Science.gov

Sample records for invertebrate vector genomics

  1. VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.

    PubMed

    Megy, Karine; Emrich, Scott J; Lawson, Daniel; Campbell, David; Dialynas, Emmanuel; Hughes, Daniel S T; Koscielny, Gautier; Louis, Christos; Maccallum, Robert M; Redmond, Seth N; Sheehan, Andrew; Topalis, Pantelis; Wilson, Derek

    2012-01-01

    VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community. PMID:22135296

  2. Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase.

    PubMed

    Megy, K; Hammond, M; Lawson, D; Bruggner, R V; Birney, E; Collins, F H

    2009-05-01

    High-throughput genome sequencing techniques have now reached vector biology with an emphasis on those species that are vectors of human pathogens. The first mosquito to be sequenced was Anopheles gambiae, the vector for Plasmodium parasites that cause malaria. Further mosquitoes have followed: Aedes aegypti (yellow fever and dengue fever vector) and Culex pipiens (lymphatic filariasis and West Nile fever). Species that are currently in sequencing include the body louse Pediculus humanus (Typhus vector), the triatomine Rhodnius prolixus (Chagas disease vector) and the tick Ixodes scapularis (Lyme disease vector). The motivations for sequencing vector genomes are to further understand vector biology, with an eye on developing new control strategies (for example novel chemical attractants or repellents) or understanding the limitations of current strategies (for example the mechanism of insecticide resistance); to analyse the mechanisms driving their evolution; and to perform an exhaustive analysis of the gene repertory. The proliferation of genomic data creates the need for efficient and accessible storage. We present VectorBase, a genomic resource centre that is both involved in the annotation of vector genomes and act as a portal for access to the genomic information (http://www.vectorbase.org).

  3. VectorBase: a home for invertebrate vectors of human pathogens.

    PubMed

    Lawson, Daniel; Arensburger, Peter; Atkinson, Peter; Besansky, Nora J; Bruggner, Robert V; Butler, Ryan; Campbell, Kathryn S; Christophides, George K; Christley, Scott; Dialynas, Emmanuel; Emmert, David; Hammond, Martin; Hill, Catherine A; Kennedy, Ryan C; Lobo, Neil F; MacCallum, M Robert; Madey, Greg; Megy, Karine; Redmond, Seth; Russo, Susan; Severson, David W; Stinson, Eric O; Topalis, Pantelis; Zdobnov, Evgeny M; Birney, Ewan; Gelbart, William M; Kafatos, Fotis C; Louis, Christos; Collins, Frank H

    2007-01-01

    VectorBase (http://www.vectorbase.org/) is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever.

  4. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

    PubMed

    Bracken-Grissom, Heather; Collins, Allen G; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Mónica; Messing, Charles; O'Brien, Stephen J; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W; Ryan, Joseph F; Schulze, Anja; Wörheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E; Diaz, M Christina; Evans, Nathaniel; Flot, Jean-François; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y; Laberge, Tammy; Lavrov, Dennis; Michonneau, François; Moroz, Leonid L; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A; Rhodes, Adelaide; Santos, Scott R; Satoh, Nori; Thacker, Robert W; Van de Peer, Yves; Voolstra, Christian R; Welch, David Mark; Winston, Judith; Zhou, Xin

    2014-01-01

    Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.

  5. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    PubMed Central

    2014-01-01

    Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture. PMID:24336862

  6. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

    PubMed

    Bracken-Grissom, Heather; Collins, Allen G; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Mónica; Messing, Charles; O'Brien, Stephen J; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W; Ryan, Joseph F; Schulze, Anja; Wörheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E; Diaz, M Christina; Evans, Nathaniel; Flot, Jean-François; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y; Laberge, Tammy; Lavrov, Dennis; Michonneau, François; Moroz, Leonid L; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A; Rhodes, Adelaide; Santos, Scott R; Satoh, Nori; Thacker, Robert W; Van de Peer, Yves; Voolstra, Christian R; Welch, David Mark; Winston, Judith; Zhou, Xin

    2014-01-01

    Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture. PMID:24336862

  7. VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.

    PubMed

    Giraldo-Calderón, Gloria I; Emrich, Scott J; MacCallum, Robert M; Maslen, Gareth; Dialynas, Emmanuel; Topalis, Pantelis; Ho, Nicholas; Gesing, Sandra; Madey, Gregory; Collins, Frank H; Lawson, Daniel

    2015-01-01

    VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/.

  8. VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

    PubMed Central

    Giraldo-Calderón, Gloria I.; Emrich, Scott J.; MacCallum, Robert M.; Maslen, Gareth; Dialynas, Emmanuel; Topalis, Pantelis; Ho, Nicholas; Gesing, Sandra; Madey, Gregory; Collins, Frank H.; Lawson, Daniel

    2015-01-01

    VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/. PMID:25510499

  9. Aquatic invertebrates as unlikely vectors of Buruli ulcer disease.

    PubMed

    Benbow, M Eric; Williamson, Heather; Kimbirauskas, Ryan; McIntosh, Mollie D; Kolar, Rebecca; Quaye, Charles; Akpabey, Felix; Boakye, D; Small, Pam; Merritt, Richard W

    2008-08-01

    Buruli ulcer is a necrotizing skin disease caused by Mycobacterium ulcerans and associated with exposure to aquatic habitats. To assess possible transmission of M. ulcerans by aquatic biting insects, we conducted a field examination of biting water bugs (Hemiptera: Naucoridae, Belostomatidae, Nepidae) in 15 disease-endemic and 12 non-disease-endemic areas of Ghana, Africa. From collections of 22,832 invertebrates, we compared composition, abundance, and associated M. ulcerans positivity among sites. Biting hemipterans were rare and represented a small percentage (usually <2%) of invertebrate communities. No significant differences were found in hemipteran abundance or pathogen positivity between disease-endemic and non-disease-endemic sites, and between abundance of biting hemipterans and M. ulcerans positivity. Therefore, although infection through insect bites is possible, little field evidence supports the assumption that biting hemipterans are primary vectors of M. ulcerans.

  10. Surfeit locus gene homologs are widely distributed in invertebrate genomes.

    PubMed

    Armes, N; Fried, M

    1996-10-01

    The mouse Surfeit locus contains six sequence-unrelated genes (Surf-1 to -6) arranged in the tightest gene cluster so far described for mammals. The organization and juxtaposition of five of the Surfeit genes (Surf-1 to -5) are conserved between mammals and birds, and this may reflect a functional or regulatory requirement for the gene clustering. We have undertaken an evolutionary study to determine whether the Surfeit genes are conserved and clustered in invertebrate genomes. Drosophila melanogaster and Caenorhabditis elegans homologs of the mouse Surf-4 gene, which encodes an integral membrane protein associated with the endoplasmic reticulum, have been isolated. The amino acid sequences of the Drosophila and C. elegans homologs are highly conserved in comparison with the mouse Surf-4 protein. In particular, a dilysine motif implicated in endoplasmic reticulum localization of the mouse protein is conserved in the invertebrate homologs. We show that the Drosophila Surf-4 gene, which is transcribed from a TATA-less promoter, is not closely associated with other Drosophila Surfeit gene homologs but rather is located upstream from sequences encoding a homolog of a yeast seryl-tRNA synthetase protein. There are at least two closely linked Surf-3/rpL7a genes or highly polymorphic alleles of a single Surf-3/rpL7a gene in the C. elegans genome. The chromosomal locations of the C. elegans Surf-1, Surf-3/rpL7a, and Surf-4 genes have been determined. In D. melanogaster the Surf-3/rpL7a, Surf-4, and Surf-5 gene homologs and in C. elegans the Surf-1, Surf-3/rpL7a, Surf-4, and Surf-5 gene homologs are located on completely different chromosomes, suggesting that any requirement for the tight clustering of the genes in the Surfeit locus is restricted to vertebrate lineages.

  11. Vectors of invasions in freshwater invertebrates and fishes

    USGS Publications Warehouse

    Fuller, Pam L.; Canning-Clode, João

    2015-01-01

    Without human assistance, the terrestrial environment and oceans represent barriers to the dispersal of freshwater aquatic organisms. The ability to overcome such barriers depends on the existence of anthropogenic vectors that can transport live organisms to new areas, and the species’ biology to survive the transportation and transplantation into the new environment (Johnson et al., 2006).

  12. Genome sequence of Brevibacillus laterosporus LMG 15441, a pathogen of invertebrates.

    PubMed

    Djukic, Marvin; Poehlein, Anja; Thürmer, Andrea; Daniel, Rolf

    2011-10-01

    Here we announce the genome sequence of the bacterium Brevibacillus laterosporus LMG 15441, which is a pathogen of invertebrates. The genome consists of one chromosome and two circular plasmids. Sequence analysis revealed a large potential to produce polyketides, nonribosomal peptides, and toxins. PMID:21914864

  13. Genome Sequence of Brevibacillus laterosporus LMG 15441, a Pathogen of Invertebrates

    PubMed Central

    Djukic, Marvin; Poehlein, Anja; Thürmer, Andrea; Daniel, Rolf

    2011-01-01

    Here we announce the genome sequence of the bacterium Brevibacillus laterosporus LMG 15441, which is a pathogen of invertebrates. The genome consists of one chromosome and two circular plasmids. Sequence analysis revealed a large potential to produce polyketides, nonribosomal peptides, and toxins. PMID:21914864

  14. Potential vertebrate reservoir hosts and invertebrate vectors of Anaplasma marginale and A. phagocytophilum in central Spain.

    PubMed

    De La Fuente, José; Naranjo, Victoria; Ruiz-Fons, Francisco; Höfle, Ursula; Fernández De Mera, Isabel G; Villanúa, Diego; Almazán, Consuelo; Torina, Alessandra; Caracappa, Santo; Kocan, Katherine M; Gortázar, Christian

    2005-01-01

    Organisms in the genus Anaplasma are obligate intracellular pathogens that multiply in both vertebrate and invertebrate hosts. The type species, A. marginale, causes bovine anaplasmosis and only infects ticks and ruminants. A. phagocytophilum causes human and animal granulocytic anaplasmosis, and genetically closely related strains show a wide host range, including ticks, ruminants, rodents, equids, canids, birds, and humans. Recent reports demonstrated that A. marginale and A. phagocytophilum co-exist in geographic areas and that concurrent infections occur in ruminants and ticks. In this study, we characterized A. marginale and A. phagocytophilum infections in wild and domestic animals, and ticks collected in central Spain by serology, PCR, and sequence of 16S rRNA genotypes. Species tested included humans, cattle, dogs, rodents, Iberian red deer, European wild boar, birds, and ticks. Species of hematophagous Diptera were analyzed as potential mechanical vectors of Anaplasma spp. A. marginale was detected in tabanids, ticks, cattle, and deer, while A. phagocytophilum was detected in ticks, deer, cattle, and birds. Concurrent infections of the two Anaplasma were found in cattle and deer. These results illustrate the complexity of the epizootiology of A. marginale and A. phagocytophilum in regions where both pathogens co-exist and share common reservoir hosts and vectors. The increasing contact between wildlife, domestic animals, and human populations increases the risk of outbreaks of human and bovine anaplasmosis, and the difficulty of implementing surveillance and control measures. PMID:16417435

  15. Zoology: Invertebrates that Parasitize Invertebrates.

    PubMed

    Giribet, Gonzalo

    2016-07-11

    The genome of an orthonectid, a group of highly modified parasitic invertebrates, is drastically reduced and compact, yet it shows the bilaterian gene toolkit. Phylogenetic analyses place the enigmatic orthonectids within Spiralia, although their exact placement remains uncertain.

  16. (New hosts and vectors for genome cloning)

    SciTech Connect

    Not Available

    1991-02-28

    The main goal of our project has been to develop new bacterial hosts and vectors for cloning human DNA in the bacterium E. coli. Because human DNA is both A+T-rich and highly repetitive, many human sequences are unstable as inserts in vectors that are propagated in bacteria. During the past eight months, we have (1) assessed what fraction of human DNA inserts in cosmid vectors is unstable, (2) developed new host strains that help stabilize unstable sequence features of human DNA, and (3) begun the development of a new generation of cloning vectors that should permit the more stable maintenance and more facile analysis of large human DNA inserts.

  17. Invertebrate lamins

    SciTech Connect

    Melcer, Shai; Gruenbaum, Yosef . E-mail: gru@vms.huji.ac.il; Krohne, Georg . E-mail: krohne@biozentrum.uni-wuerzburg.de

    2007-06-10

    Lamins are the main component of the nuclear lamina and considered to be the ancestors of all intermediate filament proteins. They are localized mainly at the nuclear periphery where they form protein complexes with integral proteins of the nuclear inner membrane, transcriptional regulators, histones and chromatin modifiers. Studying lamins in invertebrate species has unique advantages including the smaller number of lamin genes in the invertebrate genomes and powerful genetic analyses in Caenorhabditis elegans and Drosophila melanogaster. These simpler nuclear lamina systems allow direct analyses of their structure and functions. Here we give an overview of recent advances in the field of invertebrate nuclear lamins with special emphasis on their evolution, assembly and functions.

  18. (New hosts and vectors for genome cloning)

    SciTech Connect

    Not Available

    1991-01-01

    The main goal of our project remains the development of new bacterial hosts and vectors for the stable propagation of human DNA clones in E. coli. During the past six months of our current budget period, we have (1) continued to develop new hosts that permit the stable maintenance of unstable features of human DNA, and (2) developed a series of vectors for (a) cloning large DNA inserts, (b) assessing the frequency of human sequences that are lethal to the growth of E. coli, and (c) assessing the stability of human sequences cloned in M13 for large-scale sequencing projects.

  19. A genome-wide analysis of annexins from parasitic organisms and their vectors

    PubMed Central

    Cantacessi, Cinzia; Seddon, Jennifer M.; Miller, Terrence L.; Leow, Chiuan Yee; Thomas, Laëtitia; Mason, Lyndel; Willis, Charlene; Walker, Giselle; Loukas, Alex; Gasser, Robin B.; Jones, Malcolm K.; Hofmann, Andreas

    2013-01-01

    In this study, we conduct an in-depth analysis of annexin proteins from a diverse range of invertebrate taxa, including the major groups that contain the parasites and vector organisms that are harmful to humans and domestic animals. Using structure-based amino acid sequence alignments and phylogenetic analyses, we present a classification for this protein group and assign names to sequences with ambiguous annotations in public databases. Our analyses reveal six distinct annexin clades, and the mapping of genes encoding annexins to the genome of the human blood fluke Schistosoma mansoni supports the hypothesis of gene duplication as a major evolutionary event in annexin genesis. This study illuminates annexin diversity from a novel perspective using contemporary phylogenetic hypotheses of eukaryote evolution, and will aid the consolidation of annexin protein identities in public databases and provide a foundation for future functional analysis and characterisation of these proteins in parasites of socioeconomic importance. PMID:24113121

  20. Adenoviral vector DNA for accurate genome editing with engineered nucleases.

    PubMed

    Holkers, Maarten; Maggio, Ignazio; Henriques, Sara F D; Janssen, Josephine M; Cathomen, Toni; Gonçalves, Manuel A F V

    2014-10-01

    Engineered sequence-specific nucleases and donor DNA templates can be customized to edit mammalian genomes via the homologous recombination (HR) pathway. Here we report that the nature of the donor DNA greatly affects the specificity and accuracy of the editing process following site-specific genomic cleavage by transcription activator-like effector nucleases (TALENs) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 nucleases. By applying these designer nucleases together with donor DNA delivered as protein-capped adenoviral vector (AdV), free-ended integrase-defective lentiviral vector or nonviral vector templates, we found that the vast majority of AdV-modified human cells underwent scarless homology-directed genome editing. In contrast, a significant proportion of cells exposed to free-ended or to covalently closed HR substrates were subjected to random and illegitimate recombination events. These findings are particularly relevant for genome engineering approaches aiming at high-fidelity genetic modification of human cells.

  1. The Genome of Anopheles darlingi, the main neotropical malaria vector

    PubMed Central

    Marinotti, Osvaldo; Cerqueira, Gustavo C.; de Almeida, Luiz Gonzaga Paula; Ferro, Maria Inês Tiraboschi; Loreto, Elgion Lucio da Silva; Zaha, Arnaldo; Teixeira, Santuza M. R.; Wespiser, Adam R.; Almeida e Silva, Alexandre; Schlindwein, Aline Daiane; Pacheco, Ana Carolina Landim; da Silva, Artur Luiz da Costa; Graveley, Brenton R.; Walenz, Brian P.; Lima, Bruna de Araujo; Ribeiro, Carlos Alexandre Gomes; Nunes-Silva, Carlos Gustavo; de Carvalho, Carlos Roberto; Soares, Célia Maria de Almeida; de Menezes, Claudia Beatriz Afonso; Matiolli, Cleverson; Caffrey, Daniel; Araújo, Demetrius Antonio M.; de Oliveira, Diana Magalhães; Golenbock, Douglas; Grisard, Edmundo Carlos; Fantinatti-Garboggini, Fabiana; de Carvalho, Fabíola Marques; Barcellos, Fernando Gomes; Prosdocimi, Francisco; May, Gemma; de Azevedo Junior, Gilson Martins; Guimarães, Giselle Moura; Goldman, Gustavo Henrique; Padilha, Itácio Q. M.; Batista, Jacqueline da Silva; Ferro, Jesus Aparecido; Ribeiro, José M. C.; Fietto, Juliana Lopes Rangel; Dabbas, Karina Maia; Cerdeira, Louise; Agnez-Lima, Lucymara Fassarella; Brocchi, Marcelo; de Carvalho, Marcos Oliveira; Teixeira, Marcus de Melo; Diniz Maia, Maria de Mascena; Goldman, Maria Helena S.; Cruz Schneider, Maria Paula; Felipe, Maria Sueli Soares; Hungria, Mariangela; Nicolás, Marisa Fabiana; Pereira, Maristela; Montes, Martín Alejandro; Cantão, Maurício E.; Vincentz, Michel; Rafael, Miriam Silva; Silverman, Neal; Stoco, Patrícia Hermes; Souza, Rangel Celso; Vicentini, Renato; Gazzinelli, Ricardo Tostes; Neves, Rogério de Oliveira; Silva, Rosane; Astolfi-Filho, Spartaco; Maciel, Talles Eduardo Ferreira; Ürményi, Turán P.; Tadei, Wanderli Pedro; Camargo, Erney Plessmann; de Vasconcelos, Ana Tereza Ribeiro

    2013-01-01

    Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ∼100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vector–human and vector–parasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles-darlingi. PMID:23761445

  2. Biological and molecular events associated with simultaneous transmission of plant viruses by invertebrate and fungal vectors.

    PubMed

    Syller, Jerzy

    2014-05-01

    Viruses are likely to be the most dangerous parasites of living organisms because of their widespread occurrence, possible deleterious effects on their hosts and high rates of evolution. Virus host-to-host transmission is a critical step in the virus life cycle, because it enables survival in a given environment and efficient dissemination. As hosts of plant viruses are not mobile, these pathogens have adopted diverse transmission strategies involving various vector organisms, mainly arthropods, nematodes, fungi and protists. In nature, plants are often infected with more than one virus at a time, thereby creating potential sources for vectors to acquire and transmit simultaneously two or more viruses. Simultaneous transmission can result in multiple infections of new host plants, which become subsequent potential sources of the viruses, thus enhancing the spread of the diseases caused by these pathogens. Moreover, it can contribute to the maintenance of viral genetic diversity in the host communities. However, despite its possible significance, the problem of the simultaneous transmission of plant viruses by vectors has not been investigated in detail. In this review, the current knowledge on multiple viral transmissions by aphids, whiteflies, leafhoppers, planthoppers, nematodes and fungi is outlined.

  3. New Invertebrate Vectors for PST, Spirolides and Okadaic Acid in the North Atlantic

    PubMed Central

    Silva, Marisa; Barreiro, Aldo; Rodriguez, Paula; Otero, Paz; Azevedo, Joana; Alfonso, Amparo; Botana, Luis M.; Vasconcelos, Vitor

    2013-01-01

    The prevalence of poisoning events due to harmful algal blooms (HABs) has declined during the last two decades through monitoring programs and legislation, implemented mainly for bivalves. However, new toxin vectors and emergent toxins pose a challenge to public health. Several locations on the Portuguese coast were surveyed between 2009 and 2010 for three distinct biotoxin groups [saxitoxin (PST), spirolide (SPX) and okadaic acid (OA)], in 14 benthic species of mollusks and echinoderms. Our main goals were to detect new vectors and unravel the seasonal and geographical patterns of these toxins. PSTs were analyzed by the Lawrence method, SPXs by LC-MS/MS, and OA by LC-MS/MS and UPLC-MS/MS. We report 16 new vectors for these toxins in the North Atlantic. There were differences in toxin contents among species, but no significant geographical or seasonal patterns were found. Our results suggest that legislation should be adjusted to extend the monitoring of marine toxins to a wider range of species besides edible bivalves. PMID:23739043

  4. Generation of RCAS vectors useful for functional genomic analyses.

    PubMed

    Loftus, S K; Larson, D M; Watkins-Chow, D; Church, D M; Pavan, W J

    2001-10-31

    Avian leukosis type A virus-derived retroviral vectors have been used to introduce genes into cells expressing the corresponding avian receptor tv-a. This includes the use of Replication-Competent Avian sarcoma-leukosis virus (ASLV) long terminal repeat (LTR) with Splice acceptor (RCAS) vectors in the analysis of avian development, human and murine cell cultures, murine cell lineage studies and cancer biology. Previously, cloning of genes into this virus was difficult due to the large size of the vector and sparse cloning sites. To overcome some of the disadvantages of traditional cloning using the RCASBP-Y vector, we have modified the RCASBP-Y to incorporate "Gateway" site-specific recombination cloning of genes into the construct, either with or without HA epitope tags. We have found the repetitive "att" sequences, which are the targets for site-specific recombination, do not impair the production of infectious viral particles or the expression of the gene of interest. This is the first instance of site-specific recombination being used to generate retroviral gene constructs. These viral constructs will allow for the efficient transfer and expression of cDNAs needed for functional genomic analyses. PMID:11759842

  5. Retroviral Vectors: Post Entry Events and Genomic Alterations

    PubMed Central

    Nowrouzi, Ali; Glimm, Hanno; von Kalle, Christof; Schmidt, Manfred

    2011-01-01

    The curative potential of retroviral vectors for somatic gene therapy has been demonstrated impressively in several clinical trials leading to sustained long-term correction of the underlying genetic defect. Preclinical studies and clinical monitoring of gene modified hematopoietic stem and progenitor cells in patients have shown that biologically relevant vector induced side effects, ranging from in vitro immortalization to clonal dominance and oncogenesis in vivo, accompany therapeutic efficiency of integrating retroviral gene transfer systems. Most importantly, it has been demonstrated that the genotoxic potential is not identical among all retroviral vector systems designed for clinical application. Large scale viral integration site determination has uncovered significant differences in the target site selection of retrovirus subfamilies influencing the propensity for inducing genetic alterations in the host genome. In this review we will summarize recent insights gained on the mechanisms of insertional mutagenesis based on intrinsic target site selection of different retrovirus families. We will also discuss examples of side effects occurring in ongoing human gene therapy trials and future prospectives in the field. PMID:21994741

  6. Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

    PubMed Central

    2010-01-01

    Background Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strain-specific segments called regions of genomic plasticity (RGPs). Using a new web tool, RGPFinder, we investigated plasticity units in bacterial genomes, by exhaustive description of the RGPs in two Photorhabdus and two Xenorhabdus strains, belonging to the Enterobacteriaceae and interacting with invertebrates (insects and nematodes). Results RGPs account for about 60% of the genome in each of the four genomes studied. We classified RGPs into genomic islands (GIs), prophages and two new classes of RGP without the features of classical mobile genetic elements (MGEs) but harboring genes encoding enzymes catalyzing DNA recombination (RGPmob), or with no remarkable feature (RGPnone). These new classes accounted for most of the RGPs and are probably hypervariable regions, ancient MGEs with degraded mobilization machinery or non canonical MGEs for which the mobility mechanism has yet to be described. We provide evidence that not only the GIs and the prophages, but also RGPmob and RGPnone, have a mosaic structure consisting of modules. A module is a block of genes, 0.5 to 60 kb in length, displaying a conserved genomic organization among the different Enterobacteriaceae. Modules are functional units involved in host/environment interactions (22-31%), metabolism (22-27%), intracellular or intercellular DNA mobility (13-30%), drug resistance (4-5%) and antibiotic synthesis (3-6%). Finally, in silico comparisons and PCR multiplex analysis indicated that these modules served as plasticity units within the bacterial genome during genome speciation and as deletion units in clonal variants of Photorhabdus. Conclusions This led us to consider the modules, rather than the entire RGP, as the true unit of plasticity in bacterial genomes, during both short-term and long-term genome evolution. PMID:20950463

  7. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

    PubMed

    Neafsey, Daniel E; Waterhouse, Robert M; Abai, Mohammad R; Aganezov, Sergey S; Alekseyev, Max A; Allen, James E; Amon, James; Arcà, Bruno; Arensburger, Peter; Artemov, Gleb; Assour, Lauren A; Basseri, Hamidreza; Berlin, Aaron; Birren, Bruce W; Blandin, Stephanie A; Brockman, Andrew I; Burkot, Thomas R; Burt, Austin; Chan, Clara S; Chauve, Cedric; Chiu, Joanna C; Christensen, Mikkel; Costantini, Carlo; Davidson, Victoria L M; Deligianni, Elena; Dottorini, Tania; Dritsou, Vicky; Gabriel, Stacey B; Guelbeogo, Wamdaogo M; Hall, Andrew B; Han, Mira V; Hlaing, Thaung; Hughes, Daniel S T; Jenkins, Adam M; Jiang, Xiaofang; Jungreis, Irwin; Kakani, Evdoxia G; Kamali, Maryam; Kemppainen, Petri; Kennedy, Ryan C; Kirmitzoglou, Ioannis K; Koekemoer, Lizette L; Laban, Njoroge; Langridge, Nicholas; Lawniczak, Mara K N; Lirakis, Manolis; Lobo, Neil F; Lowy, Ernesto; MacCallum, Robert M; Mao, Chunhong; Maslen, Gareth; Mbogo, Charles; McCarthy, Jenny; Michel, Kristin; Mitchell, Sara N; Moore, Wendy; Murphy, Katherine A; Naumenko, Anastasia N; Nolan, Tony; Novoa, Eva M; O'Loughlin, Samantha; Oringanje, Chioma; Oshaghi, Mohammad A; Pakpour, Nazzy; Papathanos, Philippos A; Peery, Ashley N; Povelones, Michael; Prakash, Anil; Price, David P; Rajaraman, Ashok; Reimer, Lisa J; Rinker, David C; Rokas, Antonis; Russell, Tanya L; Sagnon, N'Fale; Sharakhova, Maria V; Shea, Terrance; Simão, Felipe A; Simard, Frederic; Slotman, Michel A; Somboon, Pradya; Stegniy, Vladimir; Struchiner, Claudio J; Thomas, Gregg W C; Tojo, Marta; Topalis, Pantelis; Tubio, José M C; Unger, Maria F; Vontas, John; Walton, Catherine; Wilding, Craig S; Willis, Judith H; Wu, Yi-Chieh; Yan, Guiyun; Zdobnov, Evgeny M; Zhou, Xiaofan; Catteruccia, Flaminia; Christophides, George K; Collins, Frank H; Cornman, Robert S; Crisanti, Andrea; Donnelly, Martin J; Emrich, Scott J; Fontaine, Michael C; Gelbart, William; Hahn, Matthew W; Hansen, Immo A; Howell, Paul I; Kafatos, Fotis C; Kellis, Manolis; Lawson, Daniel; Louis, Christos; Luckhart, Shirley; Muskavitch, Marc A T; Ribeiro, José M; Riehle, Michael A; Sharakhov, Igor V; Tu, Zhijian; Zwiebel, Laurence J; Besansky, Nora J

    2015-01-01

    Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts. PMID:25554792

  8. The infectious BAC genomic DNA expression library: a high capacity vector system for functional genomics

    PubMed Central

    Lufino, Michele M. P.; Edser, Pauline A. H.; Quail, Michael A.; Rice, Stephen; Adams, David J.; Wade-Martins, Richard

    2016-01-01

    Gene dosage plays a critical role in a range of cellular phenotypes, yet most cellular expression systems use heterologous cDNA-based vectors which express proteins well above physiological levels. In contrast, genomic DNA expression vectors generate physiologically-relevant levels of gene expression by carrying the whole genomic DNA locus of a gene including its regulatory elements. Here we describe the first genomic DNA expression library generated using the high-capacity herpes simplex virus-1 amplicon technology to deliver bacterial artificial chromosomes (BACs) into cells by viral transduction. The infectious BAC (iBAC) library contains 184,320 clones with an average insert size of 134.5 kb. We show in a Chinese hamster ovary (CHO) disease model cell line and mouse embryonic stem (ES) cells that this library can be used for genetic rescue studies in a range of contexts including the physiological restoration of Ldlr deficiency, and viral receptor expression. The iBAC library represents an important new genetic analysis tool openly available to the research community. PMID:27353647

  9. Genomic Changes of Chagas Disease Vector, South America

    PubMed Central

    Dujardin, Jean Pierre; Nicolini, Paula; Caraccio, María Noel; Rose, Virginia; Tellez, Tatiana; Bermúdez, Hernán; Bargues, María Dolores; Mas-Coma, Santiago; O’Connor, José Enrique; Pérez, Ruben

    2004-01-01

    We analyzed the main karyologic changes that have occurred during the dispersion of Triatoma infestans, the main vector of Chagas disease. We identified two allopatric groups, named Andean and non-Andean. The Andean specimens present C-heterochromatic blocks in most of their 22 chromosomes, whereas non-Andean specimens have only 4–7 autosomes with C-banding. These heterochromatin differences are the likely cause of a striking DNA content variation (approximately 30%) between Andean and non-Andean insects. Our study, together with previous historical and genetic data, suggests that T. infestans was originally a sylvatic species, with large quantities of DNA and heterochromatin, inhabiting the Andean region of Bolivia. However, the spread of domestic T. infestans throughout the non-Andean regions only involved insects with an important reduction of heterochromatin and DNA amounts. We propose that heterochromatin and DNA variation mainly reflected adaptive genomic changes that contribute to the ability of T. infestans to survive, reproduce, and disperse in different environments. PMID:15109410

  10. Diagnosis of vibriosis in the era of genomics: lessons from invertebrates.

    PubMed

    Le Roux, F

    2016-04-01

    Global changes linked to increases in temperature and ocean acidification, but also to more direct anthropogenic influences such as aquaculture, have caused a worldwide increase in the reports of Vibrio-associated illnesses affecting humans and also animals such as shrimp and molluscs. Investigation of the emergence of Vibrio pathogenesis events requires the analysis of microbial evolution at the gene, genome and population levels, in order to identify genomic modifications linked to increased virulence, resistance and/or prevalence, or to recent host shift. From a more applied point of view, the elucidation of virulence mechanisms is a prerequisite to devising prophylactic methods to fight infectious agents. In comparison with human pathogens, fairly little is known about the requirements for virulence in vibrios pathogenic to animals. However, the advent of genome sequencing, especially next-generation technologies, the possibility of genetically manipulating most of the Vibrio strains, and the recent availability of standardised animals for experimental infections have now compensated for the considerable delay in advancement of the knowledge of non-model pathogens such as Vibrio and have led to new scientific questions. PMID:27217182

  11. Diagnosis of vibriosis in the era of genomics: lessons from invertebrates.

    PubMed

    Le Roux, F

    2016-04-01

    Global changes linked to increases in temperature and ocean acidification, but also to more direct anthropogenic influences such as aquaculture, have caused a worldwide increase in the reports of Vibrio-associated illnesses affecting humans and also animals such as shrimp and molluscs. Investigation of the emergence of Vibrio pathogenesis events requires the analysis of microbial evolution at the gene, genome and population levels, in order to identify genomic modifications linked to increased virulence, resistance and/or prevalence, or to recent host shift. From a more applied point of view, the elucidation of virulence mechanisms is a prerequisite to devising prophylactic methods to fight infectious agents. In comparison with human pathogens, fairly little is known about the requirements for virulence in vibrios pathogenic to animals. However, the advent of genome sequencing, especially next-generation technologies, the possibility of genetically manipulating most of the Vibrio strains, and the recent availability of standardised animals for experimental infections have now compensated for the considerable delay in advancement of the knowledge of non-model pathogens such as Vibrio and have led to new scientific questions.

  12. A series of conditional shuttle vectors for targeted genomic integration in budding yeast.

    PubMed

    Chou, Chia-Ching; Patel, Michael T; Gartenberg, Marc R

    2015-05-01

    The capacity of Saccharomyces cerevisiae to repair exposed DNA ends by homologous recombination has long been used by experimentalists to assemble plasmids from DNA fragments in vivo. While this approach works well for engineering extrachromosomal vectors, it is not well suited to the generation, recovery and reuse of integrative vectors. Here, we describe the creation of a series of conditional centromeric shuttle vectors, termed pXR vectors, that can be used for both plasmid assembly in vivo and targeted genomic integration. The defining feature of pXR vectors is that the DNA segment bearing the centromere and origin of replication, termed CEN/ARS, is flanked by a pair of loxP sites. Passaging the vectors through bacteria that express Cre recombinase reduces the loxP-CEN/ARS-loxP module to a single loxP site, thereby eliminating the ability to replicate autonomously in yeast. Each vector also contains a selectable marker gene, as well as a fragment of the HO locus, which permits targeted integration at a neutral genomic site. The pXR vectors provide a convenient and robust method to assemble DNAs for targeted genomic modifications.

  13. VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites.

    PubMed

    Calabria, Andrea; Leo, Simone; Benedicenti, Fabrizio; Cesana, Daniela; Spinozzi, Giulio; Orsini, Massimilano; Merella, Stefania; Stupka, Elia; Zanetti, Gianluigi; Montini, Eugenio

    2014-01-01

    The analysis of the genomic distribution of viral vector genomic integration sites is a key step in hematopoietic stem cell-based gene therapy applications, allowing to assess both the safety and the efficacy of the treatment and to study the basic aspects of hematopoiesis and stem cell biology. Identifying vector integration sites requires ad-hoc bioinformatics tools with stringent requirements in terms of computational efficiency, flexibility, and usability. We developed VISPA (Vector Integration Site Parallel Analysis), a pipeline for automated integration site identification and annotation based on a distributed environment with a simple Galaxy web interface. VISPA was successfully used for the bioinformatics analysis of the follow-up of two lentiviral vector-based hematopoietic stem-cell gene therapy clinical trials. Our pipeline provides a reliable and efficient tool to assess the safety and efficacy of integrating vectors in clinical settings. PMID:25342980

  14. Practical utilization of recombinant AAV vector reference standards: focus on vector genomes titration by free ITR qPCR.

    PubMed

    D'Costa, Susan; Blouin, Veronique; Broucque, Frederic; Penaud-Budloo, Magalie; François, Achille; Perez, Irene C; Le Bec, Christine; Moullier, Philippe; Snyder, Richard O; Ayuso, Eduard

    2016-01-01

    Clinical trials using recombinant adeno-associated virus (rAAV) vectors have demonstrated efficacy and a good safety profile. Although the field is advancing quickly, vector analytics and harmonization of dosage units are still a limitation for commercialization. AAV reference standard materials (RSMs) can help ensure product safety by controlling the consistency of assays used to characterize rAAV stocks. The most widely utilized unit of vector dosing is based on the encapsidated vector genome. Quantitative polymerase chain reaction (qPCR) is now the most common method to titer vector genomes (vg); however, significant inter- and intralaboratory variations have been documented using this technique. Here, RSMs and rAAV stocks were titered on the basis of an inverted terminal repeats (ITRs) sequence-specific qPCR and we found an artificial increase in vg titers using a widely utilized approach. The PCR error was introduced by using single-cut linearized plasmid as the standard curve. This bias was eliminated using plasmid standards linearized just outside the ITR region on each end to facilitate the melting of the palindromic ITR sequences during PCR. This new "Free-ITR" qPCR delivers vg titers that are consistent with titers obtained with transgene-specific qPCR and could be used to normalize in-house product-specific AAV vector standards and controls to the rAAV RSMs. The free-ITR method, including well-characterized controls, will help to calibrate doses to compare preclinical and clinical data in the field.

  15. Practical utilization of recombinant AAV vector reference standards: focus on vector genomes titration by free ITR qPCR

    PubMed Central

    D’Costa, Susan; Blouin, Veronique; Broucque, Frederic; Penaud-Budloo, Magalie; François, Achille; Perez, Irene C; Le Bec, Christine; Moullier, Philippe; Snyder, Richard O; Ayuso, Eduard

    2016-01-01

    Clinical trials using recombinant adeno-associated virus (rAAV) vectors have demonstrated efficacy and a good safety profile. Although the field is advancing quickly, vector analytics and harmonization of dosage units are still a limitation for commercialization. AAV reference standard materials (RSMs) can help ensure product safety by controlling the consistency of assays used to characterize rAAV stocks. The most widely utilized unit of vector dosing is based on the encapsidated vector genome. Quantitative polymerase chain reaction (qPCR) is now the most common method to titer vector genomes (vg); however, significant inter- and intralaboratory variations have been documented using this technique. Here, RSMs and rAAV stocks were titered on the basis of an inverted terminal repeats (ITRs) sequence-specific qPCR and we found an artificial increase in vg titers using a widely utilized approach. The PCR error was introduced by using single-cut linearized plasmid as the standard curve. This bias was eliminated using plasmid standards linearized just outside the ITR region on each end to facilitate the melting of the palindromic ITR sequences during PCR. This new “Free-ITR” qPCR delivers vg titers that are consistent with titers obtained with transgene-specific qPCR and could be used to normalize in-house product-specific AAV vector standards and controls to the rAAV RSMs. The free-ITR method, including well-characterized controls, will help to calibrate doses to compare preclinical and clinical data in the field. PMID:27069952

  16. New Invertebrate Vectors of Okadaic Acid from the North Atlantic Waters—Portugal (Azores and Madeira) and Morocco

    PubMed Central

    Silva, Marisa; Rodriguez, Inés; Barreiro, Aldo; Kaufmann, Manfred; Neto, Ana Isabel; Hassouani, Meryem; Sabour, Brahim; Alfonso, Amparo; Botana, Luis M.; Vasconcelos, Vitor

    2015-01-01

    Okadaic acid and its analogues are potent phosphatase inhibitors that cause Diarrheic Shellfish Poisoning (DSP) through the ingestion of contaminated shellfish by humans. This group of toxins is transmitted worldwide but the number of poisoning incidents has declined over the last 20 years due to legislation and monitoring programs that were implemented for bivalves. In the summer of 2012 and 2013, we collected a total of 101 samples of 22 different species that were made up of benthic and subtidal organisms such echinoderms, crustaceans, bivalves and gastropods from Madeira, São Miguel Island (Azores archipelago) and the northwestern coast of Morocco. The samples were analyzed by UPLC-MS/MS. Our main objective was to detect new vectors for these biotoxins. We can report nine new vectors for these toxins in the North Atlantic: Astropecten aranciacus, Arbacia lixula, Echinaster sepositus, Holothuria sanctori, Ophidiaster ophidianus, Onchidella celtica, Aplysia depilans, Patella spp., and Stramonita haemostoma. Differences in toxin contents among the species were found. Even though low concentrations were detected, the levels of toxins that were present, especially in edible species, indicate the importance of these types of studies. Routine monitoring should be extended to comprise a wider number of vectors other than for bivalves of okadaic acid and its analogues. PMID:26670254

  17. New Invertebrate Vectors of Okadaic Acid from the North Atlantic Waters--Portugal (Azores and Madeira) and Morocco.

    PubMed

    Silva, Marisa; Rodriguez, Inés; Barreiro, Aldo; Kaufmann, Manfred; Isabel Neto, Ana; Hassouani, Meryem; Sabour, Brahim; Alfonso, Amparo; Botana, Luis M; Vasconcelos, Vitor

    2015-12-08

    Okadaic acid and its analogues are potent phosphatase inhibitors that cause Diarrheic Shellfish Poisoning (DSP) through the ingestion of contaminated shellfish by humans. This group of toxins is transmitted worldwide but the number of poisoning incidents has declined over the last 20 years due to legislation and monitoring programs that were implemented for bivalves. In the summer of 2012 and 2013, we collected a total of 101 samples of 22 different species that were made up of benthic and subtidal organisms such echinoderms, crustaceans, bivalves and gastropods from Madeira, São Miguel Island (Azores archipelago) and the northwestern coast of Morocco. The samples were analyzed by UPLC-MS/MS. Our main objective was to detect new vectors for these biotoxins. We can report nine new vectors for these toxins in the North Atlantic: Astropecten aranciacus, Arbacia lixula, Echinaster sepositus, Holothuria sanctori, Ophidiaster ophidianus, Onchidella celtica, Aplysia depilans, Patella spp., and Stramonita haemostoma. Differences in toxin contents among the species were found. Even though low concentrations were detected, the levels of toxins that were present, especially in edible species, indicate the importance of these types of studies. Routine monitoring should be extended to comprise a wider number of vectors other than for bivalves of okadaic acid and its analogues.

  18. [New hosts and vectors for genome cloning]. Progress report

    SciTech Connect

    Not Available

    1991-12-31

    The main goal of our project remains the development of new bacterial hosts and vectors for the stable propagation of human DNA clones in E. coli. During the past six months of our current budget period, we have (1) continued to develop new hosts that permit the stable maintenance of unstable features of human DNA, and (2) developed a series of vectors for (a) cloning large DNA inserts, (b) assessing the frequency of human sequences that are lethal to the growth of E. coli, and (c) assessing the stability of human sequences cloned in M13 for large-scale sequencing projects.

  19. Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis

    PubMed Central

    2014-01-01

    Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein–encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology. PMID:24763584

  20. Application of genomics for understanding plant virus-insect vector interactions and insect vector control

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ability to decipher DNA sequences provides new insights into the study of plant viruses and their interactions with host plants, including the intricate interactions that allow a virus to be transmitted by an insect vector. Next generation sequencing (NGS) provides a wealth of genetic informati...

  1. Complete genome sequence of a Klebsiella pneumoniae strain isolated from a known cotton insect boll vector

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Klebsiella pneumoniae (associated with bacterial pneumonia) was previously isolated from Nezara viridula, a significant vector of cotton boll-rot pathogens. We provide the first annotated genome sequence of the cotton opportunistic strain K. pneumoniae 5-1. This data provides guidance to study the...

  2. New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae.

    PubMed

    Laughery, Marian F; Hunter, Tierra; Brown, Alexander; Hoopes, James; Ostbye, Travis; Shumaker, Taven; Wyrick, John J

    2015-12-01

    Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology is an important tool for genome editing because the Cas9 endonuclease can induce targeted DNA double-strand breaks. Targeting of the DNA break is typically controlled by a single-guide RNA (sgRNA), a chimeric RNA containing a structural segment important for Cas9 binding and a 20mer guide sequence that hybridizes to the genomic DNA target. Previous studies have demonstrated that CRISPR-Cas9 technology can be used for efficient, marker-free genome editing in Saccharomyces cerevisiae. However, introducing the 20mer guide sequence into yeast sgRNA expression vectors often requires cloning procedures that are complex, time-consuming and/or expensive. To simplify this process, we have developed a new sgRNA expression cassette with internal restriction enzyme sites that permit rapid, directional cloning of 20mer guide sequences. Here we describe a flexible set of vectors based on this design for cloning and expressing sgRNAs (and Cas9) in yeast using different selectable markers. We anticipate that the Cas9-sgRNA expression vector with the URA3 selectable marker (pML104) will be particularly useful for genome editing in yeast, since the Cas9 machinery can be easily removed by counter-selection using 5-fluoro-orotic acid (5-FOA) following successful genome editing. The availability of new vectors that simplify and streamline the technical steps required for guide sequence cloning should help accelerate the use of CRISPR-Cas9 technology in yeast genome editing.

  3. Ensemble Feature Learning of Genomic Data Using Support Vector Machine

    PubMed Central

    Anaissi, Ali; Goyal, Madhu; Catchpoole, Daniel R.; Braytee, Ali; Kennedy, Paul J.

    2016-01-01

    The identification of a subset of genes having the ability to capture the necessary information to distinguish classes of patients is crucial in bioinformatics applications. Ensemble and bagging methods have been shown to work effectively in the process of gene selection and classification. Testament to that is random forest which combines random decision trees with bagging to improve overall feature selection and classification accuracy. Surprisingly, the adoption of these methods in support vector machines has only recently received attention but mostly on classification not gene selection. This paper introduces an ensemble SVM-Recursive Feature Elimination (ESVM-RFE) for gene selection that follows the concepts of ensemble and bagging used in random forest but adopts the backward elimination strategy which is the rationale of RFE algorithm. The rationale behind this is, building ensemble SVM models using randomly drawn bootstrap samples from the training set, will produce different feature rankings which will be subsequently aggregated as one feature ranking. As a result, the decision for elimination of features is based upon the ranking of multiple SVM models instead of choosing one particular model. Moreover, this approach will address the problem of imbalanced datasets by constructing a nearly balanced bootstrap sample. Our experiments show that ESVM-RFE for gene selection substantially increased the classification performance on five microarray datasets compared to state-of-the-art methods. Experiments on the childhood leukaemia dataset show that an average 9% better accuracy is achieved by ESVM-RFE over SVM-RFE, and 5% over random forest based approach. The selected genes by the ESVM-RFE algorithm were further explored with Singular Value Decomposition (SVD) which reveals significant clusters with the selected data. PMID:27304923

  4. Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics.

    PubMed

    Reitzel, A M; Herrera, S; Layden, M J; Martindale, M Q; Shank, T M

    2013-06-01

    Characterization of large numbers of single-nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represent a boon to test long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats in North and South America, and portions of England. We identified hundreds of SNP-containing tags in thousands of RAD loci from 30 barcoded individuals inhabiting four locations from Nova Scotia to South Carolina. Population genomic analyses using high-confidence SNPs resulted in a highly-resolved phylogeography, a result not achieved in previous studies using traditional markers. Plots of locus-specific FST against heterozygosity suggest that a majority of polymorphic sites are neutral, with a smaller proportion suggesting evidence for balancing selection. Loci inferred to be under balancing selection were mapped to the genome, where 90% were located in gene bodies, indicating potential targets of selection. The results from analyses with and without a reference genome supported similar conclusions, further highlighting RAD-seq as a method that can be efficiently applied to species lacking existing genomic resources. We discuss the utility of RAD-seq approaches in burgeoning Nematostella research as well as in other cnidarian species, particularly corals and jellyfishes, to determine phylogeographic relationships of populations and identify regions of the genome undergoing selection.

  5. Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics

    PubMed Central

    Reitzel, A.M.; Herrera, S.; Layden, M.J.; Martindale, M.Q.; Shank, T.M.

    2013-01-01

    Characterization of large numbers of single nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represent a boon to test long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats in North and South America, and portions of England. We identified hundreds of SNP-containing tags in thousands of RAD loci from 30 barcoded individuals inhabiting four locations from Nova Scotia to South Carolina. Population genomic analyses using high-confidence SNPs resulted in a highly-resolved phylogeography, a result not achieved in previous studies using traditional markers. Plots of locus-specific FST against heterozygosity suggest that a majority of polymorphic sites are neutral, with a smaller proportion suggesting evidence for balancing selection. Loci inferred to be under balancing selection were mapped to the genome, where 90% were located in gene bodies, indicating potential targets of selection. Results from analyses with and without a reference genome supported similar conclusions, further supporting RAD-seq as a method that can be efficiently applied to species lacking existing genomic resources. We discuss the utility of RAD-seq approaches in burgeoning Nematostella research as well as in other cnidarian species, particularly corals, to determine phylogeographic relationships of populations and identify regions of the genome undergoing selection. PMID:23473066

  6. Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics.

    PubMed

    Reitzel, A M; Herrera, S; Layden, M J; Martindale, M Q; Shank, T M

    2013-06-01

    Characterization of large numbers of single-nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represent a boon to test long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats in North and South America, and portions of England. We identified hundreds of SNP-containing tags in thousands of RAD loci from 30 barcoded individuals inhabiting four locations from Nova Scotia to South Carolina. Population genomic analyses using high-confidence SNPs resulted in a highly-resolved phylogeography, a result not achieved in previous studies using traditional markers. Plots of locus-specific FST against heterozygosity suggest that a majority of polymorphic sites are neutral, with a smaller proportion suggesting evidence for balancing selection. Loci inferred to be under balancing selection were mapped to the genome, where 90% were located in gene bodies, indicating potential targets of selection. The results from analyses with and without a reference genome supported similar conclusions, further highlighting RAD-seq as a method that can be efficiently applied to species lacking existing genomic resources. We discuss the utility of RAD-seq approaches in burgeoning Nematostella research as well as in other cnidarian species, particularly corals and jellyfishes, to determine phylogeographic relationships of populations and identify regions of the genome undergoing selection. PMID:23473066

  7. Comparative Genomic Analysis of Malaria Mosquito Vector-Associated Novel Pathogen Elizabethkingia anophelis

    PubMed Central

    Teo, Jeanette; Tan, Sean Yang-Yi; Liu, Yang; Tay, Martin; Ding, Yichen; Li, Yingying; Kjelleberg, Staffan; Givskov, Michael; Lin, Raymond T.P.; Yang, Liang

    2014-01-01

    Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meningoseptica. Recently, we used whole-genome sequencing to reveal that E. anophelis is the pathogenic agent for an Elizabethkingia outbreak at two ICUs. We performed comparative genomic analysis of seven hospital-isolated E. anophelis strains with five available Elizabethkingia spp. genomes deposited in the National Center for Biotechnology Information Database. A pan-genomic approach was applied to identify the core- and pan-genome for the Elizabethkingia genus. We showed that unlike the hospital-isolated pathogen E. meningoseptica ATCC 12535 strain, the hospital-isolated E. anophelis strains have genome content and organization similar to the E. anophelis Ag1 and R26 strains isolated from the midgut microbiota of the malaria mosquito vector Anopheles gambiae. Both the core- and accessory genomes of Elizabethkingia spp. possess genes conferring antibiotic resistance and virulence. Our study highlights that E. anophelis is an emerging bacterial pathogen for hospital environments. PMID:24803570

  8. CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes.

    PubMed

    Xu, Zhao; Hao, Bailin

    2009-07-01

    The CVTree web server (http://tlife.fudan.edu.cn/cvtree) presented here is a new implementation of the whole genome-based, alignment-free composition vector (CV) method for phylogenetic analysis. It is more efficient and user-friendly than the previously published version in the 2004 web server issue of Nucleic Acids Research. The development of whole genome-based alignment-free CV method has provided an independent verification to the traditional phylogenetic analysis based on a single gene or a few genes. This new implementation attempts to meet the challenge of ever increasing amount of genome data and includes in its database more than 850 prokaryotic genomes which will be updated monthly from NCBI, and more than 80 fungal genomes collected manually from several sequencing centers. This new CVTree web server provides a faster and stable research platform. Users can upload their own sequences to find their phylogenetic position among genomes selected from the server's; inbuilt database. All sequence data used in a session may be downloaded as a compressed file. In addition to standard phylogenetic trees, users can also choose to output trees whose monophyletic branches are collapsed to various taxonomic levels. This feature is particularly useful for comparing phylogeny with taxonomy when dealing with thousands of genomes.

  9. Genomic approaches for understanding dengue: insights from the virus, vector, and host.

    PubMed

    Sim, Shuzhen; Hibberd, Martin L

    2016-03-02

    The incidence and geographic range of dengue have increased dramatically in recent decades. Climate change, rapid urbanization and increased global travel have facilitated the spread of both efficient mosquito vectors and the four dengue virus serotypes between population centers. At the same time, significant advances in genomics approaches have provided insights into host-pathogen interactions, immunogenetics, and viral evolution in both humans and mosquitoes. Here, we review these advances and the innovative treatment and control strategies that they are inspiring.

  10. [Novel qPCR strategy for quantification of recombinant adeno-associated virus serotype 2 vector genome-titer].

    PubMed

    Meng, Qinglin; Zhang, Binbin; Zhang, Chun

    2013-02-01

    Adeno-associated virus (AAV) has many advantages for gene therapy over other vector systems. However, after the production of recombinant AAV (Raav) vectors, the biological titration of rAAV stocks is still cumbersome. Different investigators used laboratory-specific methods or internal reference standards that may limit preclinical and clinical applications. The inverted terminal repeats (ITR) sequences are the only cis-regulated viral elements required for rAAV packaging and remain within viral vector genomes. ITR is the excellent target sequences for qPCR quantification of rAAV titer. In this study, we developed a novel qPCR strategy to quantify rAAVs' vector genome titer via targeting the ITR2 or ITR2-CMV element. In conclusion, the method is fast and accurate for the titration of rAAV2-derived vector genomes. It will promote the standardization of rAAV titration in the future.

  11. Population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons

    PubMed Central

    Gilbert, Clément; Chateigner, Aurélien; Ernenwein, Lise; Barbe, Valérie; Bézier, Annie; Herniou, Elisabeth A.; Cordaux, Richard

    2014-01-01

    Horizontal transfer (HT) of DNA is an important factor shaping eukaryote evolution. Although several hundreds of eukaryote-to-eukaryote HTs of transposable elements (TEs) have been reported, the vectors underlying these transfers remain elusive. Here, we show that multiple copies of two TEs from the cabbage looper (Trichoplusia ni) transposed in vivo into genomes of the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) during caterpillar infection. We further demonstrate that both TEs underwent recent HT between several sympatric moth species (T. ni, Manduca sexta, Helicoverpa spp.) showing different degrees of susceptibility to AcMNPV. Based on two independent population genomics data sets (reaching a total coverage >330,000X), we report a frequency of one moth TE in ~8,500 AcMNPV genomes. Together, our results provide strong support for the role of viruses as vectors of TE HT between animals, and they call for a systematic evaluation of the frequency and impact of virus-mediated HT on the evolution of host genomes. PMID:24556639

  12. “Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes”

    PubMed Central

    Neafsey, Daniel E.; Waterhouse, Robert M.; Abai, Mohammad R.; Aganezov, Sergey S.; Alekseyev, Max A.; Allen, James E.; Amon, James; Arcà, Bruno; Arensburger, Peter; Artemov, Gleb; Assour, Lauren A.; Basseri, Hamidreza; Berlin, Aaron; Birren, Bruce W.; Blandin, Stephanie A.; Brockman, Andrew I.; Burkot, Thomas R.; Burt, Austin; Chan, Clara S.; Chauve, Cedric; Chiu, Joanna C.; Christensen, Mikkel; Costantini, Carlo; Davidson, Victoria L.M.; Deligianni, Elena; Dottorini, Tania; Dritsou, Vicky; Gabriel, Stacey B.; Guelbeogo, Wamdaogo M.; Hall, Andrew B.; Han, Mira V.; Hlaing, Thaung; Hughes, Daniel S.T.; Jenkins, Adam M.; Jiang, Xiaofang; Jungreis, Irwin; Kakani, Evdoxia G.; Kamali, Maryam; Kemppainen, Petri; Kennedy, Ryan C.; Kirmitzoglou, Ioannis K.; Koekemoer, Lizette L.; Laban, Njoroge; Langridge, Nicholas; Lawniczak, Mara K.N.; Lirakis, Manolis; Lobo, Neil F.; Lowy, Ernesto; MacCallum, Robert M.; Mao, Chunhong; Maslen, Gareth; Mbogo, Charles; McCarthy, Jenny; Michel, Kristin; Mitchell, Sara N.; Moore, Wendy; Murphy, Katherine A.; Naumenko, Anastasia N.; Nolan, Tony; Novoa, Eva M.; O'Loughlin, Samantha; Oringanje, Chioma; Oshaghi, Mohammad A.; Pakpour, Nazzy; Papathanos, Philippos A.; Peery, Ashley N.; Povelones, Michael; Prakash, Anil; Price, David P.; Rajaraman, Ashok; Reimer, Lisa J.; Rinker, David C.; Rokas, Antonis; Russell, Tanya L.; Sagnon, N'Fale; Sharakhova, Maria V.; Shea, Terrance; Simão, Felipe A.; Simard, Frederic; Slotman, Michel A.; Somboon, Pradya; Stegniy, Vladimir; Struchiner, Claudio J.; Thomas, Gregg W.C.; Tojo, Marta; Topalis, Pantelis; Tubio, José M.C.; Unger, Maria F.; Vontas, John; Walton, Catherine; Wilding, Craig S.; Willis, Judith H.; Wu, Yi-Chieh; Yan, Guiyun; Zdobnov, Evgeny M.; Zhou, Xiaofan; Catteruccia, Flaminia; Christophides, George K.; Collins, Frank H.; Cornman, Robert S.; Crisanti, Andrea; Donnelly, Martin J.; Emrich, Scott J.; Fontaine, Michael C.; Gelbart, William; Hahn, Matthew W.; Hansen, Immo A.; Howell, Paul I.; Kafatos, Fotis C.; Kellis, Manolis; Lawson, Daniel; Louis, Christos; Luckhart, Shirley; Muskavitch, Marc A.T.; Ribeiro, José M.; Riehle, Michael A.; Sharakhov, Igor V.; Tu, Zhijian; Zwiebel, Laurence J.; Besansky, Nora J.

    2015-01-01

    Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover, but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts. PMID:25554792

  13. Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector.

    PubMed

    Kabadi, Ami M; Ousterout, David G; Hilton, Isaac B; Gersbach, Charles A

    2014-10-29

    Engineered DNA-binding proteins that manipulate the human genome and transcriptome have enabled rapid advances in biomedical research. In particular, the RNA-guided CRISPR/Cas9 system has recently been engineered to create site-specific double-strand breaks for genome editing or to direct targeted transcriptional regulation. A unique capability of the CRISPR/Cas9 system is multiplex genome engineering by delivering a single Cas9 enzyme and two or more single guide RNAs (sgRNAs) targeted to distinct genomic sites. This approach can be used to simultaneously create multiple DNA breaks or to target multiple transcriptional activators to a single promoter for synergistic enhancement of gene induction. To address the need for uniform and sustained delivery of multiplex CRISPR/Cas9-based genome engineering tools, we developed a single lentiviral system to express a Cas9 variant, a reporter gene and up to four sgRNAs from independent RNA polymerase III promoters that are incorporated into the vector by a convenient Golden Gate cloning method. Each sgRNA is efficiently expressed and can mediate multiplex gene editing and sustained transcriptional activation in immortalized and primary human cells. This delivery system will be significant to enabling the potential of CRISPR/Cas9-based multiplex genome engineering in diverse cell types.

  14. Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector.

    PubMed

    Kabadi, Ami M; Ousterout, David G; Hilton, Isaac B; Gersbach, Charles A

    2014-10-29

    Engineered DNA-binding proteins that manipulate the human genome and transcriptome have enabled rapid advances in biomedical research. In particular, the RNA-guided CRISPR/Cas9 system has recently been engineered to create site-specific double-strand breaks for genome editing or to direct targeted transcriptional regulation. A unique capability of the CRISPR/Cas9 system is multiplex genome engineering by delivering a single Cas9 enzyme and two or more single guide RNAs (sgRNAs) targeted to distinct genomic sites. This approach can be used to simultaneously create multiple DNA breaks or to target multiple transcriptional activators to a single promoter for synergistic enhancement of gene induction. To address the need for uniform and sustained delivery of multiplex CRISPR/Cas9-based genome engineering tools, we developed a single lentiviral system to express a Cas9 variant, a reporter gene and up to four sgRNAs from independent RNA polymerase III promoters that are incorporated into the vector by a convenient Golden Gate cloning method. Each sgRNA is efficiently expressed and can mediate multiplex gene editing and sustained transcriptional activation in immortalized and primary human cells. This delivery system will be significant to enabling the potential of CRISPR/Cas9-based multiplex genome engineering in diverse cell types. PMID:25122746

  15. Vector algebra in the analysis of genome-wide expression data

    PubMed Central

    Kuruvilla, Finny G; Park, Peter J; Schreiber, Stuart L

    2002-01-01

    Background Data from thousands of transcription-profiling experiments in organisms ranging from yeast to humans are now publicly available. How best to analyze these data remains an important challenge. A variety of tools have been used for this purpose, including hierarchical clustering, self-organizing maps and principal components analysis. In particular, concepts from vector algebra have proven useful in the study of genome-wide expression data. Results Here we present a framework based on vector algebra for the analysis of transcription profiles that is geometrically intuitive and computationally efficient. Concepts in vector algebra such as angles, magnitudes, subspaces, singular value decomposition, bases and projections have natural and powerful interpretations in the analysis of microarray data. Angles in particular offer a rigorous method of defining 'similarity' and are useful in evaluating the claims of a microarray-based study. We present a sample analysis of cells treated with rapamycin, an immunosuppressant whose effects have been extensively studied with microarrays. In addition, the algebraic concept of a basis for a space affords the opportunity to simplify data analysis and uncover a limited number of expression vectors to span the transcriptional range of cell behavior. Conclusions This framework represents a compact, powerful and scalable construction for analysis and computation. As the amount of microarray data in the public domain grows, these vector-based methods are relevant in determining statistical significance. These approaches are also well suited to extract biologically meaningful information in the analysis of signaling networks. PMID:11897023

  16. Invertebrate Paleontology.

    ERIC Educational Resources Information Center

    Feldmann, Rodney M.

    1983-01-01

    Indicating that, although no broad conceptual notions in invertebrate paleontology were proposed during 1982, a large number of excellent papers focusing on testing, modifying, and documenting earlier speculations were published or presented at professional meetings. Highlights of papers, conferences, and research studies are provided (including…

  17. Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population.

    PubMed

    Rogers, Matthew B; Downing, Tim; Smith, Barbara A; Imamura, Hideo; Sanders, Mandy; Svobodova, Milena; Volf, Petr; Berriman, Matthew; Cotton, James A; Smith, Deborah F

    2014-01-01

    Although asexual reproduction via clonal propagation has been proposed as the principal reproductive mechanism across parasitic protozoa of the Leishmania genus, sexual recombination has long been suspected, based on hybrid marker profiles detected in field isolates from different geographical locations. The recent experimental demonstration of a sexual cycle in Leishmania within sand flies has confirmed the occurrence of hybridisation, but knowledge of the parasite life cycle in the wild still remains limited. Here, we use whole genome sequencing to investigate the frequency of sexual reproduction in Leishmania, by sequencing the genomes of 11 Leishmania infantum isolates from sand flies and 1 patient isolate in a focus of cutaneous leishmaniasis in the Çukurova province of southeast Turkey. This is the first genome-wide examination of a vector-isolated population of Leishmania parasites. A genome-wide pattern of patchy heterozygosity and SNP density was observed both within individual strains and across the whole group. Comparisons with other Leishmania donovani complex genome sequences suggest that these isolates are derived from a single cross of two diverse strains with subsequent recombination within the population. This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. This observation allowed us to estimate the relative rates of sexual and asexual reproduction within this population, to our knowledge the first quantitative estimate of these events during the Leishmania life cycle.

