatogenesis and sexual maturity.

  20. Expression analysis in a rat psychosis model identifies novel candidate genes validated in a large case–control sample of schizophrenia

    PubMed Central

    Ingason, A; Giegling, I; Hartmann, A M; Genius, J; Konte, B; Friedl, M; Ripke, S; Sullivan, P F; St. Clair, D; Collier, D A; O'Donovan, M C; Mirnics, K; Rujescu, D

    2015-01-01

    Antagonists of the N-methyl-D-aspartate (NMDA)-type glutamate receptor induce psychosis in healthy individuals and exacerbate schizophrenia symptoms in patients. In this study we have produced an animal model of NMDA receptor hypofunction by chronically treating rats with low doses of the NMDA receptor antagonist MK-801. Subsequently, we performed an expression study and identified 20 genes showing altered expression in the brain of these rats compared with untreated animals. We then explored whether the human orthologs of these genes are associated with schizophrenia in the largest schizophrenia genome-wide association study published to date, and found evidence for association for 4 out of the 20 genes: SF3B1, FOXP1, DLG2 and VGLL4. Interestingly, three of these genes, FOXP1, SF3B1 and DLG2, have previously been implicated in neurodevelopmental disorders. PMID:26460480

  1. Expression analysis in a rat psychosis model identifies novel candidate genes validated in a large case-control sample of schizophrenia.

    PubMed

    Ingason, A; Giegling, I; Hartmann, A M; Genius, J; Konte, B; Friedl, M; Ripke, S; Sullivan, P F; St Clair, D; Collier, D A; O'Donovan, M C; Mirnics, K; Rujescu, D

    2015-10-13

    Antagonists of the N-methyl-D-aspartate (NMDA)-type glutamate receptor induce psychosis in healthy individuals and exacerbate schizophrenia symptoms in patients. In this study we have produced an animal model of NMDA receptor hypofunction by chronically treating rats with low doses of the NMDA receptor antagonist MK-801. Subsequently, we performed an expression study and identified 20 genes showing altered expression in the brain of these rats compared with untreated animals. We then explored whether the human orthologs of these genes are associated with schizophrenia in the largest schizophrenia genome-wide association study published to date, and found evidence for association for 4 out of the 20 genes: SF3B1, FOXP1, DLG2 and VGLL4. Interestingly, three of these genes, FOXP1, SF3B1 and DLG2, have previously been implicated in neurodevelopmental disorders.

  2. Effects of Endogenous Salicylic Acid on Nodulation in the Model Legumes Lotus japonicus and Medicago truncatula1[W

    PubMed Central

    Stacey, Gary; McAlvin, Crystal Bickley; Kim, Sung-Yong; Olivares, José; Soto, María José

    2006-01-01

    The exogenous addition of salicylic acid (SA) was previously shown to inhibit indeterminate but not determinate-type nodulation. We sought to extend these results by modulating endogenous levels of SA through the transgenic expression of salicylate hydroxylase (NahG) in both stably transformed Lotus japonicus and composite Medicago truncatula plants. NahG expression in L. japonicus resulted in a marked reduction of SA levels. This reduction correlated with an increase in the number of infections and mean nodule number when compared to controls. However, a complicating factor was that NahG-expressing plants had greater root growth. Spot inoculations of NahG-expressing L. japonicus plants confirmed increased nodulation in these plants. Consistent with the reported inhibitory effects of exogenous SA on indeterminate-type nodulation, NahG expression in M. truncatula plants led to enhanced nodulation and infection. These data point to an important role for SA-mediated plant defense pathways in controlling nodule formation on both determinate and indeterminate nodule-forming hosts. PMID:16798946

  3. 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.

  4. 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).

  5. Different strategies of Lotus japonicus, L. corniculatus and L. tenuis to deal with complete submergence at seedling stage.

    PubMed

    Striker, G G; Izaguirre, R F; Manzur, M E; Grimoldi, A A

    2012-01-01

    Two main strategies allow plants to deal with submergence: (i) escape from below water by means of shoot elongation, or (ii) remaining quiescent under the water until water subsides and then resume growth. We investigated these strategies in seedlings of Lotus japonicus, L. corniculatus and L. tenuis subjected to control and submergence for 12 days, with a subsequent 30-day recovery period. All three species survived submergence but used different strategies. Submerged seedlings of L. japonicus exhibited an escape strategy (emerging from water) as a result of preferential carbon allocation towards shoot mass and lengthening, in detriment to root growth. In contrast, seedlings of L. corniculatus and L. tenuis became quiescent, with no biomass accumulation, no new unfolding of leaves and no shoot elongation. Upon de-submergence, seedlings of L. japonicus had the lowest recovery growth (a biomass and shoot height 58% and 40% less than controls, respectively), L. corniculatus was intermediate and L. tenuis showed the greatest recovery growth. Previously submerged seedlings of L. tenuis did not differ from their controls, either in final shoot biomass or shoot height. Thus, for the studied species, quiescence appears to be an adequate strategy for tolerance of short-term (i.e., 12 days) complete submergence, being consistent with field observations of L. tenuis colonisation of flood-prone environments.

  6. Molecular basis of multiple resistance to ACCase- and ALS-inhibiting herbicides in Alopecurus japonicus from China.

    PubMed

    Bi, Yaling; Liu, Weitang; Guo, Wenlei; Li, Lingxu; Yuan, Guohui; Du, Long; Wang, Jinxin

    2016-01-01

    Fenoxaprop-P-ethyl-resistant Alopecurus japonicus has become a recurring problem in winter wheat fields in eastern China. Growers have resorted to using mesosulfuron-methyl, an acetolactate synthase (ALS)-inhibiting herbicide, to control this weed. A single A. japonicus population (AH-15) resistant to fenoxaprop-P-ethyl and mesosulfuron-methyl was found in Anhui Province, China. The results of whole-plant dose-response experiments showed that AH-15 has evolved high-level resistance to fenoxaprop-P-ethyl (95.96-fold) and mesosulfuron-methyl (39.87-fold). It was shown via molecular analysis that resistance to both fenoxaprop-P-ethyl and mesosulfuron-methyl was due to an amino acid substitution of Ile1781 to Leu in acetyl-CoA carboxylase (ACCase) and a substitution of Trp 574 to Leu in ALS, respectively. Whole-plant bioassays indicated that the AH-15 population was resistant to the ACCase herbicides clodinafop-propargyl, clethodim, sethoxydim and pinoxaden as well as the ALS herbicides pyroxsulam, flucarbazone-Na and imazethapyr, but susceptible to the ACCase herbicide haloxyfop-R-methyl. This work reports for the first time that A. japonicus has developed resistance to ACCase- and ALS-inhibiting herbicides due to target site mutations in the ACCase and ALS genes.

  7. Effects of Surfactants and Microwave-assisted Pretreatment of Orange Peel on Extracellular Enzymes Production by Aspergillus japonicus PJ01.

    PubMed

    Li, Pei-jun; Xia, Jin-lan; Shan, Yang; Nie, Zhen-yuan; Wang, Fei-ran

    2015-06-01

    The effects of surfactants and microwave pretreatment of orange peel powder (OPP) on the production of pectinase, cellulase, and xylanase by Aspergillus japonicus PJ01 in submerged fermentation were investigated. The results showed that when OPP was pretreated only by microwave (630 W, 9 min, and liquid/solid ratio 5), the activities of exo-pectinase, carboxymethyl cellulase (CMCase), xylanase, and filter paper cellulase (FPase) were increased by 11.8, 20.6, 16.2, and 24.0 %, respectively, and when OPP was pretreated by microwave at the same conditions cited above plus PEG 4000 at the concentration of 3 g/L, the activities of the above four enzymes were enhanced by 40.2, 30.3, 40.4, and 40.0 % after 84-h cultivation, respectively. It is suggested a synergistic effect between microwave and surfactant treatment in enhancing the multiextracellular enzymes production by OPP fermentation of A. japonicus PJ01. Chemical composition and Fourier transform infrared spectroscopy (FTIR) analysis displayed that the microwave pretreatment of OPP led to the decrease of hemicellulose and essential oil contents. Scanning electron microscope (SEM) showed that OPP surface after microwave pretreatment became porous and more susceptible to be invaded by A. japonicus. The results demonstrated that pretreatment of OPP by surfactant PEG 4000 and microwave irradiation as environment-friendly way was cost-effective in enhancing the multienzyme production from agricultural waste orange peel.

  8. Anillin-related protein Mid1 regulates timely formation of the contractile ring in the fission yeast Schizosaccharomyces japonicus.

    PubMed

    Yasuda, Tsuyoshi; Takaine, Masak; Numata, Osamu; Nakano, Kentaro

    2016-06-01

    In the fission yeast Schizosaccharomyces pombe (Sp), Mid1/Dmf1 plays an important role in positioning the division site by inducing formation of the contractile ring (CR). Mid1, emanating from the nucleus located in the cell center, forms a dozen of nodes in the middle cell cortex ahead of mitosis, and actin filaments and myosin II accumulated at each node interact and assemble the CR in metaphase. Curiously, in another fission yeast S. japonicus (Sj), CR formation begins after nuclear segregation in late anaphase. Here, we investigated the role of S. japonicus Mid1 during mitosis to compare the molecular mechanisms that determine the cell division site in Schizosaccharomyces. Similar to Sp Mid1, Sj Mid1 often accumulated in the nucleus of interphase cells. Moreover, Sj Mid1 localized to cortical dots with myosin II in the future division site and formed a medial ring in mitotic cells. However, S. japonicus cells without Mid1 function still carried out symmetrical binary division. Therefore, the Mid1 dependency for positional control of the cell division site is possibly different between the two species. Meanwhile, we found that Sj Mid1 enhanced CR formation, in a manner possibly similar to that by Sp Mid1.

  9. 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.

  10. Contrasting genetic structure of closely related giant water bugs: phylogeography of Appasus japonicus and Appasus major (Insecta: Heteroptera, Belostomatidae).