  18. CD8+ T cell recognition of epitopes within the capsid of adeno-associated virus 8-based gene transfer vectors depends on vectors' genome.

    PubMed

    Wu, Te-Lang; Li, Hua; Faust, Susan M; Chi, Emily; Zhou, Shangzhen; Wright, Fraser; High, Katherine A; Ertl, Hildegund C J

    2014-01-01

    Self-complementary adeno-associated viral (AAV) vectors expressing human factor IX (hF.IX) have achieved transient or sustained correction of hemophilia B in human volunteers. High doses of AAV2 or AAV8 vectors delivered to the liver caused in several patients an increase in transaminases accompanied by a rise in AAV capsid-specific T cells and a decrease in circulating hF.IX levels suggesting immune-mediated destruction of vector-transduced cells. Kinetics of these adverse events differed in patients receiving AAV2 or AAV8 vectors causing rise in transaminases at 3 versus 8 weeks after vector injection, respectively. To test if CD8+ T cells to AAV8 vectors, which are similar to AAV2 vectors are fully-gutted vectors and thereby fail to encode structural viral proteins, could cause damage at this late time point, we tested in a series of mouse studies how long major histocompatibility (MHC) class I epitopes within AAV8 capsid can be presented to CD8+ T cells. Our results clearly show that depending on the vectors' genome, CD8+ T cells can detect such epitopes on AAV8's capsid for up to 6 months indicating that the capsid of AAV8 degrades slowly in mice.

  19. Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas.

    PubMed

    Deitz, Kevin C; Athrey, Giridhar A; Jawara, Musa; Overgaard, Hans J; Matias, Abrahan; Slotman, Michel A

    2016-01-01

    Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq) from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression. PMID:27466271

  20. Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas

    PubMed Central

    Deitz, Kevin C.; Athrey, Giridhar A.; Jawara, Musa; Overgaard, Hans J.; Matias, Abrahan; Slotman, Michel A.

    2016-01-01

    Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq) from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression. PMID:27466271

  1. Draft Genomes of Anopheles cracens and Anopheles maculatus: Comparison of Simian Malaria and Human Malaria Vectors in Peninsular Malaysia

    PubMed Central

    Chen, Junhui; Zhong, Zhen; Jian, Jianbo; Amir, Amirah; Cheong, Fei-Wen; Sum, Jia-Siang; Fong, Mun-Yik

    2016-01-01

    Anopheles cracens has been incriminated as the vector of human knowlesi malaria in peninsular Malaysia. Besides, it is a good laboratory vector of Plasmodium falciparum and P. vivax. The distribution of An. cracens overlaps with that of An. maculatus, the human malaria vector in peninsular Malaysia that seems to be refractory to P. knowlesi infection in natural settings. Whole genome sequencing was performed on An. cracens and An. maculatus collected here. The draft genome of An. cracens was 395 Mb in size whereas the size of An. maculatus draft genome was 499 Mb. Comparison with the published Malaysian An. maculatus genome suggested the An. maculatus specimen used in this study as a different geographical race. Comparative analyses highlighted the similarities and differences between An. cracens and An. maculatus, providing new insights into their biological behavior and characteristics. PMID:27347683

  2. Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

    PubMed

    Gulia-Nuss, Monika; Nuss, Andrew B; Meyer, Jason M; Sonenshine, Daniel E; Roe, R Michael; Waterhouse, Robert M; Sattelle, David B; de la Fuente, José; Ribeiro, Jose M; Megy, Karine; Thimmapuram, Jyothi; Miller, Jason R; Walenz, Brian P; Koren, Sergey; Hostetler, Jessica B; Thiagarajan, Mathangi; Joardar, Vinita S; Hannick, Linda I; Bidwell, Shelby; Hammond, Martin P; Young, Sarah; Zeng, Qiandong; Abrudan, Jenica L; Almeida, Francisca C; Ayllón, Nieves; Bhide, Ketaki; Bissinger, Brooke W; Bonzon-Kulichenko, Elena; Buckingham, Steven D; Caffrey, Daniel R; Caimano, Melissa J; Croset, Vincent; Driscoll, Timothy; Gilbert, Don; Gillespie, Joseph J; Giraldo-Calderón, Gloria I; Grabowski, Jeffrey M; Jiang, David; Khalil, Sayed M S; Kim, Donghun; Kocan, Katherine M; Koči, Juraj; Kuhn, Richard J; Kurtti, Timothy J; Lees, Kristin; Lang, Emma G; Kennedy, Ryan C; Kwon, Hyeogsun; Perera, Rushika; Qi, Yumin; Radolf, Justin D; Sakamoto, Joyce M; Sánchez-Gracia, Alejandro; Severo, Maiara S; Silverman, Neal; Šimo, Ladislav; Tojo, Marta; Tornador, Cristian; Van Zee, Janice P; Vázquez, Jesús; Vieira, Filipe G; Villar, Margarita; Wespiser, Adam R; Yang, Yunlong; Zhu, Jiwei; Arensburger, Peter; Pietrantonio, Patricia V; Barker, Stephen C; Shao, Renfu; Zdobnov, Evgeny M; Hauser, Frank; Grimmelikhuijzen, Cornelis J P; Park, Yoonseong; Rozas, Julio; Benton, Richard; Pedra, Joao H F; Nelson, David R; Unger, Maria F; Tubio, Jose M C; Tu, Zhijian; Robertson, Hugh M; Shumway, Martin; Sutton, Granger; Wortman, Jennifer R; Lawson, Daniel; Wikel, Stephen K; Nene, Vishvanath M; Fraser, Claire M; Collins, Frank H; Birren, Bruce; Nelson, Karen E; Caler, Elisabet; Hill, Catherine A

    2016-01-01

    Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent. PMID:26856261

  3. Genomic insights into the Ixodes scapularis tick vector of Lyme disease

    PubMed Central

    Gulia-Nuss, Monika; Nuss, Andrew B.; Meyer, Jason M.; Sonenshine, Daniel E.; Roe, R. Michael; Waterhouse, Robert M.; Sattelle, David B.; de la Fuente, José; Ribeiro, Jose M.; Megy, Karine; Thimmapuram, Jyothi; Miller, Jason R.; Walenz, Brian P.; Koren, Sergey; Hostetler, Jessica B.; Thiagarajan, Mathangi; Joardar, Vinita S.; Hannick, Linda I.; Bidwell, Shelby; Hammond, Martin P.; Young, Sarah; Zeng, Qiandong; Abrudan, Jenica L.; Almeida, Francisca C.; Ayllón, Nieves; Bhide, Ketaki; Bissinger, Brooke W.; Bonzon-Kulichenko, Elena; Buckingham, Steven D.; Caffrey, Daniel R.; Caimano, Melissa J.; Croset, Vincent; Driscoll, Timothy; Gilbert, Don; Gillespie, Joseph J.; Giraldo-Calderón, Gloria I.; Grabowski, Jeffrey M.; Jiang, David; Khalil, Sayed M. S.; Kim, Donghun; Kocan, Katherine M.; Koči, Juraj; Kuhn, Richard J.; Kurtti, Timothy J.; Lees, Kristin; Lang, Emma G.; Kennedy, Ryan C.; Kwon, Hyeogsun; Perera, Rushika; Qi, Yumin; Radolf, Justin D.; Sakamoto, Joyce M.; Sánchez-Gracia, Alejandro; Severo, Maiara S.; Silverman, Neal; Šimo, Ladislav; Tojo, Marta; Tornador, Cristian; Van Zee, Janice P.; Vázquez, Jesús; Vieira, Filipe G.; Villar, Margarita; Wespiser, Adam R.; Yang, Yunlong; Zhu, Jiwei; Arensburger, Peter; Pietrantonio, Patricia V.; Barker, Stephen C.; Shao, Renfu; Zdobnov, Evgeny M.; Hauser, Frank; Grimmelikhuijzen, Cornelis J. P.; Park, Yoonseong; Rozas, Julio; Benton, Richard; Pedra, Joao H. F.; Nelson, David R.; Unger, Maria F.; Tubio, Jose M. C.; Tu, Zhijian; Robertson, Hugh M.; Shumway, Martin; Sutton, Granger; Wortman, Jennifer R.; Lawson, Daniel; Wikel, Stephen K.; Nene, Vishvanath M.; Fraser, Claire M.; Collins, Frank H.; Birren, Bruce; Nelson, Karen E.; Caler, Elisabet; Hill, Catherine A.

    2016-01-01

    Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick–host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host ‘questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent. PMID:26856261

  4. Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

    PubMed

    Gulia-Nuss, Monika; Nuss, Andrew B; Meyer, Jason M; Sonenshine, Daniel E; Roe, R Michael; Waterhouse, Robert M; Sattelle, David B; de la Fuente, José; Ribeiro, Jose M; Megy, Karine; Thimmapuram, Jyothi; Miller, Jason R; Walenz, Brian P; Koren, Sergey; Hostetler, Jessica B; Thiagarajan, Mathangi; Joardar, Vinita S; Hannick, Linda I; Bidwell, Shelby; Hammond, Martin P; Young, Sarah; Zeng, Qiandong; Abrudan, Jenica L; Almeida, Francisca C; Ayllón, Nieves; Bhide, Ketaki; Bissinger, Brooke W; Bonzon-Kulichenko, Elena; Buckingham, Steven D; Caffrey, Daniel R; Caimano, Melissa J; Croset, Vincent; Driscoll, Timothy; Gilbert, Don; Gillespie, Joseph J; Giraldo-Calderón, Gloria I; Grabowski, Jeffrey M; Jiang, David; Khalil, Sayed M S; Kim, Donghun; Kocan, Katherine M; Koči, Juraj; Kuhn, Richard J; Kurtti, Timothy J; Lees, Kristin; Lang, Emma G; Kennedy, Ryan C; Kwon, Hyeogsun; Perera, Rushika; Qi, Yumin; Radolf, Justin D; Sakamoto, Joyce M; Sánchez-Gracia, Alejandro; Severo, Maiara S; Silverman, Neal; Šimo, Ladislav; Tojo, Marta; Tornador, Cristian; Van Zee, Janice P; Vázquez, Jesús; Vieira, Filipe G; Villar, Margarita; Wespiser, Adam R; Yang, Yunlong; Zhu, Jiwei; Arensburger, Peter; Pietrantonio, Patricia V; Barker, Stephen C; Shao, Renfu; Zdobnov, Evgeny M; Hauser, Frank; Grimmelikhuijzen, Cornelis J P; Park, Yoonseong; Rozas, Julio; Benton, Richard; Pedra, Joao H F; Nelson, David R; Unger, Maria F; Tubio, Jose M C; Tu, Zhijian; Robertson, Hugh M; Shumway, Martin; Sutton, Granger; Wortman, Jennifer R; Lawson, Daniel; Wikel, Stephen K; Nene, Vishvanath M; Fraser, Claire M; Collins, Frank H; Birren, Bruce; Nelson, Karen E; Caler, Elisabet; Hill, Catherine A

    2016-02-09

    Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.

  5. Conditionally Amplifiable BACs: Switching From Single-Copy to High-Copy Vectors and Genomic Clones

    PubMed Central

    Wild, Jadwiga; Hradecna, Zdenka; Szybalski, Waclaw

    2002-01-01

    The widely used, very-low-copy BAC (bacterial artificial chromosome) vectors are the mainstay of present genomic research. The principal advantage of BACs is the high stability of inserted clones, but an important disadvantage is the low yield of DNA, both for vectors alone and when carrying genomic inserts. We describe here a novel class of single-copy/high-copy (SC/HC) pBAC/oriV vectors that retain all the advantages of low-copy BAC vectors, but are endowed with a conditional and tightly controlled oriV/TrfA amplification system that allows: (1) a yield of ∼100 copies of the vector per host cell when conditionally induced with l-arabinose, and (2) analogous DNA amplification (only upon induction and with copy number depending on the insert size) of pBAC/oriV clones carrying >100-kb inserts. Amplifiable clones and libraries facilitate high-throughput DNA sequencing and other applications requiring HC plasmid DNA. To turn on DNA amplification, which is driven by the oriV origin of replication, we used copy-up mutations in the gene trfA whose expression was very tightly controlled by the araC–ParaBAD promoter/regulator system. This system is inducible by l-arabinose, and could be further regulated by glucose and fucose. Amplification of DNA upon induction with l-arabinose and its modulation by glucose are robust and reliable. Furthermore, we discovered that addition of 0.2% d-glucose to the growth medium helped toward the objective of obtaining a real SC state for all BAC systems, thus enhancing the stability of their maintenance, which became equivalent to cloning into the host chromosome. [The following individuals kindly provided reagents, samples or unpublished information as indicated in the paper: F.R. Blattner D. Helinski, S. Valla, F. Schomburg, C. Small, R. Bogden, C. Gaskins, M.P. Mayer, D.C. Schwartz, and O. Azzam.] PMID:12213781

  6. Comparative and functional genomics of the innate immune system in the malaria vector Anopheles gambiae.

    PubMed

    Christophides, George K; Vlachou, Dina; Kafatos, Fotis C

    2004-04-01

    In much of Africa, the mosquito Anopheles gambiae is the major vector of human malaria, a devastating infectious disease caused by Plasmodium parasites. Vector and parasite interact at multiple stages and locations, and the nature and effectiveness of this reciprocal interaction determines the success of transmission. Many of the interactions engage the mosquito's innate immunity, a primitive but very effective defense system. In some cases, the mosquito kills the parasite, thus blocking the transmission cycle. However, not all interactions are antagonistic; some represent immune evasion. The sequence of the A. gambiae genome revealed numerous potential components of the innate immune system, and it established that they evolve rapidly, as summarized in the present review. Their rapid evolution by gene family expansion diversification as well as the prevalence of haplotype alleles in the best-studied families may reflect selective adaptation of the immune system to the exigencies of multiple immune challenges in a variety of ecologic niches. As a follow-up to the comparative genomic analysis, the development of functional genomic methodologies has provided novel opportunities for understanding the immune system and the nature of its interactions with the parasite. In this context, identification of both Plasmodium antagonists and protectors in the mosquito represents a significant conceptual advance. In addition to providing fundamental understanding of primitive immune systems, studies of mosquito interactions with the parasite open unprecedented opportunities for novel interventions against malaria transmission. The generation of transgenic mosquitoes that resist malaria infection in the wild and the development of antimalarial 'smart sprays' capable of disrupting interactions that are protective of the parasite, or reinforcing others that are antagonistic, represent technical challenges but also immense opportunities for improvement of global health.

  7. Applying genomic and bioinformatic resources to human adenovirus genomes for use in vaccine development and for applications in vector development for gene delivery.

    PubMed

    Seto, Jason; Walsh, Michael P; Mahadevan, Padmanabhan; Zhang, Qiwei; Seto, Donald

    2010-01-01

    Technological advances and increasingly cost-effect methodologies in DNA sequencing and computational analysis are providing genome and proteome data for human adenovirus research. Applying these tools, data and derived knowledge to the development of vaccines against these pathogens will provide effective prophylactics. The same data and approaches can be applied to vector development for gene delivery in gene therapy and vaccine delivery protocols. Examination of several field strain genomes and their analyses provide examples of data that are available using these approaches. An example of the development of HAdV-B3 both as a vaccine and also as a vector is presented.

  8. Invertebrates in the Classroom.

    ERIC Educational Resources Information Center

    Abramson, Charles I.

    1986-01-01

    Describes an inexpensive program using invertebrates as subjects in conditioning demonstrations and experiments. Provides a bibliography of reviews about invertebrate learning in addition to information on obtaining required apparatus and invertebrates.

  9. Introduction: Invertebrate Neuropeptides XIII

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This publication represents an introduction to the thirteenth in a series of special issues of the Peptides journal dedicated to invertebrate neuropeptides. The issue addresses a number of aspects of invertebrate neuropeptide research including identification of novel invertebrate neuropeptide sequ...

  10. Introduction: Invertebrate Neuropeptides XVI

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This publication represents an introduction to the sixteenth in a series of special issues of the Peptides journal dedicated to invertebrate neuropeptides. The issue addresses a number of aspects of invertebrate neuropeptide research including identification of novel invertebrate neuropeptide seque...

  11. Introduction: Invertebrate Neuropeptides XV

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This publication represents an introduction to the fifteenth in a series of special issues of the Peptides journal dedicated to invertebrate neuropeptides. The issue addresses a number of aspects of invertebrate neuropeptide research including identification of novel invertebrate neuropeptide seque...

  12. Introduction: Invertebrate Neuropeptides XIV

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This publication represents an introduction to the thirteenth in a series of special issues of the Peptides journal dedicated to invertebrate neuropeptides. The issue addresses a number of aspects of invertebrate neuropeptide research including identification of novel invertebrate neuropeptide sequ...

  13. Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

    PubMed Central

    2012-01-01

    Introduction Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa. Results cDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature. Conclusions We generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable

  14. Copy number of adenoviral vector genome transduced into target cells can be measured using quantitative PCR: application to vector titration.

    PubMed

    Pei, Zheng; Kondo, Saki; Kanegae, Yumi; Saito, Izumu

    2012-01-20

    Both transfection and adenovirus vectors are commonly used in studies measuring gene expression. However, the real DNA copy number that is actually transduced into target cells cannot be measured using quantitative PCR because attached DNA present on the cell surface is difficult to distinguish from successfully transduced DNA. Here, we used Cre/loxP system to show that most of the transfected DNA was in fact attached to the cell surface; in contrast, most of the viral vector DNA used to infect the target cells was present inside the cells after the cells were washed according to the conventional infection protocol. We applied this characteristic to adenoviral vector titration. Current methods of vector titration using the growth of 293 cells are influenced by the effect of the expressed gene product as well as the cell conditions and culture techniques. The titration method proposed here indicates the copy numbers introduced to the target cells using a control vector that is infected in parallel (relative vector titer: rVT). Moreover, the new titration method is simple and reliable and may replace the current titration methods of viral vectors.

  15. CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox.

    PubMed

    Senís, Elena; Fatouros, Chronis; Große, Stefanie; Wiedtke, Ellen; Niopek, Dominik; Mueller, Ann-Kristin; Börner, Kathleen; Grimm, Dirk

    2014-11-01

    Its remarkable ease and efficiency make the CRISPR (clustered regularly interspaced short palindromic repeats) DNA editing machinery highly attractive as a new tool for experimental gene annotation and therapeutic genome engineering in eukaryotes. Here, we report a versatile set of plasmids and vectors derived from adeno-associated virus (AAV) that allow robust and specific delivery of the two essential CRISPR components - Cas9 and chimeric g(uide)RNA - either alone or in combination. All our constructs share a modular design that enables simple and stringent guide RNA (gRNA) cloning as well as rapid exchange of promoters driving Cas9 or gRNA. Packaging into potent synthetic AAV capsids permits CRISPR delivery even into hard-to-transfect targets, as shown for human T-cells. Moreover, we demonstrate the feasibility to direct Cas9 expression to or away from hepatocytes, using a liver-specific promoter or a hepatic miRNA binding site, respectively. We also report a streamlined and economical protocol for detection of CRISPR-induced mutations in less than 3 h. Finally, we provide original evidence that AAV/CRISPR vectors can be exploited for gene engineering in vivo, as exemplified in the liver of adult mice. Our new tools and protocols should foster the broad application of CRISPR technology in eukaryotic cells and organisms, and accelerate its clinical translation into humans. PMID:25186301

  16. Genetic resistance: tolerance to vector-borne diseases and the prospects and challenges of genomics.

    PubMed

    Bahbahani, H; Hanotte, O

    2015-04-01

    Vector-borne diseases in cattle and small ruminants (e.g. trypanosomosis, Rift Valley fever and East Coast fever) are associated with major economic losses in tropical countries, and particularly on the African continent. A variety of control strategies (e.g. management, vaccination and/or acaricide treatments) are used to minimise their negative impacts. These strategies are often associated with environmental, technical and/or economic drawbacks. However, several indigenous livestock populations have been reported to show a level of genetic tolerance or resistance to such disease challenges (e.g. trypanotolerant N'Dama cattle and Djallonké sheep). Use of these populations represents a sustainable alternative approach to minimising the negative impact of such infection/infestation on livestock production. This review summarises the current understanding of the genetic control of these adaptations, identifies knowledge gaps and critically examines the possible impacts of genomics approaches to the genetic improvement of tolerance and/or resistance to vector-borne diseases.

  17. Genetic resistance: tolerance to vector-borne diseases and the prospects and challenges of genomics.

    PubMed

    Bahbahani, H; Hanotte, O

    2015-04-01

    Vector-borne diseases in cattle and small ruminants (e.g. trypanosomosis, Rift Valley fever and East Coast fever) are associated with major economic losses in tropical countries, and particularly on the African continent. A variety of control strategies (e.g. management, vaccination and/or acaricide treatments) are used to minimise their negative impacts. These strategies are often associated with environmental, technical and/or economic drawbacks. However, several indigenous livestock populations have been reported to show a level of genetic tolerance or resistance to such disease challenges (e.g. trypanotolerant N'Dama cattle and Djallonké sheep). Use of these populations represents a sustainable alternative approach to minimising the negative impact of such infection/infestation on livestock production. This review summarises the current understanding of the genetic control of these adaptations, identifies knowledge gaps and critically examines the possible impacts of genomics approaches to the genetic improvement of tolerance and/or resistance to vector-borne diseases. PMID:26470457

  18. CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox.

    PubMed

    Senís, Elena; Fatouros, Chronis; Große, Stefanie; Wiedtke, Ellen; Niopek, Dominik; Mueller, Ann-Kristin; Börner, Kathleen; Grimm, Dirk

    2014-11-01

    Its remarkable ease and efficiency make the CRISPR (clustered regularly interspaced short palindromic repeats) DNA editing machinery highly attractive as a new tool for experimental gene annotation and therapeutic genome engineering in eukaryotes. Here, we report a versatile set of plasmids and vectors derived from adeno-associated virus (AAV) that allow robust and specific delivery of the two essential CRISPR components - Cas9 and chimeric g(uide)RNA - either alone or in combination. All our constructs share a modular design that enables simple and stringent guide RNA (gRNA) cloning as well as rapid exchange of promoters driving Cas9 or gRNA. Packaging into potent synthetic AAV capsids permits CRISPR delivery even into hard-to-transfect targets, as shown for human T-cells. Moreover, we demonstrate the feasibility to direct Cas9 expression to or away from hepatocytes, using a liver-specific promoter or a hepatic miRNA binding site, respectively. We also report a streamlined and economical protocol for detection of CRISPR-induced mutations in less than 3 h. Finally, we provide original evidence that AAV/CRISPR vectors can be exploited for gene engineering in vivo, as exemplified in the liver of adult mice. Our new tools and protocols should foster the broad application of CRISPR technology in eukaryotic cells and organisms, and accelerate its clinical translation into humans.

  19. Positive-selection and ligation-independent cloning vectors for large scale in planta expression for plant functional genomics.

    PubMed

    Oh, Sang-Keun; Kim, Saet-Byul; Yeom, Seon-In; Lee, Hyun-Ah; Choi, Doil

    2010-12-01

    Transient expression is an easy, rapid and powerful technique for producing proteins of interest in plants. Recombinational cloning is highly efficient but has disadvantages, including complicated, time consuming cloning procedures and expensive enzymes for large-scale gene cloning. To overcome these limitations, we developed new ligation-independent cloning (LIC) vectors derived from binary vectors including tobacco mosaic virus (pJL-TRBO), potato virus X (pGR106) and the pBI121 vector-based pMBP1. LIC vectors were modified to enable directional cloning of PCR products without restriction enzyme digestion or ligation reactions. In addition, the ccdB gene, which encodes a potent cell-killing protein, was introduced between the two LIC adapter sites in the pJL-LIC, pGR-LIC, and pMBP-LIC vectors for the efficient selection of recombinant clones. This new vector does not require restriction enzymes, alkaline phosphatase, or DNA ligase for cloning. To clone, the three LIC vectors are digested with SnaBI and treated with T4 DNA polymerase, which includes 3' to 5' exonuclease activity in the presence of only one dNTP (dGTP for the inserts and dCTP for the vector). To make recombinants, the vector plasmid and the insert PCR fragment were annealed at room temperature for 20 min prior to transformation into the host. Bacterial transformation was accomplished with 100% efficiency. To validate the new LIC vector systems, we were used to coexpressed the Phytophthora AVR and potato resistance (R) genes in N. benthamiana by infiltration of Agrobacterium. Coexpressed AVR and R genes in N. benthamiana induced the typical hypersensitive cell death resulting from in vivo interaction of the two proteins. These LIC vectors could be efficiently used for high-throughput cloning and laboratory-scale in planta expression. These vectors could provide a powerful tool for high-throughput transient expression assays for functional genomic studies in plants. PMID:21340673

  20. [Molecular mechanisms of the plague pathogenic agent interaction with invertebrates].

    PubMed

    Kutyrev, V V; Eroshenko, G A; Popov, N V; Vidiaeva, N A; Konnov, N P

    2009-01-01

    Microbe Russian Anti-Plague Research Institute, Saratov, Russia The literature data and experimental results of the authors on the molecular basis of plague agent interaction with invertebrates are discussed. The details of the plague agent life cycle, its genome organization, and molecular genetic mechanisms of its survival in flea vector and on the nematode cuticule are discussed. The experimental data about the ability to form biofilms at abiotic and biotic surfaces in the Yersinia pestis strains of the main and non-main subspecies are presented. Mechanisms of horizontal and vertical transmission of plague agent are considered. The suggestion about participation of the new member in the complex parasitic biocenosis (nematode, vector parasite) is put forward. PMID:20050160

  1. Recombinant Adeno-Associated Virus Vector Genomes Take the Form of Long-Lived, Transcriptionally Competent Episomes in Human Muscle.

    PubMed

    Schnepp, Bruce C; Chulay, Jeffrey D; Ye, Guo-Jie; Flotte, Terence R; Trapnell, Bruce C; Johnson, Philip R

    2016-01-01

    Gene augmentation therapy as a strategy to treat alpha-1 antitrypsin (AAT) deficiency has reached phase 2 clinical testing in humans. Sustained serum levels of AAT have been observed beyond one year after intramuscular administration of a recombinant adeno-associated virus (rAAV) vector expressing the AAT gene. In this study, sequential muscle biopsies obtained at 3 and 12 months after vector injection were examined for the presence of rAAV vector genomes. Each biopsy sample contained readily detectable vector DNA, the majority of which existed as double-stranded supercoiled and open circular episomes. Episomes persisted through 12 months, although at slightly lower levels than observed at 3 months. There was a clear dose response when comparing the low- and mid-vector-dose groups to the high-dose group. The highest absolute copy numbers were found in a high-dose subject, and serum AAT levels at 12 months confirmed that the high-dose group also had the highest sustained serum AAT levels. Sequence analysis revealed that the vast majority of episomes contained double-D inverted terminal repeats ranging from fully intact to severely deleted. Molecular clones of vector genomes derived directly from the biopsies were transcriptionally active, potentially identifying them as the source of serum AAT in the trial subjects.

  2. Functional neuropeptidomics in invertebrates.

    PubMed

    De Haes, Wouter; Van Sinay, Elien; Detienne, Giel; Temmerman, Liesbet; Schoofs, Liliane; Boonen, Kurt

    2015-07-01

    Neuropeptides are key messengers in almost all physiological processes. They originate from larger precursors and are extensively processed to become bioactive. Neuropeptidomics aims to comprehensively identify the collection of neuropeptides in an organism, organ, tissue or cell. The neuropeptidome of several invertebrates is thoroughly explored since they are important model organisms (and models for human diseases), disease vectors and pest species. The charting of the neuropeptidome is the first step towards understanding peptidergic signaling. This review will first discuss the latest developments in exploring the neuropeptidome. The physiological roles and modes of action of neuropeptides can be explored in two ways, which are largely orthogonal and therefore complementary. The first way consists of inferring the functions of neuropeptides by a forward approach where neuropeptide profiles are compared under different physiological conditions. Second is the reverse approach were neuropeptide collections are used to screen for receptor-binding. This is followed by localization studies and functional tests. This review will focus on how these different functional screening methods contributed to the field of invertebrate neuropeptidomics and expanded our knowledge of peptidergic signaling. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.

  3. Population and Evolutionary Genomics of Amblyomma americanum, an Expanding Arthropod Disease Vector

    PubMed Central

    Monzón, Javier D.; Atkinson, Elizabeth G.; Henn, Brenna M.; Benach, Jorge L.

    2016-01-01

    The lone star tick, Amblyomma americanum, is an important disease vector and the most frequent tick found attached to humans in the eastern United States. The lone star tick has recently experienced a rapid range expansion into the Northeast and Midwest, but despite this emerging infectious threat to wildlife, livestock, and human health, little is known about the genetic causes and consequences of the geographic expansion. In the first population genomic analysis of any tick species, we characterize the genetic diversity and population structure of A. americanum across its current geographic range, which has recently expanded. Using a high-throughput genotyping-by-sequencing approach, we discovered more than 8,000 single nucleotide polymorphisms in 90 ticks from five locations. Surprisingly, newly established populations in New York (NY) and Oklahoma (OK) are as diverse as historic range populations in North and South Carolina. However, substantial population structure occurs among regions, such that new populations in NY and OK are genetically distinct from historic range populations and from one another. Ticks from a laboratory colony are genetically distinct from wild populations, underscoring the need to account for natural variation when conducting transmission or immunological studies, many of which utilize laboratory-reared ticks. An FST-outlier analysis comparing a recently established population to a long-standing population detected numerous outlier sites, compatible with positive and balancing selection, highlighting the potential for adaptation during the range expansion. This study provides a framework for applying high-throughput DNA sequencing technologies for future investigations of ticks, which are common vectors of diseases. PMID:27190204

  4. High-throughput genomic mapping of vector integration sites in gene therapy studies.

    PubMed

    Beard, Brian C; Adair, Jennifer E; Trobridge, Grant D; Kiem, Hans-Peter

    2014-01-01

    Gene therapy has enormous potential to treat a variety of infectious and genetic diseases. To date hundreds of patients worldwide have received hematopoietic cell products that have been gene-modified with retrovirus vectors carrying therapeutic transgenes, and many patients have been cured or demonstrated disease stabilization as a result (Adair et al., Sci Transl Med 4:133ra57, 2012; Biffi et al., Science 341:1233158, 2013; Aiuti et al., Science 341:1233151, 2013; Fischer et al., Gene 525:170-173, 2013). Unfortunately, for some patients the provirus integration dysregulated the expression of nearby genes leading to clonal outgrowth and, in some cases, cancer. Thus, the unwanted side effect of insertional mutagenesis has become a major concern for retrovirus gene therapy. The careful study of retrovirus integration sites (RIS) and the contribution of individual gene-modified clones to hematopoietic repopulating cells is of crucial importance for all gene therapy studies. Supporting this, the US Food and Drug Administration (FDA) has mandated the careful monitoring of RIS in all clinical trials of gene therapy. An invaluable method was developed: linear amplification mediated-polymerase chain reaction (LAM-PCR) capable of analyzing in vitro and complex in vivo samples, capturing valuable genomic information directly flanking the site of provirus integration. Linking this method and similar methods to high-throughput sequencing has now made possible an unprecedented understanding of the integration profile of various retrovirus vectors, and allows for sensitive monitoring of their safety. It also allows for a detailed comparison of improved safety-enhanced gene therapy vectors. An important readout of safety is the relative contribution of individual gene-modified repopulating clones. One limitation of LAM-PCR is that the ability to capture the relative contribution of individual clones is compromised because of the initial linear PCR common to all current methods

  5. Aspects of pathogen genomics, diversity, epidemiology, vector dynamics, and disease management for a newly emerged disease of potato: zebra chip.

    PubMed

    Lin, Hong; Gudmestad, Neil C

    2013-06-01

    An overview is provided for the aspects of history, biology, genomics, genetics, and epidemiology of zebra chip (ZC), a destructive disease of potato (Solanum tuberosum) that represents a major threat to the potato industries in the United States as well as other potato-production regions in the world. The disease is associated with a gram-negative, phloem-limited, insect-vectored, unculturable prokaryote, 'Candidatus Liberibacter solanacearum', that belongs to the Rhizobiaceae family of α-Proteobacteria. The closest cultivated relatives of 'Ca. L. solanacearum' are members of the group of bacteria known as the α-2 subgroup. In spite of the fact that Koch's postulates sensu stricto have not been fulfilled, a great deal of progress has been made in understanding the ZC disease complex since discovery of the disease. Nevertheless, more research is needed to better understand vector biology, disease mechanisms, host response, and epidemiology in the context of vector-pathogen-plant interactions. Current ZC management strategies focus primarily on psyllid control. The ultimate control of ZC likely relies on host resistance. Unfortunately, all commercial potato cultivars are susceptible to ZC. Elucidation of the 'Ca. L. solanacearum' genome sequence has provided insights into the genetic basis of virulence and physiological and metabolic capability of this organism. Finally, the most effective, sustainable management of ZC is likely to be based on integrated strategies, including removal or reduction of vectors or inocula, improvement of host resistance to the presumptive pathogen and psyllid vectors, and novel gene-based therapeutic treatment.

  6. Genomic analyses of three malaria vectors reveals extensive shared polymorphism but contrasting population histories.

    PubMed

    O'Loughlin, Samantha M; Magesa, Stephen; Mbogo, Charles; Mosha, Franklin; Midega, Janet; Lomas, Susan; Burt, Austin

    2014-04-01

    Anopheles gambiae s.l. are important malaria vectors, but little is known about their genomic variation in the wild. Here, we present inter- and intraspecies analysis of genome-wide RADseq data, in three Anopheles gambiae s.l. species collected from East Africa. The mosquitoes fall into three genotypic clusters representing described species (A. gambiae, A. arabiensis, and A. merus) with no evidence of cryptic breeding units. Anopheles merus is the most divergent of the three species, supporting a recent new phylogeny based on chromosomal inversions. Even though the species clusters are well separated, there is extensive shared polymorphism, particularly between A. gambiae and A. arabiensis. Divergence between A. gambiae and A. arabiensis does not vary across the autosomes but is higher in X-linked inversions than elsewhere on X or on the autosomes, consistent with the suggestion that this inversion (or a gene within it) is important in reproductive isolation between the species. The 2La/2L+(a) inversion shows no more evidence of introgression between A. gambiae and A. arabiensis than the rest of the autosomes. Population differentiation within A. gambiae and A. arabiensis is weak over approximately 190-270 km, implying no strong barriers to dispersal. Analysis of Tajima's D and the allele frequency spectrum is consistent with modest population increases in A. arabiensis and A. merus, but a more complex demographic history of expansion followed by contraction in A. gambiae. Although they are less than 200 km apart, the two A. gambiae populations show evidence of different demographic histories.

  7. Analysis of the evolutionary forces shaping mitochondrial genomes of a Neotropical malaria vector complex

    PubMed Central

    Krzywinski, Jaroslaw; Li, Cong; Morris, Marion; Conn, Jan E.; Lima, José B.; Povoa, Marinete M.; Wilkerson, Richard C.

    2011-01-01

    Many vectors of human malaria belong to complexes of morphologically indistinguishable cryptic species. Here we report the analysis of the newly sequenced complete mitochondrial DNA molecules from six recognized or putative species of one such group, the Neotropical Anopheles albitarsis complex. The molecular evolution of these genomes had been driven by purifying selection, particularly strongly acting on the RNA genes. Directional mutation pressure associated with the strand-asynchronous asymmetric mtDNA replication mechanism may have shaped a pronounced DNA strand asymmetry in the nucleotide composition in these and other Anopheles species. The distribution of sequence polymorphism, coupled with the conflicting phylogenetic trees inferred from the mitochondrial DNA and from the published white gene fragment sequences, indicates that the evolution of the complex may have involved ancient mtDNA introgression. Six protein coding genes (nad5, nad4, cox3, atp6, cox1 and nad2) have high levels of sequence divergence and are likely informative for population genetics studies. Finally, the extent of the mitochondrial DNA variation within the complex supports the notion that the complex consists of a larger number of species than until recently believed. PMID:21241811

  8. RNAi and viral vectors as useful tools in the functional genomics of plants. Construction of BMV-based vectors for RNA delivery into plant cells.

    PubMed

    Wojtkowiak, Agnieszka; Siek, Anna; Alejska, Magdalena; Jarmołowski, Artur; Szweykowska-Kulińska, Zofia; Figlerowicz, Marek

    2002-01-01

    The sequencing of several complete genomes and the development of a DNA microarray technology are among the most important achievements of molecular biology. They gave the proper grounds for the development of modern functional genomics. However, there is one additional condition which needs to be satisfied to truely enable the study of how a genome works: a suitable method of selectively inducing and silencing the expression of each individual gene. The methods used so far have usually only permitted the influencing of gene expression through genetic manipulations at the DNA level (genetically modified plants). The discovery of RNA interference (RNAi) opens up completely new possibilities of research on the functioning of particular plant genes, without the necessity of altering the genome structure. In this case, interference takes place at the transcript level. Thus, at any given moment during plant development, the expression of a specific gene (or several genes) can be inhibited, even if it is important for the survival of the organism under study. To this end, a double-stranded RNA inducing the RNAi phenomenon has to be delivered into the plant cell. Here we describe the construction of four brome mosaic virus-based vectors, which, as our preliminary data indicate, can be used to transfer RNA into barley cells.

  9. Comparative Genomics- Identifying similarities and differences across three leafhopper vectors of Xylella fastidiosa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Leafhoppers are the second most important vectors of agricultural diseases, thus we examined the gene expression across three leafhopper leafhoppers, Homalodisca vitripennis, Graphocephala atropunctata, and Oncometopia nigricans, which are vectors of the plant-infecting bacterium, Xylella fastidiosa...

  10. A bifunctional invertebrate-type lysozyme from the disk abalone, Haliotis discus discus: genome organization, transcriptional profiling and biological activities of recombinant protein.

    PubMed

    Bathige, S D N K; Umasuthan, Navaneethaiyer; Kasthuri, Saranya Revathy; Whang, Ilson; Lim, Bong-Soo; Nam, Bo-Hye; Lee, Jehee

    2013-10-01

    Lysozyme is an important enzyme in the innate immune system that plays a vital role in fighting microbial infections. In the current study, we identified, cloned, and characterized a gene that encodes an invertebrate-type lysozyme from the disk abalone, Haliotis discus discus (abLysI). The full-length cDNA of abLysI consisted of 545 bp with an open reading frame of 393 bp that encodes 131 amino acids. The theoretical molecular mass of mature abLysI was 12.3 kDa with an isoelectric point of 8.03. Conserved features in other homologs, such as catalytic sites for lytic activity (Glu(30) and Asp(41)), isopeptidase activity (His(107)), and ten cysteine residues were identified in abLysI. Genomic sequence analysis with respect to its cDNA showed that abLysI was organized into four exons interrupted by three introns. Several immune-related transcription factor binding sites were discovered in the putative promoter region. Homology and phylogeny analysis of abLysI depicted high identity and closer proximity, respectively, with an annelid i-type lysozyme from Hirudo medicinalis, and indicated that abLysI is a novel molluscan i-type lysozyme. Tissue-specific expressional studies revealed that abLysI is mainly transcribed in hepatopancreas followed by mantle. In addition, abLysI mRNA expression was induced following bacterial (Vibrio parahaemolyticus and Listeria monocytogenes) and viral (viral hemorrhagic septicemia virus) challenges. Recombinantly expressed abLysI [(r)abLysI] demonstrated strong lytic activity against Micrococcus lysodeikticus, isopeptidase activity, and antibacterial activity against several Gram-positive and Gram-negative bacteria. Moreover, (r)abLysI showed optimum lytic activity at pH 4.0 and 60 °C, while exhibiting optimum isopeptidase activity at pH 7.0. Taken together, these results indicate that abLysI is potentially involved in immune responses of the disk abalone to protect it from invaders.

  11. EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae

    PubMed Central

    Baallal Jacobsen, Simo Abdessamad; Jensen, Niels B.; Kildegaard, Kanchana R.; Herrgård, Markus J.; Schneider, Konstantin; Koza, Anna; Forster, Jochen; Nielsen, Jens; Borodina, Irina

    2016-01-01

    Saccharomyces cerevisiae is widely used in the biotechnology industry for production of ethanol, recombinant proteins, food ingredients and other chemicals. In order to generate highly producing and stable strains, genome integration of genes encoding metabolic pathway enzymes is the preferred option. However, integration of pathway genes in single or few copies, especially those encoding rate-controlling steps, is often not sufficient to sustain high metabolic fluxes. By exploiting the sequence diversity in the long terminal repeats (LTR) of Ty retrotransposons, we developed a new set of integrative vectors, EasyCloneMulti, that enables multiple and simultaneous integration of genes in S. cerevisiae. By creating vector backbones that combine consensus sequences that aim at targeting subsets of Ty sequences and a quickly degrading selective marker, integrations at multiple genomic loci and a range of expression levels were obtained, as assessed with the green fluorescent protein (GFP) reporter system. The EasyCloneMulti vector set was applied to balance the expression of the rate-controlling step in the β-alanine pathway for biosynthesis of 3-hydroxypropionic acid (3HP). The best 3HP producing clone, with 5.45 g.L-1 of 3HP, produced 11 times more 3HP than the lowest producing clone, which demonstrates the capability of EasyCloneMulti vectors to impact metabolic pathway enzyme activity. PMID:26934490

  12. Construction of a genomic DNA library with a TA vector and its application in cloning of the phytoene synthase gene from the cyanobacterium Spirulina platensis M-135

    NASA Astrophysics Data System (ADS)

    Yoshikazu, Kawata; Shin-Ichi, Yano; Hiroyuki, Kojima

    1998-03-01

    An efficient and simple method for constructing a genomic DNA library using a TA cloning vector is presented. It is based on the sonicative cleavage of genomic DNA and modification of fragment ends with Taq DNA polymerase, followed by ligation using a TA vector. This method was applied for cloning of the phytoene synthase gene crt B from Spirulina platensis. This method is useful when genomic DNA cannot be efficiently digested with restriction enzymes, a problem often encountered during the construction of a genomic DNA library of cyanobacteria.

  13. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.

    PubMed

    Mesquita, Rafael D; Vionette-Amaral, Raquel J; Lowenberger, Carl; Rivera-Pomar, Rolando; Monteiro, Fernando A; Minx, Patrick; Spieth, John; Carvalho, A Bernardo; Panzera, Francisco; Lawson, Daniel; Torres, André Q; Ribeiro, Jose M C; Sorgine, Marcos H F; Waterhouse, Robert M; Montague, Michael J; Abad-Franch, Fernando; Alves-Bezerra, Michele; Amaral, Laurence R; Araujo, Helena M; Araujo, Ricardo N; Aravind, L; Atella, Georgia C; Azambuja, Patricia; Berni, Mateus; Bittencourt-Cunha, Paula R; Braz, Gloria R C; Calderón-Fernández, Gustavo; Carareto, Claudia M A; Christensen, Mikkel B; Costa, Igor R; Costa, Samara G; Dansa, Marilvia; Daumas-Filho, Carlos R O; De-Paula, Iron F; Dias, Felipe A; Dimopoulos, George; Emrich, Scott J; Esponda-Behrens, Natalia; Fampa, Patricia; Fernandez-Medina, Rita D; da Fonseca, Rodrigo N; Fontenele, Marcio; Fronick, Catrina; Fulton, Lucinda A; Gandara, Ana Caroline; Garcia, Eloi S; Genta, Fernando A; Giraldo-Calderón, Gloria I; Gomes, Bruno; Gondim, Katia C; Granzotto, Adriana; Guarneri, Alessandra A; Guigó, Roderic; Harry, Myriam; Hughes, Daniel S T; Jablonka, Willy; Jacquin-Joly, Emmanuelle; Juárez, M Patricia; Koerich, Leonardo B; Lange, Angela B; Latorre-Estivalis, José Manuel; Lavore, Andrés; Lawrence, Gena G; Lazoski, Cristiano; Lazzari, Claudio R; Lopes, Raphael R; Lorenzo, Marcelo G; Lugon, Magda D; Majerowicz, David; Marcet, Paula L; Mariotti, Marco; Masuda, Hatisaburo; Megy, Karine; Melo, Ana C A; Missirlis, Fanis; Mota, Theo; Noriega, Fernando G; Nouzova, Marcela; Nunes, Rodrigo D; Oliveira, Raquel L L; Oliveira-Silveira, Gilbert; Ons, Sheila; Orchard, Ian; Pagola, Lucia; Paiva-Silva, Gabriela O; Pascual, Agustina; Pavan, Marcio G; Pedrini, Nicolás; Peixoto, Alexandre A; Pereira, Marcos H; Pike, Andrew; Polycarpo, Carla; Prosdocimi, Francisco; Ribeiro-Rodrigues, Rodrigo; Robertson, Hugh M; Salerno, Ana Paula; Salmon, Didier; Santesmasses, Didac; Schama, Renata; Seabra-Junior, Eloy S; Silva-Cardoso, Livia; Silva-Neto, Mario A C; Souza-Gomes, Matheus; Sterkel, Marcos; Taracena, Mabel L; Tojo, Marta; Tu, Zhijian Jake; Tubio, Jose M C; Ursic-Bedoya, Raul; Venancio, Thiago M; Walter-Nuno, Ana Beatriz; Wilson, Derek; Warren, Wesley C; Wilson, Richard K; Huebner, Erwin; Dotson, Ellen M; Oliveira, Pedro L

    2015-12-01

    Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼ 702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods. PMID:26627243

  14. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

    PubMed Central

    Mesquita, Rafael D.; Vionette-Amaral, Raquel J.; Lowenberger, Carl; Rivera-Pomar, Rolando; Monteiro, Fernando A.; Minx, Patrick; Spieth, John; Carvalho, A. Bernardo; Panzera, Francisco; Lawson, Daniel; Torres, André Q.; Ribeiro, Jose M. C.; Sorgine, Marcos H. F.; Waterhouse, Robert M.; Abad-Franch, Fernando; Alves-Bezerra, Michele; Amaral, Laurence R.; Araujo, Helena M.; Aravind, L.; Atella, Georgia C.; Azambuja, Patricia; Berni, Mateus; Bittencourt-Cunha, Paula R.; Braz, Gloria R. C.; Calderón-Fernández, Gustavo; Carareto, Claudia M. A.; Christensen, Mikkel B.; Costa, Igor R.; Costa, Samara G.; Dansa, Marilvia; Daumas-Filho, Carlos R. O.; De-Paula, Iron F.; Dias, Felipe A.; Dimopoulos, George; Emrich, Scott J.; Esponda-Behrens, Natalia; Fampa, Patricia; Fernandez-Medina, Rita D.; da Fonseca, Rodrigo N.; Fontenele, Marcio; Fronick, Catrina; Fulton, Lucinda A.; Gandara, Ana Caroline; Garcia, Eloi S.; Genta, Fernando A.; Giraldo-Calderón, Gloria I.; Gomes, Bruno; Gondim, Katia C.; Granzotto, Adriana; Guarneri, Alessandra A.; Guigó, Roderic; Harry, Myriam; Hughes, Daniel S. T.; Jablonka, Willy; Jacquin-Joly, Emmanuelle; Juárez, M. Patricia; Koerich, Leonardo B.; Lange, Angela B.; Latorre-Estivalis, José Manuel; Lavore, Andrés; Lawrence, Gena G.; Lazoski, Cristiano; Lazzari, Claudio R.; Lopes, Raphael R.; Lorenzo, Marcelo G.; Lugon, Magda D.; Marcet, Paula L.; Mariotti, Marco; Masuda, Hatisaburo; Megy, Karine; Missirlis, Fanis; Mota, Theo; Noriega, Fernando G.; Nouzova, Marcela; Nunes, Rodrigo D.; Oliveira, Raquel L. L.; Oliveira-Silveira, Gilbert; Ons, Sheila; Orchard, Ian; Pagola, Lucia; Paiva-Silva, Gabriela O.; Pascual, Agustina; Pavan, Marcio G.; Pedrini, Nicolás; Peixoto, Alexandre A.; Pereira, Marcos H.; Pike, Andrew; Polycarpo, Carla; Prosdocimi, Francisco; Ribeiro-Rodrigues, Rodrigo; Robertson, Hugh M.; Salerno, Ana Paula; Salmon, Didier; Santesmasses, Didac; Schama, Renata; Seabra-Junior, Eloy S.; Silva-Cardoso, Livia; Silva-Neto, Mario A. C.; Souza-Gomes, Matheus; Sterkel, Marcos; Taracena, Mabel L.; Tojo, Marta; Tu, Zhijian Jake; Tubio, Jose M. C.; Ursic-Bedoya, Raul; Venancio, Thiago M.; Walter-Nuno, Ana Beatriz; Wilson, Derek; Warren, Wesley C.; Wilson, Richard K.; Huebner, Erwin; Dotson, Ellen M.; Oliveira, Pedro L.

    2015-01-01

    Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods. PMID:26627243

  15. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.

    PubMed

    Mesquita, Rafael D; Vionette-Amaral, Raquel J; Lowenberger, Carl; Rivera-Pomar, Rolando; Monteiro, Fernando A; Minx, Patrick; Spieth, John; Carvalho, A Bernardo; Panzera, Francisco; Lawson, Daniel; Torres, André Q; Ribeiro, Jose M C; Sorgine, Marcos H F; Waterhouse, Robert M; Montague, Michael J; Abad-Franch, Fernando; Alves-Bezerra, Michele; Amaral, Laurence R; Araujo, Helena M; Araujo, Ricardo N; Aravind, L; Atella, Georgia C; Azambuja, Patricia; Berni, Mateus; Bittencourt-Cunha, Paula R; Braz, Gloria R C; Calderón-Fernández, Gustavo; Carareto, Claudia M A; Christensen, Mikkel B; Costa, Igor R; Costa, Samara G; Dansa, Marilvia; Daumas-Filho, Carlos R O; De-Paula, Iron F; Dias, Felipe A; Dimopoulos, George; Emrich, Scott J; Esponda-Behrens, Natalia; Fampa, Patricia; Fernandez-Medina, Rita D; da Fonseca, Rodrigo N; Fontenele, Marcio; Fronick, Catrina; Fulton, Lucinda A; Gandara, Ana Caroline; Garcia, Eloi S; Genta, Fernando A; Giraldo-Calderón, Gloria I; Gomes, Bruno; Gondim, Katia C; Granzotto, Adriana; Guarneri, Alessandra A; Guigó, Roderic; Harry, Myriam; Hughes, Daniel S T; Jablonka, Willy; Jacquin-Joly, Emmanuelle; Juárez, M Patricia; Koerich, Leonardo B; Lange, Angela B; Latorre-Estivalis, José Manuel; Lavore, Andrés; Lawrence, Gena G; Lazoski, Cristiano; Lazzari, Claudio R; Lopes, Raphael R; Lorenzo, Marcelo G; Lugon, Magda D; Majerowicz, David; Marcet, Paula L; Mariotti, Marco; Masuda, Hatisaburo; Megy, Karine; Melo, Ana C A; Missirlis, Fanis; Mota, Theo; Noriega, Fernando G; Nouzova, Marcela; Nunes, Rodrigo D; Oliveira, Raquel L L; Oliveira-Silveira, Gilbert; Ons, Sheila; Orchard, Ian; Pagola, Lucia; Paiva-Silva, Gabriela O; Pascual, Agustina; Pavan, Marcio G; Pedrini, Nicolás; Peixoto, Alexandre A; Pereira, Marcos H; Pike, Andrew; Polycarpo, Carla; Prosdocimi, Francisco; Ribeiro-Rodrigues, Rodrigo; Robertson, Hugh M; Salerno, Ana Paula; Salmon, Didier; Santesmasses, Didac; Schama, Renata; Seabra-Junior, Eloy S; Silva-Cardoso, Livia; Silva-Neto, Mario A C; Souza-Gomes, Matheus; Sterkel, Marcos; Taracena, Mabel L; Tojo, Marta; Tu, Zhijian Jake; Tubio, Jose M C; Ursic-Bedoya, Raul; Venancio, Thiago M; Walter-Nuno, Ana Beatriz; Wilson, Derek; Warren, Wesley C; Wilson, Richard K; Huebner, Erwin; Dotson, Ellen M; Oliveira, Pedro L

    2015-12-01

    Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼ 702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods.

  16. Comparative genomic survey, exon-intron annotation and phylogenetic analysis of NAT-homologous sequences in archaea, protists, fungi, viruses, and invertebrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have previously published extensive genomic surveys [1-3], reporting NAT-homologous sequences in hundreds of sequenced bacterial, fungal and vertebrate genomes. We present here the results of our latest search of 2445 genomes, representing 1532 (70 archaeal, 1210 bacterial, 43 protist, 97 fungal,...

  17. Virus-Derived Gene Expression and RNA Interference Vector for Grapevine

    PubMed Central

    Kurth, Elizabeth G.; Peremyslov, Valera V.; Prokhnevsky, Alexey I.; Kasschau, Kristin D.; Miller, Marilyn; Carrington, James C.

    2012-01-01

    The improvement of the agricultural and wine-making qualities of the grapevine (Vitis vinifera) is hampered by adherence to traditional varieties, the recalcitrance of this plant to genetic modifications, and public resistance to genetically modified organism (GMO) technologies. To address these challenges, we developed an RNA virus-based vector for the introduction of desired traits into grapevine without heritable modifications to the genome. This vector expresses recombinant proteins in the phloem tissue that is involved in sugar transport throughout the plant, from leaves to roots to berries. Furthermore, the vector provides a powerful RNA interference (RNAi) capability of regulating the expression of endogenous genes via virus-induced gene-silencing (VIGS) technology. Additional advantages of this vector include superb genetic capacity and stability, as well as the swiftness of technology implementation. The most significant applications of the viral vector include functional genomics of the grapevine and disease control via RNAi-enabled vaccination against pathogens or invertebrate pests. PMID:22438553

  18. Virus-derived gene expression and RNA interference vector for grapevine.

    PubMed

    Kurth, Elizabeth G; Peremyslov, Valera V; Prokhnevsky, Alexey I; Kasschau, Kristin D; Miller, Marilyn; Carrington, James C; Dolja, Valerian V

    2012-06-01

    The improvement of the agricultural and wine-making qualities of the grapevine (Vitis vinifera) is hampered by adherence to traditional varieties, the recalcitrance of this plant to genetic modifications, and public resistance to genetically modified organism (GMO) technologies. To address these challenges, we developed an RNA virus-based vector for the introduction of desired traits into grapevine without heritable modifications to the genome. This vector expresses recombinant proteins in the phloem tissue that is involved in sugar transport throughout the plant, from leaves to roots to berries. Furthermore, the vector provides a powerful RNA interference (RNAi) capability of regulating the expression of endogenous genes via virus-induced gene-silencing (VIGS) technology. Additional advantages of this vector include superb genetic capacity and stability, as well as the swiftness of technology implementation. The most significant applications of the viral vector include functional genomics of the grapevine and disease control via RNAi-enabled vaccination against pathogens or invertebrate pests.

  19. From Agrobacterium to viral vectors: genome modification of plant cells by rare cutting restriction enzymes.

    PubMed

    Marton, Ira; Honig, Arik; Omid, Ayelet; De Costa, Noam; Marhevka, Elena; Cohen, Barry; Zuker, Amir; Vainstein, Alexander

    2013-01-01

    Researchers and biotechnologists require methods to accurately modify the genome of higher eukaryotic cells. Such modifications include, but are not limited to, site-specific mutagenesis, site-specific insertion of foreign DNA, and replacement and deletion of native sequences. Accurate genome modifications in plant species have been rather limited, with only a handful of plant species and genes being modified through the use of early genome-editing techniques. The development of rare-cutting restriction enzymes as a tool for the induction of site-specific genomic double-strand breaks and their introduction as a reliable tool for genome modification in animals, animal cells and human cell lines have paved the way for the adaptation of rare-cutting restriction enzymes to genome editing in plant cells. Indeed, the number of plant species and genes which have been successfully edited using zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and engineered homing endonucleases is on the rise. In our review, we discuss the basics of rare-cutting restriction enzyme-mediated genome-editing technology with an emphasis on its application in plant species.

  20. Pancreatic cancer modeling using retrograde viral vector delivery and in vivo CRISPR/Cas9-mediated somatic genome editing

    PubMed Central

    Chiou, Shin-Heng; Winters, Ian P.; Wang, Jing; Naranjo, Santiago; Dudgeon, Crissy; Tamburini, Fiona B.; Brady, Jennifer J.; Yang, Dian; Grüner, Barbara M.; Chuang, Chen-Hua; Caswell, Deborah R.; Zeng, Hong; Chu, Pauline; Kim, Grace E.; Carpizo, Darren R.; Kim, Seung K.; Winslow, Monte M.

    2015-01-01

    Pancreatic ductal adenocarcinoma (PDAC) is a genomically diverse, prevalent, and almost invariably fatal malignancy. Although conventional genetically engineered mouse models of human PDAC have been instrumental in understanding pancreatic cancer development, these models are much too labor-intensive, expensive, and slow to perform the extensive molecular analyses needed to adequately understand this disease. Here we demonstrate that retrograde pancreatic ductal injection of either adenoviral-Cre or lentiviral-Cre vectors allows titratable initiation of pancreatic neoplasias that progress into invasive and metastatic PDAC. To enable in vivo CRISPR/Cas9-mediated gene inactivation in the pancreas, we generated a Cre-regulated Cas9 allele and lentiviral vectors that express Cre and a single-guide RNA. CRISPR-mediated targeting of Lkb1 in combination with oncogenic Kras expression led to selection for inactivating genomic alterations, absence of Lkb1 protein, and rapid tumor growth that phenocopied Cre-mediated genetic deletion of Lkb1. This method will transform our ability to rapidly interrogate gene function during the development of this recalcitrant cancer. PMID:26178787

  1. Pancreatic cancer modeling using retrograde viral vector delivery and in vivo CRISPR/Cas9-mediated somatic genome editing.

    PubMed

    Chiou, Shin-Heng; Winters, Ian P; Wang, Jing; Naranjo, Santiago; Dudgeon, Crissy; Tamburini, Fiona B; Brady, Jennifer J; Yang, Dian; Grüner, Barbara M; Chuang, Chen-Hua; Caswell, Deborah R; Zeng, Hong; Chu, Pauline; Kim, Grace E; Carpizo, Darren R; Kim, Seung K; Winslow, Monte M

    2015-07-15

    Pancreatic ductal adenocarcinoma (PDAC) is a genomically diverse, prevalent, and almost invariably fatal malignancy. Although conventional genetically engineered mouse models of human PDAC have been instrumental in understanding pancreatic cancer development, these models are much too labor-intensive, expensive, and slow to perform the extensive molecular analyses needed to adequately understand this disease. Here we demonstrate that retrograde pancreatic ductal injection of either adenoviral-Cre or lentiviral-Cre vectors allows titratable initiation of pancreatic neoplasias that progress into invasive and metastatic PDAC. To enable in vivo CRISPR/Cas9-mediated gene inactivation in the pancreas, we generated a Cre-regulated Cas9 allele and lentiviral vectors that express Cre and a single-guide RNA. CRISPR-mediated targeting of Lkb1 in combination with oncogenic Kras expression led to selection for inactivating genomic alterations, absence of Lkb1 protein, and rapid tumor growth that phenocopied Cre-mediated genetic deletion of Lkb1. This method will transform our ability to rapidly interrogate gene function during the development of this recalcitrant cancer. PMID:26178787

  2. Generation of a replication-competent, propagation-deficient virus vector based on the transmissible gastroenteritis coronavirus genome.

    PubMed

    Ortego, Javier; Escors, David; Laude, Hubert; Enjuanes, Luis

    2002-11-01

    Replication-competent propagation-deficient virus vectors based on the transmissible gastroenteritis coronavirus (TGEV) genome that are deficient in the essential E gene have been developed by complementation within E(+) packaging cell lines. Cell lines expressing the TGEV E protein were established using the noncytopathic Sindbis virus replicon pSINrep21. In addition, cell lines stably expressing the E gene under the CMV promoter have been developed. The Sindbis replicon vector and the ectopic TGEV E protein did not interfere with the rescue of infectious TGEV from full-length cDNA. Recombinant TGEV deficient in the nonessential 3a and 3b genes and the essential E gene (rTGEV-Delta3abDeltaE) was successfully rescued in these cell lines. rTGEV-Delta3abDeltaE reached high titers (10(7) PFU/ml) in baby hamster kidney cells expressing porcine aminopeptidase N (BHK-pAPN), the cellular receptor for TGEV, using Sindbis replicon and reached titers up to 5 x 10(5) PFU/ml in cells stably expressing E protein under the control of the CMV promoter. The virus titers were proportional to the E protein expression level. The rTGEV-Delta3abDeltaE virions produced in the packaging cell line showed the same morphology and stability under different pHs and temperatures as virus derived from the full-length rTGEV genome, although a delay in virus assembly was observed by electron microscopy and virus titration in the complementation system in relation to the wild-type virus. These viruses were stably grown for >10 passages in the E(+) packaging cell lines. The availability of packaging cell lines will significantly facilitate the production of safe TGEV-derived vectors for vaccination and possibly gene therapy.

  3. Absolute determination of single-stranded and self-complementary adeno-associated viral vector genome titers by droplet digital PCR.

    PubMed

    Lock, Martin; Alvira, Mauricio R; Chen, Shu-Jen; Wilson, James M

    2014-04-01

    Accurate titration of adeno-associated viral (AAV) vector genome copies is critical for ensuring correct and reproducible dosing in both preclinical and clinical settings. Quantitative PCR (qPCR) is the current method of choice for titrating AAV genomes because of the simplicity, accuracy, and robustness of the assay. However, issues with qPCR-based determination of self-complementary AAV vector genome titers, due to primer-probe exclusion through genome self-annealing or through packaging of prematurely terminated defective interfering (DI) genomes, have been reported. Alternative qPCR, gel-based, or Southern blotting titering methods have been designed to overcome these issues but may represent a backward step from standard qPCR methods in terms of simplicity, robustness, and precision. Droplet digital PCR (ddPCR) is a new PCR technique that directly quantifies DNA copies with an unparalleled degree of precision and without the need for a standard curve or for a high degree of amplification efficiency; all properties that lend themselves to the accurate quantification of both single-stranded and self-complementary AAV genomes. Here we compare a ddPCR-based AAV genome titer assay with a standard and an optimized qPCR assay for the titration of both single-stranded and self-complementary AAV genomes. We demonstrate absolute quantification of single-stranded AAV vector genomes by ddPCR with up to 4-fold increases in titer over a standard qPCR titration but with equivalent readout to an optimized qPCR assay. In the case of self-complementary vectors, ddPCR titers were on average 5-, 1.9-, and 2.3-fold higher than those determined by standard qPCR, optimized qPCR, and agarose gel assays, respectively. Droplet digital PCR-based genome titering was superior to qPCR in terms of both intra- and interassay precision and is more resistant to PCR inhibitors, a desirable feature for in-process monitoring of early-stage vector production and for vector genome biodistribution

  4. An efficient virus-induced gene silencing vector for maize functional genomics research.

    PubMed

    Wang, Rong; Yang, Xinxin; Wang, Nian; Liu, Xuedong; Nelson, Richard S; Li, Weimin; Fan, Zaifeng; Zhou, Tao

    2016-04-01

    Maize is a major crop whose rich genetic diversity provides an advanced resource for genetic research. However, a tool for rapid transient gene function analysis in maize that may be utilized in most maize cultivars has been lacking, resulting in reliance on time-consuming stable transformation and mutation studies to obtain answers. We developed an efficient virus-induced gene silencing (VIGS) vector for maize based on a naturally maize-infecting cucumber mosaic virus (CMV) strain, ZMBJ-CMV. An infectious clone of ZMBJ-CMV was constructed, and a vascular puncture inoculation method utilizing Agrobacterium was optimized to improve its utility for CMV infection of maize. ZMBJ-CMV was then modified to function as a VIGS vector. The ZMBJ-CMV vector induced mild to moderate symptoms in many maize lines, making it useful for gene function studies in critically important maize cultivars, such as the sequenced reference inbred line B73. Using this CMV VIGS system, expression of two endogenous genes, ZmPDS and ZmIspH, was found to be decreased by 75% and 78%, respectively, compared with non-silenced tissue. Inserts with lengths of 100-300 bp produced the most complete transcriptional and visual silencing phenotypes. Moreover, genes related to autophagy, ZmATG3 and ZmATG8a, were also silenced, and it was found that they function in leaf starch degradation. These results indicate that our ZMBJ-CMV VIGS vector provides a tool for rapid and efficient gene function studies in maize. PMID:26921244

  5. Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9): genomic evidence for oscillation between invertebrates and mammals

    PubMed Central

    2011-01-01

    Background Yersinia enterocolitica strains responsible for mild gastroenteritis in humans are very diverse with respect to their metabolic and virulence properties. Strain W22703 (biotype 2, serotype O:9) was recently identified to possess nematocidal and insecticidal activity. To better understand the relationship between pathogenicity towards insects and humans, we compared the W22703 genome with that of the highly pathogenic strain 8081 (biotype1B; serotype O:8), the only Y. enterocolitica strain sequenced so far. Results We used whole-genome shotgun data to assemble, annotate and analyse the sequence of strain W22703. Numerous factors assumed to contribute to enteric survival and pathogenesis, among them osmoregulated periplasmic glucan, hydrogenases, cobalamin-dependent pathways, iron uptake systems and the Yersinia genome island 1 (YGI-1) involved in tight adherence were identified to be common to the 8081 and W22703 genomes. However, sets of ~550 genes revealed to be specific for each of them in comparison to the other strain. The plasticity zone (PZ) of 142 kb in the W22703 genome carries an ancient flagellar cluster Flg-2 of ~40 kb, but it lacks the pathogenicity island YAPIYe, the secretion system ysa and yts1, and other virulence determinants of the 8081 PZ. Its composition underlines the prominent variability of this genome region and demonstrates its contribution to the higher pathogenicity of biotype 1B strains with respect to W22703. A novel type three secretion system of mosaic structure was found in the genome of W22703 that is absent in the sequenced strains of the human pathogenic Yersinia species, but conserved in the genomes of the apathogenic species. We identified several regions of differences in W22703 that mainly code for transporters, regulators, metabolic pathways, and defence factors. Conclusion The W22703 sequence analysis revealed a genome composition distinct from other pathogenic Yersinia enterocolitica strains, thus contributing

  6. Genome-Wide Patterns of Gene Expression during Aging in the African Malaria Vector Anopheles gambiae

    PubMed Central

    Wang, Mei-Hui; Marinotti, Osvaldo; James, Anthony A.; Walker, Edward; Githure, John; Yan, Guiyun

    2010-01-01

    The primary means of reducing malaria transmission is through reduction in longevity in days of the adult female stage of the Anopheles vector. However, assessing chronological age is limited to crude physiologic methods which categorize the females binomially as either very young (nulliparous) or not very young (parous). Yet the epidemiologically relevant reduction in life span falls within the latter category. Age-grading methods that delineate chronological age, using accurate molecular surrogates based upon gene expression profiles, will allow quantification of the longevity-reducing effects of vector control tools aimed at the adult, female mosquito. In this study, microarray analyses of gene expression profiles in the African malaria vector Anopheles gambiae were conducted during natural senescence of females in laboratory conditions. Results showed that detoxification-related and stress-responsive genes were up-regulated as mosquitoes aged. A total of 276 transcripts had age-dependent expression, independently of blood feeding and egg laying events. Expression of 112 (40.6%) of these transcripts increased or decreased monotonically with increasing chronologic age. Seven candidate genes for practical age assessment were tested by quantitative gene amplification in the An. gambiae G3 strain in a laboratory experiment and the Mbita strain in field enclosures set up in western Kenya under conditions closely resembling natural ones. Results were similar between experiments, indicating that senescence is marked by changes in gene expression and that chronological age can be gauged accurately and repeatedly with this method. These results indicate that the method may be suitable for accurate gauging of the age in days of field-caught, female An. gambiae. PMID:20967211

  7. A Global Genomic Characterization of Nairoviruses Identifies Nine Discrete Genogroups with Distinctive Structural Characteristics and Host-Vector Associations

    PubMed Central

    Walker, Peter J.; Widen, Steven G.; Wood, Thomas G.; Guzman, Hilda; Tesh, Robert B.; Vasilakis, Nikolaos

    2016-01-01

    Nairoviruses are primarily tick-borne bunyaviruses, some of which are known to cause mild-to-severe febrile illness in humans or livestock. We describe the genome sequences of 11 poorly characterized nairoviruses that have ecological associations with either birds (Farallon, Punta Salinas, Sapphire II, Zirqa, Avalon, Clo Mor, Taggert, and Abu Hammad viruses), rodents (Qalyub and Bandia viruses), or camels (Dera Ghazi Khan virus). Global phylogenetic analyses of proteins encoded in the L, M, and S RNA segments of these and 20 other available nairovirus genomes identified nine well-supported genogroups (Nairobi sheep disease, Thiafora, Sakhalin, Keterah, Qalyub, Kasokero, Dera Ghazi Khan, Hughes, and Tamdy). Genogroup-specific structural variations were evident, particularly in the M segment encoding a polyprotein from which virion envelope glycoproteins (Gn and Gc) are generated by proteolytic processing. Structural variations include the extension, abbreviation, or absence sequences encoding an O-glycosylated mucin-like protein in the N-terminal domain, distinctive patterns of conserved cysteine residues in the GP38-like domain, insertion of sequences encoding a double-membrane-spanning protein (NSm) between the Gn and Gc domains, and the presence of an alternative long open reading frame encoding a viroporin-like transmembrane protein (Gx). We also observed strong genogroup-specific associations with categories of hosts and tick vectors. PMID:26903607

  8. Comparative Genomic Integration Profiling of Sleeping Beauty Transposons Mobilized With High Efficacy From Integrase-defective Lentiviral Vectors in Primary Human Cells

    PubMed Central

    Moldt, Brian; Miskey, Csaba; Staunstrup, Nicklas Heine; Gogol-Döring, Andreas; Bak, Rasmus O; Sharma, Nynne; Mátés, Lajos; Izsvák, Zsuzsanna; Chen, Wei; Ivics, Zoltán; Mikkelsen, Jacob Giehm

    2011-01-01

    It has been previously shown that integrase-defective HIV-1-based gene vectors can serve, with moderate efficiency, as substrate for DNA transposition by a transiently expressed Sleeping Beauty (SB) transposase. Here, we describe the enhanced gene transfer properties of a HIV-1/SB hybrid vector that allows efficient DNA transposition, facilitated by the hyperactive SB100X transposase, from vector DNA intermediates in primary human cells. Potent transposase-dependent integration of genetic cargo carried by the hybrid HIV-1/SB vector (up to 160-fold above background) is reported in human cell lines as well as in primary human fibroblasts and keratinocytes. The efficiency of transgene integration in context of the newly developed hybrid vector is comparable with that of conventional lentiviral vectors (LVs). Integration profiles of integrating HIV-1-derived vectors and SB transposons mobilized from LVs are investigated by deep sequencing of a large number of integration sites. A significant bias of lentiviral integrations in genes is reported, confirming that biological properties of the viral integration machinery facilitate preferred insertion into actively transcribed genomic regions. In sharp contrast, lentiviral insertions catalyzed by the SB100X transposase are far more random with respect to genes. Based on these properties, HIV-1/SB vectors may become valuable tools for genetic engineering and therapeutic gene transfer. PMID:21468003

  9. Immune memory in invertebrates.

    PubMed

    Milutinović, Barbara; Kurtz, Joachim

    2016-08-01

    Evidence for innate immune memory (or 'priming') in invertebrates has been accumulating over the last years. We here provide an in-depth review of the current state of evidence for immune memory in invertebrates, and in particular take a phylogenetic viewpoint. Invertebrates are a very heterogeneous group of animals and accordingly, evidence for the phenomenon of immune memory as well as the hypothesized molecular underpinnings differ largely for the diverse invertebrate taxa. The majority of research currently focuses on Arthropods, while evidence from many other groups of invertebrates is fragmentary or even lacking. We here concentrate on immune memory that is induced by pathogenic challenges, but also extent our view to a non-pathogenic context, i.e. allograft rejection, which can also show forms of memory and can inform us about general principles of specific self-nonself recognition. We discuss definitions of immune memory and a number of relevant aspects such as the type of antigens used, the route of exposure, and the kinetics of reactions following priming. PMID:27402055

  10. Immune memory in invertebrates.

    PubMed

    Milutinović, Barbara; Kurtz, Joachim

    2016-08-01

    Evidence for innate immune memory (or 'priming') in invertebrates has been accumulating over the last years. We here provide an in-depth review of the current state of evidence for immune memory in invertebrates, and in particular take a phylogenetic viewpoint. Invertebrates are a very heterogeneous group of animals and accordingly, evidence for the phenomenon of immune memory as well as the hypothesized molecular underpinnings differ largely for the diverse invertebrate taxa. The majority of research currently focuses on Arthropods, while evidence from many other groups of invertebrates is fragmentary or even lacking. We here concentrate on immune memory that is induced by pathogenic challenges, but also extent our view to a non-pathogenic context, i.e. allograft rejection, which can also show forms of memory and can inform us about general principles of specific self-nonself recognition. We discuss definitions of immune memory and a number of relevant aspects such as the type of antigens used, the route of exposure, and the kinetics of reactions following priming.

  11. Invertebrate FMRFamide related peptides.

    PubMed

    Krajniak, Kevin G

    2013-06-01

    In 1977 the neuropeptide FMRFamide was isolated from the clam, Macrocallista nimbosa. Since then several hundred FMRFamide-related peptides (FaRPs) have been isolated from invertebrate animals. Precursors to the FaRPs likely arose in the cnidarians. With the transition to a bilateral body plan FaRPs became a fixture in the invertebrate phyla. They have come to play a critical role as neurotransmitters, neuromodulators, and neurohormones. FaRPs regulate a variety of body functions including, feeding, digestion, circulation, reproduction, movement. The evolution of the molecular form and function of these omnipresent peptides will be considered.

  12. Scarless Genome Editing and Stable Inducible Expression Vectors for Geobacter sulfurreducens.

    PubMed

    Chan, Chi Ho; Levar, Caleb E; Zacharoff, Lori; Badalamenti, Jonathan P; Bond, Daniel R

    2015-10-01

    Metal reduction by members of the Geobacteraceae is encoded by multiple gene clusters, and the study of extracellular electron transfer often requires biofilm development on surfaces. Genetic tools that utilize polar antibiotic cassette insertions limit mutant construction and complementation. In addition, unstable plasmids create metabolic burdens that slow growth, and the presence of antibiotics such as kanamycin can interfere with the rate and extent of Geobacter biofilm growth. We report here genetic system improvements for the model anaerobic metal-reducing bacterium Geobacter sulfurreducens. A motile strain of G. sulfurreducens was constructed by precise removal of a transposon interrupting the fgrM flagellar regulator gene using SacB/sucrose counterselection, and Fe(III) citrate reduction was eliminated by deletion of the gene encoding the inner membrane cytochrome imcH. We also show that RK2-based plasmids were maintained in G. sulfurreducens for over 15 generations in the absence of antibiotic selection in contrast to unstable pBBR1 plasmids. Therefore, we engineered a series of new RK2 vectors containing native constitutive Geobacter promoters, and modified one of these promoters for VanR-dependent induction by the small aromatic carboxylic acid vanillate. Inducible plasmids fully complemented ΔimcH mutants for Fe(III) reduction, Mn(IV) oxide reduction, and growth on poised electrodes. A real-time, high-throughput Fe(III) citrate reduction assay is described that can screen numerous G. sulfurreducens strain constructs simultaneously and shows the sensitivity of imcH expression by the vanillate system. These tools will enable more sophisticated genetic studies in G. sulfurreducens without polar insertion effects or need for multiple antibiotics. PMID:26253675

  13. Scarless Genome Editing and Stable Inducible Expression Vectors for Geobacter sulfurreducens

    PubMed Central

    Chan, Chi Ho; Levar, Caleb E.; Zacharoff, Lori; Badalamenti, Jonathan P.

    2015-01-01

    Metal reduction by members of the Geobacteraceae is encoded by multiple gene clusters, and the study of extracellular electron transfer often requires biofilm development on surfaces. Genetic tools that utilize polar antibiotic cassette insertions limit mutant construction and complementation. In addition, unstable plasmids create metabolic burdens that slow growth, and the presence of antibiotics such as kanamycin can interfere with the rate and extent of Geobacter biofilm growth. We report here genetic system improvements for the model anaerobic metal-reducing bacterium Geobacter sulfurreducens. A motile strain of G. sulfurreducens was constructed by precise removal of a transposon interrupting the fgrM flagellar regulator gene using SacB/sucrose counterselection, and Fe(III) citrate reduction was eliminated by deletion of the gene encoding the inner membrane cytochrome imcH. We also show that RK2-based plasmids were maintained in G. sulfurreducens for over 15 generations in the absence of antibiotic selection in contrast to unstable pBBR1 plasmids. Therefore, we engineered a series of new RK2 vectors containing native constitutive Geobacter promoters, and modified one of these promoters for VanR-dependent induction by the small aromatic carboxylic acid vanillate. Inducible plasmids fully complemented ΔimcH mutants for Fe(III) reduction, Mn(IV) oxide reduction, and growth on poised electrodes. A real-time, high-throughput Fe(III) citrate reduction assay is described that can screen numerous G. sulfurreducens strain constructs simultaneously and shows the sensitivity of imcH expression by the vanillate system. These tools will enable more sophisticated genetic studies in G. sulfurreducens without polar insertion effects or need for multiple antibiotics. PMID:26253675

  14. Quantification of High-Capacity Helper-Dependent Adenoviral Vector Genomes In Vitro and In Vivo, Using Quantitative TaqMan Real-Time Polymerase Chain Reaction

    PubMed Central

    PUNTEL, M.; CURTIN, J.F.; ZIRGER, J.M.; MUHAMMAD, A.K.M.; XIONG, W.; LIU, C.; HU, J.; KROEGER, K.M.; CZER, P.; SCIASCIA, S.; MONDKAR, S.; LOWENSTEIN, P.R.; CASTRO, M.G.

    2006-01-01

    First-generation adenoviral (Ad) and high-capacity adenoviral (HC-Ad) vectors are efficient delivery vehicles for transferring therapeutic transgenes in vivo into tissues/organs. The initial successes reported with adenoviral vectors in preclinical trials have been limited by immune-related adverse side effects. This has been, in part, attributed to the use of poorly characterized preparations of adenoviral vectors and also to the untoward immune adverse side effects elicited when high doses of these vectors were used. HC-Ads have several advantages over Ads, including the lack of viral coding sequences, which after infection and uncoating, makes them invisible to the host’s immune system. Another advantage is their large cloning capacity (up to ~35 kb). However, accurate characterization of HC-Ad vectors, and of contaminating replication-competent adenovirus (RCA) or helper virus, is necessary before these preparations can be used safely in clinical trials. Consequently, the development of accurate, simple, and reproducible methods to standardize and validate adenoviral preparations for the presence of contaminant genomes is required. By using a molecular method that allows accurate, reproducible, and simultaneous determination of HC-Ad, contaminating helper virus, and RCA genome copy numbers based on real-time quantitative PCR, we demonstrate accurate detection of these three genomic entities, within CsCl-purified vector stocks, total DNA isolated from cells transduced in vitro, and from brain tissue infected in vivo. This approach will allow accurate assessment of the levels and biodistribution of HC-Ad and improve the safety and efficacy of clinical trials. PMID:16716110

  15. Aquarium Culture of Freshwater Invertebrates.

    ERIC Educational Resources Information Center

    Wood, Timothy S.

    1996-01-01

    Describes two methods for rearing small aquatic invertebrates using submerged surfaces in an unfiltered current of water where fish are present. Presents suggestions on how to use the invertebrate communities in the classroom. (JRH)

  16. Stalking the Neighborhood Invertebrate.

    ERIC Educational Resources Information Center

    Manley, James W.

    1982-01-01

    Describes a six-week simulation of basic research in which high school students acquire, observe, describe, illustrate, and report on an invertebrate of their choice. Includes chart used to evaluate student monographs, and comments relating to student experiences while engaged in their projects. (Author/JN)

  17. A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera

    PubMed Central

    Southgate, Paul C.; Jerry, Dean R.; Bosserelle, Cyprien; Zenger, Kyall R.

    2016-01-01

    Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850–0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1–5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2–5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their

  18. A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera.

    PubMed

    Lal, Monal M; Southgate, Paul C; Jerry, Dean R; Bosserelle, Cyprien; Zenger, Kyall R

    2016-01-01

    Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850-0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1-5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2-5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation

  19. A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera.

    PubMed

    Lal, Monal M; Southgate, Paul C; Jerry, Dean R; Bosserelle, Cyprien; Zenger, Kyall R

    2016-01-01

    Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850-0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1-5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2-5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation

  20. High-Efficiency Transduction of Primary Human Hematopoietic Stem/Progenitor Cells by AAV6 Vectors: Strategies for Overcoming Donor-Variation and Implications in Genome Editing

    PubMed Central

    Ling, Chen; Bhukhai, Kanit; Yin, Zifei; Tan, Mengqun; Yoder, Mervin C.; Leboulch, Philippe; Payen, Emmanuel; Srivastava, Arun

    2016-01-01

    We have reported that of the 10 commonly used AAV serotype vectors, AAV6 is the most efficient in transducing primary human hematopoietic stem/progenitor cells (HSPCs). However, the transduction efficiency of the wild-type (WT) AAV6 vector varies greatly in HSPCs from different donors. Here we report two distinct strategies to further increase the transduction efficiency in HSPCs from donors that are transduced less efficiently with the WT AAV6 vectors. The first strategy involved modifications of the viral capsid proteins where specific surface-exposed tyrosine (Y) and threonine (T) residues were mutagenized to generate a triple-mutant (Y705 + Y731F + T492V) AAV6 vector. The second strategy involved the use of ex vivo transduction at high cell density. The combined use of these strategies resulted in transduction efficiency exceeding ~90% in HSPCs at significantly reduced vector doses. Our studies have significant implications in the optimal use of capsid-optimized AAV6 vectors in genome editing in HSPCs. PMID:27759036

  1. Invertebrates in managed waterfowl marshes

    USGS Publications Warehouse

    Stafford, Joshua D.; Janke, Adam K.; Webb, Elisabeth B.; Chipps, Steven R.

    2016-01-01

    Invertebrates are an important food for breeding, migrating, and wintering waterfowl. Sparse study has been devoted to understanding the influence of waterfowl and wetland management on production of invertebrates for waterfowl foods; however, manipulation of hydrology and soils may change or enhance production. Fish can compete with waterfowl for invertebrate forage in wetlands and harm aquatic macrophytes; biomanipulation (e.g., stocking piscivores) may improve waterfowl habitat quality. Similarly, some terrestrial vertebrates (e.g., beaver (Castor canadensis)) may positively or negatively impact invertebrate communities in waterfowl habitats. Various challenges exist to wetland management for invertebrates for waterfowl, but the lack of data on factors influencing production may be the most limiting.

  2. Invertebrate models of alcoholism.

    PubMed

    Scholz, Henrike; Mustard, Julie A

    2013-01-01

    For invertebrates to become useful models for understanding the genetic and physiological mechanisms of alcoholism related behaviors and the predisposition towards alcoholism, several general requirements must be fulfilled. The animal should encounter ethanol in its natural habitat, so that the central nervous system of the organism will have evolved mechanisms for responding to ethanol exposure. How the brain adapts to ethanol exposure depends on its access to ethanol, which can be regulated metabolically and/or by physical barriers. Therefore, a model organism should have metabolic enzymes for ethanol degradation similar to those found in humans. The neurons and supporting glial cells of the model organism that regulate behaviors affected by ethanol should share the molecular and physiological pathways found in humans, so that results can be compared. Finally, the use of invertebrate models should offer advantages over traditional model systems and should offer new insights into alcoholism-related behaviors. In this review we will summarize behavioral similarities and identified genes and mechanisms underlying ethanol-induced behaviors in invertebrates. This review mainly focuses on the use of the nematode Caenorhabditis elegans, the honey bee Apis mellifera and the fruit fly Drosophila melanogaster as model systems. We will discuss insights gained from those studies in conjunction with their vertebrate model counterparts and the implications for future research into alcoholism and alcohol-induced behaviors.

  3. Variable immune molecules in invertebrates.

    PubMed

    Cerenius, Lage; Söderhäll, Kenneth

    2013-12-01

    Recently it has become evident that invertebrates may mount a highly variable immune response that is dependent on which pathogen is involved. The molecular mechanisms behind this diversity are beginning to be unravelled and in several invertebrate taxa immune proteins exhibiting a broad range of diversity have been found. In some cases, evidence has been gathered suggesting that this molecular diversity translates into the ability of an affected invertebrate to mount a defence that is specifically aimed at a particular pathogen.

  4. Low-copy episomal vector pFY20 and high-saturation coverage genomic libraries for the fission yeast Schizosaccharomyces pombe.

    PubMed

    Wahls, Wayne P; Davidson, Mari K

    2008-09-01

    In fission yeast, as in many organisms, episomally replicating plasmid DNA molecules can be used for a wide variety of applications. However, replicating plasmids described previously are each propagated at a high copy number per cell. Plasmid fission yeast twenty (pFY20) contains the ura4(+) gene for positive and negative selection, an origin of replication (ars1) and a stability element (stb). Although this plasmid does not have a centromere, it is propagated with a copy number of about two plasmids per haploid genome equivalent and it is transmitted with relatively high fidelity in mitosis and meiosis. This low-copy vector is useful for screens and mutational studies where overexpression (e.g. from high copy plasmids) is undesirable. We therefore constructed multiple partial-digest, size-fractionated, fission yeast genomic DNA libraries in pFY20 and in the cloning vector pBluescript KS(+). These libraries have sufficient complexity (average of 2100 genome equivalents each) for saturation screening by complementation, plasmid shuffle or hybridization. PMID:18613214

  5. Low-copy episomal vector pFY20 and high-saturation coverage genomic libraries for the fission yeast Schizosaccharomyces pombe

    PubMed Central

    Wahls, Wayne P.; Davidson, Mari K.

    2011-01-01

    In fission yeast, as in many organisms, episomally replicating plasmid DNA molecules can be used for a wide variety of applications. However, replicating plasmids described previously are each propagated at a high copy number per cell. Plasmid fission yeast twenty (pFY20) contains the ura4+ gene for positive and negative selection, an origin of replication (ars1 ) and a stability element (stb). Although this plasmid does not have a centromere, it is propagated with a copy number of about two plasmids per haploid genome equivalent and it is transmitted with relatively high fidelity in mitosis and meiosis. This low-copy vector is useful for screens and mutational studies where overexpression (e.g. from high copy plasmids) is undesirable. We therefore constructed multiple partial-digest, size-fractionated, fission yeast genomic DNA libraries in pFY20 and in the cloning vector pBluescript KS+. These libraries have sufficient complexity (average of 2100 genome equivalents each) for saturation screening by complementation, plasmid shuffle or hybridization. PMID:18613214

  6. Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island

    PubMed Central

    Fadeev, Eduard; De Pascale, Fabio; Vezzi, Alessandro; Hübner, Sariel; Aharonovich, Dikla; Sher, Daniel

    2016-01-01

    Genome sequencing is rapidly becoming a staple technique in environmental and clinical microbiology, yet computational challenges still remain, leading to many draft genomes which are typically fragmented into many contigs. We sequenced and completely assembled the genome of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compared its full genome to several draft genomes obtained using different reference-based and de novo methods. In general, the de novo assemblies clearly outperformed the reference-based or hybrid ones, covering >99% of the genes and representing essentially all of the gene functions. However, only the fully closed genome (∼4.5 Mbp) allowed us to identify the presence of a large, 148 kbp plasmid, pAM1A3. While HOT1A3 belongs to A. macleodii, typically found in surface waters (“surface ecotype”), this plasmid consists of an almost complete flexible genomic island (fGI), containing many genes involved in metal resistance previously identified in the genomes of Alteromonas mediterranea (“deep ecotype”). Indeed, similar to A. mediterranea, A. macleodii HOT1A3 grows at concentrations of zinc, mercury, and copper that are inhibitory for other A. macleodii strains. The presence of a plasmid encoding almost an entire fGI suggests that wholesale genomic exchange between heterotrophic marine bacteria belonging to related but ecologically different populations is not uncommon. PMID:27014193

  7. A versatile binary vector system with a T-DNA organisational structure conducive to efficient integration of cloned DNA into the plant genome.

    PubMed

    Gleave, A P

    1992-12-01

    A versatile gene expression cartridge and binary vector system was constructed for use in Agrobacterium-mediated plant transformation. The expression cartridge of the primary cloning vector, pART7, comprises of cauliflower mosaic virus Cabb B-JI isolate 35S promoter, a multiple cloning site and the transcriptional termination region of the octopine synthase gene. The entire cartridge can be removed from pART7 as a Not I fragment and introduced directly into the binary vector, pART27, recombinants being selected by blue/white screening for beta-galactosidase. pART27 carries the RK2 minimal replicon for maintenance in Agrobacterium, the ColE1 origin of replication for high-copy maintenance in Escherichia coli and the Tn7 spectinomycin/streptomycin resistance gene as a bacterial selectable marker. The organisational structure of the T-DNA of pART27 has been constructed taking into account the right to left border, 5' to 3' model of T-DNA transfer. The T-DNA carries the chimaeric kanamycin resistance gene (nopaline synthase promoter-neomycin phosphotransferase-nopaline synthase terminator) distal to the right border relative to the lacZ' region. Utilisation of these vectors in Agrobacterium-mediated transformation of tobacco demonstrated efficient T-DNA transfer to the plant genome.

  8. *Arsenic (+3 oxidation state) methyltransferase and the methylation of arsenicals in the invertebrate chordate ciona intestinalis

    EPA Science Inventory

    Biotransformation of inorganic arsenic (iAs) involves methylation catalyzed by arsenic (+3 oxidation state) methyltransferase (As3mt) , yielding mono-, di-, and trimethylated arsenicals. A comparative genomic approach focused on Ciona intestinaJis, an invertebrate chordate, was u...

  9. Efficient and high-throughput vector construction and Agrobacterium-mediated transformation of Arabidopsis thaliana suspension-cultured cells for functional genomics.

    PubMed

    Ogawa, Yoichi; Dansako, Tomoko; Yano, Kentaro; Sakurai, Nozomu; Suzuki, Hideyuki; Aoki, Koh; Noji, Masaaki; Saito, Kazuki; Shibata, Daisuke

    2008-02-01

    We established a large-scale, high-throughput protocol to construct Arabidopsis thaliana suspension-cultured cell lines, each of which carries a single transgene, using Agrobacterium-mediated transformation. We took advantage of RIKEN Arabidopsis full-length (RAFL) cDNA clones and the Gateway cloning system for high-throughput preparation of binary vectors carrying individual full-length cDNA sequences. Throughout all cloning steps, multiple-well plates were used to treat 96 samples simultaneously in a high-throughput manner. The optimal conditions for Agrobacterium-mediated transformation of 96 independent binary vector constructs were established to obtain transgenic cell lines efficiently. We evaluated the protocol by generating transgenic Arabidopsis T87 cell lines carrying individual 96 metabolism-related RAFL cDNA fragments, and showed that the protocol was useful for high-throughput and large-scale production of gain-of-function lines for functional genomics.

  10. Prodynorphin in invertebrates.

    PubMed

    Salzet, M; Stefano, G

    1997-12-01

    We have characterized a prodynorphin-like molecule in an invertebrate, specifically in the rhynchobdellid leech Theromyzon tessulatum. The 14270 Da protein was purified by gel permeation chromatography, anti-leucine-enkephalin-affinity column separation followed by reverse-phase HPLC. Its complete characterization was performed by Edman degradation, enzymatic treatments, and matrix assisted laser-desorption time of flight mass spectrometry. This 119 amino-acid protein exhibits 28.8% sequence identity with rat prodynorphin, 22.9% with human prodynorphin, and 21.8% with the pig molecule. Within the leech precursor, alpha-Neo-endorphin, dynorphin-A, and dynorphin B-like peptides are present at the C-terminus as in vertebrate prodynorphin. These biological active peptides exhibit 100%, 50%, and 76.6% sequence identity with their counterparts in mammals, respectively. The amount of leucine-enkephalin is identical to that found in vertebrates. Leech prodynorphin is distinguished from that found in mammals in that the N-terminus is shorter. This report constitutes the first complete biochemical characterization of a prodynorphin in invertebrates.

  11. A Hypervariable Invertebrate Allodeterminant

    PubMed Central

    Nicotra, Matthew L.; Powell, Anahid E.; Rosengarten, Rafael D.; Moreno, Maria; Grimwood, Jane; Lakkis, Fadi G.; Dellaporta, Stephen L.; Buss, Leo W.

    2009-01-01

    Summary Colonial marine invertebrates, such as sponges, corals, bryozoans, and ascidians, often live in densely-populated communities where they encounter other members of their species as they grow over their substratum. Such encounters typically lead to a natural histocompatibility response in which colonies either fuse to become a single, chimeric colony or reject and aggressively compete for space. These allorecognition phenomena mediate intraspecific competition [1–3], support allotypic diversity [4], control the level at which selection acts [5–8], and resemble allogeneic interactions in pregnancy and transplantation [9–12]. Despite the ubiquity of allorecognition in colonial phyla, however, its molecular basis has not been identified beyond what is currently known about histocompatibility in vertebrates and protochordates. We positionally cloned an allorecognition gene using inbred strains of the cnidarian, Hydractinia symbiolongicarpus, which is a model system for the study of invertebrate allorecognition. The gene identified encodes a putative transmembrane receptor expressed in all tissues capable of allorecognition that is highly polymorphic and predicts allorecognition responses in laboratory and field-derived strains. This study reveals that a previously undescribed hypervariable molecule bearing three extracellular domains with greatest sequence similarity to the immunoglobulin superfamily is an allodeterminant in a lower metazoan. PMID:19303297

  12. An invertebrate signal transducer and activator of transcription 5 (STAT5) ortholog from the disk abalone, Haliotis discus discus: Genomic structure, early developmental expression, and immune responses to bacterial and viral stresses.

    PubMed

    Bathige, S D N K; Umasuthan, Navaneethaiyer; Park, Hae-Chul; Lee, Jehee

    2016-03-01

    Signal transducer and activator of transcription (STAT) family members are key signaling molecules that transduce cellular responses from the cell membrane to the nucleus upon Janus kinase (JAK) activation. Although seven STAT members have been reported in mammals, very limited information on STAT genes in molluscans is available. In this study, we identified and characterized a STAT paralog that is homologous to STAT5 from the disk abalone, Haliotis discus discus, and designated as AbSTAT5. Comparison of the deduced amino acid sequence for AbSTAT5 (790 amino acids) with other counterparts revealed conserved residues important for functions and typical domain regions, including the N-terminal domain, coiled-coil domain, DNA-binding domain, linker domain, and Src homology 2 (SH2) domains as mammalian counterparts. Analysis of STAT phylogeny revealed that AbSTAT5 was clustered with the molluscan subgroup in STAT5 clade with distinct evolution. According to the genomic structure of AbSTAT5, the coding sequence was distributed into 20 exons with 19 introns. Immunologically essential transcription factor-binding sites, such as GATA-1, HNF, SP1, C/EBP, Oct-1, AP1, c-Jun, and Sox-2, were predicted at the 5'-proximal region of AbSTAT5. Expression of AbSTAT5 mRNA was detected in different stages of embryonic development and observed at considerably higher levels in the morula and late veliger stages. Tissue-specific expressional studies revealed that the highest level of AbSTAT5 transcripts was detected in hemocytes, followed by gill tissues. Temporal expressions of AbSTAT5 were analyzed upon live bacterial (Vibrio parahemolyticus and Listeria monocytogenes), viral (viral hemorrhagic septicemia virus), and pathogen-associated molecular pattern (lipopolysaccharides and Poly I:C) stimulations, and significant elevations indicated immune modulation. These results suggest that AbSTAT5 may be involved in maintaining innate immune responses from developmental to adult stages in

  13. An invertebrate signal transducer and activator of transcription 5 (STAT5) ortholog from the disk abalone, Haliotis discus discus: Genomic structure, early developmental expression, and immune responses to bacterial and viral stresses.

    PubMed

    Bathige, S D N K; Umasuthan, Navaneethaiyer; Park, Hae-Chul; Lee, Jehee

    2016-03-01

    Signal transducer and activator of transcription (STAT) family members are key signaling molecules that transduce cellular responses from the cell membrane to the nucleus upon Janus kinase (JAK) activation. Although seven STAT members have been reported in mammals, very limited information on STAT genes in molluscans is available. In this study, we identified and characterized a STAT paralog that is homologous to STAT5 from the disk abalone, Haliotis discus discus, and designated as AbSTAT5. Comparison of the deduced amino acid sequence for AbSTAT5 (790 amino acids) with other counterparts revealed conserved residues important for functions and typical domain regions, including the N-terminal domain, coiled-coil domain, DNA-binding domain, linker domain, and Src homology 2 (SH2) domains as mammalian counterparts. Analysis of STAT phylogeny revealed that AbSTAT5 was clustered with the molluscan subgroup in STAT5 clade with distinct evolution. According to the genomic structure of AbSTAT5, the coding sequence was distributed into 20 exons with 19 introns. Immunologically essential transcription factor-binding sites, such as GATA-1, HNF, SP1, C/EBP, Oct-1, AP1, c-Jun, and Sox-2, were predicted at the 5'-proximal region of AbSTAT5. Expression of AbSTAT5 mRNA was detected in different stages of embryonic development and observed at considerably higher levels in the morula and late veliger stages. Tissue-specific expressional studies revealed that the highest level of AbSTAT5 transcripts was detected in hemocytes, followed by gill tissues. Temporal expressions of AbSTAT5 were analyzed upon live bacterial (Vibrio parahemolyticus and Listeria monocytogenes), viral (viral hemorrhagic septicemia virus), and pathogen-associated molecular pattern (lipopolysaccharides and Poly I:C) stimulations, and significant elevations indicated immune modulation. These results suggest that AbSTAT5 may be involved in maintaining innate immune responses from developmental to adult stages in

  14. Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes

    PubMed Central

    2014-01-01

    Background Recently it has been shown that Ensifer adhaerens can be used as a plant transformation technology, transferring genes into several plant genomes when equipped with a Ti plasmid. For this study, we have sequenced the genome of Ensifer adhaerens OV14 (OV14) and compared it with those of Agrobacterium tumefaciens C58 (C58) and Sinorhizobium meliloti 1021 (1021); the latter of which has also demonstrated a capacity to genetically transform crop genomes, albeit at significantly reduced frequencies. Results The 7.7 Mb OV14 genome comprises two chromosomes and two plasmids. All protein coding regions in the OV14 genome were functionally grouped based on an eggNOG database. No genes homologous to the A. tumefaciens Ti plasmid vir genes appeared to be present in the OV14 genome. Unexpectedly, OV14 and 1021 were found to possess homologs to chromosomal based genes cited as essential to A. tumefaciens T-DNA transfer. Of significance, genes that are non-essential but exert a positive influence on virulence and the ability to genetically transform host genomes were identified in OV14 but were absent from the 1021 genome. Conclusions This study reveals the presence of homologs to chromosomally based Agrobacterium genes that support T-DNA transfer within the genome of OV14 and other alphaproteobacteria. The sequencing and analysis of the OV14 genome increases our understanding of T-DNA transfer by non-Agrobacterium species and creates a platform for the continued improvement of Ensifer-mediated transformation (EMT). PMID:24708309

  15. Rapid construction of multiple sgRNA vectors and knockout of the Arabidopsis IAA2 gene using the CRISPR/Cas9 genomic editing technology.

    PubMed

    Dingyuan, Liu; Ting, Qiu; Xiaohui, Ding; Miaomiao, Li; Muyuan, Zhu; Junhui, Wang

    2016-08-01

    IAA2 is a member of the Aux/IAA auxin responsive gene family in Arabidopsis thaliana. No iaa2 mutant has been reported until now, thus hindering its further mechanistic investigations. The normal genomic editing technology of CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) uses only a single guide RNA (sgRNA) to target one site in a specific gene, and the gene knockout efficiency is not high. Instead, multiple sgRNAs can target multiple sites; therefore, the efficiency may be improved. In the present investigation, we used the golden-gate cloning strategy and two rounds of PCR reactions to combine three sgRNAs in the same entry vector. The final expression vector was obtained by LR reactions with the destination vector containing the Cas9 expression cassette. Four out of the six sgRNAs were effective, and we also obtained a lot of insertion and deletion mutations. Compared with one sgRNA approach, multiple sgRNAs displayed higher gene-knockout efficiency and produced more germ-line mutants. Thus, we established a more rapid and efficient method and generated five mutants for further studies of IAA2 functions.

  16. Application of an efficient strategy with a phage lambda vector for constructing a physical map of the amyloplast genome of sycamore (Acer pseudoplatanus).

    PubMed

    Ngernprasirtsiri, J; Kobayashi, H

    1990-01-01

    Amyloplasts were isolated from a heterotrophic culture cell line of a woody plant, sycamore (Acer pseudoplatanus), and their DNA was purified. Conventional procedures for making a physical map were not easily applicable to the amyloplast DNA, since the yield of DNA was too low and the presence of repeated sequences interfered with the analysis. Therefore, the pieces of amyloplast DNA starting with a few micrograms of DNA were cloned in the lambda Fix vector, which is a derivative of lambda EMBL vectors improved for efficient cloning and gene walking. Cloned DNA fragments were randomly picked, mapped for restriction endonuclease sites by a refined procedure, and combined by overlapping their physical maps. The DNA library was also subjected to screening by gene walking using promoters recognized by T3 and T7 RNA polymerases in the vector to fill the gaps between sequences determined by overlapping the physical maps. In this way, we constructed the entire DNA library and the complete physical map of the amyloplast DNA. The sycamore amyloplast genome was composed of 141.7-kbp nucleotides with the same gene arrangement as that of tobacco chloroplasts.

  17. Rapid construction of multiple sgRNA vectors and knockout of the Arabidopsis IAA2 gene using the CRISPR/Cas9 genomic editing technology.

    PubMed

    Dingyuan, Liu; Ting, Qiu; Xiaohui, Ding; Miaomiao, Li; Muyuan, Zhu; Junhui, Wang

    2016-08-01

    IAA2 is a member of the Aux/IAA auxin responsive gene family in Arabidopsis thaliana. No iaa2 mutant has been reported until now, thus hindering its further mechanistic investigations. The normal genomic editing technology of CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) uses only a single guide RNA (sgRNA) to target one site in a specific gene, and the gene knockout efficiency is not high. Instead, multiple sgRNAs can target multiple sites; therefore, the efficiency may be improved. In the present investigation, we used the golden-gate cloning strategy and two rounds of PCR reactions to combine three sgRNAs in the same entry vector. The final expression vector was obtained by LR reactions with the destination vector containing the Cas9 expression cassette. Four out of the six sgRNAs were effective, and we also obtained a lot of insertion and deletion mutations. Compared with one sgRNA approach, multiple sgRNAs displayed higher gene-knockout efficiency and produced more germ-line mutants. Thus, we established a more rapid and efficient method and generated five mutants for further studies of IAA2 functions. PMID:27531614

  18. Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Culicoides biting midges (Diptera: Ceratopogonidae) are a major vector group responsible for the biological transmission of a wide variety of globally significant arboviruses, including bluetongue virus (BTV). In this review we examine current biological resources for the study of this genus, with a...

  19. Nonassociative learning in invertebrates.

    PubMed

    Byrne, John H; Hawkins, Robert D

    2015-02-26

    The simplicity and tractability of the neural circuits mediating behaviors in invertebrates have facilitated the cellular/molecular dissection of neural mechanisms underlying learning. The review has a particular focus on the general principles that have emerged from analyses of an example of nonassociative learning, sensitization in the marine mollusk Aplysia. Learning and memory rely on multiple mechanisms of plasticity at multiple sites of the neuronal circuits, with the relative contribution to memory of the different sites varying as a function of the extent of training and time after training. The same intracellular signaling cascades that induce short-term modifications in synaptic transmission can also be used to induce long-term changes. Although short-term memory relies on covalent modifications of preexisting proteins, long-term memory also requires regulated gene transcription and translation. Maintenance of long-term cellular memory involves both intracellular and extracellular feedback loops, which sustain the regulation of gene expression and the modification of targeted molecules.

  20. Associative learning in invertebrates.

    PubMed

    Hawkins, Robert D; Byrne, John H

    2015-05-01

    This work reviews research on neural mechanisms of two types of associative learning in the marine mollusk Aplysia, classical conditioning of the gill- and siphon-withdrawal reflex and operant conditioning of feeding behavior. Basic classical conditioning is caused in part by activity-dependent facilitation at sensory neuron-motor neuron (SN-MN) synapses and involves a hybrid combination of activity-dependent presynaptic facilitation and Hebbian potentiation, which are coordinated by trans-synaptic signaling. Classical conditioning also shows several higher-order features, which might be explained by the known circuit connections in Aplysia. Operant conditioning is caused in part by a different type of mechanism, an intrinsic increase in excitability of an identified neuron in the central pattern generator (CPG) for feeding. However, for both classical and operant conditioning, adenylyl cyclase is a molecular site of convergence of the two signals that are associated. Learning in other invertebrate preparations also involves many of the same mechanisms, which may contribute to learning in vertebrates as well. PMID:25877219

  1. Associative learning in invertebrates.

    PubMed

    Hawkins, Robert D; Byrne, John H

    2015-04-15

    This work reviews research on neural mechanisms of two types of associative learning in the marine mollusk Aplysia, classical conditioning of the gill- and siphon-withdrawal reflex and operant conditioning of feeding behavior. Basic classical conditioning is caused in part by activity-dependent facilitation at sensory neuron-motor neuron (SN-MN) synapses and involves a hybrid combination of activity-dependent presynaptic facilitation and Hebbian potentiation, which are coordinated by trans-synaptic signaling. Classical conditioning also shows several higher-order features, which might be explained by the known circuit connections in Aplysia. Operant conditioning is caused in part by a different type of mechanism, an intrinsic increase in excitability of an identified neuron in the central pattern generator (CPG) for feeding. However, for both classical and operant conditioning, adenylyl cyclase is a molecular site of convergence of the two signals that are associated. Learning in other invertebrate preparations also involves many of the same mechanisms, which may contribute to learning in vertebrates as well.

  2. Retinoid metabolism in invertebrates: when evolution meets endocrine disruption.

    PubMed

    André, A; Ruivo, R; Gesto, M; Castro, L Filipe C; Santos, M M

    2014-11-01

    Recent genomic and biochemical evidence in invertebrate species pushes back the origin of the retinoid metabolic and signaling modules to the last common ancestor of all bilaterians. However, the evolution of retinoid pathways are far from fully understood. In the majority of non-chordate invertebrate lineages, the ongoing functional characterization of retinoid-related genes (metabolism and signaling pathways), as well as the characterization of the endogenous retinoid content (precursors and active retinoids), is still incomplete. Despite limited, the available data supports the presence of biologically active retinoid pathways in invertebrates. Yet, the mechanisms controlling the spatial and temporal distribution of retinoids as well as their physiological significance share similarities and differences with vertebrates. For instance, retinol storage in the form of retinyl esters, a key feature for the maintenance of retinoid homeostatic balance in vertebrates, was only recently demonstrated in some mollusk species, suggesting that such ability is older than previously anticipated. In contrast, the enzymatic repertoire involved in this process is probably unlike that of vertebrates. The suggested ancestry of active retinoid pathways implies that many more metazoan species might be potential targets for endocrine disrupting chemicals. Here, we review the current knowledge about the occurrence and functionality of retinoid metabolic and signaling pathways in invertebrate lineages, paying special attention to the evolutionary origin of retinoid storage mechanisms. Additionally, we summarize existing information on the endocrine disruption of invertebrate retinoid modules by environmental chemicals. Research priorities in the field are highlighted.

  3. Site-specific integration of bacteriophage VWB genome into Streptomyces venezuelae and construction of a VWB-based integrative vector.

    PubMed

    Van Mellaert, L; Mei, L; Lammertyn, E; Schacht, S; Anné, J

    1998-12-01

    The temperate bacteriophage VWB integrates into the chromosome of Streptomyces venezuelae ETH14630 via site-specific integration. Following recombination of the VWB attP region with the chromosomal attB sequence, the host-phage junctions attL and attR are formed. Nucleotide sequence analysis of attP, attB, attL and attR revealed a 45 bp common core sequence. In attB this 45 bp sequence consists of the 3' end of a putative tRNA Arg(AGG) gene with a 3'-terminal CCA sequence which is typical for prokaryotic tRNAs. Phage DNA integration restores the putative tRNA Arg(AGG) gene in attL. However, following recombination the CCA sequence is missing as is the case for most Streptomyces tRNA genes described so far. Adjacent to VWB attP, an ORF encoding a 427 aa protein was detected. The C-terminal region of this protein shows high similarity to the conserved C-terminal domain of site-specific recombinases belonging to the integrase family. To prove the functionality of this putative integrase gene (int), an integrative vector pKT02 was constructed. This vector consists of a 2.3 kb HindIII-SphI restriction fragment of VWB DNA containing attP and int cloned in a non-replicative Escherichia coli vector carrying a thiostrepton-resistance (tsr) gene. Integration of pKT02 was obtained after transformation of Streptomyces venezuelae ETH14630 and Streptomyces lividans TK24 protoplasts. This vector will thus be useful for a number of additional Streptomyces species in which a suitable tRNA gene can be functional as integration site.

  4. Mosquito-Borne Viruses and Suppressors of Invertebrate Antiviral RNA Silencing

    PubMed Central

    O’Neal, Scott T.; Samuel, Glady Hazitha; Adelman, Zach N.; Myles, Kevin M.

    2014-01-01

    The natural maintenance cycles of many mosquito-borne viruses require establishment of persistent non-lethal infections in the invertebrate host. While the mechanisms by which this occurs are not well understood, antiviral responses directed by small RNAs are important in modulating the pathogenesis of viral infections in disease vector mosquitoes. In yet another example of an evolutionary arms race between host and pathogen, some plant and insect viruses have evolved to encode suppressors of RNA silencing (VSRs). Whether or not mosquito-borne viral pathogens encode VSRs has been the subject of debate. While at first there would seem to be little evolutionary benefit to mosquito-borne viruses encoding proteins or sequences that strongly interfere with RNA silencing, we present here a model explaining how the expression of VSRs by these viruses in the vector might be compatible with the establishment of persistence. We also discuss the challenges associated with interrogating these viruses for the presence of suppressor proteins or sequences, as well as the candidates that have been identified in the genomes of mosquito-borne pathogens thus far. PMID:25393896

  5. Arsenic Speciation of Terrestrial Invertebrates

    SciTech Connect

    Moriarty, M.M.; Koch, I.; Gordon, R.A.; Reimer, K.J. ); )

    2009-07-01

    The distribution and chemical form (speciation) of arsenic in terrestrial food chains determines both the amount of arsenic available to higher organisms, and the toxicity of this metalloid in affected ecosystems. Invertebrates are part of complex terrestrial food webs. This paper provides arsenic concentrations and arsenic speciation profiles for eight orders of terrestrial invertebrates collected at three historical gold mine sites and one background site in Nova Scotia, Canada. Total arsenic concentrations, determined by inductively coupled plasma mass spectrometry (ICP-MS), were dependent upon the classification of invertebrate. Arsenic species were determined by high-performance liquid chromatography (HPLC) ICP-MS and X-ray absorption spectroscopy (XAS). Invertebrates were found by HPLC ICP-MS to contain predominantly arsenite and arsenate in methanol/water extracts, while XAS revealed that most arsenic is bound to sulfur in vivo. Examination of the spatial distribution of arsenic within an ant tissue highlighted the differences between exogenous and endogenous arsenic, as well as the extent to which arsenic is transformed upon ingestion. Similar arsenic speciation patterns for invertebrate groups were observed across sites. Trace amounts of arsenobetaine and arsenocholine were identified in slugs, ants, and spiders.

  6. [Construction of genomic library of L. interrogans serovar lai using lambda gt11 as the vector and a study of recombiant plasmid pDL121].

    PubMed

    Liu, H; Dai, B; Jing, B; Wu, W; Li, S; Fang, Z; Zhao, H; Ye, D; Yan, R; Liu, J; Song, S; Yang, Y; Zhang, Y; Liu, F; Tu, Y; Yang, H; Huang, Z; Liang, L; Hu, L; Zhao, M

    1997-03-01

    A genomic library of L. interrogans serovar lai strain 017 has been constructed using lambda gt11 as the vector. DNA was partially digested by two blunt-end restriction enzymes, then methylated with EcoR I methylase; after EcoR I linker was added to the DNA, the linker-ended DNA was ligated to the dephosphorylated EcoR I digested lambda gt11 arms. The recombined DNA was packaged in vitro, and used to transduct E. coli Y1090 for amplification. There were 2.1 x 10(6) recombinant bacteriophages as recognized by their ability to form white plaques plated on Lac host in the presence of both IPTG and X-Ga1. A positive clone, designated lambda DL12, was screened with a rabbit anti-serum against L. interrogans serovar lai from the genomic library. The DNA from lambda DL12 was subcloned into plasmid pUC18. A recombinant (designated as pDL121) was obtained. SDS-PAGE analysis indicated that a 23 kd was expressed in E. coli JM 103 harboring pDL121. Western blotting analysis showed that a specific protein band molecular weight of 23 kd could be recognized by the rabbit antiserum against L. interrogans serovar lai strain 017. PMID:10684055

  7. Isolation of bluetongue virus serotype 1 from Culicoides vector captured in livestock farms and sequence analysis of the viral genome segment-2.

    PubMed

    Dadawala, A I; Biswas, S K; Rehman, W; Chand, K; De, A; Mathapati, B S; Kumar, P; Chauhan, H C; Chandel, B S; Mondal, B

    2012-08-01

    Bluetongue virus serotype-1 (BTV-1) was isolated from Culicoides oxystoma vectors captured on livestock farms in two places of Gujarat, India. The viruses were isolated on BHK-21 cells, which produced characteristic BTV-related cytopathic effects between 24 and 48 h post-infection. Virus antigen was demonstrated in infected cells at different passage by a BTV-specific sandwich ELISA. Further, polyacrylamide gel electrophoresis and silver staining of viral genomic RNA revealed ten double-stranded RNA segments characteristic of BTV. Serotype of the isolates was identified by virus neutralization and PCR coupled with sequencing. The isolates were designated as SKN-7 and SKN-8 and their genome segment-2 (VP2) were sequenced. Phylogenetic analyses revealed very close relationship between them although they are not identical. SKN-8 showed closer relationship with a recently isolated BTV-1 from goat. Bluetongue virus was earlier isolated from Culicoides in adjacent state more than 20 years ago, although the serotype of the virus was not determined.

  8. Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti

    PubMed Central

    2014-01-01

    Background Genetic markers are widely used to understand the biology and population dynamics of disease vectors, but often markers are limited in the resolution they provide. In particular, the delineation of population structure, fine scale movement and patterns of relatedness are often obscured unless numerous markers are available. To address this issue in the major arbovirus vector, the yellow fever mosquito (Aedes aegypti), we used double digest Restriction-site Associated DNA (ddRAD) sequencing for the discovery of genome-wide single nucleotide polymorphisms (SNPs). We aimed to characterize the new SNP set and to test the resolution against previously described microsatellite markers in detecting broad and fine-scale genetic patterns in Ae. aegypti. Results We developed bioinformatics tools that support the customization of restriction enzyme-based protocols for SNP discovery. We showed that our approach for RAD library construction achieves unbiased genome representation that reflects true evolutionary processes. In Ae. aegypti samples from three continents we identified more than 18,000 putative SNPs. They were widely distributed across the three Ae. aegypti chromosomes, with 47.9% found in intergenic regions and 17.8% in exons of over 2,300 genes. Pattern of their imputed effects in ORFs and UTRs were consistent with those found in a recent transcriptome study. We demonstrated that individual mosquitoes from Indonesia, Australia, Vietnam and Brazil can be assigned with a very high degree of confidence to their region of origin using a large SNP panel. We also showed that familial relatedness of samples from a 0.4 km2 area could be confidently established with a subset of SNPs. Conclusions Using a cost-effective customized RAD sequencing approach supported by our bioinformatics tools, we characterized over 18,000 SNPs in field samples of the dengue fever mosquito Ae. aegypti. The variants were annotated and positioned onto the three Ae. aegypti chromosomes

  9. Local Adaptation in Marine Invertebrates

    NASA Astrophysics Data System (ADS)

    Sanford, Eric; Kelly, Morgan W.

    2011-01-01

    Local adaptation in the sea was regarded historically as a rare phenomenon that was limited to a handful of species with exceptionally low dispersal potential. However, a growing body of experimental studies indicates that adaptive differentiation occurs in numerous marine invertebrates in response to selection imposed by strong gradients (and more complex mosaics) of abiotic and biotic conditions. Moreover, a surprisingly high proportion of the marine invertebrates known or suspected of exhibiting local adaptation are species with planktonic dispersal. Adaptive divergence among populations can occur over a range of spatial scales, including those that are fine-grained (i.e., meters to kilometers), reflecting a balance between scales of gene flow and selection. Addressing the causes and consequences of adaptive genetic differentiation among invertebrate populations promises to advance community ecology, climate change research, and the effective management of marine ecosystems.

  10. Invertebrate studies and their ongoing contributions to neuroscience.

    PubMed

    Sattelle, David B; Buckingham, Steven D

    2006-03-01

    Invertebrates have been deployed very successfully in experimental studies of the nervous system and neuromuscular junctions. Many important discoveries on axonal conduction, synaptic transmission, integrative neurobiology and behaviour have been made by investigations of these remarkable animals. Their advantages as model organisms for investigations of nervous systems include (a) the large diameter of neurons, glia and muscle cells of some invertebrates, thereby facilitating microelectrode recordings; (b) simple nervous systems with few neurons, enhancing the tractability of neuronal circuitry; and (c) well-defined behaviours, which lend themselves to physiological and genetic dissection. Genetic model organisms such as Drosophila melanogaster and Caenorhabditis elegans have provided powerful genetic approaches to central questions concerning nervous system development, learning and memory and the cellular and molecular basis of behaviour. The process of attributing function to particular gene products has been greatly accelerated in recent years with access to entire genome sequences and the application of reverse genetic (e.g. RNA interference, RNAi) and other post-genome technologies (e.g. microarrays). Studies of many other invertebrates, notably the honeybee (Apis mellifera), a nudibranch mollusc (Aplysia californica), locusts, lobsters, crabs, annelids and jellyfish have all assisted in the development of major concepts in neuroscience. The future is equally bright with ease of access to genome-wide reverse genetic technologies, and the development of optical recordings using voltage and intracellular calcium sensors genetically targeted to selected individual and groups of neurons. PMID:16470388

  11. The carboxylesterase/cholinesterase gene family in invertebrate deuterostomes.

    PubMed

    Johnson, Glynis; Moore, Samuel W

    2012-06-01

    Carboxylesterase/cholinesterase family members are responsible for controlling the nerve impulse, detoxification and various developmental functions, and are a major target of pesticides and chemical warfare agents. Comparative structural analysis of these enzymes is thus important. The invertebrate deuterostomes (phyla Echinodermata and Hemichordata and subphyla Urochordata and Cephalochordata) lie in the transition zone between invertebrates and vertebrates, and are thus of interest to the study of evolution. Here we have investigated the carboxylesterase/cholinesterase gene family in the sequenced genomes of Strongylocentrotus purpuratus (Echinodermata), Saccoglossus kowalevskii (Hemichordata), Ciona intestinalis (Urochordata) and Branchiostoma floridae (Cephalochordata), using sequence analysis of the catalytic apparatus and oligomerisation domains, and phylogenetic analysis. All four genomes show blurring of structural boundaries between cholinesterases and carboxylesterases, with many intermediate enzymes. Non-enzymatic proteins are well represented. The Saccoglossus and Branchiostoma genomes show evidence of extensive gene duplication and retention. There is also evidence of domain shuffling, resulting in multidomain proteins consisting either of multiple carboxylesterase domains, or of carboxylesterase/cholinesterase domains linked to other domains, including RING finger, chitin-binding, immunoglobulin, fibronectin type 3, CUB, cysteine-rich-Frizzled, caspase activation and 7tm-1, amongst others. Such gene duplication and domain shuffling in the carboxylesterase/cholinesterase family appears to be unique to the invertebrate deuterostomes, and we hypothesise that these factors may have contributed to the evolution of the morphological complexity, particularly of the nervous system and neural crest, of the vertebrates. PMID:22210164

  12. The carboxylesterase/cholinesterase gene family in invertebrate deuterostomes.

    PubMed

    Johnson, Glynis; Moore, Samuel W

    2012-06-01

    Carboxylesterase/cholinesterase family members are responsible for controlling the nerve impulse, detoxification and various developmental functions, and are a major target of pesticides and chemical warfare agents. Comparative structural analysis of these enzymes is thus important. The invertebrate deuterostomes (phyla Echinodermata and Hemichordata and subphyla Urochordata and Cephalochordata) lie in the transition zone between invertebrates and vertebrates, and are thus of interest to the study of evolution. Here we have investigated the carboxylesterase/cholinesterase gene family in the sequenced genomes of Strongylocentrotus purpuratus (Echinodermata), Saccoglossus kowalevskii (Hemichordata), Ciona intestinalis (Urochordata) and Branchiostoma floridae (Cephalochordata), using sequence analysis of the catalytic apparatus and oligomerisation domains, and phylogenetic analysis. All four genomes show blurring of structural boundaries between cholinesterases and carboxylesterases, with many intermediate enzymes. Non-enzymatic proteins are well represented. The Saccoglossus and Branchiostoma genomes show evidence of extensive gene duplication and retention. There is also evidence of domain shuffling, resulting in multidomain proteins consisting either of multiple carboxylesterase domains, or of carboxylesterase/cholinesterase domains linked to other domains, including RING finger, chitin-binding, immunoglobulin, fibronectin type 3, CUB, cysteine-rich-Frizzled, caspase activation and 7tm-1, amongst others. Such gene duplication and domain shuffling in the carboxylesterase/cholinesterase family appears to be unique to the invertebrate deuterostomes, and we hypothesise that these factors may have contributed to the evolution of the morphological complexity, particularly of the nervous system and neural crest, of the vertebrates.

  13. Aquatic Invertebrate Development Working Group

    NASA Technical Reports Server (NTRS)

    Meyers, D.

    1985-01-01

    Little definitive evidence exists to show that gravity plays a major role in embyrogenesis of aquatic invertebrates. Two reasons for this may be: (1) few studies have been done that emphasize the role of gravity; and (2) there simply may not be any gravity effect. The buoyant nature of the aquatic environment could have obscured any evolutionary effect of gravity. The small size of most eggs and their apparent lack of orientation suggests reduced gravitational influence. Therefore, it is recommended that the term development, as applied to aquatic invertebrates, be loosely defined to encompass behavioral and morphological parameters for which baseline data already exist.

  14. Introducing Vectors.

    ERIC Educational Resources Information Center

    Roche, John

    1997-01-01

    Suggests an approach to teaching vectors that promotes active learning through challenging questions addressed to the class, as opposed to subtle explanations. Promotes introducing vector graphics with concrete examples, beginning with an explanation of the displacement vector. Also discusses artificial vectors, vector algebra, and unit vectors.…

  15. Evolutionary genomics: transdomain gene transfers.

    PubMed

    Bordenstein, Seth R

    2007-11-01

    Biologists have until now conceded that bacterial gene transfer to multicellular animals is relatively uncommon in Nature. A new study showing promiscuous insertions of bacterial endosymbiont genes into invertebrate genomes ushers in a shift in this paradigm.

  16. Automated cell analysis tool for a genome-wide RNAi screen with support vector machine based supervised learning

    NASA Astrophysics Data System (ADS)

    Remmele, Steffen; Ritzerfeld, Julia; Nickel, Walter; Hesser, Jürgen

    2011-03-01

    RNAi-based high-throughput microscopy screens have become an important tool in biological sciences in order to decrypt mostly unknown biological functions of human genes. However, manual analysis is impossible for such screens since the amount of image data sets can often be in the hundred thousands. Reliable automated tools are thus required to analyse the fluorescence microscopy image data sets usually containing two or more reaction channels. The herein presented image analysis tool is designed to analyse an RNAi screen investigating the intracellular trafficking and targeting of acylated Src kinases. In this specific screen, a data set consists of three reaction channels and the investigated cells can appear in different phenotypes. The main issue of the image processing task is an automatic cell segmentation which has to be robust and accurate for all different phenotypes and a successive phenotype classification. The cell segmentation is done in two steps by segmenting the cell nuclei first and then using a classifier-enhanced region growing on basis of the cell nuclei to segment the cells. The classification of the cells is realized by a support vector machine which has to be trained manually using supervised learning. Furthermore, the tool is brightness invariant allowing different staining quality and it provides a quality control that copes with typical defects during preparation and acquisition. A first version of the tool has already been successfully applied for an RNAi-screen containing three hundred thousand image data sets and the SVM extended version is designed for additional screens.