    PubMed

    Suzuki, Tomoya; Kitano, Tadashi; Tojo, Koji

    2014-03-01

    Appasus japonicus and A. major, two belostomatid species of the giant water bug found in parts of East Asia, have very similar morphological characteristics and ecological niches, and also overlapping habitats. However, the results of our previous published study utilizing molecular phylogenetic analyses of mitochondrial and nuclear DNA revealed extensive genetic differences, which indicated that the possibility of inter-specific hybridization was extremely unlikely. We collected A. japonicus and A. major from the Japanese Archipelago, Korean Peninsula, and Russian Far East, and conducted molecular analyses of mitochondrial DNA COI and 16S rRNA to compare phylogenetic relationships between these species. Three major clades were recognized within A. japonicus. Specimens from the Korean population constituted a monophyletic clade, and were a sister group of the western region of the Japanese Archipelago. The Eastern Japanese clade was clearly differentiated. Four major clades were recognized within A. major. Specimens from the Japanese and Korean populations revealed two distinct monophyletic clades. Significant differentiation was clearly observed between their genetic structures. Furthermore, the results of mismatch distribution and Bayesian skyline plot analyses suggested the possibility of a bottleneck effect or founder effect in two of the A. major clades. Collectively, these results demonstrated both similarities and differences in these two species even though their distribution widely overlaps in East Asia, with their morphological characteristics and ecological niches being very similar. These differences in genetic structures are considered to be due to their evolutionary history.

  11. Screening of a large cohort of Leber congenital amaurosis and retinitis pigmentosa patients identifies novel LCA5 mutations and new genotype-phenotype correlations

    PubMed Central

    Sui, Ruifang; van den Born, L. Ingeborgh; Berson, Eliot L.; Ocaka, Louise A.; Davidson, Alice E.; Heckenlively, John R.; Branham, Kari; Ren, Huanan; Lopez, Irma; Maria, Maleeha; Azam, Maleeha; Henkes, Arjen; Blokland, Ellen; Qamar, Raheel; Webster, Andrew R.; Andreasson, Sten; de Baere, Elfride; Bennett, Jean; Chader, Gerald J.; Berger, Wolfgang; Golovleva, Irina; Greenberg, Jacquie; den Hollander, Anneke I.; Klaver, Caroline C.W.; Klevering, B. Jeroen; Lorenz, Birgit; Preising, Markus N.; Ramsear, Raj; Roberts, Lisa; Roepman, Ronald; Rohrschneider, Klaus; Wissinger, Bernd

    2014-01-01

    To investigate the prevalence of sequence variants in LCA5 in patients with Leber congenital amaurosis (LCA), early onset rod-cone dystrophy (EORD) and autosomal recessive retinitis pigmentosa (RP), to delineate the ocular phenotypes, and to provide an overview of all published LCA5 variants in an online database._Patients underwent standard ophthalmic evaluations after providing informed consent. In selected patients, optical coherence tomography (OCT) and fundus autofluorescence imaging was possible. DNA samples from 797 unrelated patients with LCA and 211 with the various types of RP were screened by Sanger sequence analysis of all LCA5 exons and intron/exon junctions. Some LCA patients were pre-screened by APEX technology or selected based on homozygosity mapping. In silico analyses were performed to assess the pathogenicity of the variants. Segregation analysis was performed where possible. Published and novel LCA5 variants were collected, amended for their correct nomenclature, and listed in a Leiden Open Variation Database (LOVD). Sequence analysis identified 18 new probands with 19 different LCA5 variants. Seventeen of the 19 LCA5 variants were novel. Except for two missense variants and one splice site variant, all variants were protein-truncating mutations. Most patients expressed a severe phenotype, typical of LCA. However, some LCA subjects had better vision and intact inner segment/outer segment (IS/OS) junctions on OCT imaging. In two families with LCA5 variants, the phenotype was more compatible with EORD with affected individuals displaying preserved islands of RPE. One of these milder families harbored a homozygous splice site mutation, a second family was found to have a combination of a stop mutation and a missense mutation. This is the largest LCA5 study to date. We sequenced 1008 patients (797 with LCA, 211 with arRP) and identified 18 probands with LCA5 mutations. Mutations in LCA5 are a rare cause of childhood retinal dystrophy accounting for

  12. Competencies Needed by Chief School Business Administrators. A Report on the Results, Conclusions and Implications of a Research Study to Identify the Competencies Needed by Chief School Business Administrators in Large and Small School Districts.

    ERIC Educational Resources Information Center

    McGuffey, C. W.

    A national survey sought to identify the competencies that chief school business administrators (CSBAs) in large and small school districts think are important for their job. Seventy-five respondents, out of a random stratified sample comprising 143 members of the Association of School Business Officials, ranked 264 statements in 28 major task…

  13. Function search in a large transcription factor gene family in Arabidopsis: assessing the potential of reverse genetics to identify insertional mutations in R2R3 MYB genes.

    PubMed Central

    Meissner, R C; Jin, H; Cominelli, E; Denekamp, M; Fuertes, A; Greco, R; Kranz, H D; Penfield, S; Petroni, K; Urzainqui, A; Martin, C; Paz-Ares, J; Smeekens, S; Tonelli, C; Weisshaar, B; Baumann, E; Klimyuk, V; Marillonnet, S; Patel, K; Speulman, E; Tissier, A F; Bouchez, D; Jones, J J; Pereira, A; Wisman, E

    1999-01-01

    More than 92 genes encoding MYB transcription factors of the R2R3 class have been described in Arabidopsis. The functions of a few members of this large gene family have been described, indicating important roles for R2R3 MYB transcription factors in the regulation of secondary metabolism, cell shape, and disease resistance, and in responses to growth regulators and stresses. For the majority of the genes in this family, however, little functional information is available. As the first step to characterizing these genes functionally, the sequences of >90 family members, and the map positions and expression profiles of >60 members, have been determined previously. An important second step in the functional analysis of the MYB family, through a process of reverse genetics that entails the isolation of insertion mutants, is described here. For this purpose, a variety of gene disruption resources has been used, including T-DNA-insertion populations and three distinct populations that harbor transposon insertions. We report the isolation of 47 insertions into 36 distinct MYB genes by screening a total of 73 genes. These defined insertion lines will provide the foundation for subsequent detailed functional analyses for the assignment of specific functions to individual members of the R2R3 MYB gene family. PMID:10521515

  14. Positional cloning and next-generation sequencing identified a TGM6 mutation in a large Chinese pedigree with acute myeloid leukaemia

    PubMed Central

    Pan, Li-li; Huang, Yuan-mao; Wang, Min; Zhuang, Xiao-e; Luo, Dong-feng; Guo, Shi-cheng; Zhang, Zhi-shun; Huang, Qing; Lin, Sheng-long; Wang, Shao-yuan

    2015-01-01

    An inherited predisposition to acute myeloid leukaemia (AML) is exceedingly rare, but the investigation of these families will aid in the delineation of the underlying mechanisms of the more common, sporadic cases. Three AML predisposition genes, RUNX1, CEBPA and GATA2, have been recognised, but the culprit genes in the majority of AML pedigrees remain obscure. We applied a combined strategy of linkage analysis and next-generation sequencing (NGS) technology in an autosomal-dominant AML Chinese family with 11 cases in four generations. A genome-wide linkage scan using a 500K SNP genotyping array was conducted to identify a previously unreported candidate region on 20p13 with a maximum multipoint heterogeneity LOD (HLOD) score of 3.56 (P=0.00005). Targeted NGS within this region and whole-exome sequencing (WES) revealed a missense mutation in TGM6 (RefSeq, NM_198994.2:c.1550T>G, p.(L517W)), which cosegregated with the phenotype in this family, and was absent in 530 healthy controls. The mutated amino acid was located in a highly conserved position, which may be deleterious and affect the activation of TGM6. Our results strongly support the candidacy of TGM6 as a novel familial AML-associated gene. PMID:24755948

  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.

  16. Genomic clustering of cyanogenic glucoside biosynthetic genes aids their identification in Lotus japonicus and suggests the repeated evolution of this chemical defence pathway.

    PubMed

    Takos, Adam M; Knudsen, Camilla; Lai, Daniela; Kannangara, Rubini; Mikkelsen, Lisbeth; Motawia, Mohammed S; Olsen, Carl E; Sato, Shusei; Tabata, Satoshi; Jørgensen, Kirsten; Møller, Birger L; Rook, Fred

    2011-10-01

    Cyanogenic glucosides are amino acid-derived defence compounds found in a large number of vascular plants. Their hydrolysis by specific β-glucosidases following tissue damage results in the release of hydrogen cyanide. The cyanogenesis deficient1 (cyd1) mutant of Lotus japonicus carries a partial deletion of the CYP79D3 gene, which encodes a cytochrome P450 enzyme that is responsible for the first step in cyanogenic glucoside biosynthesis. The genomic region surrounding CYP79D3 contains genes encoding the CYP736A2 protein and the UDP-glycosyltransferase UGT85K3. In combination with CYP79D3, these genes encode the enzymes that constitute the entire pathway for cyanogenic glucoside biosynthesis. The biosynthetic genes for cyanogenic glucoside biosynthesis are also co-localized in cassava (Manihot esculenta) and sorghum (Sorghum bicolor), but the three gene clusters show no other similarities. Although the individual enzymes encoded by the biosynthetic genes in these three plant species are related, they are not necessarily orthologous. The independent evolution of cyanogenic glucoside biosynthesis in several higher plant lineages by the repeated recruitment of members from similar gene families, such as the CYP79s, is a likely scenario.

  17. Stock assessment and management implications of horse mackerel ( Trachurus japonicus) in Korean waters, based on the relationships between recruitment and the ocean environment

    NASA Astrophysics Data System (ADS)

    Zhang, Chang Ik; Lee, Jae Bong

    This study presents an example of horse mackerel ( Trachurus japonicus) stock to demonstrate that marine environmental factors are important in stock assessment for the new Korean Total Allowable Catch (TAC)-based fisheries management system. The estimated survival rate ( S) of horse mackerel ranged from 0.25 to 0.36. The instantaneous coefficient of natural mortality ( M) was 0.48/year, and the age at first capture was 0.83 year. Annual biomass of horse mackerel in Korean waters was estimated by a biomass-based cohort analysis using annual catch in weight at age during 1965-1995. Yield-per-recruit and spawning biomass-per-recruit were estimated under various harvest strategies at Fmax, F0.1, F30% and F40%. A method for estimating acceptable biological catch (ABC) is proposed for dealing with the large differences in the quality and quantity of information and data available. Using recruitment of horse mackerel estimated from various spawner-recruitment relationship models combined with salinity, volume transport, and zooplankton biomass as environmental factors, the ABC under the best information available was estimated to range from 3100 to 3800 mt.

  18. Three members in JAK/STAT signal pathway from the sea cucumber Apostichopus japonicus: Molecular cloning, characterization and function analysis.

    PubMed

    Shao, Yina; Li, Chenghua; Zhang, Weiwei; Duan, Xuemei; Li, Ye; Han, Qingxi; Jin, Chunhua

    2015-10-01

    The JAK/STAT signal transduction pathway plays a critical role in host defense against bacterial infections. In the present study, we firstly cloned the full-length cDNAs of three molecules in JAK/STAT cascade, STAT5, FOXP and SOCS2, from sea cucumber Apostichopus japonicus (denoted as AjSTAT5, AjFOXP, AjSOCS2, respectively) and investigated their immune functions towards Vibrio splendidus infection and LPS exposure. The AjSTAT5 cDNA was composed of 2643 bp consisting of 787 amino acid residues which included protein interaction domain, STAT-α domain, DNA binding domain and SH2 domain. The putative AjFOXP contained a ZnF_C2H2 domain, the leucine zipper-like domain and FH domain, all of which were thought to be the representative characteristics of FOXP subfamily. The deduced amino acids sequence of AjSOCS2 included an SH2 domain and SOCS box domain similar to vertebrate SOCS counterparts. Phylogenetic trees further supported that all these three identified proteins belonged to novel members of JAK/STAT signal pathway in sea cucumber. Tissue specific expression analysis showed that three genes were ubiquitously expressed in all examined tissues. AjSTAT5 and AjFOXP were both dominantly expressed in intestine, tentacle and respiratory tree, and weak in muscle. In contrary, the peak expression of AjSOCS2 was observed in muscle and lowest in respiratory tree. The V. splendidus challenge and LPS exposure could both significantly up-regulate the mRNA expression of three genes, in which AjSOCS2 showed opposite expression trends to those of AjSTAT5 and AjFOXP. Silencing the AjSTAT5 by siRNA depressed the AjFOXP expression, but induced the expression level of AjSOCS2, revealing that AjSTAT5 might directly modulate AjFOXP, and AjSOCS2 function primarily by acting as a potent inhibitor involve in JAK/STAT pathway. The present study would expand our understanding on JAK/STAT signaling transduction pathway in modulating the innate immune responses of sea cucumber.

  19. First report of Kudoa species in the somatic muscle of the Japanese parrotfish Calotomus japonicus (Scaridae) and a description of Kudoa igami, n. sp. (Myxozoa: Multivalvulida).

    PubMed

    Shirakashi, Sho; Yamane, Koji; Ishitani, Hiroe; Yanagida, Tetsuya; Yokoyama, Hiroshi

    2014-07-01

    Three species of the Kudoid parasite (Myxozoa: Multivalvulida) were observed in the somatic muscle of Japanese parrotfish Calotomus japonicus caught off the coast of western Japan. All three species formed pseudocysts in myofibers and caused subclinical infections. The three Kudoa species were distinguished by spore morphology, as well as their 18S and 28S rDNA sequences. We identified a previously undescribed taxa Kudoa igami n. sp. with spores that were stellate with rounded peripheral edges and five to six polar capsules (prevalence 29.3%). Kudoa igami n. sp. were morphologically most similar to Kudoa neothunni but were distinguishable by a more rounded shape in the apical view. Molecular analyses demonstrated that the K. igami n. sp. is closely related to Kudoa thalassomi; however, the similarity in the 28S rDNA sequence was <96% and the spore morphology was different. We found Kudoa thalassomi in one sample (prevalence 2.4%), which is a new host and geographical record for this species. Kudoa lateolabracis, which causes postmortem myoliquefaction in Chinese sea bass Lateolabrax sp. and olive flounder Paralichthys olivaceus was found in Japanese parrotfish (prevalence 41.5%) for the first time, but did not cause myoliquefaction. We also expanded the host record for the brain-infecting Kudoa yasunagai (prevalence 94.1%). In addition, an unidentified microsporidia was observed in the somatic muscle (prevalence 23.3%).

  20. Lotus japonicus SUNERGOS1 encodes a predicted subunit A of a DNA topoisomerase VI that is required for nodule differentiation and accommodation of rhizobial infection

    PubMed Central

    Yoon, Hwi Joong; Hossain, Md Shakhawat; Held, Mark; Hou, Hongwei; Kehl, Marilyn; Tromas, Alexandre; Sato, Shusei; Tabata, Satoshi; Andersen, Stig Uggerhøj; Stougaard, Jens; Ross, Loretta; Szczyglowski, Krzysztof

    2014-01-01

    A symbiotic mutant of Lotus japonicus, called sunergos1-1 (suner1-1), originated from a har1-1 suppressor screen. suner1-1 supports epidermal infection by Mesorhizobium loti and initiates cell divisions for organogenesis of nodule primordia. However, these processes appear to be temporarily stalled early during symbiotic interaction, leading to a low nodule number phenotype. This defect is ephemeral and near wild-type nodule numbers are reached by suner1-1 at a later point after infection. Using an approach that combined map-based cloning and next-generation sequencing we have identified the causative mutation and show that the suner1-1 phenotype is determined by a weak recessive allele, with the corresponding wild-type SUNER1 locus encoding a predicted subunit A of a DNA topoisomerase VI. Our data suggest that at least one function of SUNER1 during symbiosis is to participate in endoreduplication, which is an essential step during normal differentiation of functional, nitrogen-fixing nodules. PMID:24661810

  1. Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level.

    PubMed

    Rodrigues, Jorge L M; Serres, Margrethe H; Tiedje, James M

    2011-08-01

    The use of comparative genomics for the study of different microbiological species has increased substantially as sequence technologies become more affordable. However, efforts to fully link a genotype to its phenotype remain limited to the development of one mutant at a time. In this study, we provided a high-throughput alternative to this limiting step by coupling comparative genomics to the use of phenotype arrays for five sequenced Shewanella strains. Positive phenotypes were obtained for 441 nutrients (C, N, P, and S sources), with N-based compounds being the most utilized for all strains. Many genes and pathways predicted by genome analyses were confirmed with the comparative phenotype assay, and three degradation pathways believed to be missing in Shewanella were confirmed as missing. A number of previously unknown gene products were predicted to be parts of pathways or to have a function, expanding the number of gene targets for future genetic analyses. Ecologically, the comparative high-throughput phenotype analysis provided insights into niche specialization among the five different strains. For example, Shewanella amazonensis strain SB2B, isolated from the Amazon River delta, was capable of utilizing 60 C compounds, whereas Shewanella sp. strain W3-18-1, isolated from deep marine sediment, utilized only 25 of them. In spite of the large number of nutrient sources yielding positive results, our study indicated that except for the N sources, they were not sufficiently informative to predict growth phenotypes from increasing evolutionary distances. Our results indicate the importance of phenotypic evaluation for confirming genome predictions. This strategy will accelerate the functional discovery of genes and provide an ecological framework for microbial genome sequencing projects.

  2. Large-Scale Gene Disruption in Magnaporthe oryzae Identifies MC69, a Secreted Protein Required for Infection by Monocot and Dicot Fungal Pathogens

    PubMed Central

    Saitoh, Hiromasa; Fujisawa, Shizuko; Mitsuoka, Chikako; Ito, Akiko; Hirabuchi, Akiko; Ikeda, Kyoko; Irieda, Hiroki; Yoshino, Kae; Yoshida, Kentaro; Matsumura, Hideo; Tosa, Yukio; Win, Joe; Kamoun, Sophien; Takano, Yoshitaka; Terauchi, Ryohei

    2012-01-01

    To search for virulence effector genes of the rice blast fungus, Magnaporthe oryzae, we carried out a large-scale targeted disruption of genes for 78 putative secreted proteins that are expressed during the early stages of infection of M. oryzae. Disruption of the majority of genes did not affect growth, conidiation, or pathogenicity of M. oryzae. One exception was the gene MC69. The mc69 mutant showed a severe reduction in blast symptoms on rice and barley, indicating the importance of MC69 for pathogenicity of M. oryzae. The mc69 mutant did not exhibit changes in saprophytic growth and conidiation. Microscopic analysis of infection behavior in the mc69 mutant revealed that MC69 is dispensable for appressorium formation. However, mc69 mutant failed to develop invasive hyphae after appressorium formation in rice leaf sheath, indicating a critical role of MC69 in interaction with host plants. MC69 encodes a hypothetical 54 amino acids protein with a signal peptide. Live-cell imaging suggested that fluorescently labeled MC69 was not translocated into rice cytoplasm. Site-directed mutagenesis of two conserved cysteine residues (Cys36 and Cys46) in the mature MC69 impaired function of MC69 without affecting its secretion, suggesting the importance of the disulfide bond in MC69 pathogenicity function. Furthermore, deletion of the MC69 orthologous gene reduced pathogenicity of the cucumber anthracnose fungus Colletotrichum orbiculare on both cucumber and Nicotiana benthamiana leaves. We conclude that MC69 is a secreted pathogenicity protein commonly required for infection of two different plant pathogenic fungi, M. oryzae and C. orbiculare pathogenic on monocot and dicot plants, respectively. PMID:22589729

  3. A large survey among European trainees in clinical microbiology and infectious disease on training systems and training adequacy: identifying the gaps and suggesting improvements.