  17. Opine dehydrogenases in marine invertebrates.

    PubMed

    Harcet, Matija; Perina, Drago; Pleše, Bruna

    2013-10-01

    It is well known today that opine production anaerobic pathways are analogs to the classical glycolytic pathway (lactate production pathway). These pathways, catalyzed by a group of enzymes called opine dehydrogenases (OpDHs), ensure continuous flux of glycolysis and a constant supply of ATP by maintaining the NADH/NAD(+) ratio during exercise and hypoxia, thus regulating the cytosolic redox balance in glycolysis under anoxia. OpDHs are distributed in a wide range of marine invertebrate phyla, including sponges (Porifera). Phylogenetic analyses supported with enzymatic assays strongly indicate that sponge OpDHs constitute an enzyme class unrelated to other OpDHs. Therefore, OpDHs in marine invertebrates are divided into two groups, a mollusk/annelid type and a sponge type, which belongs to the OCD/mu-crystallin family.

  18. Pharmacological Lifespan Extension of Invertebrates

    PubMed Central

    Lucanic, Mark; Lithgow, Gordon J.; Alavez, Silvestre

    2012-01-01

    There is considerable interest in identifying small, drug-like compounds that slow aging in multiple species, particularly in mammals. Such compounds may prove to be useful in treating and retarding age-related disease in humans. Just as invertebrate models have been essential in helping us understand the genetic pathways that control aging, these model organisms are also proving valuable in discovering chemical compounds that influence longevity. The nematode Caenorhabditis elegans (C. elegans) has numerous advantages for such studies including its short lifespan and has been exploited by a number of investigators to find compounds that impact aging. Here, we summarize the progress being made in identifying compounds that extend the lifespan of invertebrates, and introduce the challenges we face in translating this research into human therapies. PMID:22771382

  19. Marine Invertebrates: Communities at Risk

    PubMed Central

    Mather, Jennifer

    2013-01-01

    Our definition of the word ‘animal’ centers on vertebrates, yet 99% of the animals on the planet are invertebrates, about which we know little. In addition, although the Census of Marine Life (COML.org) has recently conducted an extensive audit of marine ecosystems, we still do not understand much about the animals of the seas. Surveys of the best-known ecosystems, in which invertebrate populations often play a key role, show that the invertebrate populations are affected by human impact. Coral animals are the foundation of coral reef systems, which are estimated to contain 30% of the species in the ocean. Physical impact and chemical changes on the water severely damage these reefs, and may lead to the removal of these important habitats. Tiny pteropod molluscs live in huge numbers in the polar seas, and their fragile shells are particularly vulnerable to ocean acidification. Their removal would mean that fishes on which we depend would have a hugely diminished food supply. In the North Sea, warming is leading to replacement of colder water copepods by warmer water species which contain less fat. This is having an effect on the birds which eat them, who enrich the otherwise poor land on which they nest. Conversely, the warming of the water and the loss of top predators such as whales and sharks has led to an explosion of the jumbo squid of the Pacific coast of North America. This is positive in the development of a squid fishery, yet negative because the squid eat fish that have been the mainstay of the fishery along that coast. These examples show how invertebrates are key in the oceans, and what might happen when global changes impact them. PMID:24832811

  20. Marine invertebrates: communities at risk.

    PubMed

    Mather, Jennifer

    2013-01-01

    Our definition of the word 'animal' centers on vertebrates, yet 99% of the animals on the planet are invertebrates, about which we know little. In addition, although the Census of Marine Life (COML.org) has recently conducted an extensive audit of marine ecosystems, we still do not understand much about the animals of the seas. Surveys of the best-known ecosystems, in which invertebrate populations often play a key role, show that the invertebrate populations are affected by human impact. Coral animals are the foundation of coral reef systems, which are estimated to contain 30% of the species in the ocean. Physical impact and chemical changes on the water severely damage these reefs, and may lead to the removal of these important habitats. Tiny pteropod molluscs live in huge numbers in the polar seas, and their fragile shells are particularly vulnerable to ocean acidification. Their removal would mean that fishes on which we depend would have a hugely diminished food supply. In the North Sea, warming is leading to replacement of colder water copepods by warmer water species which contain less fat. This is having an effect on the birds which eat them, who enrich the otherwise poor land on which they nest. Conversely, the warming of the water and the loss of top predators such as whales and sharks has led to an explosion of the jumbo squid of the Pacific coast of North America. This is positive in the development of a squid fishery, yet negative because the squid eat fish that have been the mainstay of the fishery along that coast. These examples show how invertebrates are key in the oceans, and what might happen when global changes impact them.

  1. Responses of invertebrates to temperature and water stress: A polar perspective.

    PubMed

    Everatt, Matthew J; Convey, Pete; Bale, Jeffrey S; Worland, M Roger; Hayward, Scott A L

    2015-12-01

    As small bodied poikilothermic ectotherms, invertebrates, more so than any other animal group, are susceptible to extremes of temperature and low water availability. In few places is this more apparent than in the Arctic and Antarctic, where low temperatures predominate and water is unusable during winter and unavailable for parts of summer. Polar terrestrial invertebrates express a suite of physiological, biochemical and genomic features in response to these stressors. However, the situation is not as simple as responding to each stressor in isolation, as they are often faced in combination. We consider how polar terrestrial invertebrates manage this scenario in light of their physiology and ecology. Climate change is also leading to warmer summers in parts of the polar regions, concomitantly increasing the potential for drought. The interaction between high temperature and low water availability, and the invertebrates' response to them, are therefore also explored.

  2. Pain and suffering in invertebrates?

    PubMed

    Elwood, Robert W

    2011-01-01

    All animals face hazards that cause tissue damage and most have nociceptive reflex responses that protect them from such damage. However, some taxa have also evolved the capacity for pain experience, presumably to enhance long-term protection through behavior modification based on memory of the unpleasant nature of pain. In this article I review various criteria that might distinguish nociception from pain. Because nociceptors are so taxonomically widespread, simply demonstrating their presence is not sufficient. Furthermore, investigation of the central nervous system provides limited clues about the potential to experience pain. Opioids and other analgesics might indicate a central modulation of responses but often peripheral effects could explain the analgesia; thus reduction of responses by analgesics and opioids does not allow clear discrimination between nociception and pain. Physiological changes in response to noxious stimuli or the threat of a noxious stimulus might prove useful but, to date, application to invertebrates is limited. Behavior of the organism provides the greatest insights. Rapid avoidance learning and prolonged memory indicate central processing rather than simple reflex and are consistent with the experience of pain. Complex, prolonged grooming or rubbing may demonstrate an awareness of the specific site of stimulus application. Tradeoffs with other motivational systems indicate central processing, and an ability to use complex information suggests sufficient cognitive ability for the animal to have a fitness benefit from a pain experience. Available data are consistent with the idea of pain in some invertebrates and go beyond the idea of just nociception but are not definitive. In the absence of conclusive data, more humane care for invertebrates is suggested.

  3. Arthropod use of invertebrate carrion

    SciTech Connect

    Seastedt, T.R.; Mameli, L.; Gridley, K.

    1980-08-01

    Arthropods associated with cricket carcasses placed on top and within deciduous forest litter were collected over a 12 month interval. Vespid wasps and ants quickly removed carcasses left on top of forest litter, but carcasses placed within litter persisted throughout the study. Major consumers of carcasses in litter varied seasonally; maggots dominated on fresh carcasses in summer, but fresh carcasses placed in litter in autumn were consumed by other arthropods. A gamasid mite, Hypoaspis (Laelaspis) johnieae dominated the microarthropod fauna found on exoskeleton fragments. A method for collecting invertebrate carrion feeders and measuring carrion disappearance is presented.

  4. Arthropod use of invertebrate carrion

    SciTech Connect

    Seastedt, T.R.; Mameli, L.; Gridley, K.

    1981-01-01

    Arthropods associated with cricket carcasses placed on top and within deciduous forest litter were collected for 12 months. Vespid wasps and ants quickly removed carcasses left on top of forest litter, but carcasses placed within litter persisted throughout the study. Major consumers of carcasses in litter varied seasonally; maggots dominated on fresh carcasses in summer, but fresh carcasses placed in litter in autumn were consumed by other arthropods. A gamasid mite, Hypoaspis (Laelaspis) johnieae, dominated the microarthropod fauna found on exoskeleton fragments. A method for collecting invertebrate carrion feeders and measuring carrion disappearance is presented. 15 references, 2 tables.

  5. The impact of minimally oversized adeno-associated viral vectors encoding human factor VIII on vector potency in vivo

    PubMed Central

    Kyostio-Moore, Sirkka; Berthelette, Patricia; Piraino, Susan; Sookdeo, Cathleen; Nambiar, Bindu; Jackson, Robert; Burnham, Brenda; O’Riordan, Catherine R; Cheng, Seng H; Armentano, Donna

    2016-01-01

    Recombinant adeno-associated viral (rAAV) vectors containing oversized genomes provide transgene expression despite low efficiency packaging of complete genomes. Here, we characterized the properties of oversized rAAV2/8 vectors (up to 5.4 kb) encoding human factor VIII (FVIII) under the transcriptional control of three liver promoters. All vectors provided sustained production of active FVIII in mice for 7 months and contained comparable levels of vector genomes and complete expression cassettes in liver. Therefore, for the 5.4 kb genome size range, a strong expression cassette was more important for FVIII production than the vector genome size. To evaluate the potency of slightly oversized vectors, a 5.1 kb AAVrh8R/FVIII vector was compared to a 4.6 kb (wild-type size) vector with an identical expression cassette (but containing a smaller C1-domain deleted FVIII) for 3 months in mice. The 5.1 kb vector had twofold to threefold lower levels of plasma FVIII protein and liver vector genomes than that obtained with the 4.6 kb vector. Vector genomes for both vectors persisted equally and existed primarily as high molecular weight concatemeric circular forms in liver. Taken together, these results indicate that the slightly oversized vectors containing heterogeneously packaged vector genomes generated a functional transgene product but exhibited a twofold to threefold lower in vivo potency. PMID:26958574

  6. Effects of Pollution on Freshwater Invertebrates.

    ERIC Educational Resources Information Center

    Buikema, A. L., Jr.; Herricks, E. E.

    1978-01-01

    Presents a literature review of the effects of pollution on freshwater invertebrates, covering publications of 1976-77. Some of the areas covered are: (1) toxicant effects on invertebrates; (2) microcosm and community effects, and (3) biological control of aquatic life. A list of 123 references is also presented. (HM)

  7. Invertebrates, ecosystem services and climate change.

    PubMed

    Prather, Chelse M; Pelini, Shannon L; Laws, Angela; Rivest, Emily; Woltz, Megan; Bloch, Christopher P; Del Toro, Israel; Ho, Chuan-Kai; Kominoski, John; Newbold, T A Scott; Parsons, Sheena; Joern, A

    2013-05-01

    The sustainability of ecosystem services depends on a firm understanding of both how organisms provide these services to humans and how these organisms will be altered with a changing climate. Unquestionably a dominant feature of most ecosystems, invertebrates affect many ecosystem services and are also highly responsive to climate change. However, there is still a basic lack of understanding of the direct and indirect paths by which invertebrates influence ecosystem services, as well as how climate change will affect those ecosystem services by altering invertebrate populations. This indicates a lack of communication and collaboration among scientists researching ecosystem services and climate change effects on invertebrates, and land managers and researchers from other disciplines, which becomes obvious when systematically reviewing the literature relevant to invertebrates, ecosystem services, and climate change. To address this issue, we review how invertebrates respond to climate change. We then review how invertebrates both positively and negatively influence ecosystem services. Lastly, we provide some critical future directions for research needs, and suggest ways in which managers, scientists and other researchers may collaborate to tackle the complex issue of sustaining invertebrate-mediated services under a changing climate.

  8. The structure and host entry of an invertebrate parvovirus.

    PubMed

    Meng, Geng; Zhang, Xinzheng; Plevka, Pavel; Yu, Qian; Tijssen, Peter; Rossmann, Michael G

    2013-12-01

    The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome.

  9. The Structure and Host Entry of an Invertebrate Parvovirus

    PubMed Central

    Meng, Geng; Zhang, Xinzheng; Plevka, Pavel; Yu, Qian; Tijssen, Peter

    2013-01-01

    The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome. PMID:24027306

  10. Ciona intestinalis and Oxycomanthus japonicus, representatives of marine invertebrates.

    PubMed

    Sasakura, Yasunori; Inaba, Kazuo; Satoh, Nori; Kondo, Mariko; Akasaka, Koji

    2009-10-01

    The study of marine invertebrates is useful in various biological research fields. However, genetic analyses of these animals are limited, mainly due to difficulties in culturing them, and the genetic resources of marine invertebrates have not been organized. Recently, advances have been made in the study of two deuterostomes, an ascidian Ciona intestinalis and a feather star Oxycomanthus japonicus. The draft genome sequence of Ciona intestinalis has been determined, and its compact genome, which has less redundancy of genes compared with vertebrates, provides us with a useful experimental system for analyzing the functions of genes during development. The life cycle of Ciona intestinalis is approximately 2-3 months, and the genetic techniques including a perfect inland culture system, germline transformation with a transposon Minos, enhancer detection and insertional mutagenesis, have been established. The feather star Oxycomanthus japonicus conserves the characteristics of the basic echinoderm body plan with a segmented mesoderm, which is a fascinating characteristic for understanding the evolution of echinoderms. Oxycomanthus japonicus shows strong regeneration ability and is a suitable subject for analysis of the mechanisms of regeneration. In consideration of these features, the National BioResource Project (NBRP) has started to support the supply of wild-types, transgenic lines and inbred lines of Ciona intestinalis and Oxycomanthus japonicus. PMID:19897929

  11. Endozoochory of seeds and invertebrates by migratory waterbirds in Oklahoma, USA

    USGS Publications Warehouse

    Green, Andy J.; Frisch, Dagmar; Michot, Thomas C.; Allain, Larry K.; Barrow, Wylie C.

    2013-01-01

    Given their abundance and migratory behavior, waterbirds have major potential for dispersing plants and invertebrates within North America, yet their role as vectors remains poorly understood. We investigated the numbers and types of invertebrates and seeds within freshly collected faecal samples (n = 22) of migratory dabbling ducks and shorebirds in November 2008 in two parts of Lake Texoma in southern Oklahoma. Killdeer Charadrius vociferus were transporting a higher number and diversity of both plants and invertebrates than the green-winged teal Anas carolinensis. Ten plant taxa and six invertebrate taxa were identified to at least genus level, although viability was not confirmed for most of these taxa. Bryozoan statoblasts (from four species not previously recorded from Oklahoma) were especially abundant in killdeer faeces, while the ostracod Candona simpsoni was detected as a live adult in torpor in the teal faeces. Cyperaceae and Juncaceae were the most abundant plant families represented and Cyperus strigosus seeds germinated after extraction from killdeer faeces. This snapshot study underlines the importance of waterbirds as vectors of passive dispersal of many organisms and the need for more research in this discipline.

  12. Ensembl Genomes 2016: more genomes, more complexity

    PubMed Central

    Kersey, Paul Julian; Allen, James E.; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K.; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D.; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello–Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M.; Howe, Kevin L.; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M.

    2016-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

  13. Immune Reactions Among Marine and Other Invertebrates

    ERIC Educational Resources Information Center

    Bang, Frederik B.

    1973-01-01

    Discusses the defense mechanisms and immune reaction found in invertebrates, and examines the wealth of related biological problems that need study and many of the leads that have recently been developed. (JR)

  14. Effects of pollution on freshwater invertebrates

    SciTech Connect

    Buikema, A.L. Jr.; Fenfield, E.F.; Pittinger, C.A.

    1983-06-01

    A literature review of studies on the effects of pollution on freshwater invertebrates is presented. PCBs, insecticides, and fungicides were the main pollutants studied, along with NH/sub 3/, Cd, Cr, Cu, Hg, and Zn. (JMT)

  15. Culturing larvae of marine invertebrates.

    PubMed

    Strathmann, Richard R

    2014-01-01

    Larvae of marine invertebrates cultured in the laboratory experience conditions that they do not encounter in nature, but development and survival to metamorphic competence can be obtained in such cultures. This protocol emphasizes simple methods suitable for a wide variety of larvae. Culturing larvae requires seawater of adequate quality and temperature within the tolerated range. Beyond that, feeding larvae require appropriate food, but a few kinds of algae and animals are sufficient as food for diverse larvae. Nontoxic materials include glass, many plastics, hot-melt glue, and some solvents, once evaporated. Cleaners that do not leave toxic residues after rinsing include dilute hydrochloric or acetic acid, sodium hypochlorite (commercial bleach), and ethanol. Materials that can leave toxic residues, such as formaldehyde, glutaraldehyde, detergents, and hand lotions, should be avoided, especially with batch cultures that lack continuously renewed water. Reverse filtration can be used to change water gently at varying frequencies, depending on temperature and the kinds of food that are provided. Bacterial growth can be limited by antibiotics, but antibiotics are often unnecessary. Survival and growth are increased by low concentrations of larvae and stirring of large or dense cultures. One method of stirring large numbers of containers is a rack of motor-driven paddles. Most of the methods and materials are inexpensive and portable. If necessary, a room within a few hours of the sea could be temporarily equipped for larval culture. PMID:24567204

  16. Hepatitis B Virus (HBV) Virion and Covalently Closed Circular DNA Formation in Primary Tupaia Hepatocytes and Human Hepatoma Cell Lines upon HBV Genome Transduction with Replication-Defective Adenovirus Vectors

    PubMed Central

    Ren, Shaotang; Nassal, Michael

    2001-01-01

    Hepatitis B virus (HBV), the causative agent of B-type hepatitis in humans, is a hepatotropic DNA-containing virus that replicates via reverse transcription. Because of its narrow host range, there is as yet no practical small-animal system for HBV infection. The hosts of the few related animal viruses, including woodchuck hepatitis B virus and duck hepatitis B virus, are either difficult to keep or only distantly related to humans. Some evidence suggests that tree shrews (tupaias) may be susceptible to infection with human HBV, albeit with low efficiency. Infection efficiency depends on interactions of the virus with factors on the surface and inside the host cell. To bypass restrictions during the initial entry phase, we used recombinant replication-defective adenovirus vectors, either with or without a green fluorescent protein marker gene, to deliver complete HBV genomes into primary tupaia hepatocytes. Here we show that these cells, like the human hepatoma cell lines HepG2 and Huh7, are efficiently transduced by the vectors and produce all HBV gene products required to generate the secretory antigens HBsAg and HBeAg, replication-competent nucleocapsids, and enveloped virions. We further demonstrate that covalently closed circular HBV DNA is formed. Therefore, primary tupaia hepatocytes support all steps of HBV replication following deposition of the genome in the nucleus, including the intracellular amplification cycle. These data provide a rational basis for in vivo experiments aimed at developing tupaias into a useful experimental animal system for HBV infection. PMID:11152483

  17. Anesthesia, analgesia, and euthanasia of invertebrates.

    PubMed

    Cooper, John E

    2011-01-01

    Invertebrate animals have long played an important role in biomedical research in such fields as genetics, physiology, and development. However, with few exceptions, scientists, veterinarians, and technicians have paid little attention to the anesthesia, analgesia, and euthanasia of these diverse creatures. Indeed, some standard research procedures are routinely performed without anesthesia. Yet various chemical agents are available for the immobilization or anesthesia of invertebrates, ranging from gases or volatile liquids that can be pumped into either an anesthetic chamber (for terrestrial species) or a container of water (aquatic species), to benzocaine and other substances for fish. Many invertebrates are not difficult to immobilize or anesthetize and the procedures recommended in this article appear to be safe; however, none should be considered totally risk-free. Analgesia of invertebrates is as yet a largely unexplored field; until scientific data are available, other measures can promote the well-being of these animals in the laboratory. For euthanasia, various methods (physical or chemical or a combination of both) have been recommended for different taxa of invertebrates, but most have not been properly studied under laboratory conditions and some can be problematic in the context of research procedures and tissue harvesting. Furthermore, relevant data are scattered, sometimes available only in languages other than English, and there is no international approach for seeking and collating such information. In this article I review various methods of anesthesia, analgesia, and euthanasia for terrestrial and aquatic invertebrates, as well as areas requiring further research. PMID:21709312

  18. Anesthesia, analgesia, and euthanasia of invertebrates.

    PubMed

    Cooper, John E

    2011-01-01

    Invertebrate animals have long played an important role in biomedical research in such fields as genetics, physiology, and development. However, with few exceptions, scientists, veterinarians, and technicians have paid little attention to the anesthesia, analgesia, and euthanasia of these diverse creatures. Indeed, some standard research procedures are routinely performed without anesthesia. Yet various chemical agents are available for the immobilization or anesthesia of invertebrates, ranging from gases or volatile liquids that can be pumped into either an anesthetic chamber (for terrestrial species) or a container of water (aquatic species), to benzocaine and other substances for fish. Many invertebrates are not difficult to immobilize or anesthetize and the procedures recommended in this article appear to be safe; however, none should be considered totally risk-free. Analgesia of invertebrates is as yet a largely unexplored field; until scientific data are available, other measures can promote the well-being of these animals in the laboratory. For euthanasia, various methods (physical or chemical or a combination of both) have been recommended for different taxa of invertebrates, but most have not been properly studied under laboratory conditions and some can be problematic in the context of research procedures and tissue harvesting. Furthermore, relevant data are scattered, sometimes available only in languages other than English, and there is no international approach for seeking and collating such information. In this article I review various methods of anesthesia, analgesia, and euthanasia for terrestrial and aquatic invertebrates, as well as areas requiring further research.

  19. Adeno-Associated Virus Type 2 Wild-Type and Vector-Mediated Genomic Integration Profiles of Human Diploid Fibroblasts Analyzed by Third-Generation PacBio DNA Sequencing

    PubMed Central

    Hüser, Daniela; Gogol-Döring, Andreas; Chen, Wei

    2014-01-01

    ABSTRACT Genome-wide analysis of adeno-associated virus (AAV) type 2 integration in HeLa cells has shown that wild-type AAV integrates at numerous genomic sites, including AAVS1 on chromosome 19q13.42. Multiple GAGY/C repeats, resembling consensus AAV Rep-binding sites are preferred, whereas rep-deficient AAV vectors (rAAV) regularly show a random integration profile. This study is the first study to analyze wild-type AAV integration in diploid human fibroblasts. Applying high-throughput third-generation PacBio-based DNA sequencing, integration profiles of wild-type AAV and rAAV are compared side by side. Bioinformatic analysis reveals that both wild-type AAV and rAAV prefer open chromatin regions. Although genomic features of AAV integration largely reproduce previous findings, the pattern of integration hot spots differs from that described in HeLa cells before. DNase-Seq data for human fibroblasts and for HeLa cells reveal variant chromatin accessibility at preferred AAV integration hot spots that correlates with variant hot spot preferences. DNase-Seq patterns of these sites in human tissues, including liver, muscle, heart, brain, skin, and embryonic stem cells further underline variant chromatin accessibility. In summary, AAV integration is dependent on cell-type-specific, variant chromatin accessibility leading to random integration profiles for rAAV, whereas wild-type AAV integration sites cluster near GAGY/C repeats. IMPORTANCE Adeno-associated virus type 2 (AAV) is assumed to establish latency by chromosomal integration of its DNA. This is the first genome-wide analysis of wild-type AAV2 integration in diploid human cells and the first to compare wild-type to recombinant AAV vector integration side by side under identical experimental conditions. Major determinants of wild-type AAV integration represent open chromatin regions with accessible consensus AAV Rep-binding sites. The variant chromatin accessibility of different human tissues or cell types will

  20. The Tomato Spotted Wilt Virus Genome Is Processed Differentially in its Plant Host Arachis hypogaea and its Thrips Vector Frankliniella fusca

    PubMed Central

    Fletcher, Stephen J.; Shrestha, Anita; Peters, Jonathan R.; Carroll, Bernard J.; Srinivasan, Rajagopalbabu; Pappu, Hanu R.; Mitter, Neena

    2016-01-01

    Thrips-transmitted tospoviruses are economically important viruses affecting a wide range of field and horticultural crops worldwide. Tomato spotted wilt virus (TSWV) is the type member of the Tospovirus genus with a broad host range of more than 900 plant species. Interactions between these viruses and their plant hosts and insect vectors via RNAi pathways are likely a key determinant of pathogenicity. The current investigation, for the first time, compares biogenesis of small RNAs between the plant host and insect vector in the presence or absence of TSWV. Unique viral small interfering RNA (vsiRNA) profiles are evident for Arachis hypogaea (peanut) and Frankliniella fusca (thrips vector) following infection with TSWV. Differences between vsiRNA profiles for these plant and insect species, such as the relative abundance of 21 and 22 nt vsiRNAs and locations of alignment hotspots, reflect the diverse siRNA biosynthesis pathways of their respective kingdoms. The presence of unique vsiRNAs in F. fusca samples indicates that vsiRNA generation takes place within the thrips, and not solely through uptake via feeding on vsiRNAs produced in infected A. hypogaea. The study also shows key vsiRNA profile differences for TSWV among plant families, which are evident in the case of A. hypogaea, a legume, and members of Solanaceae (S. lycopersicum and Nicotiana benthamiana). Distinctively, overall small RNA (sRNA) biogenesis in A. hypogaea is markedly affected with an absence of the 24 nt sRNAs in TSWV-infected plants, possibly leading to wide-spread molecular and phenotypic perturbations specific to this species. These findings add significant information on the host–virus–vector interaction in terms of RNAi pathways and may lead to better crop and vector specific control strategies.

  1. The Tomato Spotted Wilt Virus Genome Is Processed Differentially in its Plant Host Arachis hypogaea and its Thrips Vector Frankliniella fusca

    PubMed Central

    Fletcher, Stephen J.; Shrestha, Anita; Peters, Jonathan R.; Carroll, Bernard J.; Srinivasan, Rajagopalbabu; Pappu, Hanu R.; Mitter, Neena

    2016-01-01

    Thrips-transmitted tospoviruses are economically important viruses affecting a wide range of field and horticultural crops worldwide. Tomato spotted wilt virus (TSWV) is the type member of the Tospovirus genus with a broad host range of more than 900 plant species. Interactions between these viruses and their plant hosts and insect vectors via RNAi pathways are likely a key determinant of pathogenicity. The current investigation, for the first time, compares biogenesis of small RNAs between the plant host and insect vector in the presence or absence of TSWV. Unique viral small interfering RNA (vsiRNA) profiles are evident for Arachis hypogaea (peanut) and Frankliniella fusca (thrips vector) following infection with TSWV. Differences between vsiRNA profiles for these plant and insect species, such as the relative abundance of 21 and 22 nt vsiRNAs and locations of alignment hotspots, reflect the diverse siRNA biosynthesis pathways of their respective kingdoms. The presence of unique vsiRNAs in F. fusca samples indicates that vsiRNA generation takes place within the thrips, and not solely through uptake via feeding on vsiRNAs produced in infected A. hypogaea. The study also shows key vsiRNA profile differences for TSWV among plant families, which are evident in the case of A. hypogaea, a legume, and members of Solanaceae (S. lycopersicum and Nicotiana benthamiana). Distinctively, overall small RNA (sRNA) biogenesis in A. hypogaea is markedly affected with an absence of the 24 nt sRNAs in TSWV-infected plants, possibly leading to wide-spread molecular and phenotypic perturbations specific to this species. These findings add significant information on the host–virus–vector interaction in terms of RNAi pathways and may lead to better crop and vector specific control strategies. PMID:27656190

  2. The Tomato Spotted Wilt Virus Genome Is Processed Differentially in its Plant Host Arachis hypogaea and its Thrips Vector Frankliniella fusca.

    PubMed

    Fletcher, Stephen J; Shrestha, Anita; Peters, Jonathan R; Carroll, Bernard J; Srinivasan, Rajagopalbabu; Pappu, Hanu R; Mitter, Neena

    2016-01-01

    Thrips-transmitted tospoviruses are economically important viruses affecting a wide range of field and horticultural crops worldwide. Tomato spotted wilt virus (TSWV) is the type member of the Tospovirus genus with a broad host range of more than 900 plant species. Interactions between these viruses and their plant hosts and insect vectors via RNAi pathways are likely a key determinant of pathogenicity. The current investigation, for the first time, compares biogenesis of small RNAs between the plant host and insect vector in the presence or absence of TSWV. Unique viral small interfering RNA (vsiRNA) profiles are evident for Arachis hypogaea (peanut) and Frankliniella fusca (thrips vector) following infection with TSWV. Differences between vsiRNA profiles for these plant and insect species, such as the relative abundance of 21 and 22 nt vsiRNAs and locations of alignment hotspots, reflect the diverse siRNA biosynthesis pathways of their respective kingdoms. The presence of unique vsiRNAs in F. fusca samples indicates that vsiRNA generation takes place within the thrips, and not solely through uptake via feeding on vsiRNAs produced in infected A. hypogaea. The study also shows key vsiRNA profile differences for TSWV among plant families, which are evident in the case of A. hypogaea, a legume, and members of Solanaceae (S. lycopersicum and Nicotiana benthamiana). Distinctively, overall small RNA (sRNA) biogenesis in A. hypogaea is markedly affected with an absence of the 24 nt sRNAs in TSWV-infected plants, possibly leading to wide-spread molecular and phenotypic perturbations specific to this species. These findings add significant information on the host-virus-vector interaction in terms of RNAi pathways and may lead to better crop and vector specific control strategies. PMID:27656190

  3. Molecular characterization of DSC1 orthologs in invertebrate species.

    PubMed

    Cui, Ying-Jun; Yu, Lin-Lin; Xu, Hai-Jun; Dong, Ke; Zhang, Chuan-Xi

    2012-05-01

    DSC1 and BSC1 are two founding members of a novel family of invertebrate voltage-gated cation channels with close structural and evolutionary relationships to voltage-gated sodium and calcium channels. In this study, we searched the published genome sequences for DSC1 orthologs. DSC1 orthologs were found in all 48 insect species, and in other invertebrate species belonging to phyla Mollusca, Cnidaria, Hemichordata and Echinodermata. However, DSC1 orthologs were not found in four arachnid species, Ixodes scapularis, Rhipicephalus microplus, Tetranychus urticae and Varroa destructor, two species in Annelida or any vertebrate species. We then cloned and sequenced NlSC1 and BmSC1 full-length cDNAs from the brown planthopper (Nilaparvata lugens) and the silkworm (Bombyx mori), respectively. NlSC1 and BmSC1 share about 50% identity with DSC1, and the expression of NlSC1 and BmSC1 transcripts was most abundant in the head and antenna in adults. All DSC1 orthologs contain a unique and conserved DEEA motif, instead of the EEEE or EEDD motif in classical calcium channels or the DEKA motif in sodium channels. Phylogenetic analyses revealed that DSC1 and its orthologs form a separate group distinct from the classical voltage-gated sodium and calcium channels and constitute a unique family of cation channels. The DSC1/BSC1-family channels could be potential targets of new and safe insecticides for pest control. PMID:22321571

  4. Molecular characterization of DSC1 orthologs in invertebrate species.

    PubMed

    Cui, Ying-Jun; Yu, Lin-Lin; Xu, Hai-Jun; Dong, Ke; Zhang, Chuan-Xi

    2012-05-01

    DSC1 and BSC1 are two founding members of a novel family of invertebrate voltage-gated cation channels with close structural and evolutionary relationships to voltage-gated sodium and calcium channels. In this study, we searched the published genome sequences for DSC1 orthologs. DSC1 orthologs were found in all 48 insect species, and in other invertebrate species belonging to phyla Mollusca, Cnidaria, Hemichordata and Echinodermata. However, DSC1 orthologs were not found in four arachnid species, Ixodes scapularis, Rhipicephalus microplus, Tetranychus urticae and Varroa destructor, two species in Annelida or any vertebrate species. We then cloned and sequenced NlSC1 and BmSC1 full-length cDNAs from the brown planthopper (Nilaparvata lugens) and the silkworm (Bombyx mori), respectively. NlSC1 and BmSC1 share about 50% identity with DSC1, and the expression of NlSC1 and BmSC1 transcripts was most abundant in the head and antenna in adults. All DSC1 orthologs contain a unique and conserved DEEA motif, instead of the EEEE or EEDD motif in classical calcium channels or the DEKA motif in sodium channels. Phylogenetic analyses revealed that DSC1 and its orthologs form a separate group distinct from the classical voltage-gated sodium and calcium channels and constitute a unique family of cation channels. The DSC1/BSC1-family channels could be potential targets of new and safe insecticides for pest control.

  5. Control of breathing in invertebrate model systems.

    PubMed

    Bell, Harold J; Syed, Naweed I

    2012-07-01

    The invertebrates have adopted a myriad of breathing strategies to facilitate the extraction of adequate quantities of oxygen from their surrounding environments. Their respiratory structures can take a wide variety of forms, including integumentary surfaces, lungs, gills, tracheal systems, and even parallel combinations of these same gas exchange structures. Like their vertebrate counterparts, the invertebrates have evolved elaborate control strategies to regulate their breathing activity. Our goal in this article is to present the reader with a description of what is known regarding the control of breathing in some of the specific invertebrate species that have been used as model systems to study different mechanistic aspects of the control of breathing. We will examine how several species have been used to study fundamental principles of respiratory rhythm generation, central and peripheral chemosensory modulation of breathing, and plasticity in the control of breathing. We will also present the reader with an overview of some of the behavioral and neuronal adaptability that has been extensively documented in these animals. By presenting explicit invertebrate species as model organisms, we will illustrate mechanistic principles that form the neuronal foundation of respiratory control, and moreover appear likely to be conserved across not only invertebrates, but vertebrate species as well. PMID:23723022

  6. Cloning vector

    DOEpatents

    Guilfoyle, R.A.; Smith, L.M.

    1994-12-27

    A vector comprising a filamentous phage sequence containing a first copy of filamentous phage gene X and other sequences necessary for the phage to propagate is disclosed. The vector also contains a second copy of filamentous phage gene X downstream from a promoter capable of promoting transcription in a bacterial host. In a preferred form of the present invention, the filamentous phage is M13 and the vector additionally includes a restriction endonuclease site located in such a manner as to substantially inactivate the second gene X when a DNA sequence is inserted into the restriction site. 2 figures.

  7. Cloning vector

    DOEpatents

    Guilfoyle, Richard A.; Smith, Lloyd M.

    1994-01-01

    A vector comprising a filamentous phage sequence containing a first copy of filamentous phage gene X and other sequences necessary for the phage to propagate is disclosed. The vector also contains a second copy of filamentous phage gene X downstream from a promoter capable of promoting transcription in a bacterial host. In a preferred form of the present invention, the filamentous phage is M13 and the vector additionally includes a restriction endonuclease site located in such a manner as to substantially inactivate the second gene X when a DNA sequence is inserted into the restriction site.

  8. Symbiodinium—Invertebrate Symbioses and the Role of Metabolomics

    PubMed Central

    Gordon, Benjamin R.; Leggat, William

    2010-01-01

    Symbioses play an important role within the marine environment. Among the most well known of these symbioses is that between coral and the photosynthetic dinoflagellate, Symbiodinium spp. Understanding the metabolic relationships between the host and the symbiont is of the utmost importance in order to gain insight into how this symbiosis may be disrupted due to environmental stressors. Here we summarize the metabolites related to nutritional roles, diel cycles and the common metabolites associated with the invertebrate-Symbiodinium relationship. We also review the more obscure metabolites and toxins that have been identified through natural products and biomarker research. Finally, we discuss the key role that metabolomics and functional genomics will play in understanding these important symbioses. PMID:21116405

  9. Rice Reoviruses in Insect Vectors.

    PubMed

    Wei, Taiyun; Li, Yi

    2016-08-01

    Rice reoviruses, transmitted by leafhopper or planthopper vectors in a persistent propagative manner, seriously threaten the stability of rice production in Asia. Understanding the mechanisms that enable viral transmission by insect vectors is a key to controlling these viral diseases. This review describes current understanding of replication cycles of rice reoviruses in vector cell lines, transmission barriers, and molecular determinants of vector competence and persistent infection. Despite recent breakthroughs, such as the discoveries of actin-based tubule motility exploited by viruses to overcome transmission barriers and mutually beneficial relationships between viruses and bacterial symbionts, there are still many gaps in our knowledge of transmission mechanisms. Advances in genome sequencing, reverse genetics systems, and molecular technologies will help to address these problems. Investigating the multiple interaction systems among the virus, insect vector, insect symbiont, and plant during natural infection in the field is a central topic for future research on rice reoviruses. PMID:27296147

  10. Genome Sequence of Pantoea annatis strain CFH 7-1, which is associated with a vector-borne cotton fruit disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pantoea ananatis is a bacterium with versatile niches that vary from pathogenic to beneficial. We present the genome of strain CFH 7-1, which was recovered from a diseased greenhouse cotton boll previously caged with a field-collected cotton fleahopper (Pseudatomoscelis seriatus). These data will ...

  11. Vector quantization

    NASA Technical Reports Server (NTRS)

    Gray, Robert M.

    1989-01-01

    During the past ten years Vector Quantization (VQ) has developed from a theoretical possibility promised by Shannon's source coding theorems into a powerful and competitive technique for speech and image coding and compression at medium to low bit rates. In this survey, the basic ideas behind the design of vector quantizers are sketched and some comments made on the state-of-the-art and current research efforts.

  12. Epigenetic features in the oyster Crassostrea gigas suggestive of functionally relevant promoter DNA methylation in invertebrates

    PubMed Central

    Rivière, Guillaume

    2014-01-01

    DNA methylation is evolutionarily conserved. Vertebrates exhibit high, widespread DNA methylation whereas invertebrate genomes are less methylated, predominantly within gene bodies. DNA methylation in invertebrates is associated with transcription level, alternative splicing, and genome evolution, but functional outcomes of DNA methylation remain poorly described in lophotrochozoans. Recent genome-wide approaches improve understanding in distant taxa such as molluscs, where the phylogenetic position, and life traits of Crassostrea gigas make this bivalve an ideal model to study the physiological and evolutionary implications of DNA methylation. We review the literature about DNA methylation in invertebrates and focus on DNA methylation features in the oyster. Indeed, though our MeDIP-seq results confirm predominant intragenic methylation, the profiles depend on the oyster's developmental and reproductive stage. We discuss the perspective that oyster DNA methylation could be biased toward the 5′-end of some genes, depending on physiological status, suggesting important functional outcomes of putative promoter methylation from cell differentiation during early development to sustained adaptation of the species to the environment. PMID:24778620

  13. Wood decomposition as influenced by invertebrates.

    PubMed

    Ulyshen, Michael D

    2016-02-01

    The diversity and habitat requirements of invertebrates associated with dead wood have been the subjects of hundreds of studies in recent years but we still know very little about the ecological or economic importance of these organisms. The purpose of this review is to examine whether, how and to what extent invertebrates affect wood decomposition in terrestrial ecosystems. Three broad conclusions can be reached from the available literature. First, wood decomposition is largely driven by microbial activity but invertebrates also play a significant role in both temperate and tropical environments. Primary mechanisms include enzymatic digestion (involving both endogenous enzymes and those produced by endo- and ectosymbionts), substrate alteration (tunnelling and fragmentation), biotic interactions and nitrogen fertilization (i.e. promoting nitrogen fixation by endosymbiotic and free-living bacteria). Second, the effects of individual invertebrate taxa or functional groups can be accelerative or inhibitory but the cumulative effect of the entire community is generally to accelerate wood decomposition, at least during the early stages of the process (most studies are limited to the first 2-3 years). Although methodological differences and design limitations preclude meta-analysis, studies aimed at quantifying the contributions of invertebrates to wood decomposition commonly attribute 10-20% of wood loss to these organisms. Finally, some taxa appear to be particularly influential with respect to promoting wood decomposition. These include large wood-boring beetles (Coleoptera) and termites (Termitoidae), especially fungus-farming macrotermitines. The presence or absence of these species may be more consequential than species richness and the influence of invertebrates is likely to vary biogeographically.

  14. Infertility in male aquatic invertebrates: a review.

    PubMed

    Lewis, Ceri; Ford, Alex T

    2012-09-15

    As a result of endocrine disruptor studies, there are numerous examples of male related reproductive abnormalities observed in vertebrates. Contrastingly, within the invertebrates there have been considerably less examples both from laboratory and field investigations. This has in part been due to a focus of female related endpoints, inadequate biomarkers and the low number of studies. Whether contaminant induced male infertility is an issue within aquatic invertebrates and their wider communities therefore remains largely unknown and represents a key knowledge gap in our understanding of pollutant impacts in aquatic wildlife. This paper reviews the current knowledge regarding pollutants impacting male infertility across several aquatic invertebrate phyla; which biomarkers are currently being used and where the science needs to be expanded. The limited studies conducted so far have revealed reductions in sperm numbers, examples of poor fertilisation success, DNA damage to spermatozoa and inhibition of sperm motility that can be induced by a range of environmental contaminants. This limited data is mainly comprised from laboratory studies with only a few studies of sperm toxicity in natural populations. Clearly, there is a need for further studies in this area, to include both laboratory and field studies from clean and reference sites, with a focus on broadcast spawners and those with direct fertilisation. Biomarkers developed for measuring sperm quantity and quality in vertebrates are easily transferable to invertebrates but require optimisation for particular species. We discuss how sperm tracking and techniques for measuring DNA strand breaks and sperm viability have been successfully transferred from human infertility clinics to aquatic invertebrate ecotoxicology. Linking sperm toxicity and male infertility effects to higher level impacts on the reproductive biology and dynamics of populations requires a much greater understanding of fertilisation dynamics and

  15. HISTOLOGICAL PREPARATION OF INVERTEBRATES FOR EVALUATING CONTAMINANT EFFECTS

    EPA Science Inventory

    Although many studies in toxicologic pathology evaluate the effects of toxicants on fishes because of their similarities with other vertebrates, invertebrates can also provide insights into toxicant impacts on ecosystems. Invertebrates not only serve as food resources (e.g., ...

  16. Transcriptomics and disease vector control.

    PubMed

    Vontas, John; Ranson, Hilary; Alphey, Luke

    2010-01-01

    Next-generation sequencing can be used to compare transcriptomes under different conditions. A study in BMC Genomics applies this approach to investigating the effects of exposure to a range of xenobiotics on changes in gene expression in the larvae of Aedes aegypti, the mosquito vector of dengue fever.

  17. Libbie Henrietta Hyman: Eminent Invertebrate Zoologist.

    ERIC Educational Resources Information Center

    Morgan, Rose M.

    1998-01-01

    Reviews the life and work of the famous invertebrate zoologist Libbie Henrietta Hyman. Focuses on her work at the American Museum of History and her role as informal mentor and valued colleague and collaborator to zoologists all over the world. Contains 17 references. (DDR)

  18. The Early Years: An Invertebrate Garden

    ERIC Educational Resources Information Center

    Ashbrook, Peggy

    2008-01-01

    For farmers and gardeners, slugs and snails may be serious pests that will limit the amount of harvest, but for a child, they represent a world to be explored. To teachers, however, invertebrates are tools for broadening students' understanding about animals, the connections between animals and habitats or plants, and an engaging subject to write…

  19. Conservation status of Chinese species: (2) Invertebrates.

    PubMed

    Xie, Yan; Wang, Sung

    2007-06-01

    A total of 2441 invertebrate species were evaluated using the IUCN Red List Criteria and Regional Guidelines. Approximately 30 experts were involved in this project, which covered a wide range of species, including jellyfish, corals, planarians, snails, mollusks, bivalves, decapods, benthic crustaceans, arachnids (spiders, scorpions), butterflies, moths, beetles, sea cucumbers, sea urchins, sea stars, acorn worms and lancelets. In general, invertebrate species in China were found to be severely threatened, with 0.9% being critically endangered, 13.44% endangered and 20.63% vulnerable. All species of hermatypic corals and planarians are threatened. More than 80% of evaluated species face serious threat due to habitat destruction by coral collection, logging, non-woody vegetation collection, timber plantations, non-timber plantations, extraction and/or livestock. Other threats are intrinsic factors, harvesting by humans, alien invasive species and pollution. The main intrinsic factors contributing to the high levels of threat are limited dispersal and restricted range. No conservation measures have been taken for 70% of the threatened invertebrates evaluated. Existing conservation measures include: strengthening of national and international legislation (Convention on International Trade in Endangered Species of Wild Fauna and Flora), increasing public awareness, studying population trends/monitoring, and establishment of protected areas. The major conservation measure employed is strengthening of policies. Relative to the situation worldwide (2006 IUCN Red List), there is little information available about invertebrate extinctions in China.

  20. Effects of pollution on freshwater invertebrates

    SciTech Connect

    Buikema

    1982-06-01

    The biological effects of acid rain, chlorination, heavy metals and other forms of pollution on freshwater invertebrates are examined in this review. Several methods for evaluating chronic toxicity to pesticide residues and synthetic fuels components are reviewed. The effects of pollutants is reviewed in detail for cladocera, amphipods, isopods, decapods, aquatic insects, molluscs, worms, and protozoa.(KRM)

  1. Halogenated Indole Alkaloids from Marine Invertebrates

    PubMed Central

    Pauletti, Patrícia Mendonça; Cintra, Lucas Silva; Braguine, Caio Guedes; da Silva Filho, Ademar Alves; Silva, Márcio Luís Andrade e; Cunha, Wilson Roberto; Januário, Ana Helena

    2010-01-01

    This review discusses the isolation, structural elucidation, and biological activities of halogenated indole alkaloids obtained from marine invertebrates. Meridianins and related compounds (variolins, psammopemmins, and aplicyanins), as well as aplysinopsins and leptoclinidamines, are focused on. A compilation of the 13C-NMR spectral data of these selected natural indole alkaloids is also provided. PMID:20559487

  2. Lentiviral vectors.

    PubMed

    Giry-Laterrière, Marc; Verhoeyen, Els; Salmon, Patrick

    2011-01-01

    Lentiviral vectors have evolved over the last decade as powerful, reliable, and safe tools for stable gene transfer in a wide variety of mammalian cells. Contrary to other vectors derived from oncoretroviruses, they allow for stable gene delivery into most nondividing primary cells. In particular, lentivectors (LVs) derived from HIV-1 have gradually evolved to display many desirable features aimed at increasing both their safety and their versatility. This is why lentiviral vectors are becoming the most useful and promising tools for genetic engineering, to generate cells that can be used for research, diagnosis, and therapy. This chapter describes protocols and guidelines, for production and titration of LVs, which can be implemented in a research laboratory setting, with an emphasis on standardization in order to improve transposability of results between laboratories. We also discuss latest designs in LV technology.

  3. 76 FR 61379 - Final Recovery Plan, Bexar County Karst Invertebrates

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-04

    ... Bexar County karst invertebrates were listed as endangered species on December 26, 2000 (65 FR 81419... Fish and Wildlife Service Final Recovery Plan, Bexar County Karst Invertebrates AGENCY: Fish and... Invertebrates under the Endangered Species Act of 1973, as amended (Act). These species occur in Bexar...

  4. Prospects and challenges of CRISPR/Cas genome editing for the study and control of neglected vector-borne nematode diseases.

    PubMed

    Zamanian, Mostafa; Andersen, Erik C

    2016-09-01

    Neglected tropical diseases caused by parasitic nematodes inflict an immense health and socioeconomic burden throughout much of the developing world. Current estimates indicate that more than two billion people are infected with nematodes, resulting in the loss of 14 million disability-adjusted life years per annum. Although these parasites cause significant mortality, they primarily cause chronic morbidity through a wide range of severe clinical ailments. Treatment options for nematode infections are restricted to a small number of anthelmintic drugs, and the rapid expansion of anthelmintic mass drug administration raises concerns of drug resistance. Preservation of existing drugs is necessary, as well as the development of new treatment options and methods of control. We focus this review on how the democratization of CRISPR/Cas9 genome editing technology can be enlisted to improve our understanding of the biology of nematode parasites and our ability to treat the infections they cause. We will first explore how this robust method of genome manipulation can be used to newly exploit the powerful model nematode Caenorhabditis elegans for parasitology research. We will then discuss potential avenues to develop CRISPR/Cas9 editing protocols in filarial nematodes. Lastly, we will propose potential ways in which CRISPR/Cas9 can be used to engineer gene drives that target the transmission of mosquito-borne filarial nematodes. PMID:27300487

  5. Some highlights of research on aging with invertebrates, 2009.

    PubMed

    Partridge, Linda

    2009-09-01

    This annual review focuses on invertebrate model organisms, which shed light on new mechanisms in aging and provide excellent systems for both genome-wide and in-depth analysis. This year, protein interaction networks have been used in a new bioinformatic approach to identify novel genes that extend replicative lifespan in yeast. In an extended approach, using a new, human protein interaction network, information from the invertebrates was used to identify new, candidate genes for lifespan extension and their orthologues were validated in the nematode Caenorhabditis elegans. Chemosensation of diffusible substances from bacteria has been shown to limit lifespan in C. elegans, while a systematic study of the different methods used to implement dietary restriction in the worm has shown that they involve mechanisms that are partially distinct and partially overlapping, providing important clarification for addressing whether or not they are conserved in other organisms. A new theoretical model for the evolution of rejuvenating cell division has shown that asymmetrical division for either cell size or for damaged cell constituents results in increased fitness for most realistic levels of cellular protein damage. Work on aging-related disease has both refined our understanding of the mechanisms underlying one route to the development of Parkinson's disease and has revealed that in worms, as in mice, dietary restriction is protective against cellular proteotoxicity. Two systematic studies genetically manipulating the superoxide dismutases of C. elegans support the idea that damage from superoxide plays little or no role in aging in this organism, and have prompted discussion of other kinds of damage and other kinds of mechanisms for producing aging-related decline in function. PMID:19558590

  6. Chikungunya Virus–Vector Interactions

    PubMed Central

    Coffey, Lark L.; Failloux, Anna-Bella; Weaver, Scott C.

    2014-01-01

    Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes chikungunya fever, a severe, debilitating disease that often produces chronic arthralgia. Since 2004, CHIKV has emerged in Africa, Indian Ocean islands, Asia, Europe, and the Americas, causing millions of human infections. Central to understanding CHIKV emergence is knowledge of the natural ecology of transmission and vector infection dynamics. This review presents current understanding of CHIKV infection dynamics in mosquito vectors and its relationship to human disease emergence. The following topics are reviewed: CHIKV infection and vector life history traits including transmission cycles, genetic origins, distribution, emergence and spread, dispersal, vector competence, vector immunity and microbial interactions, and co-infection by CHIKV and other arboviruses. The genetics of vector susceptibility and host range changes, population heterogeneity and selection for the fittest viral genomes, dual host cycling and its impact on CHIKV adaptation, viral bottlenecks and intrahost diversity, and adaptive constraints on CHIKV evolution are also discussed. The potential for CHIKV re-emergence and expansion into new areas and prospects for prevention via vector control are also briefly reviewed. PMID:25421891

  7. Ethics and invertebrates: a cephalopod perspective.

    PubMed

    Mather, Jennifer A; Anderson, Roland C

    2007-05-01

    This paper first explores 3 philosophical bases for attitudes to invertebrates, Contractarian/Kantian, Utilitarian, and Rights-based, and what they lead us to conclude about how we use and care for these animals. We next discuss the problems of evaluating pain and suffering in invertebrates, pointing out that physiological responses to stress are widely similar across the animal kingdom and that most animals show behavioral responses to potentially painful stimuli. Since cephalopods are often used as a test group for consideration of pain, distress and proper conditions for captivity and handling, we evaluate their behavioral and cognitive capacities. Given these capacities, we then discuss practical issues: minimization of their pain and suffering during harvesting for food; ensuring that captive cephalopods are properly cared for, stimulated and allowed to live as full a life as possible; and, lastly, working for their conservation. PMID:17578251

  8. Modeling zinc toxicity for terrestrial invertebrates.

    PubMed

    Lock, K; Janssen, C R

    2001-09-01

    Acute and chronic ecotoxicity tests with zinc were performed with the earthworm Eisenia fetida, the potworm Enchytraeus albidus, and the springtail Folsomia candida. To assess the influence of the soil type on zinc toxicity for these soil invertebrates, these tests were carried out in a standard artificial soil, a sandy and a loamy field soil. Based on the results of this experimental work and data taken from literature, models were developed relating the ecotoxicity of zinc to the most important parameters controlling bioavailability: pH and cation exchange capacity. Models were developed for E. fetida and F. candida using the regression technique partial least squares projection to latent structures (PLS). Acute as well as chronic toxicity data of both organisms could be normalized on the basis of the pH and the cation exchange capacity of the test soils. For other terrestrial invertebrates, not enough data were available to develop reliable models.

  9. Effects of nanomaterials on marine invertebrates.

    PubMed

    Canesi, Laura; Corsi, Ilaria

    2016-09-15

    The development of nanotechnology will inevitably lead to the release of consistent amounts of nanomaterials (NMs) and nanoparticles (NPs) into marine ecosystems. Ecotoxicological studies have been carried out to identify potential biological targets of NPs, and suitable models for predicting their impact on the health of the marine environment. Recent studies in invertebrates mainly focused on NP accumulation and sub-lethal effects, rather than acute toxicity. Among marine invertebrates, bivalves represent by large the most studied group, with polychaetes and echinoderms also emerging as significant targets of NPs. However, major scientific gaps still need to be filled. In this work, factors affecting the fate of NPs in the marine environment, and their consequent uptake/accumulation/toxicity in marine invertebrates will be summarized. The results show that in different model species, NP accumulation mainly occurs in digestive tract and gills. Data on sub-lethal effects and modes of action of different types of NPs (mainly metal oxides and metal based NPs) in marine invertebrates will be reviewed, in particular on immune function, oxidative stress and embryo development. Moreover, the possibility that such effects may be influenced by NP interactions with biomolecules in both external and internal environment will be introduced. In natural environmental media, NP interactions with polysaccharides, proteins and colloids may affect their agglomeration/aggregation and consequent bioavailability. Moreover, once within the organism, NPs are known to interact with plasma proteins, forming a protein corona that can affect particle uptake and toxicity in target cells in a physiological environment. These interactions, leading to the formation of eco-bio-coronas, may be crucial in determining particle behavior and effects also in marine biota. In order to classify NPs into groups and predict the implications of their release into the marine environment, information on

  10. Effects of nanomaterials on marine invertebrates.

    PubMed

    Canesi, Laura; Corsi, Ilaria

    2016-09-15

    The development of nanotechnology will inevitably lead to the release of consistent amounts of nanomaterials (NMs) and nanoparticles (NPs) into marine ecosystems. Ecotoxicological studies have been carried out to identify potential biological targets of NPs, and suitable models for predicting their impact on the health of the marine environment. Recent studies in invertebrates mainly focused on NP accumulation and sub-lethal effects, rather than acute toxicity. Among marine invertebrates, bivalves represent by large the most studied group, with polychaetes and echinoderms also emerging as significant targets of NPs. However, major scientific gaps still need to be filled. In this work, factors affecting the fate of NPs in the marine environment, and their consequent uptake/accumulation/toxicity in marine invertebrates will be summarized. The results show that in different model species, NP accumulation mainly occurs in digestive tract and gills. Data on sub-lethal effects and modes of action of different types of NPs (mainly metal oxides and metal based NPs) in marine invertebrates will be reviewed, in particular on immune function, oxidative stress and embryo development. Moreover, the possibility that such effects may be influenced by NP interactions with biomolecules in both external and internal environment will be introduced. In natural environmental media, NP interactions with polysaccharides, proteins and colloids may affect their agglomeration/aggregation and consequent bioavailability. Moreover, once within the organism, NPs are known to interact with plasma proteins, forming a protein corona that can affect particle uptake and toxicity in target cells in a physiological environment. These interactions, leading to the formation of eco-bio-coronas, may be crucial in determining particle behavior and effects also in marine biota. In order to classify NPs into groups and predict the implications of their release into the marine environment, information on

  11. Relationship between invertebrate fauna and bromeliad size.

    PubMed

    Araújo, V A; Melo, S K; Araújo, A P A; Gomes, M L M; Carneiro, M A A

    2007-11-01

    Several bromeliads species store water and organic substrates, allowing the establishment of phytotelmata and associated fauna on their leaves. In this study, we sampled 70 individuals of Vriesea sp. (Carrière) (Bromeliaceae), in rupestrian fields in the Serra de Ouro Branco-MG, Brazil. The relationships between invertebrate species richness and abundance and size of bromeliads were tested using multiple regression. We found 19 species associated with bromeliads, mainly Diptera larvae. The abundance of the phytotelmate fauna increased principally in relation to the volume of water in the bromeliad reservoir. Phytotelmata richness was affected principally by diameter of the reservoir. There was a significant relationship between the abundance and richness of invertebrates associated with leaves with diameter and height of the plant. Invertebrate richness was better explained by abundance of individuals. These results suggest that the increase of richness was attended by higher numbers of microhabitats and more space for colonization of bigger bromeliads. Additionally, there was more chance of sampling different species in locales with greater abundance of individuals.

  12. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins

    PubMed Central

    Rosario, Karyna; Schenck, Ryan O.; Harbeitner, Rachel C.; Lawler, Stephanie N.; Breitbart, Mya

    2015-01-01

    Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses. PMID:26217327

  13. Human-mediated dispersal of aquatic invertebrates with waterproof footwear.

    PubMed

    Valls, Luis; Castillo-Escrivà, Andreu; Mesquita-Joanes, Francesc; Armengol, Xavier

    2016-02-01

    Human-mediated dispersal has rarely been considered in wetland conservation strategies at regional scales, yet high concern exists about this aspect for (inter-)national management considering invasive species in other aquatic systems. In this context, we aim at understanding the role of human-mediated dispersal by footwear in protected wetlands with high conservation value. Zooplankton and zoobenthos were sampled in 13 shallow lakes in central Spain and, at the same time, mud attached to waders was collected and later cultured in deionized water under laboratory conditions for 4 weeks. Two-hundred and four individuals belonging to 19 invertebrate taxa were recovered after hatching; Ostracoda (84 %), Cladocera (53 %), Copepoda (30 %), Anostraca (30 %), and Notostraca (7 %) were the most frequent groups among the hatched crustaceans. NMDS and PERMANOVA analyses showed significant differences between the dispersed (via footwear) and the source active metacommunity, suggesting different dispersal abilities among the species found. Human vectors facilitate dispersal among protected lakes, which could eventuality lead to biotic homogenization and faster spread of non-indigenous species. Preservation strategies and education campaigns associated to target humans in close contact with water bodies should be imperative in conservation management of protected lakes. PMID:26216143

  14. Brain and behavioral lateralization in invertebrates

    PubMed Central

    Frasnelli, Elisa

    2013-01-01

    Traditionally, only humans were thought to exhibit brain and behavioral asymmetries, but several studies have revealed that most vertebrates are also lateralized. Recently, evidence of left–right asymmetries in invertebrates has begun to emerge, suggesting that lateralization of the nervous system may be a feature of simpler brains as well as more complex ones. Here I present some examples in invertebrates of sensory and motor asymmetries, as well as asymmetries in the nervous system. I illustrate two cases where an asymmetric brain is crucial for the development of some cognitive abilities. The first case is the nematode Caenorhabditis elegans, which has asymmetric odor sensory neurons and taste perception neurons. In this worm left/right asymmetries are responsible for the sensing of a substantial number of salt ions, and lateralized responses to salt allow the worm to discriminate between distinct salt ions. The second case is the fruit fly Drosophila melanogaster, where the presence of asymmetry in a particular structure of the brain is important in the formation or retrieval of long-term memory. Moreover, I distinguish two distinct patterns of lateralization that occur in both vertebrates and invertebrates: individual-level and population-level lateralization. Theoretical models on the evolution of lateralization suggest that the alignment of lateralization at the population level may have evolved as an evolutionary stable strategy in which individually asymmetrical organisms must coordinate their behavior with that of other asymmetrical organisms. This implies that lateralization at the population-level is more likely to have evolved in social rather than in solitary species. I evaluate this new hypothesis with a specific focus on insects showing different level of sociality. In particular, I present a series of studies on antennal asymmetries in honeybees and other related species of bees, showing how insects may be extremely useful to test the

  15. Invertebrates in testing of environmental chemicals: are they alternatives?

    PubMed Central

    Lagadic, L; Caquet, T

    1998-01-01

    An enlarged interpretation of alternatives in toxicology testing includes the replacement of one animal species with another, preferably a nonmammalian species. This paper reviews the potential of invertebrates in testing environmental chemicals and provides evidence of their usefulness in alternative testing methodologies. The first part of this review addresses the use of invertebrates in laboratory toxicology testing. Problems in extrapolating results obtained in invertebrates to those obtained from vertebrates are noted, suggesting that invertebrates can essentially be used in addition to rather than as replacements for vertebrates in laboratory toxicity tests. However, evaluation of the ecologic impact of environmental chemicals must include defining end points that may frequently differ from those classically used in biomedical research. In this context, alternative approaches using invertebrates may be more pertinent. The second part of the review therefore focuses on the use of invertebrates in situ to assess the environmental impact of pollutants. Advantages of invertebrates in ecotoxicologic investigation are presented for their usefulness for seeking mechanistic links between effects occurring at the individual level and consequences for higher levels of biologic organization (e.g., population and community). In the end, it is considered that replacement of vertebrates by invertebrates in ecotoxicity testing is likely to become a reality when basic knowledge of metabolic, physiologic, and developmental patterns in the latter will be sufficient to assess the effect of a given chemical through end points that could be different between invertebrates and vertebrates. PMID:9599707

  16. Invertebrate grazers affect metal/metalloid fixation during litter decomposition.

    PubMed

    Schaller, Jörg; Brackhage, Carsten

    2015-01-01

    Plant litter and organic sediments are main sinks for metals and metalloids in aquatic ecosystems. The effect of invertebrates as key species in aquatic litter decomposition on metal/metalloid fixation by organic matter is described only for shredders, but for grazers as another important animal group less is known. Consequently, a laboratory batch experiment was conducted to examine the effect of invertebrate grazers (Lymnaea stagnalis L.) on metal/metalloid fixation/remobilization during aquatic litter decomposition. It could be shown that invertebrate grazers facilitate significantly the formation of smaller sizes of particulate organic matter (POM), as shown previously for invertebrate shredders. The metal/metalloid binding capacity of these smaller particles of POM is higher compared to leaf litter residuals. But element enrichment is not as high as shown previously for the effect by invertebrate shredders. Invertebrate grazers enhance also the mobilization of selected elements to the water, in the range also proven for invertebrate shredders but different for the different elements. Nonetheless invertebrate grazers activity during aquatic litter decomposition leads to a metal/metalloid fixation into leaf litter as part of sediment organic matter. Hence, the effect of invertebrate grazers on metal/metalloid fixation/remobilization contrasts partly with former assessments revealing the possibility of an enhanced metal/metalloid fixation.

  17. Venus Kinase Receptors: Prospects in Signaling and Biological Functions of These Invertebrate Kinases

    PubMed Central

    Dissous, Colette; Morel, Marion; Vanderstraete, Mathieu

    2014-01-01

    Venus kinase receptors (VKRs) form a family of invertebrate receptor tyrosine kinases (RTKs) initially discovered in the parasitic platyhelminth Schistosoma mansoni. VKRs are single transmembrane receptors that contain an extracellular venus fly trap structure similar to the ligand-binding domain of G protein-coupled receptors of class C, and an intracellular tyrosine kinase domain close to that of insulin receptors. VKRs are found in a large variety of invertebrates from cnidarians to echinoderms and are highly expressed in larval stages and in gonads, suggesting a role of these proteins in embryonic and larval development as well as in reproduction. VKR gene silencing could demonstrate the function of these receptors in oogenesis as well as in spermatogenesis in S. mansoni. VKRs are activated by amino acids and are highly responsive to arginine. As many other RTKs, they form dimers when activated by ligands and induce intracellular pathways involved in protein synthesis and cellular growth, such as MAPK and PI3K/Akt/S6K pathways. VKRs are not present in vertebrates or in some invertebrate species. Questions remain open about the origin of this little-known RTK family in evolution and its role in emergence and specialization of Metazoa. What is the meaning of maintenance or loss of VKR in some phyla or species in terms of development and physiological functions? The presence of VKRs in invertebrates of economical and medical importance, such as pests, vectors of pathogens, and platyhelminth parasites, and the implication of these RTKs in gametogenesis and reproduction processes are valuable reasons to consider VKRs as interesting targets in new programs for eradication/control of pests and infectious diseases, with the main advantage in the case of parasite targeting that VKR counterparts are absent from the vertebrate host kinase panel. PMID:24860549

  18. Venus kinase receptors: prospects in signaling and biological functions of these invertebrate kinases.

    PubMed

    Dissous, Colette; Morel, Marion; Vanderstraete, Mathieu

    2014-01-01

    Venus kinase receptors (VKRs) form a family of invertebrate receptor tyrosine kinases (RTKs) initially discovered in the parasitic platyhelminth Schistosoma mansoni. VKRs are single transmembrane receptors that contain an extracellular venus fly trap structure similar to the ligand-binding domain of G protein-coupled receptors of class C, and an intracellular tyrosine kinase domain close to that of insulin receptors. VKRs are found in a large variety of invertebrates from cnidarians to echinoderms and are highly expressed in larval stages and in gonads, suggesting a role of these proteins in embryonic and larval development as well as in reproduction. VKR gene silencing could demonstrate the function of these receptors in oogenesis as well as in spermatogenesis in S. mansoni. VKRs are activated by amino acids and are highly responsive to arginine. As many other RTKs, they form dimers when activated by ligands and induce intracellular pathways involved in protein synthesis and cellular growth, such as MAPK and PI3K/Akt/S6K pathways. VKRs are not present in vertebrates or in some invertebrate species. Questions remain open about the origin of this little-known RTK family in evolution and its role in emergence and specialization of Metazoa. What is the meaning of maintenance or loss of VKR in some phyla or species in terms of development and physiological functions? The presence of VKRs in invertebrates of economical and medical importance, such as pests, vectors of pathogens, and platyhelminth parasites, and the implication of these RTKs in gametogenesis and reproduction processes are valuable reasons to consider VKRs as interesting targets in new programs for eradication/control of pests and infectious diseases, with the main advantage in the case of parasite targeting that VKR counterparts are absent from the vertebrate host kinase panel.

  19. Nutrient-Specific Foraging in Invertebrate Predators

    NASA Astrophysics Data System (ADS)

    Mayntz, David; Raubenheimer, David; Salomon, Mor; Toft, Søren; Simpson, Stephen J.

    2005-01-01

    Many herbivores and omnivores adjust their food selection behavior to regulate the intake of multiple nutrients. Carnivores, however, are generally assumed to optimize the rate of prey capture rather than select prey according to nutrient composition. We showed experimentally that invertebrate predators can forage selectively for protein and lipids to redress specific nutritional imbalances. This selection can take place at different stages of prey handling: The predator may select among foods of different nutritional composition, eat more of a prey if it is rich in nutrients that the predator is deficient in, or extract specific nutrients from a single prey item.

  20. Nutrient-specific foraging in invertebrate predators.

    PubMed

    Mayntz, David; Raubenheimer, David; Salomon, Mor; Toft, Søren; Simpson, Stephen J

    2005-01-01

    Many herbivores and omnivores adjust their food selection behavior to regulate the intake of multiple nutrients. Carnivores, however, are generally assumed to optimize the rate of prey capture rather than select prey according to nutrient composition. We showed experimentally that invertebrate predators can forage selectively for protein and lipids to redress specific nutritional imbalances. This selection can take place at different stages of prey handling: The predator may select among foods of different nutritional composition, eat more of a prey if it is rich in nutrients that the predator is deficient in, or extract specific nutrients from a single prey item.

  1. Ion channels in key marine invertebrates; their diversity and potential for applications in biotechnology.

    PubMed

    Brown, Euan R; Piscopo, Stefania

    2011-01-01

    Of the intra-membrane proteins, the class that comprises voltage and ligand-gated ion channels represents the major substrate whereby signals pass between and within cells in all organisms. It has been presumed that vertebrate and particularly mammalian ion channels represent the apex of evolutionary complexity and diversity and much effort has been focused on understanding their function. However, the recent availability of cheap high throughput genome sequencing has massively broadened and deepened the quality of information across phylogeny and is radically changing this view. Here we review current knowledge on such channels in key marine invertebrates where physiological evidence is backed up by molecular sequences and expression/functional studies. As marine invertebrates represent a much greater range of phyla than terrestrial vertebrates and invertebrates together, we argue that these animals represent a highly divergent, though relatively underused source of channel novelty. As ion channels are exquisitely selective sensors for voltage and ligands, their potential and actual applications in biotechnology are manifold.

  2. Biosynthesis of polyunsaturated fatty acids in marine invertebrates: recent advances in molecular mechanisms.

    PubMed

    Monroig, Óscar; Tocher, Douglas R; Navarro, Juan C

    2013-10-21

    Virtually all polyunsaturated fatty acids (PUFA) originate from primary producers but can be modified by bioconversions as they pass up the food chain in a process termed trophic upgrading. Therefore, although the main primary producers of PUFA in the marine environment are microalgae, higher trophic levels have metabolic pathways that can produce novel and unique PUFA. However, little is known about the pathways of PUFA biosynthesis and metabolism in the levels between primary producers and fish that are largely filled by invertebrates. It has become increasingly apparent that, in addition to trophic upgrading, de novo synthesis of PUFA is possible in some lower animals. The unequivocal identification of PUFA biosynthetic pathways in many invertebrates is complicated by the presence of other organisms within them. These organisms include bacteria and algae with PUFA biosynthesis pathways, and range from intestinal flora to symbiotic relationships that can involve PUFA translocation to host organisms. This emphasizes the importance of studying biosynthetic pathways at a molecular level, and the continual expansion of genomic resources and advances in molecular analysis is facilitating this. The present paper highlights recent research into the molecular and biochemical mechanisms of PUFA biosynthesis in marine invertebrates, particularly focusing on cephalopod molluscs.

  3. Eukaryotic tRNAs fingerprint invertebrates vis-à-vis vertebrates.

    PubMed

    Mitra, Sanga; Das, Pijush; Samadder, Arpa; Das, Smarajit; Betai, Rupal; Chakrabarti, Jayprokas

    2015-01-01

    During translation, aminoacyl-tRNA synthetases recognize the identities of the tRNAs to charge them with their respective amino acids. The conserved identities of 58,244 eukaryotic tRNAs of 24 invertebrates and 45 vertebrates in genomic tRNA database were analyzed and their novel features extracted. The internal promoter sequences, namely, A-Box and B-Box, were investigated and evidence gathered that the intervention of optional nucleotides at 17a and 17b correlated with the optimal length of the A-Box. The presence of canonical transcription terminator sequences at the immediate vicinity of tRNA genes was ventured. Even though non-canonical introns had been reported in red alga, green alga, and nucleomorph so far, fairly motivating evidence of their existence emerged in tRNA genes of other eukaryotes. Non-canonical introns were seen to interfere with the internal promoters in two cases, questioning their transcription fidelity. In a first of its kind, phylogenetic constructs based on tRNA molecules delineated and built the trees of the vast and diverse invertebrates and vertebrates. Finally, two tRNA models representing the invertebrates and the vertebrates were drawn, by isolating the dominant consensus in the positional fluctuations of nucleotide compositions.

  4. Biosynthesis of Polyunsaturated Fatty Acids in Marine Invertebrates: Recent Advances in Molecular Mechanisms

    PubMed Central

    Monroig, Óscar; Tocher, Douglas R.; Navarro, Juan C.

    2013-01-01

    Virtually all polyunsaturated fatty acids (PUFA) originate from primary producers but can be modified by bioconversions as they pass up the food chain in a process termed trophic upgrading. Therefore, although the main primary producers of PUFA in the marine environment are microalgae, higher trophic levels have metabolic pathways that can produce novel and unique PUFA. However, little is known about the pathways of PUFA biosynthesis and metabolism in the levels between primary producers and fish that are largely filled by invertebrates. It has become increasingly apparent that, in addition to trophic upgrading, de novo synthesis of PUFA is possible in some lower animals. The unequivocal identification of PUFA biosynthetic pathways in many invertebrates is complicated by the presence of other organisms within them. These organisms include bacteria and algae with PUFA biosynthesis pathways, and range from intestinal flora to symbiotic relationships that can involve PUFA translocation to host organisms. This emphasizes the importance of studying biosynthetic pathways at a molecular level, and the continual expansion of genomic resources and advances in molecular analysis is facilitating this. The present paper highlights recent research into the molecular and biochemical mechanisms of PUFA biosynthesis in marine invertebrates, particularly focusing on cephalopod molluscs. PMID:24152561

  5. The invertebrate Caenorhabditis elegans biosynthesizes ascorbate.

    PubMed

    Patananan, Alexander N; Budenholzer, Lauren M; Pedraza, Maria E; Torres, Eric R; Adler, Lital N; Clarke, Steven G

    2015-03-01

    l-Ascorbate, commonly known as vitamin C, serves as an antioxidant and cofactor essential for many biological processes. Distinct ascorbate biosynthetic pathways have been established for animals and plants, but little is known about the presence or synthesis of this molecule in invertebrate species. We have investigated ascorbate metabolism in the nematode Caenorhabditis elegans, where this molecule would be expected to play roles in oxidative stress resistance and as cofactor in collagen and neurotransmitter synthesis. Using high-performance liquid chromatography and gas-chromatography mass spectrometry, we determined that ascorbate is present at low amounts in the egg stage, L1 larvae, and mixed animal populations, with the egg stage containing the highest concentrations. Incubating C. elegans with precursor molecules necessary for ascorbate synthesis in plants and animals did not significantly alter ascorbate levels. Furthermore, bioinformatic analyses did not support the presence in C. elegans of either the plant or the animal biosynthetic pathway. However, we observed the complete (13)C-labeling of ascorbate when C. elegans was grown with (13)C-labeled Escherichia coli as a food source. These results support the hypothesis that ascorbate biosynthesis in invertebrates may proceed by a novel pathway and lay the foundation for a broader understanding of its biological role.

  6. Influence of acid precipitation on stream invertebrates

    SciTech Connect

    Burton, T.M.; Allan, J.W.

    1983-09-01

    Five species of invertebrates, Asellus intermedius an isopod, Lepidostoma liba and Pycnopsyche sp., two species of caddisflies, Physa heterostropha, a snail, and a Nemoura sp., a stonefly, were tested for 30 days in 5 separate experiments for susceptibility to acidification to pH 4.0 and pH 5.0 alone or in combination with 250 to 500 micrograms Al/L. The effects of organic matter on the susceptibility of these invertebrates to acidification and aluminum toxicity were also tested. Acidification alone of natural stream water to pH 4.0 resulted in significant mortality for all 5 species. The addition of 500 micrograms Al/L significantly increased this mortality. Experiments with distilled water with inorganic chemistry adjusted to simulate natural stream water demonstrated that the absence of organic matter strongly resulted in much greater aluminum toxicity at low pH's and in somewhat greater susceptibility to acidification alone. The addition of citrate as an organic ligand decreased this effect. Thus, acidification effects for these 5 species for 30-day exposure periods only occurred at pH levels less than pH 5 and at aluminum levels greater than 250 micrograms Al/L. The threshold for effects, thus, was between pH 5 and pH 4 and between 250 and 500 micrograms Al/L. 19 references, 4 figures, 4 tables.

  7. The invertebrate Caenorhabditis elegans biosynthesizes ascorbate

    PubMed Central

    Patananan, Alexander N.; Budenholzer, Lauren M.; Pedraza, Maria E.; Torres, Eric R.; Adler, Lital N.; Clarke, Steven G.

    2015-01-01

    L-ascorbate, commonly known as vitamin C, serves as an antioxidant and cofactor essential for many biological processes. Distinct ascorbate biosynthetic pathways have been established for animals and plants, but little is known about the presence or synthesis of this molecule in invertebrate species. We have investigated ascorbate metabolism in the nematode Caenorhabditis elegans, where this molecule would be expected to play roles in oxidative stress resistance and as cofactor in collagen and neurotransmitter synthesis. Using high-performance liquid chromatography and gas-chromatography mass spectrometry, we determined that ascorbate is present at low amounts in the egg stage, L1 larvae, and mixed animal populations, with the egg stage containing the highest concentrations. Incubating C. elegans with precursor molecules necessary for ascorbate synthesis in plants and animals did not significantly alter ascorbate levels. Furthermore, bioinformatic analyses did not support the presence in C. elegans of either the plant or the animal biosynthetic pathway. However, we observed the complete 13C-labeling of ascorbate when C. elegans was grown with 13C-labeled Escherichia coli as a food source. These results support the hypothesis that ascorbate biosynthesis in invertebrates may proceed by a novel pathway and lay the foundation for a broader understanding of its biological role. PMID:25668719

  8. Cellular and molecular modifier pathways in tauopathies: the big picture from screening invertebrate models.

    PubMed

    Hannan, Shabab B; Dräger, Nina M; Rasse, Tobias M; Voigt, Aaron; Jahn, Thomas R

    2016-04-01

    including, but not limited to, phosphorylation, cytoskeleton organization, axonal transport, regulation of cellular proteostasis, transcription, RNA metabolism, cell cycle regulation, and apoptosis. We discuss the utility and application of invertebrate models in elucidating the cellular and molecular functions of novel and uncharacterized disease modifiers identified in large-scale screens as well as for investigating the function of genes identified as risk factors in genome-wide association studies from human patients in the post-genomic era. In this review, we combined and summarized several large-scale modifier screens performed in invertebrate models to identify modifiers of tau toxicity. A summary of the screens show that diverse cellular processes are implicated in the modification of tau toxicity. Kinases and phosphatases are the most predominant class of modifiers followed by components required for cellular proteostasis and axonal transport and cytoskeleton elements. PMID:26756400

  9. Invertebrate communities of small streams in northeastern Wyoming

    USGS Publications Warehouse

    Peterson, D.A.

    1990-01-01

    Invertebrate communities of small streams in an energy-mineral- development area in the Powder River structural basin of northeastern Wyoming were studied during 1980-81. The largest average density of benthic invertebrates among 11 sites was 983 invertebrates/sq ft at a site on a perennial stream, the Little Powder River at State Highway 59. The smallest average densities were 3.4 invertebrates/sq ft in Salt Creek and 16.6 invertebrates/sq ft in the Cheyenne River, two streams where the invertebrates were stressed by degraded water quality or inadequate substrate or both. The rates of invertebrate drift were fastest in three perennial streams, compared to the rates in intermittent and ephemeral streams. Analysis of the invertebrate communities using the Jaccard coefficient of community similarity and a cluster diagram showed communities inhabiting perennial streams were similar to each other, because of the taxa adapted to flowing water in riffles and runs. Communities from sites on ephemeral streams were similar to each other, because of the taxa adapted to standing water and vegetation in pools. Communities of intermittent streams did not form a group; either they were relatively similar to those of perennial or ephemeral streams or they were relatively dissimilar to other communities. The communities of the two streams stressed by degraded water quality or inadequate substrate or both, Salt Creek and the Cheyenne River, were relatively dissimilar to communities of the other streams in the study. (USGS)

  10. Attitudes toward Invertebrates: Are Educational "Bug Banquets" Effective?

    ERIC Educational Resources Information Center

    Looy, Heather; Wood, John R.

    2006-01-01

    Scientists have used educational presentations and "bug banquets" to alter widespread negative attitudes toward invertebrates. In this article, the authors explore whether such presentations have a measurable affect on attitudes. Junior high, high school, and university students completed an attitude survey focusing on invertebrates in general and…

  11. 50 CFR 17.85 - Special rules-invertebrates.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 2 2011-10-01 2011-10-01 false Special rules-invertebrates. 17.85 Section 17.85 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR....85 Special rules—invertebrates. (a) Seventeen mollusks in the Tennessee River. The species in...

  12. 50 CFR 17.85 - Special rules-invertebrates.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 2 2013-10-01 2013-10-01 false Special rules-invertebrates. 17.85 Section 17.85 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR....85 Special rules—invertebrates. (a) Seventeen mollusks in the Tennessee River. The species in...

  13. 50 CFR 17.85 - Special rules-invertebrates.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 2 2014-10-01 2014-10-01 false Special rules-invertebrates. 17.85 Section 17.85 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR....85 Special rules—invertebrates. (a) Seventeen mollusks in the Tennessee River. The species in...

  14. 50 CFR 17.85 - Special rules-invertebrates.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 2 2012-10-01 2012-10-01 false Special rules-invertebrates. 17.85 Section 17.85 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR....85 Special rules—invertebrates. (a) Seventeen mollusks in the Tennessee River. The species in...

  15. 50 CFR 17.85 - Special rules-invertebrates.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 2 2010-10-01 2010-10-01 false Special rules-invertebrates. 17.85 Section 17.85 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR....85 Special rules—invertebrates. (a) Seventeen mollusks in the Tennessee River. The species in...

  16. The Calyptogena magnifica chemoautotrophic symbiont genome

    SciTech Connect

    Newton, I.L.; Woyke, T.; Auchtung, T.A.; Dilly, G.F.; Dutton,R.J.; Fisher, M.C.; Fontanez, K.M.; Lau, E.; Stewart, F.J.; Richardson,P.M.; Barry, K.W.; Saunders, E.; Detter, J.C.; Wu, D.; Eisen, J.A.; Cavanaugh, C.M.

    2007-03-01

    Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.

  17. Genetically engineering adenoviral vectors for gene therapy.

    PubMed

    Coughlan, Lynda

    2014-01-01

    Adenoviral (Ad) vectors are commonly used for various gene therapy applications. Significant advances in the genetic engineering of Ad vectors in recent years has highlighted their potential for the treatment of metastatic disease. There are several methods to genetically modify the Ad genome to incorporate retargeting peptides which will redirect the natural tropism of the viruses, including homologous recombination in bacteria or yeast. However, homologous recombination in yeast is highly efficient and can be achieved without the need for extensive cloning strategies. In addition, the method does not rely on the presence of unique restriction sites within the Ad genome and the reagents required for this method are widely available and inexpensive. Large plasmids containing the entire adenoviral genome (~36 kbp) can be modified within Saccharomyces cerevisiae yeast and genomes easily rescued in Escherichia coli hosts for analysis or amplification. A method for two-step homologous recombination in yeast is described in this chapter.

  18. Nutraceutical functionalities of polysaccharides from marine invertebrates.

    PubMed

    Choi, Byeong-Dae; Choi, Yeung Joon

    2012-01-01

    Many researchers are seeking functional materials from marine resources. These marine resources can be used as traditional food additives, and specifically, these are based on polysaccharides. To date, there is a big opportunity to develop new high-value added products with indispensable functional characteristics, which can be used in nutraceuticals either as additives or supplements. Also, a crossover in the pharmaceutical market may be established. Some glycosaminoglycans (GAGs) mimetic-type molecules are already being utilized in the field of nutrition as well as in the cosmetics industry. This chemical is used as a dietary supplement to maintain the structure and function of cartilages, for the relief of pain caused by osteoarthritic joints, and can also be used as an anti-inflammatory agent. Recently, in relation to the prevalence of mad cow disease and avian influenza, the production of GAGs from marine invertebrates offers new market opportunities as compared with that obtained from bovine or avian livestock. PMID:22361178

  19. Peptide neuromodulation in invertebrate model systems

    PubMed Central

    Taghert, Paul H.; Nitabach, Michael N.

    2012-01-01

    Neuropeptides modulate neural circuits controlling adaptive animal behaviors and physiological processes, such as feeding/metabolism, reproductive behaviors, circadian rhythms, central pattern generation, and sensorimotor integration. Invertebrate model systems have enabled detailed experimental analysis using combined genetic, behavioral, and physiological approaches. Here we review selected examples of neuropeptide modulation in crustaceans, mollusks, insects, and nematodes, with a particular emphasis on the genetic model organisms Drosophila melanogaster and Caenorhabditis elegans, where remarkable progress has been made. On the basis of this survey, we provide several integrating conceptual principles for understanding how neuropeptides modulate circuit function, and also propose that continued progress in this area requires increased emphasis on the development of richer, more sophisticated behavioral paradigms. PMID:23040808

  20. Pesticides reduce regional biodiversity of stream invertebrates.

    PubMed

    Beketov, Mikhail A; Kefford, Ben J; Schäfer, Ralf B; Liess, Matthias

    2013-07-01

    The biodiversity crisis is one of the greatest challenges facing humanity, but our understanding of the drivers remains limited. Thus, after decades of studies and regulation efforts, it remains unknown whether to what degree and at what concentrations modern agricultural pesticides cause regional-scale species losses. We analyzed the effects of pesticides on the regional taxa richness of stream invertebrates in Europe (Germany and France) and Australia (southern Victoria). Pesticides caused statistically significant effects on both the species and family richness in both regions, with losses in taxa up to 42% of the recorded taxonomic pools. Furthermore, the effects in Europe were detected at concentrations that current legislation considers environmentally protective. Thus, the current ecological risk assessment of pesticides falls short of protecting biodiversity, and new approaches linking ecology and ecotoxicology are needed. PMID:23776226

  1. The effect of lindane on terrestrial invertebrates.

    PubMed

    Lock, K; De Schamphelaere, K A C; Janssen, C R

    2002-02-01

    Acute and chronic ecotoxicity tests with lindane were carried out using the soil invertebrates Eisenia fetida, Enchytraeus albidus, and Folsomia candida. To assess the influence of soil type on the bioavailability, these tests were carried out in a standard artificial OECD soil and in sandy and loamy field soil. For each species, differences in lindane toxicity were observed for the three soil types. These differences were, however, not related to the organic matter content. The relative differences in lindane toxicity between the soils was species-specific. These results therefore indicate that the pore-water hypothesis, i.e., the pore-water contaminant fraction being the toxicological bioavailable fraction, is not always applicable for organic substances. NOEC, NEC, as well as EC10 data were subsequently used to calculate hazardous concentrations for 5% of the species; this methodology, aimed at setting environmental quality criteria, is discussed.

  2. Pesticides reduce regional biodiversity of stream invertebrates

    PubMed Central

    Beketov, Mikhail A.; Kefford, Ben J.; Schäfer, Ralf B.; Liess, Matthias

    2013-01-01

    The biodiversity crisis is one of the greatest challenges facing humanity, but our understanding of the drivers remains limited. Thus, after decades of studies and regulation efforts, it remains unknown whether to what degree and at what concentrations modern agricultural pesticides cause regional-scale species losses. We analyzed the effects of pesticides on the regional taxa richness of stream invertebrates in Europe (Germany and France) and Australia (southern Victoria). Pesticides caused statistically significant effects on both the species and family richness in both regions, with losses in taxa up to 42% of the recorded taxonomic pools. Furthermore, the effects in Europe were detected at concentrations that current legislation considers environmentally protective. Thus, the current ecological risk assessment of pesticides falls short of protecting biodiversity, and new approaches linking ecology and ecotoxicology are needed. PMID:23776226

  3. JAKs and STATs in invertebrate model organisms.

    PubMed

    Dearolf, C R

    1999-09-01

    Invertebrate organisms provide systems to elucidate the developmental roles of Janus kinase (JAK)/signal transducers and activators of transcription (STAT) signaling pathways, thereby complementing research conducted with mammalian cells and animals. Components of the JAK/STAT protein pathway have been identified and characterized in the fruit fly Drosophila melanogaster and the cellular slime mold Dictyostelium discoideum. This review summarizes the molecular and genetic data obtained from these model organisms. In particular, a Drosophila JAK/STAT pathway regulates normal segmentation, cell proliferation, and differentiation, and hyperactivation of the pathway leads to tumor formation and leukemia-like defects. A Dictyostelium STAT regulates the development of stalk cells during the multicellular part of the life cycle. Future research utilizing these organisms should continue to provide insights into the roles and regulation of these proteins and their signaling pathways. PMID:10526575

  4. WATER TRANSPORT IN INVERTEBRATE PERIPHERAL NERVE FIBERS

    PubMed Central

    Nevis, Arnold H.

    1958-01-01

    Osmotic and diffusion permeabilities (Pf and Pd) of invertebrate nerve fibers to tritiated water were measured to determine what water flux studies could reveal about "the nerve membrane" and to directly test the possibility of active transport of water into or out of invertebrate nerve fibers. Pf/Pd ratios for lobster walking leg nerve fibers were found to be about 20 ± 7 at 14°C. Pd measurements were made for squid giant axons at 25°C. and found to yield a value of 4 x 10–4 cm.–1 sec.–1. When combined with the data of D. K. Hill for Pf, a Pf/Pd ratio of 21 ± 5 is obtained. These Pf/Pd ratios correspond to "effective pore radii" of about 16 ± 4 angstrom units, according to theories developed by Koefoed-Johnsen and Ussing and independently by Pappenheimer and his colleagues. Variations of water flux ratios with temperatures were studied and apparent activation energies calculated for both diffusion experiments and osmotic filtration experiments using the Arrhenius equation, and found to be close to 3 to 5 cal. per mole of water transferred. Cyanide (5 x 10–3 molar) and iodoacetate (1 x 10–3 molar) poisoned lobster leg nerve fibers showed no appreciable change in diffusion or osmotic filtration water effluxes. Caution in interpreting these proposed channels as simple pores was emphasized, but the possibility that such channels exist and are related to ionic flow is not incompatible with electrophysiological data. PMID:13525675

  5. Building mosaics of therapeutic plasmid gene vectors.

    PubMed

    Tolmachov, Oleg E

    2011-12-01

    Plasmids are circular or linear DNA molecules propagated extra-chromosomally in bacteria. Evolution shaped plasmids are inherently mosaic structures with individual functional units represented by distinct segments in the plasmid genome. The patchwork of plasmid genetic modules is a convenient template and a model for the generation of artificial plasmids used as vehicles for gene delivery into human cells. Plasmid gene vectors are an important tool in gene therapy and in basic biomedical research, where these vectors offer efficient transgene expression in many settings in vitro and in vivo. Plasmid vectors can be attached to nuclear directing ligands or transferred by electroporation as naked DNA to deliver the payload genes to the nuclei of the target cells. Transgene expression silencing by plasmid sequences of bacterial origin and immune stimulation by bacterial unmethylated CpG motifs can be avoided by the generation of plasmid-based minimized DNA vectors, such as minicircles. Systems of efficient site-specific integration into human chromosomes and stable episomal maintenance in human cells are being developed for further reduction of the chances for transgene silencing. The successful generation of plasmid vectors is governed by a number of vector design rules, some of which are common to all gene vectors, while others are specific to plasmid vectors. This review is focused both on the guiding principles and on the technical know-how of plasmid gene vector design. PMID:22023476

  6. Genome Maps, a new generation genome browser.

    PubMed

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  7. Genome Maps, a new generation genome browser

    PubMed Central

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  8. Genome Maps, a new generation genome browser.

    PubMed

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  9. Description of the Transcriptomes of Immune Response-Activated Hemocytes from the Mosquito Vectors Aedes aegypti and Armigeres subalbatus

    PubMed Central

    Bartholomay, Lyric C.; Cho, Wen-Long; Rocheleau, Thomas A.; Boyle, Jon P.; Beck, Eric T.; Fuchs, Jeremy F.; Liss, Paul; Rusch, Michael; Butler, Katherine M.; Wu, Roy Chen-Chih; Lin, Shih-Pei; Kuo, Hang-Yen; Tsao, I-Yu; Huang, Chiung-Yin; Liu, Tze-Tze; Hsiao, Kwang-Jen; Tsai, Shih-Feng; Yang, Ueng-Cheng; Nappi, Anthony J.; Perna, Nicole T.; Chen, Chen-Cheng; Christensen, Bruce M.

    2004-01-01

    Mosquito-borne diseases, including dengue, malaria, and lymphatic filariasis, exact a devastating toll on global health and economics, killing or debilitating millions every year (54). Mosquito innate immune responses are at the forefront of concerted research efforts aimed at defining potential target genes that could be manipulated to engineer pathogen resistance in vector populations. We aimed to describe the pivotal role that circulating blood cells (called hemocytes) play in immunity by generating a total of 11,952 Aedes aegypti and 12,790 Armigeres subalbatus expressed sequence tag (EST) sequences from immune response-activated hemocyte libraries. These ESTs collapsed into 2,686 and 2,107 EST clusters, respectively. The clusters were used to adapt the web-based interface for annotating bacterial genomes called A Systematic Annotation Package for Community Analysis of Genomes (ASAP) for analysis of ESTs. Each cluster was categorically characterized and annotated in ASAP based on sequence similarity to five sequence databases. The sequence data and annotations can be viewed in ASAP at https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm. The data presented here represent the results of the first high-throughput in vivo analysis of the transcriptome of immunocytes from an invertebrate. Among the sequences are those for numerous immunity-related genes, many of which parallel those employed in vertebrate innate immunity, that have never been described for these mosquitoes. PMID:15213157

  10. Structural analysis of the α subunit of Na(+)/K(+) ATPase genes in invertebrates.

    PubMed

    Thabet, Rahma; Rouault, J-D; Ayadi, Habib; Leignel, Vincent

    2016-01-01

    The Na(+)/K(+) ATPase is a ubiquitous pump coordinating the transport of Na(+) and K(+) across the membrane of cells and its role is fundamental to cellular functions. It is heteromer in eukaryotes including two or three subunits (α, β and γ which is specific to the vertebrates). The catalytic functions of the enzyme have been attributed to the α subunit. Several complete α protein sequences are available, but only few gene structures were characterized. We identified the genomic sequences coding the α-subunit of the Na(+)/K(+) ATPase, from the whole-genome shotgun contigs (WGS), NCBI Genomes (chromosome), Genomic Survey Sequences (GSS) and High Throughput Genomic Sequences (HTGS) databases across distinct phyla. One copy of the α subunit gene was found in Annelida, Arthropoda, Cnidaria, Echinodermata, Hemichordata, Mollusca, Placozoa, Porifera, Platyhelminthes, Urochordata, but the nematodes seem to possess 2 to 4 copies. The number of introns varied from 0 (Platyhelminthes) to 26 (Porifera); and their localization and length are also highly variable. Molecular phylogenies (Maximum Likelihood and Maximum Parsimony methods) showed some clusters constituted by (Chordata/(Echinodermata/Hemichordata)) or (Plathelminthes/(Annelida/Mollusca)) and a basal position for Porifera. These structural analyses increase our knowledge about the evolutionary events of the α subunit genes in the invertebrates.

  11. Structural analysis of the α subunit of Na(+)/K(+) ATPase genes in invertebrates.

    PubMed

    Thabet, Rahma; Rouault, J-D; Ayadi, Habib; Leignel, Vincent

    2016-01-01

    The Na(+)/K(+) ATPase is a ubiquitous pump coordinating the transport of Na(+) and K(+) across the membrane of cells and its role is fundamental to cellular functions. It is heteromer in eukaryotes including two or three subunits (α, β and γ which is specific to the vertebrates). The catalytic functions of the enzyme have been attributed to the α subunit. Several complete α protein sequences are available, but only few gene structures were characterized. We identified the genomic sequences coding the α-subunit of the Na(+)/K(+) ATPase, from the whole-genome shotgun contigs (WGS), NCBI Genomes (chromosome), Genomic Survey Sequences (GSS) and High Throughput Genomic Sequences (HTGS) databases across distinct phyla. One copy of the α subunit gene was found in Annelida, Arthropoda, Cnidaria, Echinodermata, Hemichordata, Mollusca, Placozoa, Porifera, Platyhelminthes, Urochordata, but the nematodes seem to possess 2 to 4 copies. The number of introns varied from 0 (Platyhelminthes) to 26 (Porifera); and their localization and length are also highly variable. Molecular phylogenies (Maximum Likelihood and Maximum Parsimony methods) showed some clusters constituted by (Chordata/(Echinodermata/Hemichordata)) or (Plathelminthes/(Annelida/Mollusca)) and a basal position for Porifera. These structural analyses increase our knowledge about the evolutionary events of the α subunit genes in the invertebrates. PMID:26812300

  12. The effects of PAH contamination on soil invertebrate communities

    SciTech Connect

    Snow-Ashbrook, J.L.; Erstfeld, K.M.

    1995-12-31

    Soils were collected from an abandoned industrial site to study the effects of historic polycyclic aromatic hydrocarbons (PAHs) on soil invertebrate communities. Nematode abundance and diversity, microarthropod abundance (orders Collembola and Acarina) and earthworm growth were evaluated. Physical and chemical characteristics of soils may affect both invertebrate community structure and the mobility/bioavailability of pollutants in soils. Soil characteristics were measured and included with PAH data in multiple regression analyses to identify factors which influences the responses observed in the soil invertebrate community. Positive associations were observed between eight invertebrate community endpoints and soil PAH content. For all of these endpoints but one, a higher degree of variability was explained when both PAH content and soil characteristics were considered. It is theorized that the positive response to soil PAH content may be the result of an increased abundance of PAH-degrading soil microbes. Increased microbial abundance could stimulate invertebrate communities by providing a direct food source or increasing the abundance of microbially-produced nutrients. These results suggest that both PAH content and soil characteristics significantly influenced the soil invertebrate community. It is not clear whether these factors influenced the invertebrate community independently, or whether differences in soil characteristics affected the community response by influencing the mobility or bioavailability of PAHs.

  13. Coral reef invertebrate microbiomes correlate with the presence of photosymbionts.

    PubMed

    Bourne, David G; Dennis, Paul G; Uthicke, Sven; Soo, Rochelle M; Tyson, Gene W; Webster, Nicole

    2013-07-01

    Coral reefs provide habitat for an array of marine invertebrates that host symbiotic microbiomes. Photosynthetic symbionts including Symbiodinium dinoflagellates and diatoms potentially influence the diversity of their host-associated microbiomes by releasing carbon-containing photosynthates and other organic compounds that fuel microbial metabolism. Here we used 16S ribosomal RNA (rRNA) gene amplicon pyrosequencing to characterise the microbiomes of 11 common Great Barrier Reef marine invertebrate species that host photosynthetic symbionts and five taxa in which they are absent. The presence of photosynthetic symbionts influenced the composition but not the species richness, evenness and phylogenetic diversity of invertebrate-associated microbiomes. Invertebrates without photosynthetic symbionts were dominated by Alphaproteobacteria, whereas those hosting photosynthetic symbionts were dominated by Gammaproteobacteria. Interestingly, many microbial species from photosymbiont-bearing invertebrates, including Oceanospirillales spp., Alteromonas spp., Pseudomonas spp., Halomonas spp., are implicated in the metabolism of dimethylsulfoniopropionate (DMSP). DMSP is produced in high concentrations by photosynthetic dinoflagellates and is involved in climate regulation by facilitating cloud formation. Microbiomes correlated with host taxa and replicate individuals from most sampled species grouped in distance-based redundancy analysis of retrieved 16S rRNA gene sequences. This study highlights the complex nature of invertebrate holobionts and confirms the importance of photosynthetic symbionts in structuring marine invertebrate bacterial communities.

  14. Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

    PubMed Central

    Bourne, David G; Dennis, Paul G; Uthicke, Sven; Soo, Rochelle M; Tyson, Gene W; Webster, Nicole

    2013-01-01

    Coral reefs provide habitat for an array of marine invertebrates that host symbiotic microbiomes. Photosynthetic symbionts including Symbiodinium dinoflagellates and diatoms potentially influence the diversity of their host-associated microbiomes by releasing carbon-containing photosynthates and other organic compounds that fuel microbial metabolism. Here we used 16S ribosomal RNA (rRNA) gene amplicon pyrosequencing to characterise the microbiomes of 11 common Great Barrier Reef marine invertebrate species that host photosynthetic symbionts and five taxa in which they are absent. The presence of photosynthetic symbionts influenced the composition but not the species richness, evenness and phylogenetic diversity of invertebrate-associated microbiomes. Invertebrates without photosynthetic symbionts were dominated by Alphaproteobacteria, whereas those hosting photosynthetic symbionts were dominated by Gammaproteobacteria. Interestingly, many microbial species from photosymbiont-bearing invertebrates, including Oceanospirillales spp., Alteromonas spp., Pseudomonas spp., Halomonas spp., are implicated in the metabolism of dimethylsulfoniopropionate (DMSP). DMSP is produced in high concentrations by photosynthetic dinoflagellates and is involved in climate regulation by facilitating cloud formation. Microbiomes correlated with host taxa and replicate individuals from most sampled species grouped in distance-based redundancy analysis of retrieved 16S rRNA gene sequences. This study highlights the complex nature of invertebrate holobionts and confirms the importance of photosynthetic symbionts in structuring marine invertebrate bacterial communities. PMID:23303372

  15. RNA interference-mediated intrinsic antiviral immunity in invertebrates.

    PubMed

    Nayak, Arabinda; Tassetto, Michel; Kunitomi, Mark; Andino, Raul

    2013-01-01

    In invertebrates such as insects and nematodes, RNA interference (RNAi) provides RNA-based protection against viruses. This form of immunity restricts viral replication and dissemination from infected cells and viruses, in turn, have evolved evasion mechanisms or RNAi suppressors to counteract host defenses. Recent advances indicate that, in addition to RNAi, other related small RNA pathways contribute to antiviral functions in invertebrates. This has led to a deeper understanding of fundamental aspects of small RNA-based antiviral immunity in invertebrates and its contribution to viral spread and pathogenesis.

  16. Rotations with Rodrigues' Vector

    ERIC Educational Resources Information Center

    Pina, E.

    2011-01-01

    The rotational dynamics was studied from the point of view of Rodrigues' vector. This vector is defined here by its connection with other forms of parametrization of the rotation matrix. The rotation matrix was expressed in terms of this vector. The angular velocity was computed using the components of Rodrigues' vector as coordinates. It appears…

  17. Effects of proposed physical ballast tank treatments on aquatic invertebrate resting eggs.

    PubMed

    Raikow, David F; Reid, David F; Blatchley, Ernest R; Jacobs, Gregory; Landrum, Peter F

    2007-04-01

    Adaptations in aquatic invertebrate resting eggs that confer protection from natural catastrophic events also could confer protection from treatments applied to ballast water for biological invasion vector management. To evaluate the potential efficacy of physical ballast water treatment methods, the present study examined the acute toxicity of heat (flash and holding methods), ultraviolet (UV) radiation (254 nm), and deoxygenation (acute and chronic) on resting eggs of the freshwater cladoceran Daphnia mendotae and the marine brine shrimp Artemia sp. Both D. mendotae and Artemia sp. were similarly sensitive to flash exposures of heat (100% mortality at 70 degrees C), but D. mendotae were much more sensitive to prolonged exposures. Exposure to 4,000 mJ/cm2 of UV radiation resulted in mortality rates of 59% in Artemia sp. and 91% in D. mendotae. Deoxygenation to an oxygen concentration of 1 mg/L was maximally toxic to both species. Deoxygenation suppressed hatching of D. mendotae resting eggs at oxygen concentrations of less than 5.5 mg/L and of Artemia sp. resting eggs at concentrations of less than 1 mg/L. Results suggest that UV radiation and deoxygenation are not viable treatment methods with respect to invertebrate resting eggs because of the impracticality of producing sufficient UV doses and the suppression of hatching at low oxygen concentrations. Results also suggest that the treatment temperatures required to kill resting eggs are much higher than those reported to be effective against other invertebrate life stages and species. The results, however, do not preclude the effectiveness of these treatments against other organisms or life stages. Nevertheless, if ballast tank treatment systems employing the tested methods are intended to include mitigation of viable resting eggs, then physical removal of large resting eggs and ephippia via filtration would be a necessary initial step. PMID:17447556

  18. Effects of proposed physical ballast tank treatments on aquatic invertebrate resting eggs.

    PubMed

    Raikow, David F; Reid, David F; Blatchley, Ernest R; Jacobs, Gregory; Landrum, Peter F

    2007-04-01

    Adaptations in aquatic invertebrate resting eggs that confer protection from natural catastrophic events also could confer protection from treatments applied to ballast water for biological invasion vector management. To evaluate the potential efficacy of physical ballast water treatment methods, the present study examined the acute toxicity of heat (flash and holding methods), ultraviolet (UV) radiation (254 nm), and deoxygenation (acute and chronic) on resting eggs of the freshwater cladoceran Daphnia mendotae and the marine brine shrimp Artemia sp. Both D. mendotae and Artemia sp. were similarly sensitive to flash exposures of heat (100% mortality at 70 degrees C), but D. mendotae were much more sensitive to prolonged exposures. Exposure to 4,000 mJ/cm2 of UV radiation resulted in mortality rates of 59% in Artemia sp. and 91% in D. mendotae. Deoxygenation to an oxygen concentration of 1 mg/L was maximally toxic to both species. Deoxygenation suppressed hatching of D. mendotae resting eggs at oxygen concentrations of less than 5.5 mg/L and of Artemia sp. resting eggs at concentrations of less than 1 mg/L. Results suggest that UV radiation and deoxygenation are not viable treatment methods with respect to invertebrate resting eggs because of the impracticality of producing sufficient UV doses and the suppression of hatching at low oxygen concentrations. Results also suggest that the treatment temperatures required to kill resting eggs are much higher than those reported to be effective against other invertebrate life stages and species. The results, however, do not preclude the effectiveness of these treatments against other organisms or life stages. Nevertheless, if ballast tank treatment systems employing the tested methods are intended to include mitigation of viable resting eggs, then physical removal of large resting eggs and ephippia via filtration would be a necessary initial step.

  19. Determining detection sensitivity and methods for invertebrate sampling

    EPA Science Inventory

    This meeting is intended to communicate Great Lakes invasive species early detection science to state management agencies to assist them in implementing monitoring. My presentation summaries lessons learned concerning invertebrate monitoring in the course of ORD research on earl...

  20. Biomonitors of stream quality on agricultural areas: fish versus invertebrates

    USGS Publications Warehouse

    Berkman, Hilary E.; Rabeni, Charles F.; Boyle, Terence P.

    1986-01-01

    Although the utility of using either fish or benthic invertebrates as biomonitors of stream quality has been clearly shown, there is little comparative information on the usefulness of the groups in any particular situation. We compared fish to invertebrate assemblages in their ability to reflect habitat quality of sediment-impacted streams in agricultural regions of northeast Missouri, USA. Habitat quality was measured by a combination of substrate composition, riparian type, buffer strip width, and land use. Invertebrates were more sensitive to habitat differences when structural measurements, species diversity and ordination, were used. Incorporating ecological measurements, by using the Index of Biological Integrity, increased the information obtained from the fish assemblage. The differential response of the two groups was attributed to the more direct impact of sediments on invertebrate life requisites; the impact of sedimentation on fish is considered more indirect and complex, affecting feeding and reproductive mechanisms.

  1. Logging cuts the functional importance of invertebrates in tropical rainforest.

    PubMed

    Ewers, Robert M; Boyle, Michael J W; Gleave, Rosalind A; Plowman, Nichola S; Benedick, Suzan; Bernard, Henry; Bishop, Tom R; Bakhtiar, Effendi Y; Chey, Vun Khen; Chung, Arthur Y C; Davies, Richard G; Edwards, David P; Eggleton, Paul; Fayle, Tom M; Hardwick, Stephen R; Homathevi, Rahman; Kitching, Roger L; Khoo, Min Sheng; Luke, Sarah H; March, Joshua J; Nilus, Reuben; Pfeifer, Marion; Rao, Sri V; Sharp, Adam C; Snaddon, Jake L; Stork, Nigel E; Struebig, Matthew J; Wearn, Oliver R; Yusah, Kalsum M; Turner, Edgar C

    2015-04-13

    Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. We find that the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging. These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. Our results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforests.

  2. Biogeography of Nearshore Subtidal Invertebrates in the Gulf of Maine

    EPA Science Inventory

    The biogeography of nearshore benthic invertebrates in the Gulf of Maine was studied to compare recent data with historical biogeographic studies, define physical-chemical factors affecting species distributions, and provide information needed to calibrate benthic indices of envi...

  3. Logging cuts the functional importance of invertebrates in tropical rainforest.

    PubMed

    Ewers, Robert M; Boyle, Michael J W; Gleave, Rosalind A; Plowman, Nichola S; Benedick, Suzan; Bernard, Henry; Bishop, Tom R; Bakhtiar, Effendi Y; Chey, Vun Khen; Chung, Arthur Y C; Davies, Richard G; Edwards, David P; Eggleton, Paul; Fayle, Tom M; Hardwick, Stephen R; Homathevi, Rahman; Kitching, Roger L; Khoo, Min Sheng; Luke, Sarah H; March, Joshua J; Nilus, Reuben; Pfeifer, Marion; Rao, Sri V; Sharp, Adam C; Snaddon, Jake L; Stork, Nigel E; Struebig, Matthew J; Wearn, Oliver R; Yusah, Kalsum M; Turner, Edgar C

    2015-01-01

    Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. We find that the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging. These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. Our results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforests. PMID:25865801

  4. Logging cuts the functional importance of invertebrates in tropical rainforest

    PubMed Central

    Ewers, Robert M.; Boyle, Michael J. W.; Gleave, Rosalind A.; Plowman, Nichola S.; Benedick, Suzan; Bernard, Henry; Bishop, Tom R.; Bakhtiar, Effendi Y.; Chey, Vun Khen; Chung, Arthur Y. C.; Davies, Richard G.; Edwards, David P.; Eggleton, Paul; Fayle, Tom M.; Hardwick, Stephen R.; Homathevi, Rahman; Kitching, Roger L.; Khoo, Min Sheng; Luke, Sarah H.; March, Joshua J.; Nilus, Reuben; Pfeifer, Marion; Rao, Sri V.; Sharp, Adam C.; Snaddon, Jake L.; Stork, Nigel E.; Struebig, Matthew J.; Wearn, Oliver R.; Yusah, Kalsum M.; Turner, Edgar C.

    2015-01-01

    Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. We find that the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging. These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. Our results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforests. PMID:25865801

  5. Inducing RNA interference in the arbovirus vector, Culicoides sonorensis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biting midges in the genus Culicoides are important vectors of arboviral diseases, including Epizootic Hemorrhagic Disease, Bluetongue, and likely Schmallenberg, which cause significant economic burden worldwide. Research on these vectors has been hindered by the lack of a sequenced genome, the diff...

  6. Mephedrone ("bath salt") pharmacology: insights from invertebrates.

    PubMed

    Ramoz, L; Lodi, S; Bhatt, P; Reitz, A B; Tallarida, C; Tallarida, R J; Raffa, R B; Rawls, S M

    2012-04-19

    Psychoactive bath salts (also called meph, drone, meow meow, m-CAT, bounce, bubbles, mad cow, etc.) contain a substance called mephedrone (4-methylcathinone) that may share psychostimulant properties with amphetamine and cocaine. However, there are only limited studies of the neuropharmacological profile of mephedrone. The present study used an established invertebrate (planarian) assay to test the hypothesis that acute and repeated mephedrone exposure produces psychostimulant-like behavioral effects. Acute mephedrone administration (50-1000 μM) produced stereotyped movements that were attenuated by a dopamine receptor antagonist (SCH 23390) (0.3 μM). Spontaneous discontinuation of mephedrone exposure (1, 10 μM) (60 min) resulted in an abstinence-induced withdrawal response (i.e. reduced motility). In place conditioning experiments, planarians in which mephedrone (100, 500 μM) was paired with the non-preferred environment during conditioning displayed a shift in preference upon subsequent testing. These results suggest that mephedrone produces three behavioral effects associated with psychostimulant drugs, namely dopamine-sensitive stereotyped movements, abstinence-induced withdrawal, and environmental place conditioning.

  7. Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda.

    PubMed

    Rota-Stabelli, Omar; Kayal, Ehsan; Gleeson, Dianne; Daub, Jennifer; Boore, Jeffrey L; Telford, Maximilian J; Pisani, Davide; Blaxter, Mark; Lavrov, Dennis V

    2010-01-01

    Ecdysozoa is the recently recognized clade of molting animals that comprises the vast majority of extant animal species and the most important invertebrate model organisms--the fruit fly and the nematode worm. Evolutionary relationships within the ecdysozoans remain, however, unresolved, impairing the correct interpretation of comparative genomic studies. In particular, the affinities of the three Panarthropoda phyla (Arthropoda, Onychophora, and Tardigrada) and the position of Myriapoda within Arthropoda (Mandibulata vs. Myriochelata hypothesis) are among the most contentious issues in animal phylogenetics. To elucidate these relationships, we have determined and analyzed complete or nearly complete mitochondrial genome sequences of two Tardigrada, Hypsibius dujardini and Thulinia sp. (the first genomes to date for this phylum); one Priapulida, Halicryptus spinulosus; and two Onychophora, Peripatoides sp. and Epiperipatus biolleyi; and a partial mitochondrial genome sequence of the Onychophora Euperipatoides kanagrensis. Tardigrada mitochondrial genomes resemble those of the arthropods in term of the gene order and strand asymmetry, whereas Onychophora genomes are characterized by numerous gene order rearrangements and strand asymmetry variations. In addition, Onychophora genomes are extremely enriched in A and T nucleotides, whereas Priapulida and Tardigrada are more balanced. Phylogenetic analyses based on concatenated amino acid coding sequences support a monophyletic origin of the Ecdysozoa and the position of Priapulida as the sister group of a monophyletic Panarthropoda (Tardigrada plus Onychophora plus Arthropoda). The position of Tardigrada is more problematic, most likely because of long branch attraction (LBA). However, experiments designed to reduce LBA suggest that the most likely placement of Tardigrada is as a sister group of Onychophora. The same analyses also recover monophyly of traditionally recognized arthropod lineages such as Arachnida and of

  8. Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda.

    PubMed

    Rota-Stabelli, Omar; Kayal, Ehsan; Gleeson, Dianne; Daub, Jennifer; Boore, Jeffrey L; Telford, Maximilian J; Pisani, Davide; Blaxter, Mark; Lavrov, Dennis V

    2010-07-12

    Ecdysozoa is the recently recognized clade of molting animals that comprises the vast majority of extant animal species and the most important invertebrate model organisms--the fruit fly and the nematode worm. Evolutionary relationships within the ecdysozoans remain, however, unresolved, impairing the correct interpretation of comparative genomic studies. In particular, the affinities of the three Panarthropoda phyla (Arthropoda, Onychophora, and Tardigrada) and the position of Myriapoda within Arthropoda (Mandibulata vs. Myriochelata hypothesis) are among the most contentious issues in animal phylogenetics. To elucidate these relationships, we have determined and analyzed complete or nearly complete mitochondrial genome sequences of two Tardigrada, Hypsibius dujardini and Thulinia sp. (the first genomes to date for this phylum); one Priapulida, Halicryptus spinulosus; and two Onychophora, Peripatoides sp. and Epiperipatus biolleyi; and a partial mitochondrial genome sequence of the Onychophora Euperipatoides kanagrensis. Tardigrada mitochondrial genomes resemble those of the arthropods in term of the gene order and strand asymmetry, whereas Onychophora genomes are characterized by numerous gene order rearrangements and strand asymmetry variations. In addition, Onychophora genomes are extremely enriched in A and T nucleotides, whereas Priapulida and Tardigrada are more balanced. Phylogenetic analyses based on concatenated amino acid coding sequences support a monophyletic origin of the Ecdysozoa and the position of Priapulida as the sister group of a monophyletic Panarthropoda (Tardigrada plus Onychophora plus Arthropoda). The position of Tardigrada is more problematic, most likely because of long branch attraction (LBA). However, experiments designed to reduce LBA suggest that the most likely placement of Tardigrada is as a sister group of Onychophora. The same analyses also recover monophyly of traditionally recognized arthropod lineages such as Arachnida and of

  9. Ecdysozoan Mitogenomics: Evidence for a Common Origin of the Legged Invertebrates, the Panarthropoda

    PubMed Central

    Rota-Stabelli, Omar; Kayal, Ehsan; Gleeson, Dianne; Daub, Jennifer; Boore, Jeffrey L.; Telford, Maximilian J.; Pisani, Davide; Blaxter, Mark; Lavrov, Dennis V.

    2010-01-01

    Ecdysozoa is the recently recognized clade of molting animals that comprises the vast majority of extant animal species and the most important invertebrate model organisms—the fruit fly and the nematode worm. Evolutionary relationships within the ecdysozoans remain, however, unresolved, impairing the correct interpretation of comparative genomic studies. In particular, the affinities of the three Panarthropoda phyla (Arthropoda, Onychophora, and Tardigrada) and the position of Myriapoda within Arthropoda (Mandibulata vs. Myriochelata hypothesis) are among the most contentious issues in animal phylogenetics. To elucidate these relationships, we have determined and analyzed complete or nearly complete mitochondrial genome sequences of two Tardigrada, Hypsibius dujardini and Thulinia sp. (the first genomes to date for this phylum); one Priapulida, Halicryptus spinulosus; and two Onychophora, Peripatoides sp. and Epiperipatus biolleyi; and a partial mitochondrial genome sequence of the Onychophora Euperipatoides kanagrensis. Tardigrada mitochondrial genomes resemble those of the arthropods in term of the gene order and strand asymmetry, whereas Onychophora genomes are characterized by numerous gene order rearrangements and strand asymmetry variations. In addition, Onychophora genomes are extremely enriched in A and T nucleotides, whereas Priapulida and Tardigrada are more balanced. Phylogenetic analyses based on concatenated amino acid coding sequences support a monophyletic origin of the Ecdysozoa and the position of Priapulida as the sister group of a monophyletic Panarthropoda (Tardigrada plus Onychophora plus Arthropoda). The position of Tardigrada is more problematic, most likely because of long branch attraction (LBA). However, experiments designed to reduce LBA suggest that the most likely placement of Tardigrada is as a sister group of Onychophora. The same analyses also recover monophyly of traditionally recognized arthropod lineages such as Arachnida and of

  10. Red List of macrofaunal benthic invertebrates of the Wadden Sea

    NASA Astrophysics Data System (ADS)

    Petersen, G. H.; Madsen, P. B.; Jensen, K. T.; van Bernem, K. H.; Harms, J.; Heiber, W.; Kröncke, I.; Michaelis, H.; Rachor, E.; Reise, K.; Dekker, R.; Visser, G. J. M.; Wolff, W. J.

    1996-10-01

    In the Wadden Sea, in total, 93 species of macrofaunal benthic invertebrates are threatened in at least one subregion. Of these, 72 species are threatened in the entire area and are therefore placed on the trilateral Red List. 7 species are (probably) extinct in the entire Wadden Sea area. The status of 9 species of macrofaunal invertebrates is critical, 13 species are (probably) endangered, the status of 25 species is (probably) vulnerable and of 17 species (probably) susceptible.

  11. Effects of neonicotinoids and fipronil on non-target invertebrates.

    PubMed

    Pisa, L W; Amaral-Rogers, V; Belzunces, L P; Bonmatin, J M; Downs, C A; Goulson, D; Kreutzweiser, D P; Krupke, C; Liess, M; McField, M; Morrissey, C A; Noome, D A; Settele, J; Simon-Delso, N; Stark, J D; Van der Sluijs, J P; Van Dyck, H; Wiemers, M

    2015-01-01

    We assessed the state of knowledge regarding the effects of large-scale pollution with neonicotinoid insecticides and fipronil on non-target invertebrate species of terrestrial, freshwater and marine environments. A large section of the assessment is dedicated to the state of knowledge on sublethal effects on honeybees (Apis mellifera) because this important pollinator is the most studied non-target invertebrate species. Lepidoptera (butterflies and moths), Lumbricidae (earthworms), Apoidae sensu lato (bumblebees, solitary bees) and the section "other invertebrates" review available studies on the other terrestrial species. The sections on freshwater and marine species are rather short as little is known so far about the impact of neonicotinoid insecticides and fipronil on the diverse invertebrate fauna of these widely exposed habitats. For terrestrial and aquatic invertebrate species, the known effects of neonicotinoid pesticides and fipronil are described ranging from organismal toxicology and behavioural effects to population-level effects. For earthworms, freshwater and marine species, the relation of findings to regulatory risk assessment is described. Neonicotinoid insecticides exhibit very high toxicity to a wide range of invertebrates, particularly insects, and field-realistic exposure is likely to result in both lethal and a broad range of important sublethal impacts. There is a major knowledge gap regarding impacts on the grand majority of invertebrates, many of which perform essential roles enabling healthy ecosystem functioning. The data on the few non-target species on which field tests have been performed are limited by major flaws in the outdated test protocols. Despite large knowledge gaps and uncertainties, enough knowledge exists to conclude that existing levels of pollution with neonicotinoids and fipronil resulting from presently authorized uses frequently exceed the lowest observed adverse effect concentrations and are thus likely to have large

  12. Sampling and quantifying invertebrates from drinking water distribution mains.

    PubMed

    van Lieverloo, J Hein M; Bosboom, Dick W; Bakker, Geo L; Brouwer, Anke J; Voogt, Remko; De Roos, Josje E M

    2004-03-01

    Water utilities in the Netherlands aim at controlling the multiplication of (micro-) organisms by distributing biologically stable water through biologically stable materials. Disinfectant residuals are absent or very low. To be able to assess invertebrate abundance, methods for sampling and quantifying these animals from distribution mains were optimised and evaluated. The presented method for collecting invertebrates consists of unidirectionally flushing a mains section with a flow rate of 1 ms(-1) and filtering the flushed water in two separate flows with 500 microm and 100 microm mesh plankton gauze filters. Removal efficiency from mains was evaluated in nine experiments by collecting the invertebrates removed from the mains section by intensive cleaning immediately subsequent to sampling. Of 12 taxa distinguished, all except case-building Chironomidae larvae (2%) and Oligochaeta (30%) were removed well (51-75%). Retention of invertebrates in 100 microm filters was evaluated by filtering 39 filtrates using 30 microm filters. Except for flexible and small invertebrates such as Turbellaria (13%), Nematoda (11%) and Copepoda larvae (24%), most taxa were well retained in the 100 microm filters (53-100%). During sample processing, the method for taking sub-samples with a 10 ml pipette from the suspension of samples with high sediment concentrations was found to perform well in 75% of the samples. During a 2-year national survey in the Netherlands and consecutive investigations, the method appeared to be very suitable to assess the abundance of most invertebrate taxa in drinking water distribution systems and to be practicable for relatively inexperienced sampling and lab technicians. Although the numbers of small, less abundant or sessile taxa were not accurately assessed using the method, these taxa probably should not be the primary focus of monitoring by water utilities, as consumer complaints are not likely to be caused by these invertebrates. The accuracy of

  13. Identifying and managing threatened invertebrates through assessment of coextinction risk.

    PubMed

    Moir, Melinda L; Vesk, Peter A; Brennan, Karl E C; Keith, David A; McCarthy, Michael A; Hughes, Lesley

    2011-08-01

    Invertebrates with specific host species may have a high probability of extinction when their hosts have a high probability of extinction. Some of these invertebrates are more likely to go extinct than their hosts, and under some circumstances, specific actions to conserve the host may be detrimental to the invertebrate. A critical constraint to identifying such invertebrates is uncertainty about their level of host specificity. We used two host-breadth models that explicitly incorporated uncertainty in the host specificity of an invertebrate species. We devised a decision protocol to identify actions that may increase the probability of persistence of a given dependent species. The protocol included estimates from the host-breadth models and decision nodes to identify cothreatened species. We applied the models and protocol to data on 1055 insects (186 species) associated with 2 threatened (as designated by the Australian Government) plant species and 19 plant species that are not threatened to determine whether any insect herbivores have the potential to become extinct if the plant becomes extinct. According to the host-breadth models, 18 species of insect had high host specificity to the threatened plant species. From these 18 insects, the decision protocol highlighted 6 species that had a high probability of extinction if their hosts were to become extinct (3% of all insects examined). The models and decision protocol have added objectivity and rigor to the process of deciding which dependent invertebrates require conservation action, particularly when dealing with largely unknown and speciose faunas.

  14. Invertebrate community response to a shifting mosaic of habitat

    USGS Publications Warehouse

    Engle, David M.; Fuhlendorf, S.D.; Roper, A.; Leslie, David M.

    2008-01-01

    Grazing management has focused largely on promoting vegetation homogeneity through uniform distribution of grazing to minimize area in a pasture that is either heavily disturbed or undisturbed. An alternative management model that couples grazing and fire (i.e., patch burning) to promote heterogeneity argues that grazing and fire interact through a series of positive and negative feedbacks to cause a shifting mosaic of vegetation composition and structure across the landscape. We compared patch burning with traditional homogeneity-based management in tallgrass prairie to determine the influence of the two treatments on the aboveground invertebrate community. Patch burning resulted in a temporal flush of invertebrate biomass in patches transitional between unburned and patches burned in the current year. Total invertebrate mass was about 50% greater in these transitional patches within patch-burned pastures as compared to pastures under traditional, homogeneity-based management. Moreover, the mosaic of patches in patch-burned pastures contained a wider range of invertebrate biomass and greater abundance of some invertebrate orders than did the traditionally managed pastures. Patch burning provides habitat that meets requirements for a broad range of invertebrate species, suggesting the potential for patch burning to benefit other native animal assemblages in the food chain.