    PubMed

    Yusuf, E; Ong, D S Y; Martin-Quiros, A; Skevaki, C; Cortez, J; Dedić, K; Maraolo, A E; Dušek, D; Maver, P J; Sanguinetti, M; Tacconelli, E

    2017-02-01

    The purpose of this investigation was to perform a survey among European clinical microbiology (CM) and infectious disease (ID) trainees on training satisfaction, training tools, and competency assessment. An online, anonymous survey in the English language was carried out between April and July 2015. There were 25 questions: seven in a 5-point Likert scale (1: worst scenario, 5: best scenario) and the remainder as closed multiple-choice questions in five areas (satisfaction, adequacy, system, mentorship, and evaluation of training). Included were 419 respondents (215 CM, 159 ID, and 45 combined CM/ID) from 31 European countries [mean age (standard deviation) 32.4 (5.3) years, 65.9 % women]. Regarding satisfaction on the training scheme, CM and ID scored 3.6 (0.9) and 3.2 (1.0), respectively. These scores varied between countries, ranging from 2.5 (1.0) for Italian ID to 4.3 (0.8) for Danish CM trainees. The majority of respondents considered training in management and health economics inadequate and e-learning and continuing medical education programs insufficient. Many trainees (65.3 % of CM and 62.9 % of ID) would like to have more opportunities to spend a part of their training abroad and expected their mentor to be more involved in helping with future career plans (63.5 % of CM and 53.4 % of ID) and practical skills (53.0 % of CM and 61.2 % of ID). Two-thirds of the respondents across the specialties agreed that a European exam should be developed, but half of them thought it should not be made mandatory. This survey shows high heterogeneity in training conditions in European countries, identifies perceived gaps in training, and suggests areas for improvements.

  4. Unprecedented Melioidosis Cases in Northern Australia Caused by an Asian Burkholderia pseudomallei Strain Identified by Using Large-Scale Comparative Genomics.

    PubMed

    Price, Erin P; Sarovich, Derek S; Smith, Emma J; MacHunter, Barbara; Harrington, Glenda; Theobald, Vanessa; Hall, Carina M; Hornstra, Heidie M; McRobb, Evan; Podin, Yuwana; Mayo, Mark; Sahl, Jason W; Wagner, David M; Keim, Paul; Kaestli, Mirjam; Currie, Bart J

    2015-11-25

    Melioidosis is a disease of humans and animals that is caused by the saprophytic bacterium Burkholderia pseudomallei. Once thought to be confined to certain locations, the known presence of B. pseudomallei is expanding as more regions of endemicity are uncovered. There is no vaccine for melioidosis, and even with antibiotic administration, the mortality rate is as high as 40% in some regions that are endemic for the infection. Despite high levels of recombination, phylogenetic reconstruction of B. pseudomallei populations using whole-genome sequencing (WGS) has revealed surprisingly robust biogeographic separation between isolates from Australia and Asia. To date, there have been no confirmed autochthonous melioidosis cases in Australia caused by an Asian isolate; likewise, no autochthonous cases in Asia have been identified as Australian in origin. Here, we used comparative genomic analysis of 455 B. pseudomallei genomes to confirm the unprecedented presence of an Asian clone, sequence type 562 (ST-562), in Darwin, northern Australia. First observed in Darwin in 2005, the incidence of melioidosis cases attributable to ST-562 infection has steadily risen, and it is now a common strain in Darwin. Intriguingly, the Australian ST-562 appears to be geographically restricted to a single locale and is genetically less diverse than other common STs from this region, indicating a recent introduction of this clone into northern Australia. Detailed genomic and epidemiological investigations of new clinical and environmental B. pseudomallei isolates in the Darwin region and ST-562 isolates from Asia will be critical for understanding the origin, distribution, and dissemination of this emerging clone in northern Australia.

  5. A large multi-ethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences

    PubMed Central

    Hoffmann, Thomas J.; Van Den Eeden, Stephen K.; Sakoda, Lori C.; Jorgenson, Eric; Habel, Laurel A.; Graff, Rebecca E.; Passarelli, Michael N.; Cario, Clinton L.; Emami, Nima C.; Chao, Chun R.; Ghai, Nirupa R.; Shan, Jun; Ranatunga, Dilrini K.; Quesenberry, Charles P.; Aaronson, David; Presti, Joseph; Zhaoming, Wang; Berndt, Sonja I.; Chanock, Stephen J.; McDonnell, Shannon K.; French, Amy J; Schaid, Daniel J; Thibodeau, Stephen N.; Li, Qiyuan; Freedman, Matthew L.; Penney, Kathryn L.; Mucci, Lorelei A.; Haiman, Christopher A.; Henderson, Brian E.; Seminara, Daniela; Kvale, Mark N.; Kwok, Pui-Yan; Schaefer, Catherine; Risch, Neil; Witte, John S.

    2015-01-01

    A genome-wide association study of prostate cancer in Kaiser Permanente health plan members (7,783 cases, 38,595 controls; 80.3% non-Hispanic white, 4.9% African-American, 7.0% East Asian, 7.8% Latino) revealed a new independent risk indel rs4646284 at the previously-identified locus 6q25.3 that replicated in PEGASUS (N=7,539) and MEC (N=4,679) (p=1.0×10−19, OR=1.18). Across the 6q25.3 locus, rs4646284 exhibited the strongest association with expression of SLC22A1 (p=1.3×10−23) and SLC22A3 (p=3.2×10−52). At the known 19q13.33 locus rs2659124 (p=1.3×10−13, OR=1.18) nominally replicated in PEGASUS. A risk score of 105 known risk SNPs was strongly associated with prostate cancer (p<1.0×10−8). Comparing the highest to lowest risk score deciles, the OR was 6.22 for non-Hispanic Whites, 5.82 for Latinos, 3.77 for African-Americans, and 3.38 for East Asians. In non-Hispanic whites, the 105 risk SNPs explained ~7.6% of disease heritability. The entire GWAS array explained ~33.4% of heritability, with a 4.3-fold enrichment within DNaseI hypersensitivity sites (p=0.004). PMID:26034056

  6. Unprecedented Melioidosis Cases in Northern Australia Caused by an Asian Burkholderia pseudomallei Strain Identified by Using Large-Scale Comparative Genomics

    PubMed Central

    Smith, Emma J.; MacHunter, Barbara; Harrington, Glenda; Theobald, Vanessa; Hall, Carina M.; Hornstra, Heidie M.; McRobb, Evan; Podin, Yuwana; Mayo, Mark; Sahl, Jason W.; Wagner, David M.; Keim, Paul; Kaestli, Mirjam; Currie, Bart J.

    2015-01-01

    Melioidosis is a disease of humans and animals that is caused by the saprophytic bacterium Burkholderia pseudomallei. Once thought to be confined to certain locations, the known presence of B. pseudomallei is expanding as more regions of endemicity are uncovered. There is no vaccine for melioidosis, and even with antibiotic administration, the mortality rate is as high as 40% in some regions that are endemic for the infection. Despite high levels of recombination, phylogenetic reconstruction of B. pseudomallei populations using whole-genome sequencing (WGS) has revealed surprisingly robust biogeographic separation between isolates from Australia and Asia. To date, there have been no confirmed autochthonous melioidosis cases in Australia caused by an Asian isolate; likewise, no autochthonous cases in Asia have been identified as Australian in origin. Here, we used comparative genomic analysis of 455 B. pseudomallei genomes to confirm the unprecedented presence of an Asian clone, sequence type 562 (ST-562), in Darwin, northern Australia. First observed in Darwin in 2005, the incidence of melioidosis cases attributable to ST-562 infection has steadily risen, and it is now a common strain in Darwin. Intriguingly, the Australian ST-562 appears to be geographically restricted to a single locale and is genetically less diverse than other common STs from this region, indicating a recent introduction of this clone into northern Australia. Detailed genomic and epidemiological investigations of new clinical and environmental B. pseudomallei isolates in the Darwin region and ST-562 isolates from Asia will be critical for understanding the origin, distribution, and dissemination of this emerging clone in northern Australia. PMID:26607593

  7. Transcriptome analysis of acetic-acid-treated yeast cells identifies a large set of genes whose overexpression or deletion enhances acetic acid tolerance.

    PubMed

    Lee, Yeji; Nasution, Olviyani; Choi, Eunyong; Choi, In-Geol; Kim, Wankee; Choi, Wonja

    2015-08-01

    Acetic acid inhibits the metabolic activities of Saccharomyces cerevisiae. Therefore, a better understanding of how S. cerevisiae cells acquire the tolerance to acetic acid is of importance to develop robust yeast strains to be used in industry. To do this, we examined the transcriptional changes that occur at 12 h post-exposure to acetic acid, revealing that 56 and 58 genes were upregulated and downregulated, respectively. Functional categorization of them revealed that 22 protein synthesis genes and 14 stress response genes constituted the largest portion of the upregulated and downregulated genes, respectively. To evaluate the association of the regulated genes with acetic acid tolerance, 3 upregulated genes (DBP2, ASC1, and GND1) were selected among 34 non-protein synthesis genes, and 54 viable mutants individually deleted for the downregulated genes were retrieved from the non-essential haploid deletion library. Strains overexpressing ASC1 and GND1 displayed enhanced tolerance to acetic acid, whereas a strain overexpressing DBP2 was sensitive. Fifty of 54 deletion mutants displayed enhanced acetic acid tolerance. Three chosen deletion mutants (hsps82Δ, ato2Δ, and ssa3Δ) were also tolerant to benzoic acid but not propionic and sorbic acids. Moreover, all those five (two overexpressing and three deleted) strains were more efficient in proton efflux and lower in membrane permeability and internal hydrogen peroxide content than controls. Individually or in combination, those physiological changes are likely to contribute at least in part to enhanced acetic acid tolerance. Overall, information of our transcriptional profile was very useful to identify molecular factors associated with acetic acid tolerance.

  8. 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

  9. Local and scientific knowledge for assessing the use of fallows and mature forest by large mammals in SE Brazil: identifying singularities in folkecology

    PubMed Central

    2014-01-01

    Background Local ecological knowledge (LEK) has been discussed in terms of its similarities to and its potential to complement normative scientific knowledge. In this study, we compared the knowledge of a Brazilian quilombola population regarding the habitat use and life habits of large mammals with in situ recordings of the species. We also tested the hypothesis that quilombola LEK has a special focus on the anthropogenic portion of the landscape. Methods The habitats investigated were anthropogenic secondary forests and mature forests in the southeastern Atlantic coast of Brazil. We conducted the faunal survey using the camera-trap method. The sampling effort consisted of deploying 1,217 cameras/day in the mature forests and 1,189 cameras/day in the secondary forests. Statistical comparisons regarding the habitat use of the species were based on the randomization procedure. We interviewed 36 men who were more than 40 years old in the three communities studied. Informal, semi-structured and structured interviews were used. Two variables were considered in the LEK analyses: level of internal agreement and level of convergence with the scientific data. Results The camera trap sampling resulted in a total of 981 records. Animals such as opossums, tayras, armadillos and deer showed a non-selective pattern in the use of habitats. In contrast, the coati was more common in mature forests. We found that nearly 40% of the interviewees’ responses converged with the scientific data on the use of habitats. However, the LEK on the species’ life habits was highly convergent with the scientific data. The hypothesis that secondary forests would have a greater relevance for local knowledge was validated for four of the five analyzed species. Conclusions We suggest two principal considerations of ecological and ethnoecological interest: (1) In the Atlantic Forest of the Ribeira Valley, the secondary forests resulting from shifting cultivation were as attractive to the species

  10. 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.

  11. Edible mushroom (Flammulina velutipes) extract inhibits melanosis in Kuruma shrimp (Marsupenaeus japonicus).

    PubMed

    Encarnacion, Angel B; Fagutao, Fernand; Hirayama, Jinto; Terayama, Makoto; Hirono, Ikuo; Ohshima, Toshiaki

    2011-01-01

    This study compared the potential of an aqueous extract of an edible mushroom (Flammulina velutipes) to prevent melanosis in cultured Kuruma shrimp (Marsupenaeus japonicus) with other antimelanosic compounds in vivo. The mushroom extract contained 9.1 mg/mL ergothioneine (ESH). Immersion of live full-grown shrimp in a 0.5% w/v solution of mushroom extract significantly reduced PPO activity in shrimp hemolymph. In addition, expression of the prophenoloxidase (proPO) gene decreased in hemocytes, suggesting that the extract blocked the activation of the proPO cascade. Consequently, the development of melanosis in the treated shrimp was significantly suppressed during ice storage. Treatment with a 0.05% w/v solution of sodium ascorbate and 4-hexyl-1,3-benzenediol had the same effect. In vitro experiments showed that ESH effectively inhibited PPO activity and activation of the proPO cascade in hemocyte lysate supernatant. This study suggests that in vivo application of F. velutipes mushroom extract is an effective natural alternative to synthetic antimelanosic agents to inhibit postmortem melanosis in shrimp. Practical Application: The extract of an edible mushroom (F. velutipes) containing ergothioneine can be a promising natural alternative to synthetic antimelanosic agents used to prevent postharvest melanosis in shrimp and other crustaceans. Furthermore, utilization of the mushroom trimmings could also help address the growing concerns on the disposal of such agricultural wastes and instead use it into a novel purpose as a source of antimelanosic and antioxidants for food and industrial application.

  12. 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.

  13. 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.

  14. Ultrastructure of putative germ granules in the penaeid shrimp Marsupenaeus japonicus.

    PubMed

    Grattan, R M; McCulloch, R J; Sellars, M J; Hertzler, P L

    2013-03-01

    Knowledge about the specification of the germ line in penaeid shrimp would allow development of techniques to control germ cell formation and/or fate to produce reproductively sterile shrimp for genetic copyright purposes. Recent studies have traced the localization of an RNA-enriched intracellular body (ICB) in the putative germ line of four penaeid shrimp species. It is hypothesized that the ICB may serve as a putative germ granule and marker of germ line fate. In this study semi-thin and ultra-thin sections of Marsupenaeus japonicus embryos were prepared, and the dimensions and ultrastructure of the ICB was examined at different stages of embryogenesis. The ICB was an aggregation of electron dense granules, small vesicles and multi-vesicular bodies (MVBs), similar to germ granules from other species. Lamellar membranes and mitochondria were localized at the periphery of the ICB. Using fluorescence microscopy, microtubules were also observed between the centrosome and the ICB. The localization of the ICB in the D lineage and putative germ cell line, the enrichment of RNA in the ICB, and the ultrastructural similarities to other germ granules characterized in this study support the hypothesis that the ICB contains germ granules.

  15. 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.

  16. 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.

  17. Stress responses to rapid temperature changes of the juvenile sea cucumber ( Apostichopus japonicus Selenka)

    NASA Astrophysics Data System (ADS)

    Yunwei, Dong; Tingting, Ji; Shuanglin, Dong

    2007-07-01

    Activities of hexokinase (HK), pyruvate kinase (PK), superoxide dismutase (SOD) and catalase (CAT) and Hsp70 level were measured to evaluate the response of the commercially important sea cucumber ( Apostichopus japonicus Selenka) to rapid temperature changes in laboratory. Animals were subjected to a higher temperature (from 10 to 20°C) (Tinc treatment) or to a lower temperature (from 20 to 10°C) (Tdec treatment) for 72h. At 1, 3, 12, 24, 72h of exposure, animals were removed and prepared for further analysis. Results showed that the effect of acute temperature changes on enzyme activities was significant. In Tinc treatment, activities of SOD and CAT increased immediately. The significant enhancement of SOD and CAT activities suggested that oxidative stress increases significantly when ambient temperature increasing from 10 to 20°C. The up-regulation of Hsp70 in Tinc and Tdec treatments indicated that Hsp70 was a bioindicator of thermal stress in the sea cucumber, and the expression pattern depended on the thermal treatment.

  18. Effect of Phragmites japonicus harvest frequency and timing on dry matter yield and nutritive value.

    PubMed

    Tanaka, Takashi S T; Irbis, Chagan; Kumagai, Hajime; Wang, Pengyun; Li, Kunzhi; Inamura, Tatsuya

    2017-02-01

    Phragmites is a cosmopolitan perennial emergent macrophyte that is distributed worldwide. In recent years, Phragmites has attracted attention for its potential use as roughage. Given the increasing demand for feed and the number of constructed wetlands (CWs) vegetated with Phragmites, Phragmites is expected to play an important role in roughage production. Thus, it is vital to understand the effects of harvest timing and frequency on dry matter yield, nutritive value, and nitrogen (N) removal to establish appropriate vegetation management. In two CWs in Southwest China, four treatments with different harvesting frequencies were evaluated in monospecific areas of P. japonicus. The four treatments included no harvest, single harvest at 6 months, two harvests at 2 and 4 months, and three harvests at 2, 4, and 6 months. A sharp decline in the total digestible nutrients (TDN) concentration and the rate of increase in dry matter (DM) yield was associated with the heading timings, and the seasonal variations in TDN were likely influenced by carbohydrate accumulation in the stems. The three harvest treatment contributed to substantially improve the N and DM yields without decreasing the nutritive value but negatively affected the growth in the following year. Therefore, not only the combinations of harvest timing and frequency but also other management practices, including partial harvesting, may be needed to optimize CW performance and roughage production.

  19. 58-F, a flavanone from Ophiopogon japonicus, prevents hepatocyte death by decreasing lysosomal membrane permeability

    PubMed Central

    Yan, Xiaofeng; Ye, Tingjie; Hu, Xudong; Zhao, Pei; Wang, Xiaoling

    2016-01-01

    Lysosome membrane permeabilization (LMP) has been implicated in cell death. In the present study, we investigated the relationship between cell death and H2O2-/CCl4-induced LMP in hepatocytes in vitro and following acute liver injury in vivo. The key finding was that H2O2 triggered LMP by oxidative stress, as evidenced by a suppression of LAMP1 expression, a reduction in LysoTracker Green and AO staining, and the leakage of proton and cathepsin B/D from the lysosome to the cytoplasm, resulting in cell death. CCl4 also triggered hepatocyte death by decreasing lysosome LAMP1 expression and by inducing the accumulation of products of peroxidative lipids and oxidized proteins. Furthermore, a novel compound 5,8-dimethoxy-6-methyl-7-hydroxy-3-3(2-hydroxy-4-methoxybenzyl) chroman-4-one (58-F) was extracted from Ophiopogon japonicus and served as a potential therapeutic drug. In vivo and in vitro results showed that 58-F effectively rescued hepatocytes by decreasing LMP and by inducing lysosomal enzyme translocation to the cytosol. PMID:27306715

  20. 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 Vmax 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

  1. Influence of sulfation on anti-myocardial ischemic activity of Ophiopogon japonicus polysaccharide.

    PubMed

    Zheng, Qin; Feng, Yi; Xu, De-Sheng; Lin, Xiao; Chen, Yan-Zuo

    2009-01-01

    Ophiopogon japonicus polysaccharide (FOJ-5) from Radix ophiopogonis has shown anti-myocardial ischemic action in vitro and in vivo in our previous studies. In order to clarify the influence of chemical modifications on the action, a series of sulfated FOJ-5 (FOJ-5-S) with different substitution degrees were prepared and the anti-myocardial ischemic action of the natural FOJ-5 and the FOJ-5-S were studied in vitro and in vivo. Langendorff isolated rat hearts and acute myocardial ischemic rats induced by isoprenaline were employed as myocardial ischemic models in our experiments. The amplitude and frequency of cardiac contraction, coronary blood flow at different time points after ischemia/reperfusion were measured in vitro. The ST segment shift in electrocardiogram and lactate dehydrogenase level in blood plasma were observed on the in vivo model. The results indicated that FOJ-5 and FOJ-5-S had the anti-myocardial ischemic action compared with non-treated vehicle groups. Furthermore, it was found that FOJ-5-S had significant action on the in vivo model compared with FOJ-5 (P < 0.05). And the obtained results from the further study also indicated that only when the degree of substitution was in a certain range, the FOJ-5-S had excellent anti-myocardial ischemic activity.

  2. 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.

  3. [Seasonal variation of functional diversity of aquatic microbial community in Apostichopus japonicus cultural pond].