  15. Trypanosoma rangeli uptakes the main lipoprotein from the hemolymph of its invertebrate host.

    PubMed

    Folly, Evelize; Cunha e Silva, Narcisa L; Lopes, Angela H C S; Silva-Neto, Mário A C; Atella, Georgia C

    2003-10-17

    During its life cycle Trypanosoma rangeli crosses the hemolymph of its invertebrate host. In the present study, we demonstrate for the first time the uptake of lipophorin (Lp), the main lipid-transporting particle of insect hemolymph. We observed that living T. rangeli parasites uptake lipids from both 32P- and 3H-, or 125I-labeled Lp. However, the parasites do not uptake any other hemolymphatic protein such as 32P-labeled vitellogenin. The presence of a specific receptor to Lp in the parasite surface is suggested based on experiments using 125I-Lp. We also investigated the intracellular fate of lipids using Texas Red-labeled phosphatidylethanolamine-Lp. Parasites were observed under confocal microscope and displayed fluorescent-labeled lipids close to the flagellar pocket and in vesicles at the posterior region. In conclusion, this study raises a novel set of molecular events which takes place during vector-parasite interaction.

  16. Saxitoxins and okadaic acid group: accumulation and distribution in invertebrate marine vectors from Southern Chile.

    PubMed

    García, Carlos; Pérez, Francisco; Contreras, Cristóbal; Figueroa, Diego; Barriga, Andrés; López-Rivera, Américo; Araneda, Oscar F; Contreras, Héctor R

    2015-01-01

    Harmful algae blooms (HABs) are the main source of marine toxins in the aquatic environment surrounding the austral fjords in Chile. Huichas Island (Aysén) has an history of HABs spanning more than 30 years, but there is limited investigation of the bioaccumulation of marine toxins in the bivalves and gastropods from the Region of Aysén. In this study, bivalves (Mytilus chilenses, Choromytilus chorus, Aulacomya ater, Gari solida, Tagelus dombeii and Venus antiqua) and carnivorous gastropods (Argobuccinum ranelliformes and Concholepas concholepas) were collected from 28 sites. Researchers analysed the accumulation of STX-group toxins using a LC with a derivatisation post column (LC-PCOX), while lipophilic toxins (OA-group, azapiracids, pectenotoxins and yessotoxins) were analysed using LC-MS/MS with electrospray ionisation (+/-) in visceral (hepatopancreas) and non-visceral tissues (mantle, adductor muscle, gills and foot). Levels of STX-group and OA-group toxins varied among individuals from the same site. Among all tissue samples, the highest concentrations of STX-group toxins were noted in the hepatopancreas in V. antiqua (95 ± 0.1 μg STX-eq 100 g(-1)), T. dombeii (148 ± 1.4 μg STX-eq 100 g(-1)) and G. solida (3232 ± 5.2 μg STX-eq 100 g(-1); p < 0.05); in the adductor muscle in M. chilensis (2495 ± 6.4 μg STX-eq 100 g(-1); p < 0.05) and in the foot in C. concholepas (81 ± 0.7 μg STX-eq 100 g(-1)) and T. dombeii (114 ± 1.2 μg STX-eq 100 g(-1)). The highest variability of toxins was detected in G. solida, where high levels of carbamate derivatives were identified (GTXs, neoSTX and STX). In addition to the detected hydrophilic toxins, OA-group toxins were detected (OA and DTX-1) with an average ratio of ≈1:1. The highest levels of OA-group toxins were in the foot of C. concholepas, with levels of 400.3 ± 3.6 μg OA eq kg(-1) (p < 0.05) and with a toxic profile composed of 90% OA. A wide range of OA-group toxins was detected in M. chilensis with a toxicity < 80 μg OA eq kg(-1), but with 74% of those toxins detected in the adductor muscle. In all evaluated species, there was no detection of lipophilic toxins associated with biotransformation in molluscs and carnivorous gastropods. In addition, the STX-group and OA-group toxin concentrations in shellfish was not associated with the presence of HAB. The ranking of toxin concentration in the tissues of most species was: digestive glands > mantle > adductor muscle for the STX-group toxins and foot > digestive gland for the OA-group toxins. These results gave a better understanding of the variability and compartmentalisation of STX-group and OA-group toxins in different bivalve and gastropod species from the south of Chile, and the analyses determined that tissues could play an important role in the biotransformation of STX-group toxins and the retention of OA-group toxins. PMID:25769036

  17. Saxitoxins and okadaic acid group: accumulation and distribution in invertebrate marine vectors from Southern Chile.

    PubMed

    García, Carlos; Pérez, Francisco; Contreras, Cristóbal; Figueroa, Diego; Barriga, Andrés; López-Rivera, Américo; Araneda, Oscar F; Contreras, Héctor R

    2015-01-01

    Harmful algae blooms (HABs) are the main source of marine toxins in the aquatic environment surrounding the austral fjords in Chile. Huichas Island (Aysén) has an history of HABs spanning more than 30 years, but there is limited investigation of the bioaccumulation of marine toxins in the bivalves and gastropods from the Region of Aysén. In this study, bivalves (Mytilus chilenses, Choromytilus chorus, Aulacomya ater, Gari solida, Tagelus dombeii and Venus antiqua) and carnivorous gastropods (Argobuccinum ranelliformes and Concholepas concholepas) were collected from 28 sites. Researchers analysed the accumulation of STX-group toxins using a LC with a derivatisation post column (LC-PCOX), while lipophilic toxins (OA-group, azapiracids, pectenotoxins and yessotoxins) were analysed using LC-MS/MS with electrospray ionisation (+/-) in visceral (hepatopancreas) and non-visceral tissues (mantle, adductor muscle, gills and foot). Levels of STX-group and OA-group toxins varied among individuals from the same site. Among all tissue samples, the highest concentrations of STX-group toxins were noted in the hepatopancreas in V. antiqua (95 ± 0.1 μg STX-eq 100 g(-1)), T. dombeii (148 ± 1.4 μg STX-eq 100 g(-1)) and G. solida (3232 ± 5.2 μg STX-eq 100 g(-1); p < 0.05); in the adductor muscle in M. chilensis (2495 ± 6.4 μg STX-eq 100 g(-1); p < 0.05) and in the foot in C. concholepas (81 ± 0.7 μg STX-eq 100 g(-1)) and T. dombeii (114 ± 1.2 μg STX-eq 100 g(-1)). The highest variability of toxins was detected in G. solida, where high levels of carbamate derivatives were identified (GTXs, neoSTX and STX). In addition to the detected hydrophilic toxins, OA-group toxins were detected (OA and DTX-1) with an average ratio of ≈1:1. The highest levels of OA-group toxins were in the foot of C. concholepas, with levels of 400.3 ± 3.6 μg OA eq kg(-1) (p < 0.05) and with a toxic profile composed of 90% OA. A wide range of OA-group toxins was detected in M. chilensis with a toxicity < 80 μg OA eq kg(-1), but with 74% of those toxins detected in the adductor muscle. In all evaluated species, there was no detection of lipophilic toxins associated with biotransformation in molluscs and carnivorous gastropods. In addition, the STX-group and OA-group toxin concentrations in shellfish was not associated with the presence of HAB. The ranking of toxin concentration in the tissues of most species was: digestive glands > mantle > adductor muscle for the STX-group toxins and foot > digestive gland for the OA-group toxins. These results gave a better understanding of the variability and compartmentalisation of STX-group and OA-group toxins in different bivalve and gastropod species from the south of Chile, and the analyses determined that tissues could play an important role in the biotransformation of STX-group toxins and the retention of OA-group toxins.

  18. Evolutionary concepts in ecotoxicology: tracing the genetic background of differential cadmium sensitivities in invertebrate lineages.

    PubMed

    Dallinger, Reinhard; Höckner, Martina

    2013-07-01

    In many toxicological and ecotoxicological studies and experimental setups, the investigator is mainly interested in traditional parameters such as toxicity data and effects of toxicants on molecular, cellular or physiological functions of individuals, species or statistical populations. It is clear, however, that such approaches focus on the phenotype level of animal species, whilst the genetic and evolutionary background of reactions to environmental toxicants may remain untold. In ecotoxicological risk assessment, moreover, species sensitivities towards pollutants are often regarded as random variables in a statistical approach. Beyond statistics, however, toxicant sensitivity of every species assumes a biological significance, especially if we consider that sensitivity traits have developed in lineages of species with common evolutionary roots. In this article, the genetic and evolutionary background of differential Cd sensitivities among invertebrate populations and species and their potential of adaptation to environmental Cd exposure will be highlighted. Important evolutionary and population genetic concepts such as genome structure and their importance for evolutionary adaptation, population structure of affected individuals, as well as micro and macroevolutionary mechanisms of Cd resistance in invertebrate lineages will be stressed by discussing examples of work from our own laboratory along with a review of relevant literature data and a brief discussion of open questions along with some perspectives for further research. Both, differences and similarities in Cd sensitivity traits of related invertebrate species can only be understood if we consider the underlying evolutionary processes and genetic (or epigenetic) mechanisms. Keeping in mind this perception can help us to better understand and interpret more precisely why the sensitivity of some species or species groups towards a certain toxicant (or metal) may be ranked in the lower or higher range of

  19. Genome size and chromosome number in velvet worms (Onychophora).

    PubMed

    Jeffery, Nicholas W; Oliveira, Ivo S; Gregory, T Ryan; Rowell, David M; Mayer, Georg

    2012-12-01

    The Onychophora (velvet worms) represents a small group of invertebrates (~180 valid species), which is commonly united with Tardigrada and Arthropoda in a clade called Panarthropoda. As with the majority of invertebrate taxa, genome size data are very limited for the Onychophora, with only one previously published estimate. Here we use both flow cytometry and Feulgen image analysis densitometry to provide genome size estimates for seven species of velvet worms from both major subgroups, Peripatidae and Peripatopsidae, along with karyotype data for each species. Genome sizes in these species range from roughly 5-19 pg, with densitometric estimates being slightly larger than those obtained by flow cytometry for all species. Chromosome numbers range from 2n = 8 to 2n = 54. No relationship is evident between genome size, chromosome number, or reproductive mode. Various avenues for future genomic research are presented based on these results.

  20. Genome size and chromosome number in velvet worms (Onychophora).

    PubMed

    Jeffery, Nicholas W; Oliveira, Ivo S; Gregory, T Ryan; Rowell, David M; Mayer, Georg

    2012-12-01

    The Onychophora (velvet worms) represents a small group of invertebrates (~180 valid species), which is commonly united with Tardigrada and Arthropoda in a clade called Panarthropoda. As with the majority of invertebrate taxa, genome size data are very limited for the Onychophora, with only one previously published estimate. Here we use both flow cytometry and Feulgen image analysis densitometry to provide genome size estimates for seven species of velvet worms from both major subgroups, Peripatidae and Peripatopsidae, along with karyotype data for each species. Genome sizes in these species range from roughly 5-19 pg, with densitometric estimates being slightly larger than those obtained by flow cytometry for all species. Chromosome numbers range from 2n = 8 to 2n = 54. No relationship is evident between genome size, chromosome number, or reproductive mode. Various avenues for future genomic research are presented based on these results. PMID:23307271

  1. Accumulation and inactivation of avian influenza virus by the filter-feeding invertebrate Daphnia magna.

    PubMed

    Meixell, Brandt W; Borchardt, Mark A; Spencer, Susan K

    2013-12-01

    The principal mode of avian influenza A virus (AIV) transmission among wild birds is thought to occur via an indirect fecal-oral route, whereby individuals are exposed to virus from the environment through contact with virus-contaminated water. AIV can remain viable for an extended time in water; however, little is known regarding the influence of the biotic community (i.e., aquatic invertebrates) on virus persistence and infectivity in aquatic environments. We conducted laboratory experiments to investigate the ability of an aquatic filter-feeding invertebrate, Daphnia magna, to accumulate virus from AIV-dosed water under the hypothesis that they represent a potential vector of AIV to waterfowl hosts. We placed live daphnids in test tubes dosed with low-pathogenicity AIV (H3N8 subtype isolated from a wild duck) and sampled Daphnia tissue and the surrounding water using reverse transcription-quantitative PCR (RT-qPCR) at 3- to 120-min intervals for up to 960 min following dosing. Concentrations of viral RNA averaged 3 times higher in Daphnia tissue than the surrounding water shortly after viral exposure, but concentrations decreased exponentially through time for both. Extracts from Daphnia tissue were negative for AIV by cell culture, whereas AIV remained viable in water without Daphnia present. Our results suggest daphnids can accumulate AIV RNA and effectively remove virus particles from water. Although concentrations of viral RNA were consistently higher in Daphnia tissue than the water, additional research is needed on the time scale of AIV inactivation after Daphnia ingestion to fully elucidate Daphnia's role as a potential vector of AIV infection to aquatic birds.

  2. Accumulation and Inactivation of Avian Influenza Virus by the Filter-Feeding Invertebrate Daphnia magna

    PubMed Central

    Borchardt, Mark A.; Spencer, Susan K.

    2013-01-01

    The principal mode of avian influenza A virus (AIV) transmission among wild birds is thought to occur via an indirect fecal-oral route, whereby individuals are exposed to virus from the environment through contact with virus-contaminated water. AIV can remain viable for an extended time in water; however, little is known regarding the influence of the biotic community (i.e., aquatic invertebrates) on virus persistence and infectivity in aquatic environments. We conducted laboratory experiments to investigate the ability of an aquatic filter-feeding invertebrate, Daphnia magna, to accumulate virus from AIV-dosed water under the hypothesis that they represent a potential vector of AIV to waterfowl hosts. We placed live daphnids in test tubes dosed with low-pathogenicity AIV (H3N8 subtype isolated from a wild duck) and sampled Daphnia tissue and the surrounding water using reverse transcription-quantitative PCR (RT-qPCR) at 3- to 120-min intervals for up to 960 min following dosing. Concentrations of viral RNA averaged 3 times higher in Daphnia tissue than the surrounding water shortly after viral exposure, but concentrations decreased exponentially through time for both. Extracts from Daphnia tissue were negative for AIV by cell culture, whereas AIV remained viable in water without Daphnia present. Our results suggest daphnids can accumulate AIV RNA and effectively remove virus particles from water. Although concentrations of viral RNA were consistently higher in Daphnia tissue than the water, additional research is needed on the time scale of AIV inactivation after Daphnia ingestion to fully elucidate Daphnia's role as a potential vector of AIV infection to aquatic birds. PMID:24038705

  3. Invertebrate Models for Coenzyme Q10 Deficiency

    PubMed Central

    Fernández-Ayala, Daniel J.M.; Jiménez-Gancedo, Sandra; Guerra, Ignacio; Navas, Plácido

    2014-01-01

    The human syndrome of coenzyme Q (CoQ) deficiency is a heterogeneous mitochondrial disease characterized by a diminution of CoQ content in cells and tissues that affects all the electron transport processes CoQ is responsible for, like the electron transference in mitochondria for respiration and ATP production and the antioxidant capacity that it exerts in membranes and lipoproteins. Supplementation with external CoQ is the main attempt to address these pathologies, but quite variable results have been obtained ranging from little response to a dramatic recovery. Here, we present the importance of modeling human CoQ deficiencies in animal models to understand the genetics and the pathology of this disease, although the election of an organism is crucial and can sometimes be controversial. Bacteria and yeast harboring mutations that lead to CoQ deficiency are unable to grow if they have to respire but develop without any problems on media with fermentable carbon sources. The complete lack of CoQ in mammals causes embryonic lethality, whereas other mutations produce tissue-specific diseases as in humans. However, working with transgenic mammals is time and cost intensive, with no assurance of obtaining results. Caenorhabditis elegans and Drosophila melanogaster have been used for years as organisms to study embryonic development, biogenesis, degenerative pathologies, and aging because of the genetic facilities and the speed of working with these animal models. In this review, we summarize several attempts to model reliable human CoQ deficiencies in invertebrates, focusing on mutant phenotypes pretty similar to those observed in human patients. PMID:25126050

  4. New methods to titrate EIAV-based lentiviral vectors.

    PubMed

    Martin-Rendon, Enca; White, Linda J; Olsen, Anna; Mitrophanous, Kyriacos A; Mazarakis, Nicholas D

    2002-05-01

    Ideally, gene transfer vectors used in clinical protocols should only express the gene of interest. So far most vectors have contained marker genes to aid their titration. We have used quantitative real-time PCR to titrate equine infectious anemia virus (EIAV) vectors for gene therapy applications. Viral RNA was isolated from vector preparations and analyzed in a one-step RT-PCR reaction in which reverse transcription and amplification were combined in one tube. The PCR assay of vector stocks was quantitative and linear over four orders of magnitude. In tandem, the integration efficiency of these vectors has also been determined by real-time PCR, measuring the number of vector genomes in the target cells. We have found that these methods permit reliable and sensitive titration of lentiviral vectors independent from the expression of a transgene. They also allow us to determine the integration efficiency of different vector genomes. This technology has proved very useful, especially in the absence of marker genes and where vectors express multiple genes.

  5. Understanding Singular Vectors

    ERIC Educational Resources Information Center

    James, David; Botteron, Cynthia

    2013-01-01

    matrix yields a surprisingly simple, heuristical approximation to its singular vectors. There are correspondingly good approximations to the singular values. Such rules of thumb provide an intuitive interpretation of the singular vectors that helps explain why the SVD is so…

  6. The LBP/BPI multigenic family in invertebrates: Evolutionary history and evidences of specialization in mollusks.

    PubMed

    Baron, Olga Lucia; Deleury, Emeline; Reichhart, Jean-Marc; Coustau, Christine

    2016-04-01

    LBPs (lipopolysaccharide binding proteins) and BPIs (bactericidal permeability increasing proteins) are important proteins involved in defense against bacterial pathogens. We recently discovered a novel biocidal activity of a LBP/BPI from the gastropod Biomphalaria glabrata and demonstrated its role in parental immune protection of eggs, highlighting the importance of LBP/BPIs in invertebrate immunity. Here we characterize four additional LBP/BPI from B. glabrata, presenting conserved sequence architecture and exon-intron structure. Searches of invertebrate genomes revealed that existence of LBP/BPIs is not a conserved feature since they are absent from phyla such as arthropods and platyhelminths. Analyses of LBP/BPI transcripts from selected mollusk species showed recent parallel duplications in some species, including B. glabrata. In this snail species, LBP/BPI members vary in their expression tissue localization as well as their change in expression levels after immune challenges (Gram-negative bacterium; Gram-positive bacterium or yeast). These results, together with the predicted protein features provide evidences of functional specialization of LBP/BPI family members in molluscs.

  7. Environmental epigenetics: A promising venue for developing next-generation pollution biomonitoring tools in marine invertebrates.

    PubMed

    Suarez-Ulloa, Victoria; Gonzalez-Romero, Rodrigo; Eirin-Lopez, Jose M

    2015-09-15

    Environmental epigenetics investigates the cause-effect relationships between specific environmental factors and the subsequent epigenetic modifications triggering adaptive responses in the cell. Given the dynamic and potentially reversible nature of the different types of epigenetic marks, environmental epigenetics constitutes a promising venue for developing fast and sensible biomonitoring programs. Indeed, several epigenetic biomarkers have been successfully developed and applied in traditional model organisms (e.g., human and mouse). Nevertheless, the lack of epigenetic knowledge in other ecologically and environmentally relevant organisms has hampered the application of these tools in a broader range of ecosystems, most notably in the marine environment. Fortunately, that scenario is now changing thanks to the growing availability of complete reference genome sequences along with the development of high-throughput DNA sequencing and bioinformatic methods. Altogether, these resources make the epigenetic study of marine organisms (and more specifically marine invertebrates) a reality. By building on this knowledge, the present work provides a timely perspective highlighting the extraordinary potential of environmental epigenetic analyses as a promising source of rapid and sensible tools for pollution biomonitoring, using marine invertebrates as sentinel organisms. This strategy represents an innovative, groundbreaking approach, improving the conservation and management of natural resources in the oceans.

  8. Rhotrix Vector Spaces

    ERIC Educational Resources Information Center

    Aminu, Abdulhadi

    2010-01-01

    By rhotrix we understand an object that lies in some way between (n x n)-dimensional matrices and (2n - 1) x (2n - 1)-dimensional matrices. Representation of vectors in rhotrices is different from the representation of vectors in matrices. A number of vector spaces in matrices and their properties are known. On the other hand, little seems to be…

  9. Invertebrates as model organisms for research on aging biology

    PubMed Central

    Murthy, Mahadev; Ram, Jeffrey L.

    2015-01-01

    Invertebrate model systems, such as nematodes and fruit flies, have provided valuable information about the genetics and cellular biology involved in aging. However, limitations of these simple, genetically tractable organisms suggest the need for other model systems, some of them invertebrate, to facilitate further advances in the understanding of mechanisms of aging and longevity in mammals, including humans. This paper introduces 10 review articles about the use of invertebrate model systems for the study of aging by authors who participated in an ‘NIA-NIH symposium on aging in invertebrate model systems’ at the 2013 International Congress for Invertebrate Reproduction and Development. In contrast to the highly derived characteristics of nematodes and fruit flies as members of the superphylum Ecdysozoa, cnidarians, such as Hydra, are more ‘basal’ organisms that have a greater number of genetic orthologs in common with humans. Moreover, some other new model systems, such as the urochordate Botryllus schlosseri, the tunicate Ciona, and the sea urchins (Echinodermata) are members of the Deuterostomia, the same superphylum that includes all vertebrates, and thus have mechanisms that are likely to be more closely related to those occurring in humans. Additional characteristics of these new model systems, such as the recent development of new molecular and genetic tools and a more similar pattern to humans of regeneration and stem cell function suggest that these new model systems may have unique advantages for the study of mechanisms of aging and longevity. PMID:26241448

  10. Piscicides and invertebrates: after 70 years, does anyone really know?

    USGS Publications Warehouse

    Vinson, M.R.; Dinger, E.C.; Vinson, D.K.

    2010-01-01

    The piscicides rotenone and antimycin have been used for more than 70 years to manage fish populations by eliminating undesirable fish species. The effects of piscicides on aquatic invertebrate assemblages are considered negligible by some and significant by others. This difference of opinion has created contentious situations and delayed native fish restoration projects. We review the scientific evidence and report that short-term ( 1 year) impacts are largely unknown. Recovery of invertebrate assemblages following treatments ranged from a few months for abundances of common taxa to several years for rarer taxa. Variation in reported effects was primarily due to natural variation among species and habitats and a lack of adequate pre- and post-treatment sampling which prevents determining the true impacts to invertebrate assemblages. The factors most likely to influence impacts and recovery of aquatic invertebrate assemblages following piscicide treatments are: (1) concentration, duration, and breadth of the piscicide treatment; (2) invertebrate morphology and life history characteristics, including surface area to volume ratios, type of respiration organs, generation time, and propensity to disperse; (3) refugia presence; and (4) distance from colonization sources.

  11. Indigenous ectosymbiotic bacteria associated with diverse hydrothermal vent invertebrates.

    PubMed

    Goffredi, Shana K

    2010-08-01

    Symbioses involving bacteria and invertebrates contribute to the biological diversity and high productivity of both aquatic and terrestrial environments. Well-known examples from chemosynthetic deep-sea hydrothermal vent environments involve ectosymbiotic microbes associated with the external surfaces of marine invertebrates. Some of these ectosymbioses confer protection or defence from predators or the environment itself, some are nutritional in nature, and many still are of unknown function. Several recently discovered hydrothermal vent invertebrates, including two populations of yeti crab (Kiwa spp.), a limpet (Symmetromphalus aff. hageni), and the scaly-foot snail (as yet undescribed), support a consortium of diverse bacteria. Comparisons of these ectosymbioses to those previously described revealed similarities among the associated microorganisms, suggesting that certain microbes are indigenous to the surfaces of marine invertebrates. In particular, members of the Thiovulgaceae (epsilonproteobacteria) and Thiotrichaceae (gammaproteobacteria) appear to preferentially form ectosymbioses with vent crustaceans and gastropods. Interactions between specific Proteobacteria and the surfaces of many marine invertebrates likely have ecological and evolutionary significance at these chemically challenging habitats.

  12. Invertebrates that aestivate in dry basins of Carolina bay wetlands.

    SciTech Connect

    Dietz-Brantley, Susan, E.; Taylor, Barbera, E.; Batzer, Darold, P.; DeBiase, Adrienne, E.

    2002-12-01

    Dietz-Brantley, S.E., B.E. Taylor, D.P. Batzer, and A.E. DeBiase. 2002. Invertebrates that aestivate in dry basins of carolina bay wetlands. Wetlands 22(4):767-775. Water levels fluctuate widely in Carolina bay wetlands and most dry periodically. Aquatic organisims inhabiting these wetlands have the capacity to either resist desication or to recolonize newly flooded habitats. The objective of this study was to determine which invertebrates aestivate in the soil of dry Carolina bays and to describe how differences in habitat affect the composition of aestivating invertebrates. Eight Carolina bays located on the Savannah River Site (SRS) near Aiken, South Carolina, USA were examined for this study. Although all of the wetlands dried seasonally, three of the wetlands were relatively wet (inundated 47-92% of the year on average), one was intermediate, and four were relatively dry (inundated 20% of the year on average). Sections of soil were removed from each bay during August and November when all sites were dry, placed into tubs, flooded, and covered with fine mesh. Invertebrates were sampled from the water biweekly for four weeks. Invertebrate assemblages were contrasted between naturally inundated bays and rehydrated samples, wetter and drier bays, August and November collections, and remnant ditches and the main basins.

  13. Lysosomal enzymes and their receptors in invertebrates: an evolutionary perspective.

    PubMed

    Kumar, Nadimpalli Siva; Bhamidimarri, Poorna M

    2015-01-01

    Lysosomal biogenesis is an important process in eukaryotic cells to maintain cellular homeostasis. The key components that are involved in the biogenesis such as the lysosomal enzymes, their modifications and the mannose 6-phosphate receptors have been well studied and their evolutionary conservation across mammalian and non-mammalian vertebrates is clearly established. Invertebrate lysosomal biogenesis pathway on the other hand is not well studied. Although, details on mannose 6-phosphate receptors and enzymes involved in lysosomal enzyme modifications were reported earlier, a clear cut pathway has not been established. Recent research on the invertebrate species involving biogenesis of lysosomal enzymes suggests a possible conserved pathway in invertebrates. This review presents certain observations based on these processes that include biochemical, immunological and functional studies. Major conclusions include conservation of MPR-dependent pathway in higher invertebrates and recent evidence suggests that MPR-independent pathway might have been more prominent among lower invertebrates. The possible components of MPR-independent pathway that may play a role in lysosomal enzyme targeting are also discussed here.

  14. Key factors for the emergence of collective decision in invertebrates.

    PubMed

    Jeanson, Raphaël; Dussutour, Audrey; Fourcassié, Vincent

    2012-01-01

    In many species of group living invertebrates, in particular arthropods, collective decisions can emerge from the combined actions of individuals and the direct or indirect interactions between individuals. These decisions allow groups of individuals to respond quickly and accurately to changes that occur in their environment. Examples of such decisions are found in a variety of invertebrate taxa and in many different contexts, e.g., exploring a new territory, foraging for food, finding a suitable location where to aggregate or to establish a nest, defending oneself against predators, etc. In this paper we review the collective decisions that have been documented in different invertebrate taxa where individuals are known to live temporarily or permanently in social or gregarious groups. We first present some simple examples of collective decisions involving the choice between two alternatives. We then define the fundamental rules required for these collective decisions to emerge throughout the invertebrate taxon, from simple organisms such as caterpillars, to animals endowed with highly developed perceptive and cognitive capacities such as ants and bees. The presentation of these rules gives us the opportunity to illustrate one of the pitfalls of the study of collective choice in animals by showing through computer simulations how a choice between two alternatives can be misinterpreted as the result of the action of self-organized mechanisms. In the second part, we discuss the peculiarities of collective decisions in invertebrates, their properties, and characteristics. We conclude by discussing the issue of individual complexity in collective decision-making process.

  15. A thesaurus for soil invertebrate trait-based approaches.

    PubMed

    Pey, Benjamin; Laporte, Marie-Angélique; Nahmani, Johanne; Auclerc, Apolline; Capowiez, Yvan; Caro, Gaël; Cluzeau, Daniel; Cortet, Jérôme; Decaëns, Thibaud; Dubs, Florence; Joimel, Sophie; Guernion, Muriel; Briard, Charlène; Grumiaux, Fabien; Laporte, Baptiste; Pasquet, Alain; Pelosi, Céline; Pernin, Céline; Ponge, Jean-François; Salmon, Sandrine; Santorufo, Lucia; Hedde, Mickaël

    2014-01-01

    Soil invertebrates are known to be much involved in soil behaviour and therefore in the provision of ecosystem services. Functional trait-based approaches are methodologies which can be used to understand soil invertebrates' responses to their environment. They (i) improve the predictions and (ii) are less dependent on space and time. The way traits have been used recently has led to misunderstandings in the integration and interpretation of data. Trait semantics are especially concerned. The aim of this paper is to propose a thesaurus for soil invertebrate trait-based approaches. T-SITA, an Internet platform, is the first initiative to deal with the semantics of traits and ecological preferences for soil invertebrates. It reflects the agreement of a scientific expert community to fix semantic properties (e.g. definition) of approximately 100 traits and ecological preferences. In addition, T-SITA has been successfully linked with a fully operational database of soil invertebrate traits. Such a link enhances data integration and improves the scientific integrity of data. PMID:25310431

  16. Key Factors for the Emergence of Collective Decision in Invertebrates

    PubMed Central

    Jeanson, Raphaël; Dussutour, Audrey; Fourcassié, Vincent

    2012-01-01

    In many species of group living invertebrates, in particular arthropods, collective decisions can emerge from the combined actions of individuals and the direct or indirect interactions between individuals. These decisions allow groups of individuals to respond quickly and accurately to changes that occur in their environment. Examples of such decisions are found in a variety of invertebrate taxa and in many different contexts, e.g., exploring a new territory, foraging for food, finding a suitable location where to aggregate or to establish a nest, defending oneself against predators, etc. In this paper we review the collective decisions that have been documented in different invertebrate taxa where individuals are known to live temporarily or permanently in social or gregarious groups. We first present some simple examples of collective decisions involving the choice between two alternatives. We then define the fundamental rules required for these collective decisions to emerge throughout the invertebrate taxon, from simple organisms such as caterpillars, to animals endowed with highly developed perceptive and cognitive capacities such as ants and bees. The presentation of these rules gives us the opportunity to illustrate one of the pitfalls of the study of collective choice in animals by showing through computer simulations how a choice between two alternatives can be misinterpreted as the result of the action of self-organized mechanisms. In the second part, we discuss the peculiarities of collective decisions in invertebrates, their properties, and characteristics. We conclude by discussing the issue of individual complexity in collective decision-making process. PMID:22933990

  17. Mobilization and Mechanism of Transcription of Integrated Self-Inactivating Lentiviral Vectors

    PubMed Central

    Hanawa, Hideki; Persons, Derek A.; Nienhuis, Arthur W.

    2005-01-01

    Permanent genetic modification of replicating primitive hematopoietic cells by an integrated vector has many potential therapeutic applications. Both oncoretroviral and lentiviral vectors have a predilection for integration into transcriptionally active genes, creating the potential for promoter activation or gene disruption. The use of self-inactivating (SIN) vectors in which a deletion of the enhancer and promoter sequences from the 3′ long terminal repeat (LTR) is copied over into the 5′ LTR during vector integration is designed to improve safety by reducing the risk of mobilization of the vector genome and the influence of the LTR on nearby cellular promoters. Our results indicate that SIN vectors are mobilized in cells expressing lentiviral proteins, with the frequency of mobilization influenced by features of the vector design. The mechanism of transcription of integrated vector genomes was evaluated using a promoter trap design with a vector encoding tat but lacking an upstream promoter in a cell line in which drug resistance depended on tat expression. In six clones studied, all transcripts originated from cryptic promoters either upstream or within the vector genome. We estimate that approximately 1 in 3,000 integrated vector genomes is transcribed, leading to the inference that activation of cryptic promoters must depend on local features of chromatin structure and the constellation of nearby regulatory elements as well as the nature of the regulatory elements within the vector. PMID:15956585

  18. Preventing and exploiting the oncogenic potential of integrating gene vectors.

    PubMed

    Modlich, Ute; Baum, Christopher

    2009-04-01

    Gene therapy requires efficient gene delivery to cure or prevent disease by modifying the genome of somatic cells. However, gene vectors, which insert themselves into the host genome in order to achieve persistent protein expression, can trigger oncogenesis by upregulating cellular protooncogenes. This adverse event, known as insertional mutagenesis, has become a major hurdle in the field. Vectors developed on the basis of lentiviruses are considered to be less genotoxic than the hitherto used gamma-retroviral vectors. For their report in this issue of the JCI, Montini et al. utilized a tumor-prone mouse model to identify the genetic determinants of insertional mutagenesis (see the related article beginning on page 964). They report that the lentiviral integration pattern and additional improvements in vector design reduce the genotoxic risk. These findings will inform future vector design with the goal of limiting genotoxicity for gene therapy or increasing genotoxicity for protooncogene discovery.

  19. Optimization of a method for chromatin immunoprecipitation assays in the marine invertebrate chordate Ciona

    PubMed Central

    Aihara, Hitoshi; Katikala, Lavanya; Zeller, Robert W.; Di Gregorio, Anna; Nibu, Yutaka

    2013-01-01

    Chromatin immunoprecipitation (ChIP) assays allow the efficient characterization of the in vivo occupancy of genomic regions by DNA-binding proteins, and thus facilitate the prediction of cis-regulatory sequences in silico and guide their validation in vivo. For these reasons, these assays and their permutations (e.g., ChIP-on-chip, ChIP-Sequencing) are currently being extended to several non-mainstream model organisms, as the availability of specific antibodies increases. Here we describe the development of a polyclonal antibody against the Brachyury protein of the marine invertebrate chordate Ciona intestinalis and provide a detailed ChIP protocol that should be easily adaptable to other marine organisms. PMID:23592257

  20. Genome sequence of a crustacean iridovirus, IIV31, isolated from the pill bug, Armadillidium vulgare.

    PubMed

    Piégu, Benoît; Guizard, Sébastien; Yeping, Tan; Cruaud, Corinne; Asgari, Sassan; Bideshi, Dennis K; Federici, Brian A; Bigot, Yves

    2014-07-01

    Members of the family Iridoviridae are animal viruses that infect only invertebrates and poikilothermic vertebrates. The invertebrate iridovirus 31 (IIV31) was originally isolated from adult pill bugs, Armadillidium vulgare (class Crustacea, order Isopoda, suborder Oniscidea), found in southern California on the campus of the University of California, Riverside, USA. IIV31 virions are icosahedral, have a diameter of about 135 nm, and contain a dsDNA genome 220.222 kbp in length, with 35.09 mol % G+C content and 203 ORFs. Here, we describe the complete genome sequence of this virus and its annotation. This is the eighth genome sequence of an IIV reported. PMID:24722681

  1. Genome sequence of a crustacean iridovirus, IIV31, isolated from the pill bug, Armadillidium vulgare.

    PubMed

    Piégu, Benoît; Guizard, Sébastien; Yeping, Tan; Cruaud, Corinne; Asgari, Sassan; Bideshi, Dennis K; Federici, Brian A; Bigot, Yves

    2014-07-01

    Members of the family Iridoviridae are animal viruses that infect only invertebrates and poikilothermic vertebrates. The invertebrate iridovirus 31 (IIV31) was originally isolated from adult pill bugs, Armadillidium vulgare (class Crustacea, order Isopoda, suborder Oniscidea), found in southern California on the campus of the University of California, Riverside, USA. IIV31 virions are icosahedral, have a diameter of about 135 nm, and contain a dsDNA genome 220.222 kbp in length, with 35.09 mol % G+C content and 203 ORFs. Here, we describe the complete genome sequence of this virus and its annotation. This is the eighth genome sequence of an IIV reported.

  2. Calcium signals and oocyte maturation in marine invertebrates.

    PubMed

    Deguchi, Ryusaku; Takeda, Noriyo; Stricker, Stephen A

    2015-01-01

    In various oocytes and eggs of animals, transient elevations in cytoplasmic calcium ion concentrations are known to regulate key processes during fertilization and the completion of meiosis. However, whether or not calcium transients also help to reinitiate meiotic progression at the onset of oocyte maturation remains controversial. This article summarizes reports of calcium signals playing essential roles during maturation onset (=germinal vesicle breakdown, GVBD) in several kinds of marine invertebrate oocytes. Conversely, other data from the literature, as well as previously unpublished findings for jellyfish oocytes, fail to support the view that calcium signals are required for GVBD. In addition to assessing the effects of calcium transients on GVBD in marine invertebrate oocytes, the ability of maturing oocytes to enhance their calcium-releasing capabilities after GVBD is also reviewed. Furthermore, possible explanations are proposed for the contradictory results that have been obtained regarding calcium signals during oocyte maturation in marine invertebrates. PMID:26679945

  3. Pro-oxidant and antioxidant processes in aquatic invertebrates.

    PubMed

    Canesi, Laura

    2015-03-01

    Most aquatic organisms behave as conformers with respect to environmental variables, including changes in O2 availability. Aquatic species that show tolerance to hypoxia/anoxia or hyperoxia can be excellent models for investigating physiological and biochemical adaptations that deal with changing O2 and consequent changes in metabolic rate and production of reactive oxygen species (ROS). Here, I summarize selected data on ROS production and antioxidant defenses in a model marine invertebrate, the bivalve Mytilus, under different environmental and physiological conditions. An example of other bivalves adapted to particular environments (the Antarctic Sea) is also reported. These studies contributed to the knowledge on pro-oxidant and antioxidant processes in aquatic invertebrates from comparative and environmental perspectives. A common role for metallothioneins in antioxidant protection in mammals and aquatic invertebrates is underlined in different conditions, from human disease to responses to environmental exposure to heavy metals.

  4. Sequence diversity and evolution of antimicrobial peptides in invertebrates.

    PubMed

    Tassanakajon, Anchalee; Somboonwiwat, Kunlaya; Amparyup, Piti

    2015-02-01

    Antimicrobial peptides (AMPs) are evolutionarily ancient molecules that act as the key components in the invertebrate innate immunity against invading pathogens. Several AMPs have been identified and characterized in invertebrates, and found to display considerable diversity in their amino acid sequence, structure and biological activity. AMP genes appear to have rapidly evolved, which might have arisen from the co-evolutionary arms race between host and pathogens, and enabled organisms to survive in different microbial environments. Here, the sequence diversity of invertebrate AMPs (defensins, cecropins, crustins and anti-lipopolysaccharide factors) are presented to provide a better understanding of the evolution pattern of these peptides that play a major role in host defense mechanisms.

  5. The genetics of host-virus coevolution in invertebrates.

    PubMed

    Obbard, Darren J; Dudas, Gytis

    2014-10-01

    Although viral infection and antiviral defence are ubiquitous, genetic data are currently unavailable from the vast majority of animal phyla-potentially biasing our overall perspective of the coevolutionary process. Rapid adaptive evolution is seen in some insect antiviral genes, consistent with invertebrate-virus 'arms-race' coevolution, but equivalent signatures of selection are hard to detect in viruses. We find that, despite the large differences in vertebrate, invertebrate, and plant immune responses, comparison of viral evolution fails to identify any difference among these hosts in the impact of positive selection. The best evidence for invertebrate-virus coevolution is currently provided by large-effect polymorphisms for host resistance and/or viral evasion, as these often appear to have arisen and spread recently, and can be favoured by virus-mediated selection.

  6. Experimental evidence of pollination in marine flowers by invertebrate fauna

    PubMed Central

    van Tussenbroek, Brigitta I.; Villamil, Nora; Márquez-Guzmán, Judith; Wong, Ricardo; Monroy-Velázquez, L. Verónica; Solis-Weiss, Vivianne

    2016-01-01

    Pollen transport by water-flow (hydrophily) is a typical, and almost exclusive, adaptation of plants to life in the marine environment. It is thought that, unlike terrestrial environments, animals are not involved in pollination in the sea. The male flowers of the tropical marine angiosperm Thalassia testudinum open-up and release pollen in mucilage at night when invertebrate fauna is active. Here we present experimental evidence that, in the absence of water-flow, these invertebrates visit the flowers, carry and transfer mucilage mass with embedded pollen from the male flowers to the stigmas of the female flowers. Pollen tubes are formed on the stigmas, indicating that pollination is successful. Thus, T. testudinum has mixed abiotic–biotic pollination. We propose a zoobenthophilous pollination syndrome (pollen transfer in the benthic zone by invertebrate animals) which shares many characteristics with hydrophily, but flowers are expected to open-up during the night. PMID:27680661

  7. Protozoa interaction with aquatic invertebrate: interest for watercourses biomonitoring.

    PubMed

    Palos Ladeiro, M; Bigot, A; Aubert, D; Hohweyer, J; Favennec, L; Villena, I; Geffard, A

    2013-02-01

    Toxoplasma gondii, Cryptosporidium parvum, and Giardia duodenalis are human waterborne protozoa. These worldwide parasites had been detected in various watercourses as recreational, surface, drinking, river, and seawater. As of today, water protozoa detection was based on large water filtration and on sample concentration. Another tool like aquatic invertebrate parasitism could be used for sanitary and environmental biomonitoring. In fact, organisms like filter feeders could already filtrate and concentrate protozoa directly in their tissues in proportion to ambient concentration. So molluscan shellfish can be used as a bioindicator of protozoa contamination level in a site since they were sedentary. Nevertheless, only a few researches had focused on nonspecific parasitism like protozoa infection on aquatic invertebrates. Objectives of this review are twofold: Firstly, an overview of protozoa in worldwide water was presented. Secondly, current knowledge of protozoa parasitism on aquatic invertebrates was detailed and the lack of data of their biological impact was pointed out.

  8. Invertebrates as a source of emerging human pathogens.

    PubMed

    Waterfield, Nicholas R; Wren, Brendan W; Ffrench-Constant, Richard H

    2004-10-01

    Despite their importance, little is known about the origins of many emerging human pathogens. However, given the age and current predominance of invertebrates, it is likely that bacteria-invertebrate interactions are not only a present source of human pathogens but have also shaped their evolution. Pathogens of invertebrate and unicellular organisms represent an extensive reservoir of bacterial strains equipped with virulence factors that evolved to overcome the innate immune responses of their hosts. This reservoir might represent a source of new human pathogenic strains and might also foster the spread of novel virulence factors into existing human commensal or pathogenic bacteria. This article examines the available evidence for this concept by examining pairs of closely related bacteria, one of which is benign, but insect associated, and one of which is a human pathogen.

  9. From bouncy legs to poisoned arrows: elastic movements in invertebrates.

    PubMed

    Patek, S N; Dudek, D M; Rosario, M V

    2011-06-15

    Elastic mechanisms in the invertebrates are fantastically diverse, yet much of this diversity can be captured by examining just a few fundamental physical principles. Our goals for this commentary are threefold. First, we aim to synthesize and simplify the fundamental principles underlying elastic mechanisms and show how different configurations of basic building blocks can be used for different functions. Second, we compare single rapid movements and rhythmic movements across six invertebrate examples - ranging from poisonous cnidarians to high-jumping froghoppers - and identify remarkable functional properties arising from their underlying elastic systems. Finally, we look to the future of this field and find two prime areas for exciting new discoveries - the evolutionary dynamics of elastic mechanisms and biomimicry of invertebrate elastic materials and mechanics. PMID:21613512

  10. Competition of Invertebrates Mixed Culture in the Closed Aquatic System

    NASA Astrophysics Data System (ADS)

    Pisman, Tamara

    The study considers the experimental model of interactions between invertebrates (the cilates Paramecium caudatum, Paramecium bursaria and the rotifers Brachionis plicatilis) in the closed aquatic system. The infusoria P.caudatum can feed on yeast, bacteria and chlorella; in this experiment growth and reproduction were maintained by bacteria only. The P.bursaria - zoochlorella endosymbiosis is a natural model of a simple biotic cycle. P.bursaria consumes glucose and oxygen released by zoochlorella in the process of biosynthesis and releases nitrogenous compounds and carbon dioxide necessary for algal photosynthesis. The rotifers Br. plicatilis can consume algae, bacteria and detritus. Thus in experiment with the mixed culture of invertebrates they can use different food sources. However with any initial percentage of the invertebrates the end portion of P.bursaria reaches 90-99

  11. Land Use and Hydrogeological Characteristics Influence Groundwater Invertebrate Communities.

    PubMed

    Tione, María Laura; Bedano, José Camilo; Blarasin, Mónica

    2016-08-01

    We examine the influence of land use and hydrogeological characteristics on the abundance, composition and structure of groundwater invertebrate communities in a loessic aquifer from Argentina. Seven wells, selected according to surrounding land use and hydrogeological characteristics, were sampled twice. Groundwater was characterized as sodium bicarbonate, bicarbonate sulfate or sulfate type. NO3(-) was detected in all samples. Land use in the area surrounding the well, unsaturated zone thickness and geochemical characteristics of groundwater influenced the abundance, composition and community structure of groundwater invertebrates. Copepoda, Oligochaeta, Cladocera, Ostracoda and Amphipoda were highly influenced by land use, particularly by point pollution sources that produced higher abundance and changes in taxonomic composition. The lowest invertebrate abundance was observed at the wells situated in areas with the thickest unsaturated zone. Groundwater salinity and geochemical type influenced the presence of certain species, particularly Stygonitocrella sp. PMID:27456146

  12. Calcium signals and oocyte maturation in marine invertebrates.

    PubMed

    Deguchi, Ryusaku; Takeda, Noriyo; Stricker, Stephen A

    2015-01-01

    In various oocytes and eggs of animals, transient elevations in cytoplasmic calcium ion concentrations are known to regulate key processes during fertilization and the completion of meiosis. However, whether or not calcium transients also help to reinitiate meiotic progression at the onset of oocyte maturation remains controversial. This article summarizes reports of calcium signals playing essential roles during maturation onset (=germinal vesicle breakdown, GVBD) in several kinds of marine invertebrate oocytes. Conversely, other data from the literature, as well as previously unpublished findings for jellyfish oocytes, fail to support the view that calcium signals are required for GVBD. In addition to assessing the effects of calcium transients on GVBD in marine invertebrate oocytes, the ability of maturing oocytes to enhance their calcium-releasing capabilities after GVBD is also reviewed. Furthermore, possible explanations are proposed for the contradictory results that have been obtained regarding calcium signals during oocyte maturation in marine invertebrates.

  13. A generalized model for estimating the energy density of invertebrates

    USGS Publications Warehouse

    James, Daniel A.; Csargo, Isak J.; Von Eschen, Aaron; Thul, Megan D.; Baker, James M.; Hayer, Cari-Ann; Howell, Jessica; Krause, Jacob; Letvin, Alex; Chipps, Steven R.

    2012-01-01

    Invertebrate energy density (ED) values are traditionally measured using bomb calorimetry. However, many researchers rely on a few published literature sources to obtain ED values because of time and sampling constraints on measuring ED with bomb calorimetry. Literature values often do not account for spatial or temporal variability associated with invertebrate ED. Thus, these values can be unreliable for use in models and other ecological applications. We evaluated the generality of the relationship between invertebrate ED and proportion of dry-to-wet mass (pDM). We then developed and tested a regression model to predict ED from pDM based on a taxonomically, spatially, and temporally diverse sample of invertebrates representing 28 orders in aquatic (freshwater, estuarine, and marine) and terrestrial (temperate and arid) habitats from 4 continents and 2 oceans. Samples included invertebrates collected in all seasons over the last 19 y. Evaluation of these data revealed a significant relationship between ED and pDM (r2  =  0.96, p < 0.0001), where ED (as J/g wet mass) was estimated from pDM as ED  =  22,960pDM − 174.2. Model evaluation showed that nearly all (98.8%) of the variability between observed and predicted values for invertebrate ED could be attributed to residual error in the model. Regression of observed on predicted values revealed that the 97.5% joint confidence region included the intercept of 0 (−103.0 ± 707.9) and slope of 1 (1.01 ± 0.12). Use of this model requires that only dry and wet mass measurements be obtained, resulting in significant time, sample size, and cost savings compared to traditional bomb calorimetry approaches. This model should prove useful for a wide range of ecological studies because it is unaffected by taxonomic, seasonal, or spatial variability.

  14. Predicting subtle behavioral responses of invertebrates to soil contaminants

    SciTech Connect

    Donkin, S.G.

    1995-12-31

    At concentration levels well below those which cause death and injury to soil invertebrates, a toxic chemical plume may yet effectively damage a soil ecosystem by triggering avoidance behavior among sensitive invertebrates as they move along the concentration gradient. The result may be a soil ecosystem lacking the benefits of effective nutrient cycling and mineralization which a thriving invertebrate population provides. While determining actual detection limits of invertebrates for chemical gradients in soils is experimentally difficult, theoretical calculations have suggested that such limits may be extremely low, and hence many organisms may sense and avoid concentrations of chemicals far below levels commonly considered acceptable. The minimum gradient (G) that can be detected by a receptor depends on the receptor radius (R), the chemical concentration (C), the diffusion constant of the chemical (D), the velocity of the organism (v), and the time over which the receptor integrates the chemical signal (t). In addition, the characteristics of that gradient are determined by interactions between the chemical and the soil particles (sorption/desorption), and advection through the pore spaces. The example of lead (Pb), a neurotoxic metal with demonstrated behavioral effects on the free-living nematode Caenorhabditis elegans, is used to model a chemical migrating through a soil. Based on experimentally determined Pb concentrations which elicited avoidance behavior in nematodes, and sorption characteristics of defined Pb-soil systems, the minimum detectable gradient (G) produced by a solubilized Pb plume in several soils was modeled. The results predict maximum allowable Pb levels in a soil if a healthy invertebrate community is desired, and suggest areas for further research into the subtle behavioral effects of environmental toxicants ore sensitive invertebrates.

  15. Copper hazards to fish, wildlife and invertebrates: a synoptic review

    USGS Publications Warehouse

    Eisler, Ronald

    1998-01-01

    Selective review and synthesis of the technical literature on copper and copper salts in the environment and their effects primarily on fishes, birds, mammals, terrestrial and aquatic invertebrates, and other natural resources. The subtopics include copper sources and uses; chemical and biochemical properties; concentrations of copper in field collections of abiotic materials and living organisms; effects of copper deficiency; lethal and sublethal effects on terrestrial plants and invertebrates, aquatic organisms, birds and mammals, including effects on survival, growth, reproduction, behavior, metabolism, carcinogenicity, matagenicity, and teratogenicity; proposed criteria for the protection of human health and sensitive natural resources; and recommendations for additional research.

  16. Meroterpenes from Marine Invertebrates: Structures, Occurrence, and Ecological Implications

    PubMed Central

    Menna, Marialuisa; Imperatore, Concetta; D’Aniello, Filomena; Aiello, Anna

    2013-01-01

    Meroterpenes are widely distributed among marine organisms; they are particularly abundant within brown algae, but other important sources include microorganisms and invertebrates. In the present review the structures and bioactivities of meroterpenes from marine invertebrates, mainly sponges and tunicates, are summarized. More than 300 molecules, often complex and with unique skeletons originating from intra- and inter-molecular cyclizations, and/or rearrangements, are illustrated. The reported syntheses are mentioned. The issue of a potential microbial link to their biosynthesis is also shortly outlined. PMID:23685889

  17. Analytical Ultracentrifugation as an Approach to Characterize Recombinant Adeno-Associated Viral Vectors.

    PubMed

    Burnham, Brenda; Nass, Shelley; Kong, Elton; Mattingly, MaryEllen; Woodcock, Denise; Song, Antonius; Wadsworth, Samuel; Cheng, Seng H; Scaria, Abraham; O'Riordan, Catherine R

    2015-12-01

    Recombinant adeno-associated viral (rAAV) vectors represent a novel class of biopharmaceutical drugs. The production of clinical-grade rAAV vectors for gene therapy would benefit from analytical methods that are able to monitor drug product quality with regard to homogeneity, purity, and manufacturing consistency. Here, we demonstrate the novel application of analytical ultracentrifugation (AUC) to characterize the homogeneity of preparations of rAAV vectors. We show that a single sedimentation velocity run of rAAV vectors detected and quantified a number of different viral species, such as vectors harboring an intact genome, lacking a vector genome (empty particles), and containing fragmented or incomplete vector genomes. This information is obtained by direct boundary modeling of the AUC data generated from refractometric or UV detection systems using the computer program SEDFIT. Using AUC, we show that multiple parameters contributed to vector quality, including the AAV genome form (i.e., self-complementary vs. single-stranded), vector genome size, and the production and purification methods. Hence, AUC is a critical tool for identifying optimal production and purification processes and for monitoring the physical attributes of rAAV vectors to ensure their quality.

  18. Index Sets and Vectorization

    SciTech Connect

    Keasler, J A

    2012-03-27

    Vectorization is data parallelism (SIMD, SIMT, etc.) - extension of ISA enabling the same instruction to be performed on multiple data items simultaeously. Many/most CPUs support vectorization in some form. Vectorization is difficult to enable, but can yield large efficiency gains. Extra programmer effort is required because: (1) not all algorithms can be vectorized (regular algorithm structure and fine-grain parallelism must be used); (2) most CPUs have data alignment restrictions for load/store operations (obey or risk incorrect code); (3) special directives are often needed to enable vectorization; and (4) vector instructions are architecture-specific. Vectorization is the best way to optimize for power and performance due to reduced clock cycles. When data is organized properly, a vector load instruction (i.e. movaps) can replace 'normal' load instructions (i.e. movsd). Vector operations can potentially have a smaller footprint in the instruction cache when fewer instructions need to be executed. Hybrid index sets insulate users from architecture specific details. We have applied hybrid index sets to achieve optimal vectorization. We can extend this concept to handle other programming models.

  19. Genome Sequencing Fishes out Longevity Genes.

    PubMed

    Lakhina, Vanisha; Murphy, Coleen T

    2015-12-01

    Understanding the molecular basis underlying aging is critical if we are to fully understand how and why we age-and possibly how to delay the aging process. Up until now, most longevity pathways were discovered in invertebrates because of their short lifespans and availability of genetic tools. Now, Reichwald et al. and Valenzano et al. independently provide a reference genome for the short-lived African turquoise killifish, establishing its role as a vertebrate system for aging research. PMID:26638067

  20. Genome Sequencing Fishes out Longevity Genes.

    PubMed

    Lakhina, Vanisha; Murphy, Coleen T

    2015-12-01

    Understanding the molecular basis underlying aging is critical if we are to fully understand how and why we age-and possibly how to delay the aging process. Up until now, most longevity pathways were discovered in invertebrates because of their short lifespans and availability of genetic tools. Now, Reichwald et al. and Valenzano et al. independently provide a reference genome for the short-lived African turquoise killifish, establishing its role as a vertebrate system for aging research.

  1. Application of multiple index development approaches to benthic invertebrate data from the Virginian Biogeographic Province

    EPA Science Inventory

    Benthic invertebrate indices have commonly been utilized to assess benthic invertebrate communities. These indices have been constructed using different techniques, but have shown different levels of application success. For example, the EMAP Virginian Province Index did not pe...

  2. Invertebrate colonization of leaves and roots within sediments of intermittent coastal plain streams across hydrologic phases

    EPA Science Inventory

    We compared benthic invertebrate assemblages colonizing three types of buried substrates (leaves, roots and plastic roots) among three intermittent Coastal Plain streams over a one year period. Invertebrate density was significantly lower in root litterbags than in plastic root l...

  3. WETLAND INVERTEBRATE COMMUNITY RESPONSES TO VARYING EMERGENT LITTER IN A PRAIRIE POTHOLE EMERGENT MARSH

    EPA Science Inventory

    Plant litter produced in the interior of dense emergent stands may directly or indirectly influence invertebrate communities. Low litter may provide structure and refuge to invertebrates while high litter may shade out vegetation and algae and decrease oxygen concentrations. With...

  4. Bacteriophage lambda as a cloning vector.

    PubMed

    Chauthaiwale, V M; Therwath, A; Deshpande, V V

    1992-12-01

    Extensive research has been directed toward the development of multipurpose lambda vectors for cloning ever since the potential of using coliphage lambda as a cloning vector was recognized in the late 1970s. An understanding of the intrinsic molecular organization and of the genetic events which determine lysis or lysogeny in lambda has allowed investigators to modify it to suit the specific requirements of gene manipulations. Unwanted restriction sites have been altered and arranged together into suitable polylinkers. The development of a highly efficient in vitro packaging system has permitted the introduction of chimeric molecules into hosts. Biological containment of recombinants has been achieved by introducing amber mutations into the lambda genome and by using specific amber suppressor hosts. Taking advantage of the limited range of genome size (78 to 105% of the wild-type size) for its efficient packaging, an array of vectors has been devised to accommodate inserts of a wide size range, the limit being 24 kbp in Charon 40. The central dispensable fragment of the lambda genome can be replaced by a fragment of heterologous DNA, leading to the construction of replacement vectors such as Charon and EMBL. Alternatively, small DNA fragments can be inserted without removing the dispensable region of the lambda genome, as in lambda gt10 and lambda gt11 vectors. In addition, the introduction of many other desirable properties, such as NotI and SfiI sites in polylinkers (e.g., lambda gt22), T7 and T3 promoters for the in vitro transcription (e.g., lambda DASH), and the mechanism for in vivo excision of the intact insert (e.g., lambda ZAP), has facilitated both cloning and subsequent analysis. In most cases, the recombinants can be differentiated from the parental phages by their altered phenotype. Libraries constructed in lambda vectors are screened easily with antibody or nucleic acid probes since several thousand clones can be plated on a single petri dish. Besides

  5. Retroviral vector production.

    PubMed

    Miller, A Dusty

    2014-01-01

    In this unit, the basic protocol generates stable cell lines that produce retroviral vectors that carry selectable markers. Also included are an alternate protocol that applies when the retroviral vector does not carry a selectable marker, and another alternate protocol for rapidly generating retroviral vector preparations by transient transfection. A support protocol describes construction of the retroviral vectors. The methods for generating virus from retroviral vector plasmids rely on the use of packaging cells that synthesize all of the retroviral proteins but do not produce replication-competent virus. Additional protocols detail plasmid transfection, virus titration, assay for replication-competent virus, and histochemical staining to detect transfer of a vector encoding alkaline phosphatase.

  6. Vectorization of a Treecode

    NASA Astrophysics Data System (ADS)

    Makino, Junichiro

    1990-03-01

    Vectorized algorithms for the force calculation and tree construction in the Barnes-Hut tree algorithm are described. The basic idea for the vectorization of the force calculation is to vectorize the tree traversal across particles, so that all particles in the system traverse the tree simultaneously. The tree construction algorithm also makes use of the fact that particles can be treated in parallel. Thus these algorithms take advantage of the internal parallelism in the N-body system and the tree algorithm most effectively. As a natural result, these algorithms can be used on a wide range of vector/parallel architectures, including current supercomputers and highly parallel architectures such as the Connection Machine. The vectorized code runs about five times faster than the non-vector code on a Cyber 205 for an N-body system with N = 8192.

  7. Simian virus-40 as a gene therapy vector.

    PubMed

    Vera, Maria; Fortes, Puri

    2004-05-01

    Simian virus-40 (SV40), an icosahedral papovavirus, has recently been modified to serve as a gene delivery vector. Recombinant SV40 vectors (rSV40) are good candidates for gene transfer, as they display some unique features: SV40 is a well-known virus, nonreplicative vectors are easy-to-make, and can be produced in titers of 10(12) IU/ml. They also efficiently transduce both resting and dividing cells, deliver persistent transgene expression to a wide range of cell types, and are nonimmunogenic. Present disadvantages of rSV40 vectors for gene therapy are a small cloning capacity and the possible risks related to random integration of the viral genome into the host genome. Considerable efforts have been devoted to modifing this virus and setting up protocols for viral production. Preliminary therapeutic results obtained both in tissue culture cells and in animal models for heritable and acquired diseases indicate that rSV40 vectors are promising gene transfer vehicles. This article reviews the work performed with SV40 viruses as recombinant vectors for gene transfer. A summary of the structure, genomic organization, and life cycle of wild-type SV40 viruses is presented. Furthermore, the strategies utilized for the development, production, and titering of rSV40 vectors are discussed. Last, the therapeutic applications developed to date are highlighted. PMID:15169607

  8. Support vector tracking.

    PubMed

    Avidan, Shai

    2004-08-01

    Support Vector Tracking (SVT) integrates the Support Vector Machine (SVM) classifier into an optic-flow-based tracker. Instead of minimizing an intensity difference function between successive frames, SVT maximizes the SVM classification score. To account for large motions between successive frames, we build pyramids from the support vectors and use a coarse-to-fine approach in the classification stage. We show results of using SVT for vehicle tracking in image sequences.

  9. Detection of betanodaviruses in apparently healthy aquarium fishes and invertebrates.

    PubMed

    Gomez, Dennis Kaw; Lim, Dong Joo; Baeck, Gun Wook; Youn, Hee Jeong; Shin, Nam Shik; Youn, Hwa Young; Hwang, Cheol Yong; Park, Jun Hong; Park, Se Chang

    2006-12-01

    Betanodaviruses are the causative agents of viral nervous necrosis (VNN) in cultured marine fish. A total of 237 apparently healthy aquarium fish, marine (65 species) and freshwater (12 species) fishes and marine invertebrates (4 species), which were stocked in a commercial aquarium in Seoul, South Korea, were collected from November 2005 to February 2006. The brains of the fish and other tissues of the invertebrates were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR to detect betanodavirus. Positive nested PCR results were obtained from the brains of 8 marine fish species (shrimp fish Aeoliscus strigatus, milkfish Chanos chanos, three spot damsel Dascyllus trimaculatus, Japanese anchovy Engraulis japonicus, pinecone fish Monocentris japonica, blue ribbon eel Rhinomuraena quaesita, look down fish Selene vomer, yellow tang Zebrasoma flavesenes), 1 marine invertebrate species (spiny lobster Pamulirus versicolor), and 2 freshwater fish species (South American leaf fish Monocirrhus polyacanthus and red piranha Pygocentrus nattereri). The detection rate in nested PCR was 11/237 (4.64%). These subclinically infected aquarium fish and invertebrates may constitute an inoculum source of betanodaviruses for cultured fishes in the Korean Peninsula. PMID:17106229

  10. Invertebrates: Revealing a Hidden World in the Year of Biodiversity

    ERIC Educational Resources Information Center

    Sanders, Dawn

    2010-01-01

    Biodiversity means the variety of life in all its forms. It includes the variety of species and ecosystems in the world, and genetic variation. Invertebrates are one of the largest and most accessible groups of animals for primary children to study. In this article, the author explains why and how children should engage with the idea of…

  11. Use of Invertebrate Animals to Teach Physiological Principles.

    ERIC Educational Resources Information Center

    Deyrup-Olsen, Ingrith; Linder, Thomas M.