    PubMed

    Yan, Fa-Jun; Tian, Xiang-Li; Dong, Shuang-Lin; Yang, Gang

    2014-05-01

    The functional diversity of aquatic microbial communities in sea cucumber (Apostichopus japonicus) cultural ponds was examined in this paper. The Biolog plate technique and redundancy analysis (RDA) method were used to evaluate seasonal changes and their relationships with environmental factors. The results showed that both total amount and types of carbon sources utilized by microbes in the sea cucumber cultural ponds varied seasonally, and were the highest in summer and lowest in winter, with polymers being the main type of carbon sources. Principal component analysis revealed that the carbon utilization diversity of the microbial communities varied significantly over the seasonal courses. A total of 10 categories of carbon sources were significantly related to the principal component 1, among which were polymers, carbohydrates, carboxylic acids, amino acids, and amines. Significant seasonal changes were detected for all carbon utilization diversity indices of the microbial communities, including Shannon, McIntosh, Simpson, and S-E. However, seasonal variations were different among the microbial diversity indices. RDA analysis revealed that TP, NO(3-)-N, TN, and PO4(3-)-P were the critical environmental factors influencing the seasonal changes in functional diversity of aquatic microbial community in sea cucumber cultural ponds.

  4. Recovery and properties of a fructooligosaccharides-producing beta-fructofuranosidase from Aspergillus japonicus CCRC 38011.

    PubMed

    Su, Y C; Sheu, C S

    1993-04-01

    The fungus (Aspergillus japonicus CCRC 38011) was found to be able to produce beta-fructofuranosidase with high transfructosylating activity (Ut), a key enzyme involved in synthesis of fructooligosaccharides from sucrose. The Ut productivities of this microorganism were 191.5 units/ml broth in a 6-L jar-fermentor and 256.1 units/ml broth in a 1000-L pilot-fermentor in a modified medium containing 8% sucrose as a carbon source. Most of the Ut of this microorganism was found to be bound with mycelia. Incubation and sonication treatment extracted this enzyme from mycelia with maximum efficiencies of 66.3% and 44.3%, respectively. On the other hand, homogenization and freeze-thawing treatment had only a small effect on enzyme extraction. The soluble enzyme extracted from mycelia by incubation at pH 5.0 and 40 degrees C for 3 hours could be easily recovered and purified by acetone precipitation. The recovery of Ut from the crude enzyme solution was 99.5% by mixing the solution with an equal volume of acetone at 4 degrees C, followed by centrifugation. The purification factor of acetone precipitation was 15.8. The optimum pH and temperature of Ut was 5.0 and 65-70 degrees C, respectively. The enzyme was stable at a pH between 4.0 and 5.0 and at a temperature below 60 degrees C.

  5. 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.

  6. 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.

  7. 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.

  8. The hydraulic mechanism in the hind wing veins of Cybister japonicus Sharp (order: Coleoptera).

    PubMed

    Sun, Jiyu; Wu, Wei; Ling, Mingze; Bhushan, Bharat; Tong, Jin

    2016-01-01

    The diving beetles (Dytiscidae, Coleoptera) are families of water beetles. When they see light, they fly to the light source directly from the water. Their hind wings are thin and fragile under the protection of their elytra (forewings). When the beetle is at rest the hind wings are folded over the abdomen of the beetle and when in flight they unfold to provide the necessary aerodynamic forces. In this paper, the unfolding process of the hind wing of Cybister japonicus Sharp (order: Coleoptera) was investigated. The motion characteristics of the blood in the veins of the structure system show that the veins have microfluidic control over the hydraulic mechanism of the unfolding process. A model is established, and the hind wing extending process is simulated. The blood flow and pressure changes are discussed. The driving mechanism for hydraulic control of the folding and unfolding actions of beetle hind wings is put forward. This can assist the design of new deployable micro air vehicles and bioinspired deployable systems.

  9. The hydraulic mechanism in the hind wing veins of Cybister japonicus Sharp (order: Coleoptera)

    PubMed Central

    Wu, Wei; Ling, Mingze; Tong, Jin

    2016-01-01

    Summary The diving beetles (Dytiscidae, Coleoptera) are families of water beetles. When they see light, they fly to the light source directly from the water. Their hind wings are thin and fragile under the protection of their elytra (forewings). When the beetle is at rest the hind wings are folded over the abdomen of the beetle and when in flight they unfold to provide the necessary aerodynamic forces. In this paper, the unfolding process of the hind wing of Cybister japonicus Sharp (order: Coleoptera) was investigated. The motion characteristics of the blood in the veins of the structure system show that the veins have microfluidic control over the hydraulic mechanism of the unfolding process. A model is established, and the hind wing extending process is simulated. The blood flow and pressure changes are discussed. The driving mechanism for hydraulic control of the folding and unfolding actions of beetle hind wings is put forward. This can assist the design of new deployable micro air vehicles and bioinspired deployable systems. PMID:27547607

  10. A novel ABA insensitive mutant of Lotus japonicus with a wilty phenotype displays unaltered nodulation regulation.

    PubMed

    Biswas, Bandana; Chan, Pick Kuen; Gresshoff, Peter M

    2009-05-01

    An ABA insensitive mutant, Beyma, was isolated in Lotus japonicus MG-20 from an EMS mutagenesis population using root growth inhibition to applied ABA as the screening criterion. (The name 'Beyma' was taken from the Australian Aboriginal language, Wagiman, beyma, meaning 'drying up'.) The stable mutant that segregates as a dominant Mendelian mutation is insensitive to ABA induced inhibition of germination, vegetative growth, stomatal opening, as well as nodulation. Tissue ABA levels were normal, suggesting a sensitivity rather than biosynthesis mutation. It is slow-growing (50-70% of wild-type MG-20) and has a near-constitutive wilty phenotype associated with its inability to regulate stomatal opening. Whilst showing a wide range of ABA insensitive phenotypes, Beyma did not show alteration of nodule number control, as, in the absence of added ABA, the number and patterning (but not size) of nodules formed in the mutant were similar to that of MG-20. Split root experiments on MG-20 showed that application of ABA on one side of the root inhibited nodulation locally but not systemically. We propose that ABA is not involved directly in systemic autoregulation of nodulation (AON).

  11. Lotus japonicus symRK-14 uncouples the cortical and epidermal symbiotic program.

    PubMed

    Kosuta, Sonja; Held, Mark; Hossain, Md Shakhawat; Morieri, Giulia; Macgillivary, Amanda; Johansen, Christopher; Antolín-Llovera, Meritxell; Parniske, Martin; Oldroyd, Giles E D; Downie, Allan J; Karas, Bogumil; Szczyglowski, Krzysztof

    2011-09-01

    SYMRK is a leucine-rich-repeat (LRR)-receptor kinase that mediates intracellular symbioses of legumes with rhizobia and arbuscular mycorrhizal fungi. It participates in signalling events that lead to epidermal calcium spiking, an early cellular response that is typically considered as central for intracellular accommodation and nodule organogenesis. Here, we describe the Lotus japonicus symRK-14 mutation that alters a conserved GDPC amino-acid sequence in the SYMRK extracellular domain. Normal infection of the epidermis by fungal or bacterial symbionts was aborted in symRK-14. Likewise, epidermal responses of symRK-14 to bacterial signalling, including calcium spiking, NIN gene expression and infection thread formation, were significantly reduced. In contrast, no major negative effects on the formation of nodule primordia and cortical infection were detected. Cumulatively, our data show that the symRK-14 mutation uncouples the epidermal and cortical symbiotic program, while indicating that the SYMRK extracellular domain participates in transduction of non-equivalent signalling events. The GDPC sequence was found to be highly conserved in LRR-receptor kinases in legumes and non-legumes, including the evolutionarily distant bryophytes. Conservation of the GDPC sequence in nearly one-fourth of LRR-receptor-like kinases in the genome of Arabidopsis thaliana suggests, however, that this sequence might also play an important non-symbiotic function in this plant.

  12. Gonadal development and gonadotropin gene expression during puberty in cultured chub mackerel (Scomber japonicus).

    PubMed

    Nyuji, Mitsuo; Kodama, Ryoko; Kato, Keitaro; Yamamoto, Shinji; Yamaguchi, Akihiko; Matsuyama, Michiya

    2014-06-01

    Understanding puberty is important for establishing aquaculture in fish. In this study, we analyzed the timing and completion of pubertal development along with changes in pituitary gonadotropin genes (fshb and lhb) in cultured chub mackerel (Scomber japonicus). At 45 days post-hatching (dph), gonadal sex differentiation was observed. The onset of puberty occurred at 192 dph in females with the start of vitellogenesis, whereas it occurred at 164 dph in males, with the beginning of spermatogenesis (proliferation and differentiation of germ cells). The completion of puberty was at 326 dph in females when vitellogenesis completed, and it was at 338 dph in males during spermiation. All fish sampled during the spawning season completed pubertal development. In the pituitary of female fish, fshb expression was activated during early secondary growth and was maintained high throughout vitellogenesis, whereas lhb expression was highest at the completion of vitellogenesis. In male fish, fshb and lhb expression were activated from the onset of spermatogenesis and further activated during late pubertal development; fshb remained high between late spermatogenesis and spermiation, whereas lhb was highest during spermiation.

  13. Exposure to Deepwater Horizon weathered crude oil increases routine metabolic demand in chub mackerel, Scomber japonicus.

    PubMed

    Klinger, Dane H; Dale, Jonathan J; Machado, Benjamin E; Incardona, John P; Farwell, Charles J; Block, Barbara A

    2015-09-15

    During the 2010 Deepwater Horizon incident, the continuous release of crude oil from the damaged Macondo 252 wellhead on the ocean floor contaminated surface water habitats for pelagic fish for more than 12weeks. The spill occurred across pelagic, neritic and benthic waters, impacting a variety of ecosystems. Chemical components of crude oil are known to disrupt cardiac function in juvenile fish, and here we investigate the effects of oil on the routine metabolic rate of chub mackerel, Scomber japonicus. Mackerel were exposed to artificially weathered Macondo 252 crude oil, prepared as a Water Accommodated Fraction (WAF), for 72 or 96h. Routine metabolic rates were determined pre- and post-exposure using an intermittent-flow, swim tunnel respirometer. Routine energetic demand increased in all mackerels in response to crude oil and reached statistical significance relative to unexposed controls at 96h. Chemical analyses of bile from exposed fish revealed elevated levels of fluorescent metabolites, confirming the bioavailability of polycyclic aromatic hydrocarbons (PAHs) in the exposure WAF. The observed increase in metabolic demand is likely attributable to the bioenergetic costs of contaminant detoxification. These results indicate that short-term exposure (i.e. days) to oil has sub-lethal toxicity to mackerel and results in physiological stress during the active spill phase of the incident.