    1991-01-01

    The advantages of using invertebrates in teaching physiological principles are discussed. The ability to illustrate with greater clarity physiological principles, the range and variety of physiological processes available for examination, and the unlimited possibilities for student research are topics of discussion. (KR)

  12. Trends in Children's Concepts of Vertebrate and Invertebrate.

    ERIC Educational Resources Information Center

    Braund, Martin

    1998-01-01

    Presents the results of a cross-age study of 7- to 15-year-old children on their thinking about vertebrate and invertebrate animals. Suggests experiences that could be included in the school science curriculum and argues for more classroom work relating structure with function in order to address students' conceptual difficulties. (Contains 18…

  13. Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary

    PubMed Central

    2010-01-01

    Background Invertebrate nervous systems are highly disparate between different taxa. This is reflected in the terminology used to describe them, which is very rich and often confusing. Even very general terms such as 'brain', 'nerve', and 'eye' have been used in various ways in the different animal groups, but no consensus on the exact meaning exists. This impedes our understanding of the architecture of the invertebrate nervous system in general and of evolutionary transformations of nervous system characters between different taxa. Results We provide a glossary of invertebrate neuroanatomical terms with a precise and consistent terminology, taxon-independent and free of homology assumptions. This terminology is intended to form a basis for new morphological descriptions. A total of 47 terms are defined. Each entry consists of a definition, discouraged terms, and a background/comment section. Conclusions The use of our revised neuroanatomical terminology in any new descriptions of the anatomy of invertebrate nervous systems will improve the comparability of this organ system and its substructures between the various taxa, and finally even lead to better and more robust homology hypotheses. PMID:21062451

  14. Detection of betanodaviruses in apparently healthy aquarium fishes and invertebrates.

    PubMed

    Gomez, Dennis Kaw; Lim, Dong Joo; Baeck, Gun Wook; Youn, Hee Jeong; Shin, Nam Shik; Youn, Hwa Young; Hwang, Cheol Yong; Park, Jun Hong; Park, Se Chang

    2006-12-01

    Betanodaviruses are the causative agents of viral nervous necrosis (VNN) in cultured marine fish. A total of 237 apparently healthy aquarium fish, marine (65 species) and freshwater (12 species) fishes and marine invertebrates (4 species), which were stocked in a commercial aquarium in Seoul, South Korea, were collected from November 2005 to February 2006. The brains of the fish and other tissues of the invertebrates were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR to detect betanodavirus. Positive nested PCR results were obtained from the brains of 8 marine fish species (shrimp fish Aeoliscus strigatus, milkfish Chanos chanos, three spot damsel Dascyllus trimaculatus, Japanese anchovy Engraulis japonicus, pinecone fish Monocentris japonica, blue ribbon eel Rhinomuraena quaesita, look down fish Selene vomer, yellow tang Zebrasoma flavesenes), 1 marine invertebrate species (spiny lobster Pamulirus versicolor), and 2 freshwater fish species (South American leaf fish Monocirrhus polyacanthus and red piranha Pygocentrus nattereri). The detection rate in nested PCR was 11/237 (4.64%). These subclinically infected aquarium fish and invertebrates may constitute an inoculum source of betanodaviruses for cultured fishes in the Korean Peninsula.

  15. Vectorized Monte Carlo

    SciTech Connect

    Brown, F.B.

    1981-01-01

    Examination of the global algorithms and local kernels of conventional general-purpose Monte Carlo codes shows that multigroup Monte Carlo methods have sufficient structure to permit efficient vectorization. A structured multigroup Monte Carlo algorithm for vector computers is developed in which many particle events are treated at once on a cell-by-cell basis. Vectorization of kernels for tracking and variance reduction is described, and a new method for discrete sampling is developed to facilitate the vectorization of collision analysis. To demonstrate the potential of the new method, a vectorized Monte Carlo code for multigroup radiation transport analysis was developed. This code incorporates many features of conventional general-purpose production codes, including general geometry, splitting and Russian roulette, survival biasing, variance estimation via batching, a number of cutoffs, and generalized tallies of collision, tracklength, and surface crossing estimators with response functions. Predictions of vectorized performance characteristics for the CYBER-205 were made using emulated coding and a dynamic model of vector instruction timing. Computation rates were examined for a variety of test problems to determine sensitivities to batch size and vector lengths. Significant speedups are predicted for even a few hundred particles per batch, and asymptotic speedups by about 40 over equivalent Amdahl 470V/8 scalar codes arepredicted for a few thousand particles per batch. The principal conclusion is that vectorization of a general-purpose multigroup Monte Carlo code is well worth the significant effort required for stylized coding and major algorithmic changes.

  16. Engineering HSV-1 vectors for gene therapy.

    PubMed

    Goins, William F; Huang, Shaohua; Cohen, Justus B; Glorioso, Joseph C

    2014-01-01

    Virus vectors have been employed as gene transfer vehicles for various preclinical and clinical gene therapy applications, and with the approval of Glybera (alipogene tiparvovec) as the first gene therapy product as a standard medical treatment (Yla-Herttuala, Mol Ther 20: 1831-1832, 2013), gene therapy has reached the status of being a part of standard patient care. Replication-competent herpes simplex virus (HSV) vectors that replicate specifically in actively dividing tumor cells have been used in Phase I-III human trials in patients with glioblastoma multiforme, a fatal form of brain cancer, and in malignant melanoma. In fact, T-VEC (talimogene laherparepvec, formerly known as OncoVex GM-CSF) displayed efficacy in a recent Phase III trial when compared to standard GM-CSF treatment alone (Andtbacka et al. J Clin Oncol 31: sLBA9008, 2013) and may soon become the second FDA-approved gene therapy product used in standard patient care. In addition to the replication-competent oncolytic HSV vectors like T-VEC, replication-defective HSV vectors have been employed in Phase I-II human trials and have been explored as delivery vehicles for disorders such as pain, neuropathy, and other neurodegenerative conditions. Research during the last decade on the development of HSV vectors has resulted in the engineering of recombinant vectors that are totally replication defective, nontoxic, and capable of long-term transgene expression in neurons. This chapter describes methods for the construction of recombinant genomic HSV vectors based on the HSV-1 replication-defective vector backbones, steps in their purification, and their small-scale production for use in cell culture experiments as well as preclinical animal studies.

  17. Genetic variation in arthropod vectors of disease-causing organisms: obstacles and opportunities.

    PubMed Central

    Gooding, R H

    1996-01-01

    An overview of the genetic variation in arthropods that transmit pathogens to vertebrates is presented, emphasizing the genetics of vector-pathogen relationships and the biochemical genetics of vectors. Vector-pathogen interactions are reviewed briefly as a prelude to a discussion of the genetics of susceptibility and refractoriness in vectors. Susceptibility to pathogens is controlled by maternally inherited factors, sex-linked dominant alleles, and dominant and recessive autosomal genes. There is widespread interpopulation (including intercolony) and temporal variation in susceptibility to pathogens. The amount of biochemical genetic variation in vectors is similar to that found in other invertebrates. However, the amount varies widely among species, among populations within species, and temporally within populations. Biochemical genetic studies show that there is considerable genetic structuring of many vectors at the local, regional, and global levels. It is argued that genetic variation in vectors is critical in understanding vector-pathogen interactions and that genetic variation in vectors creates both obstacles to and opportunities for application of genetic techniques to the control of vectors. PMID:8809462

  18. Marine Invertebrate Xenobiotic-Activated Nuclear Receptors: Their Application as Sensor Elements in High-Throughput Bioassays for Marine Bioactive Compounds

    PubMed Central

    Richter, Ingrid; Fidler, Andrew E.

    2014-01-01

    Developing high-throughput assays to screen marine extracts for bioactive compounds presents both conceptual and technical challenges. One major challenge is to develop assays that have well-grounded ecological and evolutionary rationales. In this review we propose that a specific group of ligand-activated transcription factors are particularly well-suited to act as sensors in such bioassays. More specifically, xenobiotic-activated nuclear receptors (XANRs) regulate transcription of genes involved in xenobiotic detoxification. XANR ligand-binding domains (LBDs) may adaptively evolve to bind those bioactive, and potentially toxic, compounds to which organisms are normally exposed to through their specific diets. A brief overview of the function and taxonomic distribution of both vertebrate and invertebrate XANRs is first provided. Proof-of-concept experiments are then described which confirm that a filter-feeding marine invertebrate XANR LBD is activated by marine bioactive compounds. We speculate that increasing access to marine invertebrate genome sequence data, in combination with the expression of functional recombinant marine invertebrate XANR LBDs, will facilitate the generation of high-throughput bioassays/biosensors of widely differing specificities, but all based on activation of XANR LBDs. Such assays may find application in screening marine extracts for bioactive compounds that could act as drug lead compounds. PMID:25421319

  19. Invertebrate community composition differs between invasive herb alligator weed and native sedges

    NASA Astrophysics Data System (ADS)

    Bassett, Imogen E.; Paynter, Quentin; Beggs, Jacqueline R.

    2012-05-01

    Chemical and/or architectural differences between native and exotic plants may influence invertebrate community composition. According to the enemy release hypothesis, invasive weeds should host fewer and less specialised invertebrates than native vegetation. Invertebrate communities were compared on invasive Alternanthera philoxeroides (alligator weed) and native sedges (Isolepis prolifer and Schoenoplectus tabernaemontani) in a New Zealand lake. A. philoxeroides is more architecturally and chemically similar to I. prolifer than to S. tabernaemontani. Lower invertebrate abundance, richness and proportionally fewer specialists were predicted on A. philoxeroides compared to native sedges, but with greatest differences between A. philoxeroides and S. tabernaemontani. A. philoxeroides is more architecturally and chemically similar to I. prolifer than to S. tabernaemontani. Invertebrate abundance showed taxa-specific responses, rather than consistently lower abundance on A. philoxeroides. Nevertheless, as predicted, invertebrate fauna of A. philoxeroides was more similar to that of I. prolifer than to S. tabernaemontani. The prediction of a depauperate native fauna on A. philoxeroides received support from some but not all taxa. All vegetation types hosted generalist-dominated invertebrate communities with simple guild structures. The enemy release hypothesis thus had minimal ability to predict patterns in this system. Results suggest the extent of architectural and chemical differences between native and invasive vegetation may be useful in predicting the extent to which they will host different invertebrate communities. However, invertebrate ecology also affects whether invertebrate taxa respond positively or negatively to weed invasion. Thus, exotic vegetation may support distinct invertebrate communities despite similar overall invertebrate abundance to native vegetation.

  20. One-step PCR amplification of complete arthropod mitochondrial genomes.

    PubMed

    Hwang, U W; Park, C J; Yong, T S; Kim, W

    2001-06-01

    A new PCR primer set which enables one-step amplification of complete arthropod mitochondrial genomes was designed from two conserved 16S rDNA regions for the long PCR technique. For this purpose, partial 16S rDNAs amplified with universal primers 16SA and 16SB were newly sequenced from six representative arthropods: Armadillidium vulgare and Macrobrachium nipponense (Crustacea), Anopheles sinensis (Insecta), Lithobius forficatus and Megaphyllum sp. (Myriapoda), and Limulus polyphemus (Chelicerata). The genomic locations of two new primers, HPK16Saa and HPK16Sbb, correspond to positions 13314-13345 and 12951-12984, respectively, in the Drosophila yakuba mitochondrial genome. The usefulness of the primer set was experimentally examined and confirmed with five of the representative arthropods, except for A. vulgare, which has a linearized mitochondrial genome. With this set, therefore, we could easily and rapidly amplify complete mitochondrial genomes with small amounts of arthropod DNA. Although the primers suggested here were examined only with arthropod groups, a possibility of successful application to other invertebrates is very high, since the high degree of sequence conservation is shown on the primer sites in other invertebrates. Thus, this primer set can serve various research fields, such as molecular evolution, population genetics, and molecular phylogenetics based on DNA sequences, RFLP, and gene rearrangement of mitochondrial genomes in arthropods and other invertebrates. PMID:11399145

  1. The Overlooked Biodiversity of Flower-Visiting Invertebrates

    PubMed Central

    Wardhaugh, Carl W.; Stork, Nigel E.; Edwards, Will; Grimbacher, Peter S.

    2012-01-01

    Estimates suggest that perhaps 40% of all invertebrate species are found in tropical rainforest canopies. Extrapolations of total diversity and food web analyses have been based almost exclusively on species inhabiting the foliage, under the assumption that foliage samples are representative of the entire canopy. We examined the validity of this assumption by comparing the density of invertebrates and the species richness of beetles across three canopy microhabitats (mature leaves, new leaves and flowers) on a one hectare plot in an Australian tropical rainforest. Specifically, we tested two hypotheses: 1) canopy invertebrate density and species richness are directly proportional to the amount of resource available; and 2) canopy microhabitats represent discrete resources that are utilised by their own specialised invertebrate communities. We show that flowers in the canopy support invertebrate densities that are ten to ten thousand times greater than on the nearby foliage when expressed on a per-unit resource biomass basis. Furthermore, species-level analyses of the beetle fauna revealed that flowers support a unique and remarkably rich fauna compared to foliage, with very little species overlap between microhabitats. We reject the hypothesis that the insect fauna on mature foliage is representative of the greater canopy community even though mature foliage comprises a very large proportion of canopy plant biomass. Although the significance of the evolutionary relationship between flowers and insects is well known with respect to plant reproduction, less is known about the importance of flowers as resources for tropical insects. Consequently, we suggest that this constitutes a more important piece of the ‘diversity jigsaw puzzle’ than has been previously recognised and could alter our understanding of the evolution of plant-herbivore interactions and food web dynamics, and provide a better foundation for accurately estimating global species richness. PMID

  2. Mallard duckling growth and survival in relation to aquatic invertebrates

    USGS Publications Warehouse

    Cox, R.R.; Hanson, M.A.; Roy, C.C.; Euliss, N.H.; Johnson, D.H.; Butler, Malcolm G.

    1998-01-01

    Identification and assessment of the relative importance of factors affecting duckling growth and survival are essential for effective management of mallards on breeding areas. For each of 3 years (1993-95), we placed F1-generation wild mallard (Anas platyrhynchos) females on experimental wetlands and allowed them to mate, nest, and rear broods for 17 days. We manipulated invertebrate densities by introducing fathead minnows (Pimephales promelas) at high densities in half of the wetlands on which broods were confined. Day-17 body mass of surviving ducklings (n = 183) was greater for ducklings that were heavier at hatch; the difference averaged 1.7 g at day 17 for each 1.0 g at hatch (P = 0.047). Growth ratio (the proportion of body mass attained by ducklings when they were last measured relative to that predicted for wild female mallard ducklings) also was positively related to body mass at hatch (P = 0.004). Mean day-17 body mass and mean growth ratio of ducklings per brood (each adjusted for body mass at hatch) were positively related to numbers of aquatic invertebrates (Ps < 0.001) and negatively related to variance in the daily minimum air temperature during the exposure period (Ps < 0.020). Early growth of mallards was more sensitive to variation in numbers of invertebrates than to air temperature or biomass of invertebrates. Duckling survival was positively related to growth ratio (P < 0.001). Our study provides parameter estimates that are essential for modeling growth and survival of mallard ducklings. We emphasize the need for conserving brood-rearing wetlands in the Prairie Pothole Region that are capable of supporting high densities of aquatic invertebrates.

  3. Crawling to Collapse: Ecologically Unsound Ornamental Invertebrate Fisheries

    PubMed Central

    Rhyne, Andrew; Rotjan, Randi; Bruckner, Andrew; Tlusty, Michael

    2009-01-01

    Background Fishery management has historically been an inexact and reactionary discipline, often taking action only after a critical stock suffers overfishing or collapse. The invertebrate ornamental fishery in the State of Florida, with increasing catches over a more diverse array of species, is poised for collapse. Current management is static and the lack of an adaptive strategy will not allow for adequate responses associated with managing this multi-species fishery. The last decade has seen aquarium hobbyists shift their display preference from fish-only tanks to miniature reef ecosystems that include many invertebrate species, creating increased demand without proper oversight. The once small ornamental fishery has become an invertebrate-dominated major industry supplying five continents. Methodology/Principal Findings Here, we analyzed the Florida Marine Life Fishery (FLML) landing data from 1994 to 2007 for all invertebrate species. The data were organized to reflect both ecosystem purpose (in the wild) and ecosystem services (commodities) for each reported species to address the following question: Are ornamental invertebrates being exploited for their fundamental ecosystem services and economic value at the expense of reef resilience? We found that 9 million individuals were collected in 2007, 6 million of which were grazers. Conclusions/Significance The number of grazers now exceeds, by two-fold, the number of specimens collected for curio and ornamental purposes altogether, representing a major categorical shift. In general, landings have increased 10-fold since 1994, though the number of licenses has been dramatically reduced. Thus, despite current management strategies, the FLML Fishery appears to be crawling to collapse. PMID:20027312

  4. Effects of stream enclosures on drifting invertebrates and fish growth

    USGS Publications Warehouse

    Zimmerman, J.K.H.; Vondracek, B.

    2006-01-01

    Stream ecologists often use enclosure experiments to investigate predator-prey interactions and competition within and among fish species. The design of enclosures, manipulation of species densities, and method of replication may influence experimental results. We designed an experiment with enclosure cages (1 m2, 6-mm mesh) to examine the relative influence of fish size, density, and prey availability on growth of brown trout (Salmo trutta), brook trout (Salvelinus fontinalis), and slimy sculpin (Cottus cognatus) within enclosures in Valley Creek, Minnesota. In addition, we examined water flow and invertebrate drift entering enclosures and in open riffles to investigate whether enclosures reduced the supply of invertebrate prey. Growth of small (age-0) brook and brown trout was not influenced by fish density, but growth of larger (age-1) trout generally decreased as density increased. Sculpin growth was not related to fish size or density, but increased with mean size of invertebrates in the drift. Enclosures reduced water flow and tended to reduce invertebrate drift rate, although total drift rate (ind./min), total drift density (ind./m3), and mean size of invertebrates were not significantly different inside enclosures compared to adjacent stream riffles. Enclosures had no effect on drift rate or size of Gammarus pseudolimnaeus, the main prey item for trout and sculpin in Valley Creek. Overall, our analyses indicated that reductions of prey availability by enclosures did not influence fish growth. Trout growth may have been limited at larger sizes and densities because of increased activity costs of establishing and defending territories, whereas sculpin growth was related to availability of large prey, a factor not influenced by enclosures. ?? 2006 by The North American Benthological Society.

  5. The overlooked biodiversity of flower-visiting invertebrates.

    PubMed

    Wardhaugh, Carl W; Stork, Nigel E; Edwards, Will; Grimbacher, Peter S

    2012-01-01

    Estimates suggest that perhaps 40% of all invertebrate species are found in tropical rainforest canopies. Extrapolations of total diversity and food web analyses have been based almost exclusively on species inhabiting the foliage, under the assumption that foliage samples are representative of the entire canopy. We examined the validity of this assumption by comparing the density of invertebrates and the species richness of beetles across three canopy microhabitats (mature leaves, new leaves and flowers) on a one hectare plot in an Australian tropical rainforest. Specifically, we tested two hypotheses: 1) canopy invertebrate density and species richness are directly proportional to the amount of resource available; and 2) canopy microhabitats represent discrete resources that are utilised by their own specialised invertebrate communities. We show that flowers in the canopy support invertebrate densities that are ten to ten thousand times greater than on the nearby foliage when expressed on a per-unit resource biomass basis. Furthermore, species-level analyses of the beetle fauna revealed that flowers support a unique and remarkably rich fauna compared to foliage, with very little species overlap between microhabitats. We reject the hypothesis that the insect fauna on mature foliage is representative of the greater canopy community even though mature foliage comprises a very large proportion of canopy plant biomass. Although the significance of the evolutionary relationship between flowers and insects is well known with respect to plant reproduction, less is known about the importance of flowers as resources for tropical insects. Consequently, we suggest that this constitutes a more important piece of the 'diversity jigsaw puzzle' than has been previously recognised and could alter our understanding of the evolution of plant-herbivore interactions and food web dynamics, and provide a better foundation for accurately estimating global species richness.

  6. Mosquito genomics: progress and challenges.

    PubMed

    Severson, David W; Behura, Susanta K

    2012-01-01

    The whole-genome sequencing of mosquitoes has facilitated our understanding of fundamental biological processes at their basic molecular levels and holds potential for application to mosquito control and prevention of mosquito-borne disease transmission. Draft genome sequences are available for Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus. Collectively, these represent the major vectors of African malaria, dengue fever and yellow fever viruses, and lymphatic filariasis, respectively. Rapid advances in genome technologies have revealed detailed information on genome architecture as well as phenotype-specific transcriptomics and proteomics. These resources allow for detailed comparative analyses within and across populations as well as species. Next-generation sequencing technologies will likely promote a proliferation of genome sequences for additional mosquito species as well as for individual insects. Here we review the current status of genome research in mosquitoes and identify potential areas for further investigations.

  7. Vector processing unit

    SciTech Connect

    Garcia, L.C.; Tjon-Pian-Gi, D.C.; Tucker, S.G.; Zajac, M.W.

    1988-12-13

    This patent describes a data processing system comprising: memory means for storing instruction words of operands; a central processing unit (CPU) connected to the memory means for fetching and decoding instructions and controlling execution of instructions, including transfer of operands to and from the memory means, the control of execution of instructions is effected by a CPU clock and microprogram control means connected to the CPU clock for generating periodic execution control signals in synchronism with the CPU clock; vector processing means tightly coupled to the CPU for effecting data processing on vector data; and interconnection means, connecting the CPU and the vector processing means, including operand transfer lines for transfer of vector data between the CPU and the vector processing means, control lines, status lines for signalling conditions of the vector processor means to the CPU, and a vector timing signal line connected to one of the execution control signals from the microprogram control means, whereby the vector processing means receives periodic execution control signals at the clock rate and is synchronized with the CPU clock on a clock pulse by clock pulse basis during execution of instructions.

  8. Vector generator scan converter

    DOEpatents

    Moore, J.M.; Leighton, J.F.

    1988-02-05

    High printing speeds for graphics data are achieved with a laser printer by transmitting compressed graphics data from a main processor over an I/O channel to a vector generator scan converter which reconstructs a full graphics image for input to the laser printer through a raster data input port. The vector generator scan converter includes a microprocessor with associated microcode memory containing a microcode instruction set, a working memory for storing compressed data, vector generator hardware for drawing a full graphic image from vector parameters calculated by the microprocessor, image buffer memory for storing the reconstructed graphics image and an output scanner for reading the graphics image data and inputting the data to the printer. The vector generator scan converter eliminates the bottleneck created by the I/O channel for transmitting graphics data from the main processor to the laser printer, and increases printer speed up to thirty fold. 7 figs.

  9. Vector generator scan converter

    DOEpatents

    Moore, James M.; Leighton, James F.

    1990-01-01

    High printing speeds for graphics data are achieved with a laser printer by transmitting compressed graphics data from a main processor over an I/O (input/output) channel to a vector generator scan converter which reconstructs a full graphics image for input to the laser printer through a raster data input port. The vector generator scan converter includes a microprocessor with associated microcode memory containing a microcode instruction set, a working memory for storing compressed data, vector generator hardward for drawing a full graphic image from vector parameters calculated by the microprocessor, image buffer memory for storing the reconstructed graphics image and an output scanner for reading the graphics image data and inputting the data to the printer. The vector generator scan converter eliminates the bottleneck created by the I/O channel for transmitting graphics data from the main processor to the laser printer, and increases printer speed up to thirty fold.

  10. Vector theories in cosmology

    SciTech Connect

    Esposito-Farese, Gilles; Pitrou, Cyril; Uzan, Jean-Philippe

    2010-03-15

    This article provides a general study of the Hamiltonian stability and the hyperbolicity of vector field models involving both a general function of the Faraday tensor and its dual, f(F{sup 2},FF-tilde), as well as a Proca potential for the vector field, V(A{sup 2}). In particular it is demonstrated that theories involving only f(F{sup 2}) do not satisfy the hyperbolicity conditions. It is then shown that in this class of models, the cosmological dynamics always dilutes the vector field. In the case of a nonminimal coupling to gravity, it is established that theories involving Rf(A{sup 2}) or Rf(F{sup 2}) are generically pathologic. To finish, we exhibit a model where the vector field is not diluted during the cosmological evolution, because of a nonminimal vector field-curvature coupling which maintains second-order field equations. The relevance of such models for cosmology is discussed.

  11. Vector generator scan converter

    SciTech Connect

    Moore, J.M.; Leighton, J.F.

    1990-04-17

    This patent describes high printing speeds for graphics data that are achieved with a laser printer by transmitting compressed graphics data from a main processor over an I/O (input/output) channel to a vector generator scan converter which reconstructs a full graphics image for input to the laser printer through a raster data input port. The vector generator scan converter includes a microprocessor with associated microcode memory containing a microcode instruction set, a working memory for storing compressed data, vector generator hardware for drawing a full graphic image from vector parameters calculated by the microprocessor, image buffer memory for storing the reconstructed graphics image and an output scanner for reading the graphics image data and inputting the data to the printer. The vector generator scan converter eliminates the bottleneck created by the I/O channel for transmitting graphics data from the main processor to the laser printer, and increases printer speed up to thirty fold.

  12. Deletion of A44L, A46R and C12L Vaccinia Virus Genes from the MVA Genome Improved the Vector Immunogenicity by Modifying the Innate Immune Response Generating Enhanced and Optimized Specific T-Cell Responses.

    PubMed

    Holgado, María Pía; Falivene, Juliana; Maeto, Cynthia; Amigo, Micaela; Pascutti, María Fernanda; Vecchione, María Belén; Bruttomesso, Andrea; Calamante, Gabriela; Del Médico-Zajac, María Paula; Gherardi, María Magdalena

    2016-01-01

    MVA is an attenuated vector that still retains immunomodulatory genes. We have previously reported its optimization after deleting the C12L gene, coding for the IL-18 binding-protein. Here, we analyzed the immunogenicity of MVA vectors harboring the simultaneous deletion of A44L, related to steroid synthesis and A46R, a TLR-signaling inhibitor (MVAΔA44L-A46R); or also including a deletion of C12L (MVAΔC12L/ΔA44L-A46R). The absence of biological activities of the deleted genes in the MVA vectors was demonstrated. Adaptive T-cell responses against VACV epitopes, evaluated in spleen and draining lymph-nodes of C57Bl/6 mice at acute/memory phases, were of higher magnitude in those animals that received deleted MVAs compared to MVAwt. MVAΔC12L/ΔA44L-A46R generated cellular specific memory responses of higher quality characterized by bifunctionality (CD107a/b⁺/IFN-γ⁺) and proliferation capacity. Deletion of selected genes from MVA generated innate immune responses with higher levels of determining cytokines related to T-cell response generation, such as IL-12, IFN-γ, as well as IL-1β and IFN-β. This study describes for the first time that simultaneous deletion of the A44L, A46R and C12L genes from MVA improved its immunogenicity by enhancing the host adaptive and innate immune responses, suggesting that this approach comprises an appropriate strategy to increase the MVA vaccine potential. PMID:27223301

  13. Deletion of A44L, A46R and C12L Vaccinia Virus Genes from the MVA Genome Improved the Vector Immunogenicity by Modifying the Innate Immune Response Generating Enhanced and Optimized Specific T-Cell Responses

    PubMed Central

    Holgado, María Pía; Falivene, Juliana; Maeto, Cynthia; Amigo, Micaela; Pascutti, María Fernanda; Vecchione, María Belén; Bruttomesso, Andrea; Calamante, Gabriela; del Médico-Zajac, María Paula; Gherardi, María Magdalena

    2016-01-01

    MVA is an attenuated vector that still retains immunomodulatory genes. We have previously reported its optimization after deleting the C12L gene, coding for the IL-18 binding-protein. Here, we analyzed the immunogenicity of MVA vectors harboring the simultaneous deletion of A44L, related to steroid synthesis and A46R, a TLR-signaling inhibitor (MVAΔA44L-A46R); or also including a deletion of C12L (MVAΔC12L/ΔA44L-A46R). The absence of biological activities of the deleted genes in the MVA vectors was demonstrated. Adaptive T-cell responses against VACV epitopes, evaluated in spleen and draining lymph-nodes of C57Bl/6 mice at acute/memory phases, were of higher magnitude in those animals that received deleted MVAs compared to MVAwt. MVAΔC12L/ΔA44L-A46R generated cellular specific memory responses of higher quality characterized by bifunctionality (CD107a/b+/IFN-γ+) and proliferation capacity. Deletion of selected genes from MVA generated innate immune responses with higher levels of determining cytokines related to T-cell response generation, such as IL-12, IFN-γ, as well as IL-1β and IFN-β. This study describes for the first time that simultaneous deletion of the A44L, A46R and C12L genes from MVA improved its immunogenicity by enhancing the host adaptive and innate immune responses, suggesting that this approach comprises an appropriate strategy to increase the MVA vaccine potential. PMID:27223301

  14. The structural diversity and promise of antiparasitic marine invertebrate-derived small molecules

    PubMed Central

    Watts, Katharine R; Tenney, Karen; Crews, Phillip

    2010-01-01

    This review focuses on six important parasitic diseases that adversely affect the health and lives of over one billion people worldwide. In light of the global human impact of these neglected tropical diseases (NTDs), several initiatives and campaigns have been mounted to eradicate these infections once and for all. Currently available therapeutics summarized herein are either ineffective and/or have severe and deleterious side effects. Resistant strains continue to emerge and there is an overall unmet and urgent need for new antiparasitic drugs. Marine-derived small molecules (MDSMs) from invertebrates comprise an extremely diverse and promising source of compounds from a wide variety of structural classes. New discoveries of marine natural product privileged structures and compound classes that are being made via natural product library screening using whole cell in vitro assays are highlighted. It is striking to note that for the first time in history the entire genomes of all six parasites have been sequenced and additional transcriptome and proteomic analyses are available. Furthermore, open and shared, publicly available databases of the genome sequences, compounds, screening assays, and druggable molecular targets are being used by the worldwide research community. A combined assessment of all of the above factors, especially of current discoveries in marine natural products, implies a brighter future with more effective, affordable, and benign antiparasitic therapeutics. PMID:20956079

  15. Simian virus 40 (SV40) large T antigen-dependent amplification of an Epstein-Barr virus-SV40 hybrid shuttle vector integrated into the human HeLa cell genome.

    PubMed

    Stary, A; Sarasin, A

    1992-07-01

    We analysed the DNA rearrangements that occurred during the integration and amplification of an Epstein-Barr virus (EBV)-simian virus 40 (SV40) hybrid shuttle vector in human cells. The human HeLa cell line was episomally transformed with the EBV-SV40 p205-GTI plasmid. After a 2 month culture in a selective medium, a HeLa cell-derived population (H-G1 cells) was obtained in which the p205-GTI vector was integrated as a single intact copy deleted in the EBV latent origin of replication (OriP). Sequencing data showed that the endpoints of the plasmid sequences, at the plasmid-cell DNA junctions, are located within the two essential elements of EBV OriP, which may form several secondary structures. This result suggests that a specific DNA sequence (OriP) or palindromic structures could play a role in this integration process. This represents the first fully characterized site of integration of an EBV vector in human cells. The transient expression of the SV40 large T antigen in H-G1 cells leads to the appearance of episomal molecules with an extremely heterogeneous size pattern. Individual analysis of these episomes after rescue in bacteria indicated that they retained sequences of both the p205-GTI plasmid and cellular DNA. Comparison of the structure of these circular DNAs with those of the integrated p205-GTI copy indicated that large T antigen expression in human cells leads to the amplification of the integrated shuttle vector according to the 'onion skin' model developed for transformed rodent cells. Indeed, amplified sequences were colinear with the integrated p205-GTI copy and its surrounding cellular sequences, distributed almost equally around the SV40 replication origin, and circularized by illegitimate recombination which did not involve specific nucleotide sequences. This system is of interest in that it enables easy recovery of individual recombined molecules in host bacteria. Each isolated clone contains a unique recombination junction which is easily

  16. Line Integral of a Vector.

    ERIC Educational Resources Information Center

    Balabanian, Norman

    This programed booklet is designed for the engineering student who understands and can use vector and unit vector notation, components of a vector, parallel law of vector addition, and the dot product of two vectors. Content begins with work done by a force in moving a body a certain distance along some path. For each of the examples and problem…

  17. The First United Workshop on Microsporidia from Invertebrate and Vertebrate Hosts.

    PubMed

    Weiss, Louis M

    2005-05-01

    The phylum Microsporidia is a large group of parasitic unicellular eukaryotes that infect a wide range of invertebrate and vertebrate taxa. These organisms are significant human and veterinary pathogens with impacts on medicine, agriculture and aquaculture. Scientists working on these pathogens represent diverse disciplines that have had limited opportunities for detailed interactions. A NATO Advanced Research Workshop 'Emergent Pathogens in the 21st Century: First United Workshop on Microsporidia from Invertebrate and Vertebrate Hosts' was held July 12-15, 2004 at the Institute of Parasitology of the Academy of Sciences of the Czech Republic to bring together experts in insect, fish, veterinary and human microsporidiosis for the exchange of information on these pathogens. At this meeting, discussions were held on issues related to taxonomy and phylogeny. It was recognized that microsporidia are related to fungi, but the strong opinion of the participants was that the International Code of Zoological Nomenclature should continue to be applied for taxonomic descriptions of the Microsporidia and that they be treated as an independent group emerging from a paraphyletic fungi. There continues to be exponential growth in the pace and volume of research on these ubiquitous intracellular protists. The small genomes of these organisms and the reduction in the size of many of their genes are of interest to many disciplines. Many microsporidia are dimorphic and the mechanisms underlying these morphologic changes remain to be elucidated. Epidemiologic studies to clarify the source of human microsporidiosis and ecologic studies to understand the multifaceted relationship of the Microsporidia and their hosts are important avenues of investigation. Studies on the Microsporidia should prove useful to many fields of biologic investigation.

  18. Polycistronic viral vectors.

    PubMed

    de Felipe, P

    2002-09-01

    Traditionally, vectors for gene transfer/therapy experiments were mono- or bicistronic. In the latter case, vectors express the gene of interest coupled with a marker gene. An increasing demand for more complex polycistronic vectors has arisen in recent years to obtain complex gene transfer/therapy effects. In particular, this demand is stimulated by the hope of a more powerful effect from combined gene therapy than from single gene therapy in a process whose parallels lie in the multi-drug combined therapies for cancer or AIDS. In the 1980's we had only splicing signals and internal promoters to construct such vectors: now a new set of biotechnological tools enables us to design new and more reliable bicistronic and polycistronic vectors. This article focuses on the description and comparison of the strategies for co-expression of two genes in bicistronic vectors, from the oldest to the more recently described: internal promoters, splicing, reinitiation, IRES, self-processing peptides (e.g. foot-and-mouth disease virus 2A), proteolytic cleavable sites (e.g. fusagen) and fusion of genes. I propose a classification of these strategies based upon either the use of multiple transcripts (with transcriptional mechanisms), or single transcripts (using translational/post-translational mechanisms). I also examine the different attempts to utilize these strategies in the construction of polycistronic vectors and the main problems encountered. Several potential uses of these polycistronic vectors, both in basic research and in therapy-focused applications, are discussed. The importance of the study of viral gene expression strategies and the need to transfer this knowledge to vector design is highlighted.

  19. Fractal vector optical fields.

    PubMed

    Pan, Yue; Gao, Xu-Zhen; Cai, Meng-Qiang; Zhang, Guan-Lin; Li, Yongnan; Tu, Chenghou; Wang, Hui-Tian

    2016-07-15

    We introduce the concept of a fractal, which provides an alternative approach for flexibly engineering the optical fields and their focal fields. We propose, design, and create a new family of optical fields-fractal vector optical fields, which build a bridge between the fractal and vector optical fields. The fractal vector optical fields have polarization states exhibiting fractal geometry, and may also involve the phase and/or amplitude simultaneously. The results reveal that the focal fields exhibit self-similarity, and the hierarchy of the fractal has the "weeding" role. The fractal can be used to engineer the focal field. PMID:27420485

  20. Innate immunity against moulds: lessons learned from invertebrate models.

    PubMed

    Ben-Ami, Ronen

    2011-01-01

    The emergence over the past two decades of invasive mycoses as a significant problem in immunocompromised patients underscores the importance of deciphering innate immunity against filamentous fungi. However, the complexity and cost of traditionally used mammalian model hosts presents a bottleneck that has limited the rate of advances in this field. In contrast, invertebrate model hosts have several important advantages, including simple immune systems, genetic tractability, and amenity to high-throughput experiments. The application of these models to studies of host-pathogen interactions is contingent on two tenets: (1) host innate defenses are preserved across widely disparate taxa, and (2) similar fungal virulence factors are operative in insects and in mammals. Validation of these principles paved the way for the use of invertebrates as facile models for studying invasive mould infections. These studies have helped shape our understanding of human pattern recognition receptors, phagocytic cell function and antimicrobial proteins, and their roles in host defense against filamentous fungi.

  1. Elastic arteries in invertebrates: mechanics of the octopus aorta.

    PubMed

    Shadwick, R E; Gosline, J M

    1981-08-14

    The aorta of the octopus, Octopus dofleini, is a highly distensible, elastic tube. The circumferential elastic modulus increases with inflation in the physiological range from abut 10(4) to 10(5) newtons per square meter. Rubber-like fibers have been isolated, apparently for the first time, from the aorta of an invertebrate. These fibers have an elastic modulus, like elastin, of about 4 x 10(5) newtons per square meter and are present in sufficient quantity to account for the elastic properties of the intact vessel under physiological conditions. Thus the circulatory system of an invertebrate animal provides an "elastic reservoir" (much like that of the vertebrate system), which increases the efficiency of the circulation. PMID:7256277

  2. Comparative acute toxicities of surfactants to aquatic invertebrates

    SciTech Connect

    Lewis, M.A.; Suprenant, D.

    1983-06-01

    Investigations of the toxicity of surfactants to aquatic invertebrates have been limited primarily to determining the effects on a few species. In this study, the 48-hr LC50 values for three surfactants are reported for six species of aquatic invertebrates. The acute toxicities (LC50) for each surfactant (mg/liter) varied 159 to 580 X and were as follows: C11.8LAS (anionic), 1.7 (Dero sp.) to 270 (Asellus sp.); C14-15 alkylethoxylate (nonionic), 1.0 (Dugesia sp.) to 6.8 (Rhabditis sp.); CTAC (cationic), 0.1 (Gammarus sp.) to 58 (Asellus sp.). When compared to previously developed data, Daphnia magna was typically found to be the most sensitive of all species tested, including fish, to the surfactants.

  3. Enterococcus infection biology: lessons from invertebrate host models.

    PubMed

    Yuen, Grace J; Ausubel, Frederick M

    2014-03-01

    The enterococci are commensals of the gastrointestinal tract of many metazoans, from insects to humans. While they normally do not cause disease in the intestine, they can become pathogenic when they infect sites outside of the gut. Recently, the enterococci have become important nosocomial pathogens, with the majority of human enterococcal infections caused by two species, Enterococcus faecalis and Enterococcus faecium. Studies using invertebrate infection models have revealed insights into the biology of enterococcal infections, as well as general principles underlying host innate immune defense. This review highlights recent findings on Enterococcus infection biology from two invertebrate infection models, the greater wax moth Galleria mellonella and the free-living bacteriovorous nematode Caenorhabditis elegans. PMID:24585051

  4. Street lighting changes the composition of invertebrate communities.

    PubMed

    Davies, Thomas W; Bennie, Jonathan; Gaston, Kevin J

    2012-10-23

    Artificial lighting has been used to illuminate the nocturnal environment for centuries and continues to expand with urbanization and economic development. Yet, the potential ecological impact of the resultant light pollution has only recently emerged as a major cause for concern. While investigations have demonstrated that artificial lighting can influence organism behaviour, reproductive success and survivorship, none have addressed whether it is altering the composition of communities. We show, for the first time, that invertebrate community composition is affected by proximity to street lighting independently of the time of day. Five major invertebrate groups contributed to compositional differences, resulting in an increase in the number of predatory and scavenging individuals in brightly lit communities. Our results indicate that street lighting changes the environment at higher levels of biological organization than previously recognized, raising the potential that it can alter the structure and function of ecosystems.

  5. Vascular endothelial growth factors: A comparison between invertebrates and vertebrates.

    PubMed

    Kipryushina, Yulia O; Yakovlev, Konstantin V; Odintsova, Nelly A

    2015-12-01

    This review aims to summarize recent data concerning the structure and role of the members of the vascular endothelial growth factor (VEGF) and vascular endothelial growth factor receptor (VEGFR) families in the context of early development, organogenesis and regeneration, with a particular emphasis on the role of these factors in the development of invertebrates. Homologs of VEGF and/or VEGFR have been found in all Eumetazoa, in both Radiata and Bilateria, where they are expressed in the descendants of different germ layers and play a pivotal role in the development of animals with and without a vascular system. VEGF is a well-known angiogenesis regulator, but this factor also control cell migration during neurogenesis and the development of branching organs (the trachea) in invertebrate and vertebrate species. A possible explanation for the origin of Vegf/Vegfr in the animal kingdom and a pathway of Vegf/Vegfr evolution are discussed.

  6. Spawning, copulation and inbreeding coefficients in marine invertebrates

    PubMed Central

    Addison, J.A; Hart, M.W

    2005-01-01

    Patterns of population genetic variation have frequently been understood as consequences of life history covariates such as dispersal ability and breeding systems (e.g. selfing). For example, marine invertebrates show enormous variation in life history traits that are correlated with the extent of gene flow between populations and the magnitude of differentiation among populations at neutral genetic markers (FST). Here we document an unexpected correlation between marine invertebrate life histories and deviation from Hardy–Weinberg equilibrium (non-zero values of FIS, the inbreeding coefficient). FIS values were significantly higher in studies of species with free-spawned planktonic sperm than in studies of species that copulate or have some form of direct sperm transfer to females or benthic egg masses. This result was robust to several different analytical approaches. We note several mechanisms that might contribute to this pattern, and appeal for more studies and ideas that might help to explain our observations. PMID:17148230

  7. Differential niche dynamics among major marine invertebrate clades

    PubMed Central

    Hopkins, Melanie J; Simpson, Carl; Kiessling, Wolfgang

    2014-01-01

    The degree to which organisms retain their environmental preferences is of utmost importance in predicting their fate in a world of rapid climate change. Notably, marine invertebrates frequently show strong affinities for either carbonate or terrigenous clastic environments. This affinity is due to characteristics of the sediments as well as correlated environmental factors. We assessed the conservatism of substrate affinities of marine invertebrates over geological timescales, and found that niche conservatism is prevalent in the oceans, and largely determined by the strength of initial habitat preference. There is substantial variation in niche conservatism among major clades with corals and sponges being among the most conservative. Time-series analysis suggests that niche conservatism is enhanced during times of elevated nutrient flux, whereas niche evolution tends to occur after mass extinctions. Niche evolution is not necessarily elevated in genera exhibiting higher turnover in species composition. PMID:24313951

  8. Viral Vectors for in Vivo Gene Transfer

    NASA Astrophysics Data System (ADS)

    Thévenot, E.; Dufour, N.; Déglon, N.

    The transfer of DNA into the nucleus of a eukaryotic cell (gene transfer) is a central theme of modern biology. The transfer is said to be somatic when it refers to non-germline organs of a developed individual, and germline when it concerns gametes or the fertilised egg of an animal, with the aim of transmitting the relevant genetic modification to its descendents [1]. The efficient introduction of genetic material into a somatic or germline cell and the control of its expression over time have led to major advances in understanding how genes work in vivo, i.e., in living organisms (functional genomics), but also to the development of innovative therapeutic methods (gene therapy). The efficiency of gene transfer is conditioned by the vehicle used, called the vector. Desirable features for a vector are as follows: Easy to produce high titer stocks of the vector in a reproducible way. Absence of toxicity related to transduction (transfer of genetic material into the target cell, and its expression there) and no immune reaction of the organism against the vector and/or therapeutic protein. Stability in the expression of the relevant gene over time, and the possibility of regulation, e.g., to control expression of the therapeutic protein on the physiological level, or to end expression at the end of treatment. Transduction of quiescent cells should be as efficient as transduction of dividing cells. Vectors currently used fall into two categories: non-viral and viral vectors. In non-viral vectors, the DNA is complexed with polymers, lipids, or cationic detergents (described in Chap. 3). These vectors have a low risk of toxicity and immune reaction. However, they are less efficient in vivo than viral vectors when it comes to the number of cells transduced and long-term transgene expression. (Naked DNA transfer or electroporation is rather inefficient in the organism. This type of gene transfer will not be discussed here, and the interested reader is referred to the

  9. When growth models are not universal: evidence from marine invertebrates

    PubMed Central

    Hirst, Andrew G.; Forster, Jack

    2013-01-01

    The accumulation of body mass, as growth, is fundamental to all organisms. Being able to understand which model(s) best describe this growth trajectory, both empirically and ultimately mechanistically, is an important challenge. A variety of equations have been proposed to describe growth during ontogeny. Recently, the West Brown Enquist (WBE) equation, formulated as part of the metabolic theory of ecology, has been proposed as a universal model of growth. This equation has the advantage of having a biological basis, but its ability to describe invertebrate growth patterns has not been well tested against other, more simple models. In this study, we collected data for 58 species of marine invertebrate from 15 different taxa. The data were fitted to three growth models (power, exponential and WBE), and their abilities were examined using an information theoretic approach. Using Akaike information criteria, we found changes in mass through time to fit an exponential equation form best (in approx. 73% of cases). The WBE model predominantly overestimates body size in early ontogeny and underestimates it in later ontogeny; it was the best fit in approximately 14% of cases. The exponential model described growth well in nine taxa, whereas the WBE described growth well in one of the 15 taxa, the Amphipoda. Although the WBE has the advantage of being developed with an underlying proximate mechanism, it provides a poor fit to the majority of marine invertebrates examined here, including species with determinate and indeterminate growth types. In the original formulation of the WBE model, it was tested almost exclusively against vertebrates, to which it fitted well; the model does not however appear to be universal given its poor ability to describe growth in benthic or pelagic marine invertebrates. PMID:23945691

  10. Transmission of solar ultraviolet radiation through invertebrate exteriors

    SciTech Connect

    Karentz, D.; Gast, T. )

    1993-01-01

    The occurrence of springtime ozone depletion over the Antarctic has created concern about the effects of increases ultraviolet-B on marine organisms, particularly in intertidal and subtidal populations. The first line of defense that an animal has to solar radiation exposure is its outer covering. This paper examines four species of antarctic invertebrates to determine the amount of UV protection provided by their external covering (the sea urchin, the sea star; the limpet; and the tunicate). 5 refs., 3 figs.

  11. When growth models are not universal: evidence from marine invertebrates.

    PubMed

    Hirst, Andrew G; Forster, Jack

    2013-10-01

    The accumulation of body mass, as growth, is fundamental to all organisms. Being able to understand which model(s) best describe this growth trajectory, both empirically and ultimately mechanistically, is an important challenge. A variety of equations have been proposed to describe growth during ontogeny. Recently, the West Brown Enquist (WBE) equation, formulated as part of the metabolic theory of ecology, has been proposed as a universal model of growth. This equation has the advantage of having a biological basis, but its ability to describe invertebrate growth patterns has not been well tested against other, more simple models. In this study, we collected data for 58 species of marine invertebrate from 15 different taxa. The data were fitted to three growth models (power, exponential and WBE), and their abilities were examined using an information theoretic approach. Using Akaike information criteria, we found changes in mass through time to fit an exponential equation form best (in approx. 73% of cases). The WBE model predominantly overestimates body size in early ontogeny and underestimates it in later ontogeny; it was the best fit in approximately 14% of cases. The exponential model described growth well in nine taxa, whereas the WBE described growth well in one of the 15 taxa, the Amphipoda. Although the WBE has the advantage of being developed with an underlying proximate mechanism, it provides a poor fit to the majority of marine invertebrates examined here, including species with determinate and indeterminate growth types. In the original formulation of the WBE model, it was tested almost exclusively against vertebrates, to which it fitted well; the model does not however appear to be universal given its poor ability to describe growth in benthic or pelagic marine invertebrates.

  12. Pesticide runoff from energy crops: A threat to aquatic invertebrates?

    PubMed

    Bunzel, Katja; Schäfer, Ralf B; Thrän, Daniela; Kattwinkel, Mira

    2015-12-15

    The European Union aims to reach a 10% share of biofuels in the transport sector by 2020. The major burden is most likely to fall on already established annual energy crops such as rapeseed and cereals for the production of biodiesel and bioethanol, respectively. Annual energy crops are typically cultivated in intensive agricultural production systems, which require the application of pesticides. Agricultural pesticides can have adverse effects on aquatic invertebrates in adjacent streams. We assessed the relative ecological risk to aquatic invertebrates associated with the chemical pest management from six energy crops (maize, potato, sugar beet, winter barley, winter rapeseed, and winter wheat) as well as from mixed cultivation scenarios. The pesticide exposure related to energy crops and cultivation scenarios was estimated as surface runoff for 253 small stream sites in Central Germany using a GIS-based runoff potential model. The ecological risk for aquatic invertebrates, an important organism group for the functioning of stream ecosystems, was assessed using acute toxicity data (48-h LC50 values) of the crustacean Daphnia magna. We calculated the Ecological Risk from potential Pesticide Runoff (ERPR) for all three main groups of pesticides (herbicides, fungicides, and insecticides). Our findings suggest that the crops potato, sugar beet, and rapeseed pose a higher ecological risk to aquatic invertebrates than maize, barley, and wheat. As maize had by far the lowest ERPR values, from the perspective of pesticide pollution, its cultivation as substrate for the production of the gaseous biofuel biomethane may be preferable compared to the production of, for example, biodiesel from rapeseed.

  13. [Body mass and excretion of phosphorus in aqueous invertebrates].

    PubMed

    Golubkov, S M

    2014-01-01

    Empirical materials on the dependence of the intensity of mineral phosphorus excretion (Ex) on the body mass (W) in invertebrates are summarized. The parameters of the average dependence of Ex on Win animals at 20 degrees C are determined. The main factors that influence the parameters ofthis dependence are discussed. It is shown that the decrease of Ex with an increase of Win animals is, as a rule, more significant compared with the decrease in the intensity of metabolism.

  14. Effects of Electromagnetic Fields on Fish and Invertebrates

    SciTech Connect

    Schultz, Irvin R.; Woodruff, Dana L.; Marshall, Kathryn E.; Pratt, William J.; Roesijadi, Guritno

    2010-10-13

    In this progress report, we describe the preliminary experiments conducted with three fish and one invertebrate species to determine the effects of exposure to electromagnetic fields. During fiscal year 2010, experiments were conducted with coho salmon (Onchrohychus kisutch), California halibut (Paralicthys californicus), Atlantic halibut (Hippoglossus hippoglossus), and Dungeness crab (Cancer magister). The work described supports Task 2.1.3: Effects on Aquatic Organisms, Subtask 2.1.3.1: Electromagnetic Fields.

  15. Pesticide runoff from energy crops: A threat to aquatic invertebrates?

    PubMed

    Bunzel, Katja; Schäfer, Ralf B; Thrän, Daniela; Kattwinkel, Mira

    2015-12-15

    The European Union aims to reach a 10% share of biofuels in the transport sector by 2020. The major burden is most likely to fall on already established annual energy crops such as rapeseed and cereals for the production of biodiesel and bioethanol, respectively. Annual energy crops are typically cultivated in intensive agricultural production systems, which require the application of pesticides. Agricultural pesticides can have adverse effects on aquatic invertebrates in adjacent streams. We assessed the relative ecological risk to aquatic invertebrates associated with the chemical pest management from six energy crops (maize, potato, sugar beet, winter barley, winter rapeseed, and winter wheat) as well as from mixed cultivation scenarios. The pesticide exposure related to energy crops and cultivation scenarios was estimated as surface runoff for 253 small stream sites in Central Germany using a GIS-based runoff potential model. The ecological risk for aquatic invertebrates, an important organism group for the functioning of stream ecosystems, was assessed using acute toxicity data (48-h LC50 values) of the crustacean Daphnia magna. We calculated the Ecological Risk from potential Pesticide Runoff (ERPR) for all three main groups of pesticides (herbicides, fungicides, and insecticides). Our findings suggest that the crops potato, sugar beet, and rapeseed pose a higher ecological risk to aquatic invertebrates than maize, barley, and wheat. As maize had by far the lowest ERPR values, from the perspective of pesticide pollution, its cultivation as substrate for the production of the gaseous biofuel biomethane may be preferable compared to the production of, for example, biodiesel from rapeseed. PMID:26282752

  16. Philosophical background of attitudes toward and treatment of invertebrates.

    PubMed

    Mather, Jennifer A

    2011-01-01

    People who interact with or make decisions about invertebrate animals have an attitude toward them, although they may not have consciously worked it out. Three philosophical approaches underlie this attitude. The first is the contractarian, which basically contends that animals are only automata and that we humans need not concern ourselves with their welfare except for our own good, because cruelty and neglect demean us. A second approach is the utilitarian, which focuses on gains versus losses in interactions between animals, including humans. Given the sheer numbers of invertebrates-they constitute 99% of the animals on the planet- this attitude implicitly requires concern for them and consideration in particular of whether they can feel pain. Third is the rights-based approach, which focuses on humans-treatment of animals by calling for an assessment of their quality of life in each human-animal interaction. Here scholars debate to what extent different animals have self-awareness or even consciousness, which may dictate our treatment of them. Regardless of the philosophical approach to invertebrates, information and education about their lives are critical to an understanding of how humans ought to treat them.

  17. Zebra mussel effects on benthic invertebrates: physical or biotic?

    USGS Publications Warehouse

    Botts, P. Silver; Patterson, Benjamin A.; Schloesser, Don W.

    1996-01-01

    In soft sediments, Dreissena spp. create firm substrate in the form of aggregates of living mussels (druses) that roll free on the sediments. Druses provide physical structure which increases habitat heterogeneity, and the mussels increase benthic organic matter through the production of pseudofeces and feces. Descriptive and experimental studies were used to determine: 1) whether the density of benthic invertebrates in soft sediments increased in the presence of druses, and 2) whether the invertebrate assemblage responded to the physical structure provided by a druse or to some biotic effect associated with the presence of living mussels. In core samples collected biweekly during summer in Presque Isle Bay, Erie, Pennsylvania, amphipods, chironomids, oligochaetes, turbellarians, and hydrozoans were significantly more abundant in sand with druses than in bare sand. When mesh bags containing either a living druse, non-living druse, or no druse were incubated in the bay for 33 d, we found that chironomids were significantly more abundant in treatments with living druses than with non-living druses, and in treatments with non-living druses than with no druse; turbellarians, amphipods, and hydrozoans were significantly more abundant in treatments with living or non-living druses than with no druse; oligochaetes showed no significant differences among treatments. This study demonstrates that most taxa of benthic invertebrates in soft substrate respond specifically to the physical structure associated with aggregates of mussel shells, but further study is needed to examine chironomid responses to some biotic effect dependent on the presence of living mussels.

  18. Improved ultrastructure of marine invertebrates using non-toxic buffers.

    PubMed

    Montanaro, Jacqueline; Gruber, Daniela; Leisch, Nikolaus

    2016-01-01

    Many marine biology studies depend on field work on ships or remote sampling locations where sophisticated sample preservation techniques (e.g., high-pressure freezing) are often limited or unavailable. Our aim was to optimize the ultrastructural preservation of marine invertebrates, especially when working in the field. To achieve chemically-fixed material of the highest quality, we compared the resulting ultrastructure of gill tissue of the mussel Mytilus edulis when fixed with differently buffered EM fixatives for marine specimens (seawater, cacodylate and phosphate buffer) and a new fixative formulation with the non-toxic PHEM buffer (PIPES, HEPES, EGTA and MgCl2). All buffers were adapted for immersion fixation to form an isotonic fixative in combination with 2.5% glutaraldehyde. We showed that PHEM buffer based fixatives resulted in equal or better ultrastructure preservation when directly compared to routine standard fixatives. These results were also reproducible when extending the PHEM buffered fixative to the fixation of additional different marine invertebrate species, which also displayed excellent ultrastructural detail. We highly recommend the usage of PHEM-buffered fixation for the fixation of marine invertebrates. PMID:27069800

  19. The ecotoxicological significance of genotoxicity in marine invertebrates.

    PubMed

    Depledge, M H

    1998-03-13

    Attention is drawn to the goals of genetic ecotoxicology, in particular, the need to relate genotoxicity in individuals to population and community level consequences. The evidence for pollutant-induced genotoxicity in marine invertebrates is reviewed. Neoplasia is apparently rare in marine invertebrates and only limited evidence is available to suggest that chemical genotoxins act as causative agents. It is unknown why marine invertebrates exhibit low tumour incidences and are much more tolerant of ionising radiation than their vertebrate counterparts. The importance of the genotoxic disease syndrome is highlighted. Disentangling phenotypic manifestations of genotoxic damage and that due to direct metabolic toxicity provides a major challenge for the future. Further work is required to assess the significance of interspecific and interindividual variability in susceptibility to genotoxicity, especially with regard to the evolution of resistant populations and communities of marine organisms at contaminated sites. Only by addressing the issues highlighted above can proper risk assessments of genotoxic agents be performed to minimise threats to human and ecosystem health.

  20. The invertebrate ecology of the Chalk aquifer in England (UK)

    NASA Astrophysics Data System (ADS)

    Maurice, L.; Robertson, A. R.; White, D.; Knight, L.; Johns, T.; Edwards, F.; Arietti, M.; Sorensen, J. P. R.; Weitowitz, D.; Marchant, B. P.; Bloomfield, J. P.

    2016-03-01

    The Chalk is an important water supply aquifer, yet ecosystems within it remain poorly understood. Boreholes (198) in seven areas of England (UK) were sampled to determine the importance of the Chalk aquifer as a habitat, and to improve understanding of how species are distributed. Stygobitic macro-invertebrates were remarkably common, and were recorded in 67 % of boreholes in unconcealed Chalk, although they were not recorded in Chalk that is concealed by low-permeability strata and thus likely to be confined. Most species were found in shallow boreholes (<21 m) and boreholes with deep (>50 m) water tables, indicating that the habitat is vertically extensive. Stygobites were present in more boreholes in southern England than northern England (77 % compared to 38 %). Only two species were found in northern England compared to six in southern England, but overall seven of the eight stygobitic macro-invertebrate species found in England were detected in the Chalk. Two species are common in southern England, but absent from northern England despite the presence of a continuous habitat prior to the Devensian glaciation. This suggests that either they did not survive glaciations in the north where glaciers were more extensive, or dispersal rates are slow and they have never colonised northern England. Subsurface ecosystems comprising aquatic macro-invertebrates and meiofauna, as well as the microbial organisms they interact with, are likely to be widespread in the Chalk aquifer. They represent an important contribution to biodiversity, and may influence biogeochemical cycles and provide other ecosystem services.

  1. Mucin-Type O-Glycosylation in Invertebrates.

    PubMed

    Staudacher, Erika

    2015-06-09

    O-Glycosylation is one of the most important posttranslational modifications of proteins. It takes part in protein conformation, protein sorting, developmental processes and the modulation of enzymatic activities. In vertebrates, the basics of the biosynthetic pathway of O-glycans are already well understood. However, the regulation of the processes and the molecular aspects of defects, especially in correlation with cancer or developmental abnormalities, are still under investigation. The knowledge of the correlating invertebrate systems and evolutionary aspects of these highly conserved biosynthetic events may help improve the understanding of the regulatory factors of this pathway. Invertebrates display a broad spectrum of glycosylation varieties, providing an enormous potential for glycan modifications which may be used for the design of new pharmaceutically active substances. Here, overviews of the present knowledge of invertebrate mucin-type O-glycan structures and the currently identified enzymes responsible for the biosynthesis of these oligosaccharides are presented, and the few data dealing with functional aspects of O-glycans are summarised.

  2. RUNX factors in development: lessons from invertebrate model systems.

    PubMed

    Braun, Toby; Woollard, Alison

    2009-01-01

    Runt-related (RUNX) transcription factors are evolutionarily conserved regulators of cell proliferation, differentiation and stem cell maintenance. They are critical for the correct development and function of a variety of human tissues, including during haematopoiesis. RUNX genes regulate various aspects of proliferation control, stem cell maintenance, lineage commitment and regulation of differentiation; disruptions in the correct function of RUNX genes have been associated with human pathologies, most prominently cancer. Because of the high context dependency and partial redundancy of vertebrate RUNX genes, invertebrate model systems have been studied in the hope of finding an ancestral function. Here we review the progress of these studies in three invertebrate systems, the fruit fly Drosophila melanogaster, the sea urchin Strongylocentrotus purpuratus and the nematode Caenorhabditis elegans. All essential aspects of RUNX function in vertebrates have counterparts in invertebrates, confirming the usefulness of these studies in simpler organisms. The fact that not all RUNX functions are conserved in all systems, though, underscores the importance of choosing the right model to ask specific questions. PMID:19447650

  3. The distribution of dimethylsulfoniopropionate in tropical Pacific coral reef invertebrates

    NASA Astrophysics Data System (ADS)

    van Alstyne, Kathryn L.; Schupp, Peter; Slattery, Marc

    2006-08-01

    Dimethylsulfoniopropionate (DMSP) is an important component of the global sulfur cycle and may be involved, via its cleavage product dimethylsulfide, in climate regulation. Although it is common in many algae, reports of DMSP in animals, particularly tropical invertebrates, are limited. This study examined the distribution of DMSP in a diverse group of coral reef invertebrates. DMSP was present in all 22 species of cnidarians and ranged from 9 to 723 μmol g-1 of dry mass (DM) with a mean (± 1SD) of 110 ± 180 μmol g-1 DM. It was not detected in a flatworm and an ascidian or in two of five sponges. Concentrations in sponges ranged from undetectable to 16 μmol g-1 DM with a mean of 4 ± 7 μmol g-1 DM. Within the cnidarians, DMSP concentrations did not differ among orders. Among cnidarian species, DMSP concentrations were correlated with symbiotic zooxanthellae densities. Within cnidarian species, DMSP concentrations of individuals were positively correlated with zooxanthellae densities in three of the four species examined. We speculate that DMSP is dietarily derived in sponges and derived from zooxanthellae in the cnidarians. The functions of DMSP in coral reef invertebrates are not known.