  14. 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.

  15. Early Lotus japonicus root transcriptomic responses to symbiotic and pathogenic fungal exudates

    PubMed Central

    Giovannetti, Marco; Mari, Alfredo; Novero, Mara; Bonfante, Paola

    2015-01-01

    The objective of this study is to evaluate Lotus japonicus transcriptomic responses to arbuscular mycorrhizal (AM) germinated spore exudates (GSEs), responsible for activating nuclear Ca2+ spiking in plant root epidermis. A microarray experiment was performed comparing gene expression in Lotus rootlets treated with GSE or water after 24 and 48 h. The transcriptional pattern of selected genes that resulted to be regulated in the array was further evaluated upon different treatments and timings. In particular, Lotus rootlets were treated with: GSE from the pathogenic fungus Colletotrichum trifolii; short chitin oligomers (COs; acknowledged AM fungal signals) and long COs (as activators of pathogenic responses). This experimental set up has revealed that AM GSE generates a strong transcriptomic response in Lotus roots with an extensive defense-related response after 24 h and a subsequent down-regulation after 48 h. A similar subset of defense-related genes resulted to be up-regulated also upon treatment with C. trifolii GSE, although with an opposite trend. Surprisingly, long COs activated both defense-like and symbiosis-related genes. Among the genes regulated in the microarray, promoter-GUS assay showed that LjMATE1 activates in epidermal cells and root hairs. PMID:26175746

  16. 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

  17. Assessing the identity and expression level of the cytochrome P450 20A1 (CYP20A1) gene in the BPA-, BDE-47, and WAF-exposed copepods Tigriopus japonicus and Paracyclopina nana.

    PubMed

    Han, Jeonghoon; Kim, Duck-Hyun; Seo, Jung Soo; Kim, Il-Chan; Nelson, David R; Puthumana, Jayesh; Lee, Jae-Seong

    2017-03-01

    CYP20A1 is a member of the cytochrome P450 (CYP) superfamily, identified as an orphan P450 without any assigned biological function; hence, its continued status as an "orphan" gene. In order to address this shortcoming in our understanding of this superfamily, we sought to characterize the CYP20A1 gene in the copepods Tigriopus japonicus (Tj-CYP20A1) and Paracyclopina nana (Pn-CYP20A1) at their mRNA transcriptional level. We assessed the response of this gene's expression in various developmental stages and in response to treatment with bisphenol A (BPA), 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47), and water accommodated fractions (WAFs) of crude oil. As shown in the vertebrate CYP20A1, both Tj-CYP20A1 and Pn-CYP20A1 contained characteristic conserved motifs and domain regions (I helix, K helix and heme-binding motifs) with unusual amino acid sequences apparent in their gene structure. Also molecular characterization of the putative responsive elements in the promoter regions was performed. We observed transcriptional up-regulation of these genes during post-embryonic developmental stages including sex-specific up-regulation in adults. In addition, concentration- and time-dependent mRNA transcripts in response to xenobiotics (BPA, BDE-47, and WAFs) were seen. This study focuses on the molecular elucidation of CYP20A1 genes and their interactions with xenobiotics in the copepods T. japonicus and P. nana that provides important insight into the biological importance of CYP20A1 in invertebrates.

  18. Ochratoxigenic Black Species of Aspergilli in Grape Fruits of Northern Italy Identified by an Improved PCR-RFLP Procedure

    PubMed Central

    Spadaro, Davide; Patharajan, Subban; Lorè, Alessia; Garibaldi, Angelo; Gullino, Maria Lodovica

    2012-01-01

    A collection of 356 isolates of Aspergillus spp. collected during 2006 and 2007 from grapevines in northern Italy were identified through Internal Transcribed Spacer based Restriction Fragment Length Polymorphism (ITS-RFLP) and tested for ochratoxin A (OTA) production. Restriction endonuclease digestion of the ITS products using the endonucleases HhaI, HinfI and RsaI, distinguished five different RFLPs. From each pattern, three samples were sequenced and the nucleotide sequences showed different species corresponding to Aspergillus niger, A. carbonarius, A. tubingensis, A. japonicus and A. aculeatus. By comparing the sequences of the ITS regions, also the uniseriate species A. japonicus and A. aculeatus could be differentiated by HinfI digestion of the ITS products. Among the aspergilli, A. niger was the major species associated with grapes during 2006 (57.4%), while A. carbonarius was the major species during 2007 (46.6%). All the strains of Aspergillus were tested for their ability to produce OTA on Yeast extract sucrose medium (YES), as it was tested as an optimal substrate for the evaluation of OTA production by black aspergilli. Out of 356 isolates, 63 (17.7%) isolates produced OTA ranging from 0.05 to 3.0 µg mL−1. Most of the ochratoxigenic isolates were A. carbonarius (46) in both years, but also some strains of A. tubingensis (11) and A. japonicus (6) produced lower amounts of OTA. PMID:22474565

  19. 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.

  20. 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.

  1. Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): gene rearrangement and phylogeny within Caridea.

    PubMed

    Shen, Xin; Li, Xiao; Sha, Zhongli; Yan, Binlun; Xu, Qihua

    2012-07-01

    The complete sequence of the mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus Miers (Crustacea: Decapoda: Caridea) is presented here. A comparative analysis based on the currently available mitochondrial genomic data revealed many previously unknown characteristics of the mitochondrial genomes of caridean shrimps. The A. japonicus mitochondrial genome is 16487 bp long and contains the typical set of 37 metazoan genes. The gene arrangements in the mitochondrial genomes of four previously studied carideans (Macrobrachium rosenbergii, M. nipponense, M. lanchesteri and Halocaridina rubra) were found to be identical to the pancrustacean ground pattern; thus, it was considered that gene rearrangements probably did not occur in the suborder Caridea. In the present study, a translocation of the trnE gene involving inversion was found in Alpheus mitochondrial genomes. This phenomenon has not been reported in any other crustacean mitochondrial genome that has been studied so far; however, the translocation of one transfer RNA gene (trnP or trnT) was reported in the mitochondrial genome of Exopalaemon carinicauda. When the ratios of the nonsynonymous and synonymous substitutions rates (Ka/Ks) for the 13 protein coding genes from two Alpheus species (A. japonicus and A. distinguendus) and three Macrobrachium species (M. rosenbergii, M. nipponense, M. lanchesteri) were calculated, the Ka/Ks values for all the protein coding genes in Alpheus and Macrobrachium mitochondrial genomes were found to be less than 1 (between 0.0048 and 0.2057), indicating that a strong purification selection had occurred. The phylogenetic tree that was constructed based on the mitochondrial protein coding genes in the genomes of nine related species indicated that Palaemonidae and Alpheidae formed a monophyly and shared a statistically significant relationship, (Palaemonidae+Alpheidae)+Atyidae, at the family level.

  2. 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.

  3. Comparative quantitative proteomics unveils putative mechanisms involved into mercury toxicity and tolerance in Tigriopus japonicus under multigenerational exposure scenario.

    PubMed

    Xu, Xiaoqun; Shi, Lin; Wang, Minghua

    2016-11-01

    In our earlier work, Tigriopus japonicus were subjected to different mercuric chloride treatments (0-50 μg/L in the seawater) for five generations (F0-F4), and they were subsequently resumed under clean environments for one generation, i.e., F5. Accumulative effects were hypothesized to participate in mercury (Hg) multigenerational toxicity, however phenotypic plasticity could be responsible for metal resistance in this copepod against the long term exposure. Here, we specifically investigated the proteome profiles in the F0, F2, and F5 copepods of the control and 50 μg/L metal treatment, respectively, so as to elucidate the action mechanisms for Hg toxicity/tolerance in T. japonicus under the long term exposure. Functional enrichment analysis showed that a quite different proteomic response was observed in F5 compared with F0 and F2. Namely, the vast majority of enrichments were correlated with the down-regulated proteins in F0 and F2, whereas the enrichments for F5 were mostly attributable to the up-regulated proteins, suggesting that different mechanisms are responsible for Hg toxicity and tolerance (i.e., phenotypic plasticity). Hg toxicity prohibited many proteins in F0 and F2 which are related to several critical processes/pathways, e.g., protein translation, macromolecule metabolic process, DNA replication, cell cycle, cuticle organization, vitellogenesis, etc. In F5, many up-regulated proteins were enriched into compensatory systems, such as carbohydrate metabolism, myosin reorganizations, and stress-related defense pathway. Notably, glycolysis (an oxygen-independent pathway) was enhanced for energy allocation into metal detoxification and tolerance. Taken together, proteomics provides novel mechanistic insights into phenotypic plasticity used by T. japonicus when challenged with cumulative effects due to Hg multigenerational toxicity.

  4. Analysis of the Lotus japonicus nuclear pore NUP107-160 subcomplex reveals pronounced structural plasticity and functional redundancy

    PubMed Central

    Binder, Andreas; Parniske, Martin

    2013-01-01

    Mutations in the Lotus japonicus nucleoporin genes, NUP85, NUP133, and NENA (SEH1), lead to defects in plant-microbe symbiotic signaling. The homologous proteins in yeast and vertebrates are part of the conserved NUP84/NUP107-160 subcomplex, which is an essential component of the nuclear pore scaffold and has a pivotal role in nuclear pore complex (NPC) assembly. Loss and down-regulation of NUP84/NUP107-160 members has previously been correlated with a variety of growth and molecular defects, however, in L. japonicus only surprisingly specific phenotypes have been reported. We investigated whether Lotus nup85, nup133, and nena mutants exhibit general defects in NPC composition and distribution. Whole mount immunolocalization confirmed a typical nucleoporin-like localization for NUP133, which was unchanged in the nup85-1 mutant. Severe NPC clustering and aberrations in the nuclear envelope have been reported for Saccharomyces cerevisiae nup85 and nup133 mutants. However, upon transmission electron microscopy analysis of L. japonicus nup85, nup133 and nena, we detected only a slight reduction in the average distances between neighboring NPCs in nup133. Using quantitative immunodetection on protein-blots we observed that loss of individual nucleoporins affected the protein levels of other NUP107–160 complex members. Unlike the single mutants, nup85/nup133 double mutants exhibited severe temperature dependent growth and developmental defects, suggesting that the loss of more than one NUP107–160 member affects basal functions of the NPC. PMID:24478780

  5. The prevalence of non-indigenous parasitic copepod (Neoergasilus japonicus) spreads with fishes of pet trade in Kerman, Iran.

    PubMed

    Mirzaei, Mohammad; Khovand, Hosein; Kheirandish, Reza

    2016-12-01

    Ergasilids are copepods living in the river mouth of freshwaters and parasitic on Teleost fish family in both natural and artificial environments. So far, 5 species of the copepod have been discovered that belong to the genus Neoergasilus. This copepod is most likely to be disseminated through aquarium trades, aquaculture and over-nutrition, or construction of sand carrying water. The females of Ergasilidae are external parasites attaching to the anal and dorsal fins and sometimes to gills and nasal cavities of fish living in freshwaters. In total, 552 pieces of ornamental fish (301 males and 251 females) with length of 5-10 cm from fish (Poecilia sphenops) species (Singapore, Sandy, Dirigible and scorpion's tail) were collected from ornamental fish stores in different regions of Kerman, Iran during 1 year in 2012-2013 and tested in order to examine Neoergasilus japonicus infestation. From 188 adult females Neoergasilus japonicus specimens recorded on the fish host, 8 (4.26 %) were on the anal, 120 (63.83 %) on the dorsal, 10 (5.32 %), on the pectoral, 45 (23.94 %) on the pelvic, and 5 (2.66 %) on the caudal fins. In this study, the prevalence of parasitic copepod infestation from Dec. to May was 26.31, 27.69, 26.19, 14, 18.75, and 7.5 %, respectively. There was no significant difference between infestation prevalence in indigenous and non-native fishes (P = 0.18). There were significant differences between different months of year in the prevalence and intensity of Neoergasilus japonicas (P < 0.05). There was significant difference between frequency distribution of Neoergasilus Japonicus infestation in different organs (P < 0.05). The male fish infestation (16.3 %) was significantly higher than female fish infestation (5.6 %) (P < 0.05). Considering that the Neoergasilus japonicus was first observed in native and nonnative ornamental fish in Kerman, further studies should be conducted on the copepod infestation in stores supplying ornamental fish

  6. Identifying Hazards

    EPA Pesticide Factsheets

    The federal government has established a system of labeling hazardous materials to help identify the type of material and threat posed. Summaries of information on over 300 chemicals are maintained in the Envirofacts Master Chemical Integrator.

  7. [Effects of two organic pollutants on biomarker system of fish Lateolabrax japonicus and the pollution assessment].

    PubMed

    Wang, You; Jiang, Shuang; Zhao, Xiao-wei; Zhao, Yan-fang; Wu, Peng; Cao, Xi-hua; Tang, Xue-xi

    2010-03-01

    Responses of a select suite of protective enzymes in Lateolabrax japonicus including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (Gpx), reduced glutathione (GSH) glutathione S-transferase (GST), nitric oxide synthase (iNOS) in liver tissue and brain acetylcholinesterase (AChE), which could work as sensitively biochemical biomarkers were analyzed when exposed to different concentrations of sodium dodecylbenzene sulfonate (SDBS) and benzo[a]pyrene (B[a]P) under controlled laboratory conditions. Results showed that: (1) The biochemical biomarkers included in this investigation, different responses occurred in the enzymatic activities when exposed to different pollutants: the activities of SOD, GST, Gpx and GSH content were significantly induced by B[a]P (p < 0.05) while others present little different as compared to the control. Differently, SDBS exposure greatly affected the activities of CAT, Gpx, iNOS and AChE while showed little effect on the other evaluated biomarkers. Gpx was the most sensitive biomarker that sensitively indicated the organic pollution stress. (2) The simultaneous assay on heat shock protein 70 (Hsp70) expression was conducted by flow cytometry (FCM) and result presented that Hsp 70 expression could be effectively induced by SDBS as compared to the control throughout the experiment; however, B[a]P obviously induced Hsp70 during the first 12 d and then decreased to the level of the control. (3) The evaluated method of biomarker system combined with principal component analysis (PCA) could effectively distinguish different pollutants under controlled laboratory conditions and might be a promising and warning method for the early assessment of environmental change exposed to different organic pollutions.

  8. Hepatozoon ursi n. sp. (Apicomplexa: Hepatozoidae) in Japanese black bear (Ursus thibetanus japonicus).

    PubMed

    Kubo, Masahito; Uni, Shigehiko; Agatsuma, Takeshi; Nagataki, Mitsuru; Panciera, Roger J; Tsubota, Toshio; Nakamura, Sachiko; Sakai, Hiroki; Masegi, Toshiaki; Yanai, Tokuma

    2008-09-01

    Morphological and genetic features of a new Hepatozoon species, Hepatozoon ursi n. sp., in Japanese black bear (Ursus thibetanus japonicus) were studied. Schizogonic developmental stages were observed in the lungs of Japanese black bears. The schizonts were sub-spherical in shape and 45.7+/-4.6 x 42.7+/-4.5 microm in size. Each mature schizont contained approximately 80-130 merozoites and 0-5 residual bodies. The merozoites were 7.0+/-0.7 x 1.8+/-0.3 microm in size. Intraleukocytic gametocytes were slightly curved, cigar-like in shape and had a beak-like protrusion at one end. The size of the gametocytes was 10.9+/-0.3 x 3.3+/-0.2 microm. The analyses of the18S rRNA gene sequences supported the hypothesis that H. ursi n. sp. is different from other Hepatozoon species. Mature Hepatozoon oocysts were detected in two species of ticks (Haemaphysalis japonica and Haemaphysalis flava) collected on the bears infected with H. ursi n. sp. Two measured oocysts were 263.2 x 234.0 microm and 331.8 x 231.7 microm, respectively. The oocysts contained approximately 40 and 50 sporocysts, respectively. The sporocysts were sub-spherical in shape and 31.2+/-2.5 x 27.0+/-2.9 microm in size. Each sporocyst contained at least 8-16 sporozoites, with the sporozoites being 12.2+/-1.4 x 3.5+/-0.5 microm in size. H. ursi n. sp. is the first Hepatozoon species recorded from the family Ursidae.

  9. 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.

  10. Molecular cloning, characterization and expression analysis of melanotransferrin from the sea cucumber Apostichopus japonicus.

    PubMed

    Qiu, Xuemei; Li, Dong; Cui, Jun; Liu, Yang; Wang, Xiuli

    2014-06-01

    Melanotransferrin (MTf), a member of the transferrin families, plays an important role in immune response. But the research about MTf in sea cucumber is limited till now. In this study, the Melanotransferrin (Aj-MTf) gene was firstly cloned and characterized from the sea cucumber Apostichoupus japonicus by reverse transcriptase polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends. The full-length cDNA of Aj-MTf is 2,840 bp in length and contains a 2,184 bp open reading frame that encodes a polypeptide of 727 amino acids. An iron-responsive element-like structure is located at the 5'-UTR of Aj-MTf cDNA. Sequence analysis shows that the Aj-MTf contains two conserved domains, and the binding-iron (III) sites, including eight amino acid residues (D81,Y109,Y215,H283,D425,Y454,Y565 and H634) and three N-linked glycosylation sites (N121V122S123,N173A174S175 and N673S674T675). Quantitative real-time polymerase chain reaction (qRT-PCR) analyses suggested that the Aj-MTf expressions in the coelomic fluid, body cavity wall and respiratory trees were significantly changed from 4 to 24 h post lipopolysaccharide (LPS) injection. The mRNA levels of Aj-MTf in coelomic fluid was significantly up-regulated at 12 and 24 h in treatment group, and Aj-MTf shared a similar expression pattern with C-type lectin in coelomic fluid, while both genes appears to gradually increase after 4 h of LPS injection. These results indicate that the Aj-MTf plays a pivotal role in immune responses to the LPS challenge in sea cucumber, and provide new information that it is complementary to the sea cucumber immune genes and initiate new researches concerning the genetic basis of the holothurian immune response.

  11. Transmitting Tissue ECM Distribution and Composition, and Pollen Germinability in Sarcandra glabra and Chloranthus japonicus (Chloranthaceae)

    PubMed Central

    HRISTOVA, KATERINA; LAM, MATTHEW; FEILD, TAYLOR; SAGE, TAMMY L.

    2005-01-01

    • Background and Aims Free-flowing surface exudates at the stigmatic (wet versus dry stigma) and adaxial epidermis at the site of angiospermy in carpels of Chloranthaceous species have been proposed to comprise a continuous extracellular matrix (ECM) operating in pollen tube transmission to the ovary. The aim of this research was to establish the spatial distribution and histo/immunochemical composition of the ECM involved in pollen tube growth in Sarcandra glabra and Chloranthus japonicus (Chloranthaceae). • Methods Following confirmation of the pollen tube pathway, the histo/immunochemical make-up of the ECM was determined with histochemistry on fresh tissue to detect cuticle, esterase, proteins, pectins, and lipids and immunolocalization at the level of the TEM on sections from cryofixed/freeze-substituted tissue to detect molecules recognized by antibodies to homogalacturonans (JIM7, 5), arabinogalactan-proteins (JIM13) and cysteine-rich adhesion (SCA). • Key Results Pollen germinability is low in both species. When grains germinate, they do so on an ECM comprised of an esterase-positive cuticle proper (dry versus wet stigma). Pollen tubes do not track the surface ECM of stigma or adaxial epidermal cells at the site of angiospermy. Instead, tubes grow between stigmatic cells and subsequently along the inner tangential walls of the stigmatic and adaxial carpel cells at the site of angiospermy. Pollen tubes enter the ovary locule at the base of the funiculus. The stigmatic ECM is distinct by virtue of the presence of anti-JIM5 aggregates, lipids, and a protein recognized by anti-SCA. • Conclusions The Chloranthaceae joins a growing number of basal angiosperm taxa whereby pollen tubes germinate on a dry versus wet stigma to subsequently grow intercellularly en route to the ovary thereby challenging traditional views that the archetype pollen tube pathway was composed of the surface of stigma and adaxial epidermal cells covered with a free-flowing exudate

  12. 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.

  13. 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 actin