  4. Improved ultrastructure of marine invertebrates using non-toxic buffers

    PubMed Central

    Montanaro, Jacqueline; Gruber, Daniela

    2016-01-01

    Many marine biology studies depend on field work on ships or remote sampling locations where sophisticated sample preservation techniques (e.g., high-pressure freezing) are often limited or unavailable. Our aim was to optimize the ultrastructural preservation of marine invertebrates, especially when working in the field. To achieve chemically-fixed material of the highest quality, we compared the resulting ultrastructure of gill tissue of the mussel Mytilus edulis when fixed with differently buffered EM fixatives for marine specimens (seawater, cacodylate and phosphate buffer) and a new fixative formulation with the non-toxic PHEM buffer (PIPES, HEPES, EGTA and MgCl2). All buffers were adapted for immersion fixation to form an isotonic fixative in combination with 2.5% glutaraldehyde. We showed that PHEM buffer based fixatives resulted in equal or better ultrastructure preservation when directly compared to routine standard fixatives. These results were also reproducible when extending the PHEM buffered fixative to the fixation of additional different marine invertebrate species, which also displayed excellent ultrastructural detail. We highly recommend the usage of PHEM-buffered fixation for the fixation of marine invertebrates. PMID:27069800

  5. The DNA virus Invertebrate iridescent virus 6 is a target of the Drosophila RNAi machinery.

    PubMed

    Bronkhorst, Alfred W; van Cleef, Koen W R; Vodovar, Nicolas; Ince, Ikbal Agah; Blanc, Hervé; Vlak, Just M; Saleh, Maria-Carla; van Rij, Ronald P

    2012-12-18

    RNA viruses in insects are targets of an RNA interference (RNAi)-based antiviral immune response, in which viral replication intermediates or viral dsRNA genomes are processed by Dicer-2 (Dcr-2) into viral small interfering RNAs (vsiRNAs). Whether dsDNA virus infections are controlled by the RNAi pathway remains to be determined. Here, we analyzed the role of RNAi in DNA virus infection using Drosophila melanogaster infected with Invertebrate iridescent virus 6 (IIV-6) as a model. We show that Dcr-2 and Argonaute-2 mutant flies are more sensitive to virus infection, suggesting that vsiRNAs contribute to the control of DNA virus infection. Indeed, small RNA sequencing of IIV-6-infected WT and RNAi mutant flies identified abundant vsiRNAs that were produced in a Dcr-2-dependent manner. We observed a highly uneven distribution with strong clustering of vsiRNAs to small defined regions (hotspots) and modest coverage at other regions (coldspots). vsiRNAs mapped in similar proportions to both strands of the viral genome, suggesting that long dsRNA derived from convergent overlapping transcripts serves as a substrate for Dcr-2. In agreement, strand-specific RT-PCR and Northern blot analyses indicated that antisense transcripts are produced during infection. Moreover, we show that vsiRNAs are functional in silencing reporter constructs carrying fragments of the IIV-6 genome. Together, our data indicate that RNAi provides antiviral defense against dsDNA viruses in animals. Thus, RNAi is the predominant antiviral defense mechanism in insects that provides protection against all major classes of viruses. PMID:23151511

  6. Three-dimensional visualisation of developmental stages of an apicomplexan fish blood parasite in its invertebrate host

    PubMed Central

    2011-01-01

    Background Although widely used in medicine, the application of three-dimensional (3D) imaging to parasitology appears limited to date. In this study, developmental stages of a marine fish haemogregarine, Haemogregarina curvata (Apicomplexa: Adeleorina), were investigated in their leech vector, Zeylanicobdella arugamensis; this involved 3D visualisation of brightfield and confocal microscopy images of histological sections through infected leech salivary gland cells. Findings 3D assessment demonstrated the morphology of the haemogregarine stages, their spatial layout, and their relationship with enlarged host cells showing reduced cellular content. Haemogregarine meronts, located marginally within leech salivary gland cells, had small tail-like connections to the host cell limiting membrane; this parasite-host cell interface was not visible in two-dimensional (2D) light micrographs and no records of a similar connection in apicomplexan development have been traced. Conclusions This is likely the first account of the use of 3D visualisation to study developmental stages of an apicomplexan parasite in its invertebrate vector. Elucidation of the extent of development of the haemogregarine within the leech salivary cells, together with the unusual connections between meronts and the host cell membrane, illustrates the future potential of 3D visualisation in parasite-vector biology. PMID:22107751

  7. Bloch vector projection noise

    NASA Technical Reports Server (NTRS)

    Wang, Li-Jun; Bacon, A. M.; Zhao, H.-Z.; Thomas, J. E.

    1994-01-01

    In the optical measurement of the Bloch vector components describing a system of N two-level atoms, the quantum fluctuations in these components are coupled into the measuring optical field. This paper develops the quantum theory of optical measurement of Bloch vector projection noise. The preparation and probing of coherence in an effective two-level system consisting of the two ground states in an atomic three-level lambda-scheme are analyzed.

  8. Poynting-vector filter

    SciTech Connect

    Carrigan, Charles R.

    2011-08-02

    A determination is made of frequency components associated with a particular bearing or location resulting from sources emitting electromagnetic-wave energy for which a Poynting-Vector can be defined. The broadband frequency components associated with a specific direction or location of interest are isolated from other components in the power spectrum that are not associated with the direction or location of interest. The collection of pointing vectors can be used to characterize the source.

  9. Matrotrophy and placentation in invertebrates: a new paradigm.

    PubMed

    Ostrovsky, Andrew N; Lidgard, Scott; Gordon, Dennis P; Schwaha, Thomas; Genikhovich, Grigory; Ereskovsky, Alexander V

    2016-08-01

    Matrotrophy, the continuous extra-vitelline supply of nutrients from the parent to the progeny during gestation, is one of the masterpieces of nature, contributing to offspring fitness and often correlated with evolutionary diversification. The most elaborate form of matrotrophy-placentotrophy-is well known for its broad occurrence among vertebrates, but the comparative distribution and structural diversity of matrotrophic expression among invertebrates is wanting. In the first comprehensive analysis of matrotrophy across the animal kingdom, we report that regardless of the degree of expression, it is established or inferred in at least 21 of 34 animal phyla, significantly exceeding previous accounts and changing the old paradigm that these phenomena are infrequent among invertebrates. In 10 phyla, matrotrophy is represented by only one or a few species, whereas in 11 it is either not uncommon or widespread and even pervasive. Among invertebrate phyla, Platyhelminthes, Arthropoda and Bryozoa dominate, with 162, 83 and 53 partly or wholly matrotrophic families, respectively. In comparison, Chordata has more than 220 families that include or consist entirely of matrotrophic species. We analysed the distribution of reproductive patterns among and within invertebrate phyla using recently published molecular phylogenies: matrotrophy has seemingly evolved at least 140 times in all major superclades: Parazoa and Eumetazoa, Radiata and Bilateria, Protostomia and Deuterostomia, Lophotrochozoa and Ecdysozoa. In Cycliophora and some Digenea, it may have evolved twice in the same life cycle. The provisioning of developing young is associated with almost all known types of incubation chambers, with matrotrophic viviparity more widespread (20 phyla) than brooding (10 phyla). In nine phyla, both matrotrophic incubation types are present. Matrotrophy is expressed in five nutritive modes, of which histotrophy and placentotrophy are most prevalent. Oophagy, embryophagy and

  10. Matrotrophy and placentation in invertebrates: a new paradigm.

    PubMed

    Ostrovsky, Andrew N; Lidgard, Scott; Gordon, Dennis P; Schwaha, Thomas; Genikhovich, Grigory; Ereskovsky, Alexander V

    2016-08-01

    Matrotrophy, the continuous extra-vitelline supply of nutrients from the parent to the progeny during gestation, is one of the masterpieces of nature, contributing to offspring fitness and often correlated with evolutionary diversification. The most elaborate form of matrotrophy-placentotrophy-is well known for its broad occurrence among vertebrates, but the comparative distribution and structural diversity of matrotrophic expression among invertebrates is wanting. In the first comprehensive analysis of matrotrophy across the animal kingdom, we report that regardless of the degree of expression, it is established or inferred in at least 21 of 34 animal phyla, significantly exceeding previous accounts and changing the old paradigm that these phenomena are infrequent among invertebrates. In 10 phyla, matrotrophy is represented by only one or a few species, whereas in 11 it is either not uncommon or widespread and even pervasive. Among invertebrate phyla, Platyhelminthes, Arthropoda and Bryozoa dominate, with 162, 83 and 53 partly or wholly matrotrophic families, respectively. In comparison, Chordata has more than 220 families that include or consist entirely of matrotrophic species. We analysed the distribution of reproductive patterns among and within invertebrate phyla using recently published molecular phylogenies: matrotrophy has seemingly evolved at least 140 times in all major superclades: Parazoa and Eumetazoa, Radiata and Bilateria, Protostomia and Deuterostomia, Lophotrochozoa and Ecdysozoa. In Cycliophora and some Digenea, it may have evolved twice in the same life cycle. The provisioning of developing young is associated with almost all known types of incubation chambers, with matrotrophic viviparity more widespread (20 phyla) than brooding (10 phyla). In nine phyla, both matrotrophic incubation types are present. Matrotrophy is expressed in five nutritive modes, of which histotrophy and placentotrophy are most prevalent. Oophagy, embryophagy and

  11. RNAi in Arthropods: Insight into the Machinery and Applications for Understanding the Pathogen-Vector Interface

    PubMed Central

    Barnard, Annette-Christi; Nijhof, Ard M.; Fick, Wilma; Stutzer, Christian; Maritz-Olivier, Christine

    2012-01-01

    The availability of genome sequencing data in combination with knowledge of expressed genes via transcriptome and proteome data has greatly advanced our understanding of arthropod vectors of disease. Not only have we gained insight into vector biology, but also into their respective vector-pathogen interactions. By combining the strengths of postgenomic databases and reverse genetic approaches such as RNAi, the numbers of available drug and vaccine targets, as well as number of transgenes for subsequent transgenic or paratransgenic approaches, have expanded. These are now paving the way for in-field control strategies of vectors and their pathogens. Basic scientific questions, such as understanding the basic components of the vector RNAi machinery, is vital, as this allows for the transfer of basic RNAi machinery components into RNAi-deficient vectors, thereby expanding the genetic toolbox of these RNAi-deficient vectors and pathogens. In this review, we focus on the current knowledge of arthropod vector RNAi machinery and the impact of RNAi on understanding vector biology and vector-pathogen interactions for which vector genomic data is available on VectorBase. PMID:24705082

  12. Syngeneic AAV pseudo-vectors potentiates full vector transduction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An excessive amount of empty capsids are generated during regular AAV vector production process. These pseudo-vectors often remain in final vectors used for animal studies or clinical trials. The potential effects of these pseudo-vectors on AAV transduction have been a major concern. In the current ...

  13. Concurrent micro-RNA mediated silencing of tick-borne flavivirus replication in tick vector and in the brain of vertebrate host

    PubMed Central

    Tsetsarkin, Konstantin A.; Liu, Guangping; Kenney, Heather; Hermance, Meghan; Thangamani, Saravanan; Pletnev, Alexander G.

    2016-01-01

    Tick-borne viruses include medically important zoonotic pathogens that can cause life-threatening diseases. Unlike mosquito-borne viruses, whose impact can be restrained via mosquito population control programs, for tick-borne viruses only vaccination remains the reliable means of disease prevention. For live vaccine viruses a concern exists, that spillovers from viremic vaccinees could result in introduction of genetically modified viruses into sustainable tick-vertebrate host transmission cycle in nature. To restrict tick-borne flavivirus (Langat virus, LGTV) vector tropism, we inserted target sequences for tick-specific microRNAs (mir-1, mir-275 and mir-279) individually or in combination into several distant regions of LGTV genome. This caused selective attenuation of viral replication in tick-derived cells. LGTV expressing combinations of target sequences for tick- and vertebrate CNS-specific miRNAs were developed. The resulting viruses replicated efficiently and remained stable in simian Vero cells, which do not express these miRNAs, however were severely restricted to replicate in tick-derived cells. In addition, simultaneous dual miRNA targeting led to silencing of virus replication in live Ixodes ricinus ticks and abolished virus neurotropism in highly permissive newborn mice. The concurrent restriction of adverse replication events in vertebrate and invertebrate hosts will, therefore, ensure the environmental safety of live tick-borne virus vaccine candidates. PMID:27620807

  14. Concurrent micro-RNA mediated silencing of tick-borne flavivirus replication in tick vector and in the brain of vertebrate host.

    PubMed

    Tsetsarkin, Konstantin A; Liu, Guangping; Kenney, Heather; Hermance, Meghan; Thangamani, Saravanan; Pletnev, Alexander G

    2016-01-01

    Tick-borne viruses include medically important zoonotic pathogens that can cause life-threatening diseases. Unlike mosquito-borne viruses, whose impact can be restrained via mosquito population control programs, for tick-borne viruses only vaccination remains the reliable means of disease prevention. For live vaccine viruses a concern exists, that spillovers from viremic vaccinees could result in introduction of genetically modified viruses into sustainable tick-vertebrate host transmission cycle in nature. To restrict tick-borne flavivirus (Langat virus, LGTV) vector tropism, we inserted target sequences for tick-specific microRNAs (mir-1, mir-275 and mir-279) individually or in combination into several distant regions of LGTV genome. This caused selective attenuation of viral replication in tick-derived cells. LGTV expressing combinations of target sequences for tick- and vertebrate CNS-specific miRNAs were developed. The resulting viruses replicated efficiently and remained stable in simian Vero cells, which do not express these miRNAs, however were severely restricted to replicate in tick-derived cells. In addition, simultaneous dual miRNA targeting led to silencing of virus replication in live Ixodes ricinus ticks and abolished virus neurotropism in highly permissive newborn mice. The concurrent restriction of adverse replication events in vertebrate and invertebrate hosts will, therefore, ensure the environmental safety of live tick-borne virus vaccine candidates. PMID:27620807

  15. Vector and Axial Vector Pion Form Factors

    NASA Astrophysics Data System (ADS)

    Vitz, Michael; PEN Collaboration

    2015-04-01

    Radiative pion decay π+ -->e+ νγ (RPD) provides critical input to chiral perturbation theory (χPT). Aside from the uninteresting ``inner bremsstrahlung'' contribution from QED, the RPD rate contains ``structure dependent'' terms given by FV and FA, the vector and axial-vector pion form factors, respectively. The two appear in the decay rate in combinations FV -FA and FV +FA , i.e., in the so-called SD- and SD+ terms, respectively. The latter has been measured to high precision by the PIBETA collaboration. We report on the analysis of new data, measured by the PEN collaboration in runs between 2008 and 2010 at the Paul Scherrer Institute, Switzerland. We particularly focus on the possibility of improvement in the determination of the SD- term. Precise determinations of FV and FA test the validity of the CVC hypothesis, provide numerical input for the l9 +l10 terms in the χPT lagrangian, and constrain potential non-(V - A) terms, such as a possible tensor term FT. NSF grants PHY-0970013, 1307328, and others.

  16. Bunyavirus-vector interactions.

    PubMed

    Beaty, B J; Bishop, D H

    1988-06-01

    Recent advances in the genetics and molecular biology of bunyaviruses have been applied to understanding bunyavirus-vector interactions. Such approaches have revealed which virus gene and gene products are important in establishing infections in vectors and in transmission of viruses. However, much more information is required to understand the molecular mechanisms of persistent infections of vectors which are lifelong but apparently exert no untoward effect. In fact, it seems remarkable that LAC viral antigen can be detected in almost every cell in an ovarian follicle, yet no untoward effect on fecundity and no teratology is seen. Similarly the lifelong infection of the vector would seem to provide ample opportunity for bunyavirus evolution by genetic drift and, under the appropriate circumstances, by segment reassortment. The potential for bunyavirus evolution by segment reassortment in vectors certainly exists. For example the Group C viruses in a small forest in Brazil seem to constitute a gene pool, with the 6 viruses related alternately by HI/NT and CF reactions, which assay respectively M RNA and S RNA gene products (Casals and Whitman, 1960; Shope and Causey, 1962). Direct evidence for naturally occurring reassortant bunyaviruses has also been obtained. Oligonucleotide fingerprint analyses of field isolates of LAC virus and members of the Patois serogroup of bunyaviruses have demonstrated that reassortment does occur in nature (El Said et al., 1979; Klimas et al., 1981; Ushijima et al., 1981). Determination of the genotypic frequencies of viruses selected by the biological interactions of viruses and vectors after dual infection and segment reassortment is an important issue. Should a virus result that efficiently interacts with alternate vector species, the virus could be expressed in different circumstances with serious epidemiologic consequences. Dual infection of vectors with different viruses is not unlikely, because many bunyaviruses are sympatric in

  17. Lentiviral Vectors and Cystic Fibrosis Gene Therapy

    PubMed Central

    Castellani, Stefano; Conese, Massimo

    2010-01-01

    Cystic fibrosis (CF) is a chronic autosomic recessive syndrome, caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene, a chloride channel expressed on the apical side of the airway epithelial cells. The lack of CFTR activity brings a dysregulated exchange of ions and water through the airway epithelium, one of the main aspects of CF lung disease pathophysiology. Lentiviral (LV) vectors, of the Retroviridae family, show interesting properties for CF gene therapy, since they integrate into the host genome and allow long-lasting gene expression. Proof-of-principle that LV vectors can transduce the airway epithelium and correct the basic electrophysiological defect in CF mice has been given. Initial data also demonstrate that LV vectors can be repeatedly administered to the lung and do not give rise to a gross inflammatory process, although they can elicit a T cell-mediated response to the transgene. Future studies will clarify the efficacy and safety profile of LV vectors in new complex animal models with CF, such as ferrets and pigs. PMID:21994643

  18. Detection of Biochemical Pathways by Probabilistic Matching of Phyletic Vectors

    PubMed Central

    Li, Hua; Kristensen, David M.; Coleman, Michael K.; Mushegian, Arcady

    2009-01-01

    A phyletic vector, also known as a phyletic (or phylogenetic) pattern, is a binary representation of the presences and absences of orthologous genes in different genomes. Joint occurrence of two or more genes in many genomes results in closely similar binary vectors representing these genes, and this similarity between gene vectors may be used as a measure of functional association between genes. Better understanding of quantitative properties of gene co-occurrences is needed for systematic studies of gene function and evolution. We used the probabilistic iterative algorithm Psi-square to find groups of similar phyletic vectors. An extended Psi-square algorithm, in which pseudocounts are implemented, shows better sensitivity in identifying proteins with known functional links than our earlier hierarchical clustering approach. At the same time, the specificity of inferring functional associations between genes in prokaryotic genomes is strongly dependent on the pathway: phyletic vectors of the genes involved in energy metabolism and in de novo biosynthesis of the essential precursors tend to be lumped together, whereas cellular modules involved in secretion, motility, assembly of cell surfaces, biosynthesis of some coenzymes, and utilization of secondary carbon sources tend to be identified with much greater specificity. It appears that the network of gene coinheritance in prokaryotes contains a giant connected component that encompasses most biosynthetic subsystems, along with a series of more independent modules involved in cell interaction with the environment. PMID:19390636

  19. Observations on the history of non-insect invertebrate pathology from the perspective of a participant.

    PubMed

    Sparks, Albert K

    2005-05-01

    This paper discusses diseases of commercially important non-insect invertebrates from both a historical and a personal perspective. Early studies of curious scientists such as Metchnikoff using invertebrate systems led to important discoveries with much wider impact. As commercial culture of oysters, shrimp, and other invertebrates grew, so did studies of their diseases. Here, the impact of pioneering scientists and important new techniques on our understanding of these diseases is described.

  20. [Effects of invertebrate bioturbation on vertical hydraulic conductivity of streambed for a river].

    PubMed

    Ren, Chao-Liang; Song, Jin-Xi; Yang, Xiao-Gang; Xue, Jian

    2013-11-01

    Streambed hydraulic conductivity is a key factor influencing water exchange between surface water and groundwater. However, the streambed invertebrate bioturbation has a great effect on the hydraulic conductivity. In order to determine the impact of invertebrate bioturbation on streambed hydraulic conductivity, the investigation of invertebrate bioturbation and in-situ test of vertical hydraulic conductivity of streambed are simultaneously conducted at five points along the main stream of the Weihe River. Firstly, correlation between the streambed vertical hydraulic conductivity and grain size distribution is analyzed. Secondly, type and density of the invertebrate and their correlation to hydraulic conductivity are determined. Finally, the effect of invertebrate bioturbation on the streambed hydraulic conductivity is illustrated. The results show that the vertical hydraulic conductivity and biological density of invertebrate are 18.479 m x d(-1) and 139 ind x m(-2), respectively for the Caotan site, where sediment composition with a large amount of sand and gravel particles. For Meixian site, the sediment constitutes a large amount of silt and clay particles, in which the vertical hydraulic conductivity and biological density of invertebrate are 2.807 m x d(-1) and 2 742 ind x m(-2) respectively. Besides, for the low permeability of four sites (Meixian, Xianyang, Lintong and Huaxian), grain size particles are similar while the vertical hydraulic conductivity and biological density of invertebrate are significantly different from one site to another. However, for each site, the vertical hydraulic conductivity closely related to biological density of invertebrate, the Pearson correlation coefficient is 0.987. It can be concluded that both grain size particles and invertebrate bioturbation influence sediment permeability. For example, higher values of streambed hydraulic conductivity from strong permeability site mainly due to the large amount of large-size particles

  1. Vector financial rogue waves

    NASA Astrophysics Data System (ADS)

    Yan, Zhenya

    2011-11-01

    The coupled nonlinear volatility and option pricing model presented recently by Ivancevic is investigated, which generates a leverage effect, i.e., stock volatility is (negatively) correlated to stock returns, and can be regarded as a coupled nonlinear wave alternative of the Black-Scholes option pricing model. In this Letter, we analytically propose vector financial rogue waves of the coupled nonlinear volatility and option pricing model without an embedded w-learning. Moreover, we exhibit their dynamical behaviors for chosen different parameters. The vector financial rogue wave (rogon) solutions may be used to describe the possible physical mechanisms for the rogue wave phenomena and to further excite the possibility of relative researches and potential applications of vector rogue waves in the financial markets and other related fields.

  2. Vectorized garbage collection

    SciTech Connect

    Appel, A.W.; Bendiksen, A.

    1988-01-01

    Garbage collection can be done in vector mode on supercomputers like the Cray-2 and the Cyber 205. Both copying collection and mark-and-sweep can be expressed as breadth-first searches in which the queue can be processed in parallel. The authors have designed a copying garbage collector whose inner loop works entirely in vector mode. The only significant limitation of the algorithm is that if the size of the records is not constant, the implementation becomes much more complicated. The authors give performance measurements of the algorithm as implemented for Lisp CONS cells on the Cyber 205. Vector-mode garbage collection performs up to 9 times faster than scalar-mode collection.

  3. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.

    PubMed

    Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

    2014-12-19

    Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.

  4. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.

    PubMed

    Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

    2014-01-01

    Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. PMID:25523484

  5. Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera.

    PubMed

    Lal, Monal M; Southgate, Paul C; Jerry, Dean R; Zenger, Kyall R

    2016-02-01

    Population genomic investigations on highly dispersive marine organisms typically require thousands of genome-wide SNP loci to resolve fine-scale population structure and detect signatures of selection. This information is important for species conservation efforts and stock management in both wild and captive populations, as well as genome mapping and genome wide association studies. Double digest Restriction site-Associated DNA Sequencing (ddRADseq) is a recent tool for delivering genome wide SNPs for non-model organisms. However, its application to marine invertebrate taxa has been limited, particularly given the complex and highly repetitive nature of many of these organisms' genomes. This study develops and evaluates an optimised ddRADseq technique together with associated analyses for generating genome-wide SNP data, and performs population genomic analyses to inform aquaculture and fishery management of a marine bivalve, the black-lip pearl oyster Pinctada margaritifera. A total of 5243 high-quality genome-wide SNP markers were detected, and used to assess population structure, genome diversity, detect Fst outliers and perform association testing in 156 individuals belonging to three wild and one hatchery produced populations from the Fiji Islands. Shallow but significant population structure was revealed among all wild populations (average pairwise Fst=0.046) when visualised with DAPC and an individual network analysis (NetView P), with clear evidence of a genetic bottleneck in the hatchery population (NeLD=6.1), compared to wild populations (NeLD>192.5). Fst outlier detection revealed 42-62 highly differentiated SNPs (p<0.02), while case-control association discovered up to 152 SNPs (p<0.001). Both analyses were able to successfully differentiate individuals between the orange and black tissue colour morphotypes characteristic of this species. BLAST searches revealed that five of these SNPs were associated with a melanin biosynthesis pathway, demonstrating

  6. Hemichordate genomes and deuterostome origins.

    PubMed

    Simakov, Oleg; Kawashima, Takeshi; Marlétaz, Ferdinand; Jenkins, Jerry; Koyanagi, Ryo; Mitros, Therese; Hisata, Kanako; Bredeson, Jessen; Shoguchi, Eiichi; Gyoja, Fuki; Yue, Jia-Xing; Chen, Yi-Chih; Freeman, Robert M; Sasaki, Akane; Hikosaka-Katayama, Tomoe; Sato, Atsuko; Fujie, Manabu; Baughman, Kenneth W; Levine, Judith; Gonzalez, Paul; Cameron, Christopher; Fritzenwanker, Jens H; Pani, Ariel M; Goto, Hiroki; Kanda, Miyuki; Arakaki, Nana; Yamasaki, Shinichi; Qu, Jiaxin; Cree, Andrew; Ding, Yan; Dinh, Huyen H; Dugan, Shannon; Holder, Michael; Jhangiani, Shalini N; Kovar, Christie L; Lee, Sandra L; Lewis, Lora R; Morton, Donna; Nazareth, Lynne V; Okwuonu, Geoffrey; Santibanez, Jireh; Chen, Rui; Richards, Stephen; Muzny, Donna M; Gillis, Andrew; Peshkin, Leonid; Wu, Michael; Humphreys, Tom; Su, Yi-Hsien; Putnam, Nicholas H; Schmutz, Jeremy; Fujiyama, Asao; Yu, Jr-Kai; Tagawa, Kunifumi; Worley, Kim C; Gibbs, Richard A; Kirschner, Marc W; Lowe, Christopher J; Satoh, Noriyuki; Rokhsar, Daniel S; Gerhart, John

    2015-11-26

    Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor. PMID:26580012

  7. Hemichordate genomes and deuterostome origins

    PubMed Central

    Simakov, Oleg; Kawashima, Takeshi; Marlétaz, Ferdinand; Jenkins, Jerry; Koyanagi, Ryo; Mitros, Therese; Hisata, Kanako; Bredeson, Jessen; Shoguchi, Eiichi; Gyoja, Fuki; Yue, Jia-Xing; Chen, Yi-Chih; Freeman, Robert M.; Sasaki, Akane; Hikosaka-Katayama, Tomoe; Sato, Atsuko; Fujie, Manabu; Baughman, Kenneth W.; Levine, Judith; Gonzalez, Paul; Cameron, Christopher; Fritzenwanker, Jens H.; Pani, Ariel M.; Goto, Hiroki; Kanda, Miyuki; Arakaki, Nana; Yamasaki, Shinichi; Qu, Jiaxin; Cree, Andrew; Ding, Yan; Dinh, Huyen H.; Dugan, Shannon; Holder, Michael; Jhangiani, Shalini N.; Kovar, Christie L.; Lee, Sandra L.; Lewis, Lora R.; Morton, Donna; Nazareth, Lynne V.; Okwuonu, Geoffrey; Santibanez, Jireh; Chen, Rui; Richards, Stephen; Muzny, Donna M.; Gillis, Andrew; Peshkin, Leonid; Wu, Michael; Humphreys, Tom; Su, Yi-Hsien; Putnam, Nicholas H.; Schmutz, Jeremy; Fujiyama, Asao; Yu, Jr-Kai; Tagawa, Kunifumi; Worley, Kim C.; Gibbs, Richard A.; Kirschner, Marc W.; Lowe, Christopher J.; Satoh, Noriyuki; Rokhsar, Daniel S.; Gerhart, John

    2015-01-01

    Acorn worms, also known as enteropneust (literally, ‘gut-breathing’) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal ‘gill’ slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor. PMID:26580012

  8. The occurrence of chitin in the hemocytes of invertebrates

    PubMed Central

    Heath-Heckman, Elizabeth A.C.; McFall-Ngai, Margaret J.

    2011-01-01

    The light-organ symbiosis of Euprymna scolopes, the Hawaiian bobtail squid, is a useful model for the study of animal–microbe interactions. Recent analyses have demonstrated that chitin breakdown products play a role in communication between E. scolopes and its bacterial symbiont Vibrio fischeri. In this study, we sought to determine the source of chitin in the symbiotic organ. We used a commercially available chitin-binding protein (CBP) conjugated to fluorescein to label the polymeric chitin in host tissues. Confocal microscopy revealed that the only cells in contact with the symbionts that labeled with the probe were the macrophage-like hemocytes, which traffic into the light-organ crypts where the bacteria reside. Labeling of extracted hemocytes by CBP was markedly decreased following treatment with purified chitinase, providing further evidence that the labeled molecule is polymeric chitin. Further, CBP-positive areas co-localized with both a halide peroxidase antibody and Lysotracker, a lysosomal marker, suggesting that the chitin-like biomolecule occurs in the lysosome or acidic vacuoles. Reverse transcriptase polymerase chain reaction (PCR) of hemocytes revealed mRNA coding for a chitin synthase, suggesting that the hemocytes synthesize chitin de novo. Finally, upon surveying blood cells from other invertebrate species, we observed CBP-positive regions in all granular blood cells examined, suggesting that this feature is a shared character among the invertebrates; the vertebrate blood cells that we sampled did not label with CBP. Although the function of the chitin-like material remains undetermined, its presence and subcellular location in invertebrate hemocytes suggests a conserved role for this polysaccharide in the immune system of diverse animals. PMID:21723107

  9. Macro-invertebrate decline in surface water polluted with imidacloprid.

    PubMed

    Van Dijk, Tessa C; Van Staalduinen, Marja A; Van der Sluijs, Jeroen P

    2013-01-01

    Imidacloprid is one of the most widely used insecticides in the world. Its concentration in surface water exceeds the water quality norms in many parts of the Netherlands. Several studies have demonstrated harmful effects of this neonicotinoid to a wide range of non-target species. Therefore we expected that surface water pollution with imidacloprid would negatively impact aquatic ecosystems. Availability of extensive monitoring data on the abundance of aquatic macro-invertebrate species, and on imidacloprid concentrations in surface water in the Netherlands enabled us to test this hypothesis. Our regression analysis showed a significant negative relationship (P<0.001) between macro-invertebrate abundance and imidacloprid concentration for all species pooled. A significant negative relationship was also found for the orders Amphipoda, Basommatophora, Diptera, Ephemeroptera and Isopoda, and for several species separately. The order Odonata had a negative relationship very close to the significance threshold of 0.05 (P = 0.051). However, in accordance with previous research, a positive relationship was found for the order Actinedida. We used the monitoring field data to test whether the existing three water quality norms for imidacloprid in the Netherlands are protective in real conditions. Our data show that macrofauna abundance drops sharply between 13 and 67 ng l(-1). For aquatic ecosystem protection, two of the norms are not protective at all while the strictest norm of 13 ng l(-1) (MTR) seems somewhat protective. In addition to the existing experimental evidence on the negative effects of imidacloprid on invertebrate life, our study, based on data from large-scale field monitoring during multiple years, shows that serious concern about the far-reaching consequences of the abundant use of imidacloprid for aquatic ecosystems is justified.

  10. A database of lotic invertebrate traits for North America

    USGS Publications Warehouse

    Vieira, Nicole K.M.; Poff, N. LeRoy; Carlisle, Daren M.; Moulton, Stephen R.; Koski, Marci L.; Kondratieff, Boris C.

    2006-01-01

    The assessment and study of stream communities may be enhanced if functional characteristics such as life-history, habitat preference, and reproductive strategy were more widely available for specific taxa. Species traits can be used to develop these functional indicators because many traits directly link functional roles of organisms with controlling environmental factors (for example, flow, substratum, temperature). In addition, some functional traits may not be constrained by taxonomy and are thus applicable at multiple spatial scales. Unfortunately, a comprehensive summary of traits for North American invertebrate taxa does not exist. Consequently, the U.S. Geological Survey's National Water-Quality Assessment Program in cooperation with Colorado State University compiled a database of traits for North American invertebrates. A total of 14,127 records for over 2,200 species, 1,165 genera, and 249 families have been entered into the database from 967 publications, texts and reports. Quality-assurance procedures indicated error rates of less than 3 percent in the data entry process. Species trait information was most complete for insect taxa. Traits describing resource acquisition and habitat preferences were most frequently reported, whereas those describing physiological tolerances and reproductive biology were the least frequently reported in the literature. The database is not exhaustive of the literature for North American invertebrates and is biased towards aquatic insects, but it represents a first attempt to compile traits in a web-accessible database. This report describes the database and discusses important decisions necessary for identifying ecologically relevant, environmentally sensitive, non-redundant, and statistically tractable traits for use in bioassessment programs.

  11. Macro-Invertebrate Decline in Surface Water Polluted with Imidacloprid

    PubMed Central

    Van Dijk, Tessa C.; Van Staalduinen, Marja A.; Van der Sluijs, Jeroen P.

    2013-01-01

    Imidacloprid is one of the most widely used insecticides in the world. Its concentration in surface water exceeds the water quality norms in many parts of the Netherlands. Several studies have demonstrated harmful effects of this neonicotinoid to a wide range of non-target species. Therefore we expected that surface water pollution with imidacloprid would negatively impact aquatic ecosystems. Availability of extensive monitoring data on the abundance of aquatic macro-invertebrate species, and on imidacloprid concentrations in surface water in the Netherlands enabled us to test this hypothesis. Our regression analysis showed a significant negative relationship (P<0.001) between macro-invertebrate abundance and imidacloprid concentration for all species pooled. A significant negative relationship was also found for the orders Amphipoda, Basommatophora, Diptera, Ephemeroptera and Isopoda, and for several species separately. The order Odonata had a negative relationship very close to the significance threshold of 0.05 (P = 0.051). However, in accordance with previous research, a positive relationship was found for the order Actinedida. We used the monitoring field data to test whether the existing three water quality norms for imidacloprid in the Netherlands are protective in real conditions. Our data show that macrofauna abundance drops sharply between 13 and 67 ng l−1. For aquatic ecosystem protection, two of the norms are not protective at all while the strictest norm of 13 ng l−1 (MTR) seems somewhat protective. In addition to the existing experimental evidence on the negative effects of imidacloprid on invertebrate life, our study, based on data from large-scale field monitoring during multiple years, shows that serious concern about the far-reaching consequences of the abundant use of imidacloprid for aquatic ecosystems is justified. PMID:23650513

  12. Statistical models to evaluate invertebrate-plant trophic interactions in arable systems.

    PubMed

    Bohan, D A; Hawes, C; Haughton, A J; Denholm, I; Champion, G T; Perry, J N; Clark, S J

    2007-06-01

    Over the past 40 years there have been marked shifts in arable farmland management that are widely believed to have had a considerable impact on flowering plants and invertebrates and the small mammals and birds that rely upon them. It is not yet possible to predict the dynamics of plants and invertebrates either with past or future changes in farmland management. This study investigates whether a basic invertebrate classification, formed of broad trophic groups, can be used to describe interactions between invertebrates and their resource plants and evaluate management impacts for genetically modified, herbicide-tolerant (GMHT) and conventional herbicide management in both spring- and winter-sown oilseed rape. It is argued that the analyses validate trophic-based approaches for describing the dynamics of invertebrates in farmland and that linear models might be used to describe the changes in invertebrate trophic group abundance in farmland when driven by primary producer abundance or biomass and interactions between invertebrates themselves. The analyses indicate that invertebrate dynamics under GMHT management are not unique, but similar to conventional management occurring over different resource ranges, and that dynamics differed considerably between spring- and winter-sown oilseed rape. Thus, herbicide management was of much lower impact on trophic relationships than sowing date. Results indicate that invertebrate dynamics in oilseed rape are regulated by a combination of top-down and bottom-up trophic processes.

  13. Bunyavirus-Vector Interactions

    PubMed Central

    Horne, Kate McElroy; Vanlandingham, Dana L.

    2014-01-01

    The Bunyaviridae family is comprised of more than 350 viruses, of which many within the Hantavirus, Orthobunyavirus, Nairovirus, Tospovirus, and Phlebovirus genera are significant human or agricultural pathogens. The viruses within the Orthobunyavirus, Nairovirus, and Phlebovirus genera are transmitted by hematophagous arthropods, such as mosquitoes, midges, flies, and ticks, and their associated arthropods not only serve as vectors but also as virus reservoirs in many cases. This review presents an overview of several important emerging or re-emerging bunyaviruses and describes what is known about bunyavirus-vector interactions based on epidemiological, ultrastructural, and genetic studies of members of this virus family. PMID:25402172

  14. The use of chromatin insulators to improve the expression and safety of integrating gene transfer vectors.

    PubMed

    Emery, David W

    2011-06-01

    The therapeutic application of recombinant retroviruses and other integrating gene transfer vectors has been limited by problems of vector expression and vector-mediated genotoxicity. These problems arise in large part from the interactions between vector sequences and the genomic environment surrounding sites of integration. Strides have been made in overcoming both of these problems through the modification of deleterious vector sequences, the inclusion of better enhancers and promoters, and the use of alternative virus systems. However, these modifications often add other restrictions on vector design, which in turn can further limit therapeutic applications. As an alternative, several groups have been investigating a class of DNA regulatory elements known as chromatin insulators. These elements provide a means of blocking the interaction between an integrating vector and the target cell genome in a manner that is independent of the vector transgene, regulatory elements, or virus of origin. This review outlines the background, rationale, and evidence for using chromatin insulators to improve the expression and safety of gene transfer vectors. Also reviewed are topological factors that constrain the use of insulators in integrating gene transfer vectors, alternative sources of insulators, and the role of chromatin insulators as one of several components for optimal vector design.

  15. MAR characteristic motifs mediate episomal vector in CHO cells.

    PubMed

    Lin, Yan; Li, Zhaoxi; Wang, Tianyun; Wang, Xiaoyin; Wang, Li; Dong, Weihua; Jing, Changqin; Yang, Xianjun

    2015-04-01

    An ideal gene therapy vector should enable persistent transgene expression without limitations in safety and reproducibility. Recent researches' insight into the ability of chromosomal matrix attachment regions (MARs) to mediate episomal maintenance of genetic elements allowed the development of a circular episomal vector. Although a MAR-mediated engineered vector has been developed, little is known on which motifs of MAR confer this function during interaction with the host genome. Here, we report an artificially synthesized DNA fragment containing only characteristic motif sequences that served as an alternative to human beta-interferon matrix attachment region sequence. The potential of the vector to mediate gene transfer in CHO cells was investigated. The short synthetic MAR motifs were found to mediate episomal vector at a low copy number for many generations without integration into the host genome. Higher transgene expression was maintained for at least 4 months. In addition, MAR was maintained episomally and conferred sustained EGFP expression even in nonselective CHO cells. All the results demonstrated that MAR characteristic sequence-based vector can function as stable episomes in CHO cells, supporting long-term and effective transgene expression.

  16. Pentachlorophenol Hazards to Fish, Wildlife, and Invertebrates: A Synoptic Review

    USGS Publications Warehouse

    Eisler, R.

    1989-01-01

    Pentachlorophenol (PCP) is now widely used as a wood preservative, and this has contributed to the detection of PCP residues in air, rain, groundwaters, surface waters, fish and aquatic invertebrates, and in human urine, blood, and milk of nursing mothers. This report briefly reviews the technical literature on ecological and toxicological aspects of PCP in the environment, with emphasis on fishery and wildlife resources. Subtopics include sources and uses, chemical properties, fate, background concentrations, lethal and sublethal effects, and current recommendations for resource protection

  17. Nickel Hazards to Fish, Wildlife and Invertebrates: A Synoptic Review

    USGS Publications Warehouse

    Eisler, R.

    1998-01-01

    This account is a selective review and synthesis of the technical literature on nickel and nickel salts in the environment and their effects on terrestrial plants and invertebrates, aquatic plants and animals, avian and mammalian wildlife, and other natural resources, The subtopics include nickel sources and uses; physical, chemical, and metabolic properties of nickel; nickel concentrations in field collections of abiotic materials and living organisms; nickel deficiency effects; lethal and sublethal effects, including effects on survival, growth, reproduction, metabolism, mutagenicity, teratogenicity, and carcinogenicity; currently proposed nickel criteria for the protection of human health and sensitive natural resources; and recommendations for additional research.

  18. Recent Advances in Drug Discovery from South African Marine Invertebrates.

    PubMed

    Davies-Coleman, Michael T; Veale, Clinton G L

    2015-10-01

    Recent developments in marine drug discovery from three South African marine invertebrates, the tube worm Cephalodiscus gilchristi, the ascidian Lissoclinum sp. and the sponge Topsentia pachastrelloides, are presented. Recent reports of the bioactivity and synthesis of the anti-cancer secondary metabolites cephalostatin and mandelalides (from C. gilchristi and Lissoclinum sp., respectively) and various analogues are presented. The threat of drug-resistant pathogens, e.g., methicillin-resistant Staphylococcus aureus (MRSA), is assuming greater global significance, and medicinal chemistry strategies to exploit the potent MRSA PK inhibition, first revealed by two marine secondary metabolites, cis-3,4-dihydrohamacanthin B and bromodeoxytopsentin from T. pachastrelloides, are compared. PMID:26473891

  19. [Venomous and poisonous animals. V. Envenomations by venomous marine invertebrates].

    PubMed

    Bédry, R; de Haro, L

    2007-06-01

    Epidemiological information about marine envenomation is generally less extensive in Europe than in tropical countries where this type of injury is more severe and the need for medical attention is more frequent. For this reason use of the regional poison control centers in the areas where envenomation occurs must be encouraged. The purpose of this review is to describe envenomation by poisonous marine invertebrates (cephalopods, sea urchins, cone shells, jellyfish, anemones, star-fish, corals, and worms). Understanding of these envenomation syndromes is important not only in tropical areas but also in Europe where importation of dangerous species has increased in recent years.

  20. Recent Advances in Drug Discovery from South African Marine Invertebrates

    PubMed Central

    Davies-Coleman, Michael T.; Veale, Clinton G. L.

    2015-01-01

    Recent developments in marine drug discovery from three South African marine invertebrates, the tube worm Cephalodiscus gilchristi, the ascidian Lissoclinum sp. and the sponge Topsentia pachastrelloides, are presented. Recent reports of the bioactivity and synthesis of the anti-cancer secondary metabolites cephalostatin and mandelalides (from C. gilchristi and Lissoclinum sp., respectively) and various analogues are presented. The threat of drug-resistant pathogens, e.g., methicillin-resistant Staphylococcus aureus (MRSA), is assuming greater global significance, and medicinal chemistry strategies to exploit the potent MRSA PK inhibition, first revealed by two marine secondary metabolites, cis-3,4-dihydrohamacanthin B and bromodeoxytopsentin from T. pachastrelloides, are compared. PMID:26473891

  1. Alice in microbes' land: adaptations and counter-adaptations of vector-borne parasitic protozoa and their hosts.

    PubMed

    Caljon, Guy; De Muylder, Géraldine; Durnez, Lies; Jennes, Wim; Vanaerschot, Manu; Dujardin, Jean-Claude

    2016-09-01

    In the present review, we aim to provide a general introduction to different facets of the arms race between pathogens and their hosts/environment, emphasizing its evolutionary aspects. We focus on vector-borne parasitic protozoa, which have to adapt to both invertebrate and vertebrate hosts. Using Leishmania, Trypanosoma and Plasmodium as main models, we review successively (i) the adaptations and counter-adaptations of parasites and their invertebrate host, (ii) the adaptations and counter-adaptations of parasites and their vertebrate host and (iii) the impact of human interventions (chemotherapy, vaccination, vector control and environmental changes) on these adaptations. We conclude by discussing the practical impact this knowledge can have on translational research and public health. PMID:27400870

  2. Alice in microbes' land: adaptations and counter-adaptations of vector-borne parasitic protozoa and their hosts.

    PubMed

    Caljon, Guy; De Muylder, Géraldine; Durnez, Lies; Jennes, Wim; Vanaerschot, Manu; Dujardin, Jean-Claude

    2016-09-01

    In the present review, we aim to provide a general introduction to different facets of the arms race between pathogens and their hosts/environment, emphasizing its evolutionary aspects. We focus on vector-borne parasitic protozoa, which have to adapt to both invertebrate and vertebrate hosts. Using Leishmania, Trypanosoma and Plasmodium as main models, we review successively (i) the adaptations and counter-adaptations of parasites and their invertebrate host, (ii) the adaptations and counter-adaptations of parasites and their vertebrate host and (iii) the impact of human interventions (chemotherapy, vaccination, vector control and environmental changes) on these adaptations. We conclude by discussing the practical impact this knowledge can have on translational research and public health.

  3. Brevibacillus laterosporus, a Pathogen of Invertebrates and a Broad-Spectrum Antimicrobial Species

    PubMed Central

    Ruiu, Luca

    2013-01-01

    Brevibacillus laterosporus, a bacterium characterized by the production of a unique canoe-shaped lamellar body attached to one side of the spore, is a natural inhabitant of water, soil and insects. Its biopesticidal potential has been reported against insects in different orders including Coleoptera, Lepidoptera, Diptera and against nematodes and mollusks. In addition to its pathogenicity against invertebrates, different B. laterosporus strains show a broad-spectrum antimicrobial activity including activity against phytopathogenic bacteria and fungi. A wide variety of molecules, including proteins and antibiotics, have been associated with the observed pathogenicity and mode of action. Before being considered as a biological control agent against plant pathogens, the antifungal and antibacterial properties of certain B. laterosporus strains have found medical interest, associated with the production of antibiotics with therapeutic effects. The recent whole genome sequencing of this species revealed its potential to produce polyketides, nonribosomal peptides, and toxins. Another field of growing interest is the use of this bacterium for bioremediation of contaminated sites by exploiting its biodegradation properties. The aim of the present review is to gather and discuss all recent findings on this emerging entomopathogen, giving a wider picture of its complex and broad-spectrum biocontrol activity. PMID:26462431

  4. Hierarchical population genetic structure in a direct developing antarctic marine invertebrate.

    PubMed

    Hoffman, Joseph I; Clarke, Andrew; Clark, Melody S; Peck, Lloyd S

    2013-01-01

    Understanding the relationship between life-history variation and population structure in marine invertebrates is not straightforward. This is particularly true of polar species due to the difficulty of obtaining samples and a paucity of genomic resources from which to develop nuclear genetic markers. Such knowledge, however, is essential for understanding how different taxa may respond to climate change in the most rapidly warming regions of the planet. We therefore used over two hundred polymorphic Amplified Fragment Length Polymorphisms (AFLPs) to explore population connectivity at three hierachical spatial scales in the direct developing Antarctic topshell Margarella antarctica. To previously published data from five populations spanning a 1500 km transect along the length of the Western Antarctic Peninsula, we added new AFLP data for four populations separated by up to 6 km within Ryder Bay, Adelaide Island. Overall, we found a nonlinear isolation-by-distance pattern, suggestive of weaker population structure within Ryder Bay than is present over larger spatial scales. Nevertheless, significantly positive F st values were obtained in all but two of ten pairwise population comparisons within the bay following Bonferroni correction for multiple tests. This is in contrast to a previous study of the broadcast spawner Nacella concinna that found no significant genetic differences among several of the same sites. By implication, the topshell's direct-developing lifestyle may constrain its ability to disperse even over relatively small geographic scales.

  5. The Evolution and Variety of RFamide-Type Neuropeptides: Insights from Deuterostomian Invertebrates

    PubMed Central

    Elphick, Maurice R.; Mirabeau, Olivier

    2014-01-01

    Five families of neuropeptides that have a C-terminal RFamide motif have been identified in vertebrates: (1) gonadotropin-inhibitory hormone (GnIH), (2) neuropeptide FF (NPFF), (3) pyroglutamylated RFamide peptide (QRFP), (4) prolactin-releasing peptide (PrRP), and (5) Kisspeptin. Experimental demonstration of neuropeptide–receptor pairings combined with comprehensive analysis of genomic and/or transcriptomic sequence data indicate that, with the exception of the deuterostomian PrRP system, the evolutionary origins of these neuropeptides can be traced back to the common ancestor of bilaterians. Here, we review the occurrence of homologs of vertebrate RFamide-type neuropeptides and their receptors in deuterostomian invertebrates – urochordates, cephalochordates, hemichordates, and echinoderms. Extending analysis of the occurrence of the RFamide motif in other bilaterian neuropeptide families reveals RFamide-type peptides that have acquired modified C-terminal characteristics in the vertebrate lineage (e.g., NPY/NPF), neuropeptide families where the RFamide motif is unique to protostomian members (e.g., CCK/sulfakinins), and RFamide-type peptides that have been lost in the vertebrate lineage (e.g., luqins). Furthermore, the RFamide motif is also a feature of neuropeptide families with a more restricted phylogenetic distribution (e.g., the prototypical FMRFamide-related neuropeptides in protostomes). Thus, the RFamide motif is both an ancient and a convergent feature of neuropeptides, with conservation, acquisition, or loss of this motif occurring in different branches of the animal kingdom. PMID:24994999

  6. Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing.

    PubMed

    Kapranov, Philipp; Chen, Lingxia; Dederich, Debra; Dong, Biao; He, Jie; Steinmann, Kathleen E; Moore, Andrea R; Thompson, John F; Milos, Patrice M; Xiao, Weidong

    2012-01-01

    The single-stranded genome of adeno-associated viral (AAV) vectors is one of the key factors leading to slow-rising but long-term transgene expression kinetics. Previous molecular studies have established what is now considered a textbook molecular model of AAV genomes with two copies of inverted tandem repeats at either end. In this study, we profiled hundreds of thousands of individual molecules of AAV vector DNA directly isolated from capsids, using single-molecule sequencing (SMS), which avoids any intermediary steps such as plasmid cloning. The sequence profile at 3' ends of both the regular and oversized vector did show the presence of an inverted terminal repeat (ITR), which provided direct confirmation that AAV vector packaging initiates from its 3' end. Furthermore, the vector 5'-terminus profile showed inconsistent termination for oversized vectors. Such incomplete vectors would not be expected to undergo canonical synthesis of the second strand of their genomic DNA and thus could function only via annealing of complementary strands of DNA. Furthermore, low levels of contaminating plasmid DNA were also detected. SMS may become a valuable tool during the development phase of vectors that are candidates for clinical use and for facilitating/accelerating studies on vector biology. PMID:21875357

  7. Multigene Phylogenetics Reveals Temporal Diversification of Major African Malaria Vectors

    PubMed Central

    Kamali, Maryam; Marek, Paul E.; Peery, Ashley; Antonio-Nkondjio, Christophe; Ndo, Cyrille; Tu, Zhijian; Simard, Frederic; Sharakhov, Igor V.

    2014-01-01

    The major vectors of malaria in sub-Saharan Africa belong to subgenus Cellia. Yet, phylogenetic relationships and temporal diversification among African mosquito species have not been unambiguously determined. Knowledge about vector evolutionary history is crucial for correct interpretation of genetic changes identified through comparative genomics analyses. In this study, we estimated a molecular phylogeny using 49 gene sequences for the African malaria vectors An. gambiae, An. funestus, An. nili, the Asian malaria mosquito An. stephensi, and the outgroup species Culex quinquefasciatus and Aedes aegypti. To infer the phylogeny, we identified orthologous sequences uniformly distributed approximately every 5 Mb in the five chromosomal arms. The sequences were aligned and the phylogenetic trees were inferred using maximum likelihood and neighbor-joining methods. Bayesian molecular dating using a relaxed log normal model was used to infer divergence times. Trees from individual genes agreed with each other, placing An. nili as a basal clade that diversified from the studied malaria mosquito species 47.6 million years ago (mya). Other African malaria vectors originated more recently, and independently acquired traits related to vectorial capacity. The lineage leading to An. gambiae diverged 30.4 mya, while the African vector An. funestus and the Asian vector An. stephensi were the most closely related sister taxa that split 20.8 mya. These results were supported by consistently high bootstrap values in concatenated phylogenetic trees generated individually for each chromosomal arm. Genome-wide multigene phylogenetic analysis is a useful approach for discerning historic relationships among malaria vectors, providing a framework for the correct interpretation of genomic changes across species, and comprehending the evolutionary origins of this ubiquitous and deadly insect-borne disease. PMID:24705448

  8. Sequencing of a new target genome: the Pediculus humanus humanus (Phthiraptera: Pediculidae) genome project.

    PubMed

    Pittendrigh, B R; Clark, J M; Johnston, J S; Lee, S H; Romero-Severson, J; Dasch, G A

    2006-11-01

    The human body louse, Pediculus humanus humanus (L.), and the human head louse, Pediculus humanus capitis, belong to the hemimetabolous order Phthiraptera. The body louse is the primary vector that transmits the bacterial agents of louse-borne relapsing fever, trench fever, and epidemic typhus. The genomes of the bacterial causative agents of several of these aforementioned diseases have been sequenced. Thus, determining the body louse genome will enhance studies of host-vector-pathogen interactions. Although not important as a major disease vector, head lice are of major social concern. Resistance to traditional pesticides used to control head and body lice have developed. It is imperative that new molecular targets be discovered for the development of novel compounds to control these insects. No complete genome sequence exists for a hemimetabolous insect species primarily because hemimetabolous insects often have large (2000 Mb) to very large (up to 16,300 Mb) genomes. Fortuitously, we determined that the human body louse has one of the smallest genome sizes known in insects, suggesting it may be a suitable choice as a minimal hemimetabolous genome in which many genes have been eliminated during its adaptation to human parasitism. Because many louse species infest birds and mammals, the body louse genome-sequencing project will facilitate studies of their comparative genomics. A 6-8X coverage of the body louse genome, plus sequenced expressed sequence tags, should provide the entomological, evolutionary biology, medical, and public health communities with useful genetic information.

  9. Support vector machines

    NASA Technical Reports Server (NTRS)

    Garay, Michael J.; Mazzoni, Dominic; Davies, Roger; Wagstaff, Kiri

    2004-01-01

    Support Vector Machines (SVMs) are a type of supervised learning algorith,, other examples of which are Artificial Neural Networks (ANNs), Decision Trees, and Naive Bayesian Classifiers. Supervised learning algorithms are used to classify objects labled by a 'supervisor' - typically a human 'expert.'.

  10. Vector potential methods

    NASA Technical Reports Server (NTRS)

    Hafez, M.

    1989-01-01

    Vector potential and related methods, for the simulation of both inviscid and viscous flows over aerodynamic configurations, are briefly reviewed. The advantages and disadvantages of several formulations are discussed and alternate strategies are recommended. Scalar potential, modified potential, alternate formulations of Euler equations, least-squares formulation, variational principles, iterative techniques and related methods, and viscous flow simulation are discussed.

  11. Killing vectors and anisotropy

    SciTech Connect

    Krisch, J. P.; Glass, E. N.

    2009-08-15

    We consider an action that can generate fluids with three unequal stresses for metrics with a spacelike Killing vector. The parameters in the action are directly related to the stress anisotropies. The field equations following from the action are applied to an anisotropic cosmological expansion and an extension of the Gott-Hiscock cosmic string.

  12. Production of lentiviral vectors

    PubMed Central

    Merten, Otto-Wilhelm; Hebben, Matthias; Bovolenta, Chiara

    2016-01-01

    Lentiviral vectors (LV) have seen considerably increase in use as gene therapy vectors for the treatment of acquired and inherited diseases. This review presents the state of the art of the production of these vectors with particular emphasis on their large-scale production for clinical purposes. In contrast to oncoretroviral vectors, which are produced using stable producer cell lines, clinical-grade LV are in most of the cases produced by transient transfection of 293 or 293T cells grown in cell factories. However, more recent developments, also, tend to use hollow fiber reactor, suspension culture processes, and the implementation of stable producer cell lines. As is customary for the biotech industry, rather sophisticated downstream processing protocols have been established to remove any undesirable process-derived contaminant, such as plasmid or host cell DNA or host cell proteins. This review compares published large-scale production and purification processes of LV and presents their process performances. Furthermore, developments in the domain of stable cell lines and their way to the use of production vehicles of clinical material will be presented. PMID:27110581

  13. Gene transfer vector

    SciTech Connect

    Puhler, A.; Simon, R.

    1987-08-11

    A Tn-Mob vector is described comprising: (a) A replicon functional E. coli; and (b) A Tn-Mob element comprising a transposon containing (i) a functional selection marker, and (ii) a Mob-site and oriT located in a region of the transposon that is not essential to transposability.

  14. Redshifts and Killing vectors

    NASA Astrophysics Data System (ADS)

    Harvey, Alex; Schucking, Engelbert; Surowitz, Eugene J.

    2006-11-01

    Current approaches to physics stress the importance of conservation laws due to spacetime and internal symmetries. In special and general relativity the generators of these symmetries are known as Killing vectors. We use them for the rigorous determination of gravitational and cosmological redshifts.

  15. Vector-borne diseases.

    PubMed

    Gubler, D J

    2009-08-01

    Vector-borne diseases have been the scourge of man and animals since the beginning of time. Historically, these are the diseases that caused the great plagues such as the 'Black Death' in Europe in the 14th Century and the epidemics of yellow fever that plagued the development of the New World. Others, such as Nagana, contributed to the lack of development in Africa for many years. At the turn of the 20th Century, vector-borne diseases were among the most serious public and animal health problems in the world. For the most part, these diseases were controlled by the middle of the 20th Century through the application of knowledge about their natural history along with the judicious use of DDT (dichlorodiphenyltrichloroethane) and other residual insecticides to interrupt the transmission cycle between arthropod and vertebrate host. However, this success initiated a period of complacency in the 1960s and 1970s, which resulted in the redirection of resources away from prevention and control of vector-borne diseases. The 1970s was also a time in which there were major changes to public health policy. Global trends, combined with changes in animal husbandry, urbanisation, modern transportation and globalisation, have resulted in a global re-emergence of epidemic vector-borne diseases affecting both humans and animals over the past 30 years. PMID:20128467

  16. Vector-borne diseases.

    PubMed

    Gubler, D J

    2009-08-01

    Vector-borne diseases have been the scourge of man and animals since the beginning of time. Historically, these are the diseases that caused the great plagues such as the 'Black Death' in Europe in the 14th Century and the epidemics of yellow fever that plagued the development of the New World. Others, such as Nagana, contributed to the lack of development in Africa for many years. At the turn of the 20th Century, vector-borne diseases were among the most serious public and animal health problems in the world. For the most part, these diseases were controlled by the middle of the 20th Century through the application of knowledge about their natural history along with the judicious use of DDT (dichlorodiphenyltrichloroethane) and other residual insecticides to interrupt the transmission cycle between arthropod and vertebrate host. However, this success initiated a period of complacency in the 1960s and 1970s, which resulted in the redirection of resources away from prevention and control of vector-borne diseases. The 1970s was also a time in which there were major changes to public health policy. Global trends, combined with changes in animal husbandry, urbanisation, modern transportation and globalisation, have resulted in a global re-emergence of epidemic vector-borne diseases affecting both humans and animals over the past 30 years.

  17. Singular Vectors' Subtle Secrets

    ERIC Educational Resources Information Center

    James, David; Lachance, Michael; Remski, Joan

    2011-01-01

    Social scientists use adjacency tables to discover influence networks within and among groups. Building on work by Moler and Morrison, we use ordered pairs from the components of the first and second singular vectors of adjacency matrices as tools to distinguish these groups and to identify particularly strong or weak individuals.

  18. Vector-Borne Bacterial Plant Pathogens: Interactions with Hemipteran Insects and Plants.

    PubMed

    Perilla-Henao, Laura M; Casteel, Clare L

    2016-01-01

    Hemipteran insects are devastating pests of crops due to their wide host range, rapid reproduction, and ability to transmit numerous plant-infecting pathogens as vectors. While the field of plant-virus-vector interactions has flourished in recent years, plant-bacteria-vector interactions remain poorly understood. Leafhoppers and psyllids are by far the most important vectors of bacterial pathogens, yet there are still significant gaps in our understanding of their feeding behavior, salivary secretions, and plant responses as compared to important viral vectors, such as whiteflies and aphids. Even with an incomplete understanding of plant-bacteria-vector interactions, some common themes have emerged: (1) all known vector-borne bacteria share the ability to propagate in the plant and insect host; (2) particular hemipteran families appear to be incapable of transmitting vector-borne bacteria; (3) all known vector-borne bacteria have highly reduced genomes and coding capacity, resulting in host-dependence; and (4) vector-borne bacteria encode proteins that are essential for colonization of specific hosts, though only a few types of proteins have been investigated. Here, we review the current knowledge on important vector-borne bacterial pathogens, including Xylella fastidiosa, Spiroplasma spp., Liberibacter spp., and 'Candidatus Phytoplasma spp.'. We then highlight recent approaches used in the study of vector-borne bacteria. Finally, we discuss the application of this knowledge for control and future directions that will need to be addressed in the field of vector-plant-bacteria interactions.

  19. Vector-Borne Bacterial Plant Pathogens: Interactions with Hemipteran Insects and Plants.

    PubMed

    Perilla-Henao, Laura M; Casteel, Clare L

    2016-01-01

    Hemipteran insects are devastating pests of crops due to their wide host range, rapid reproduction, and ability to transmit numerous plant-infecting pathogens as vectors. While the field of plant-virus-vector interactions has flourished in recent years, plant-bacteria-vector interactions remain poorly understood. Leafhoppers and psyllids are by far the most important vectors of bacterial pathogens, yet there are still significant gaps in our understanding of their feeding behavior, salivary secretions, and plant responses as compared to important viral vectors, such as whiteflies and aphids. Even with an incomplete understanding of plant-bacteria-vector interactions, some common themes have emerged: (1) all known vector-borne bacteria share the ability to propagate in the plant and insect host; (2) particular hemipteran families appear to be incapable of transmitting vector-borne bacteria; (3) all known vector-borne bacteria have highly reduced genomes and coding capacity, resulting in host-dependence; and (4) vector-borne bacteria encode proteins that are essential for colonization of specific hosts, though only a few types of proteins have been investigated. Here, we review the current knowledge on important vector-borne bacterial pathogens, including Xylella fastidiosa, Spiroplasma spp., Liberibacter spp., and 'Candidatus Phytoplasma spp.'. We then highlight recent approaches used in the study of vector-borne bacteria. Finally, we discuss the application of this knowledge for control and future directions that will need to be addressed in the field of vector-plant-bacteria interactions. PMID:27555855

  20. Lichen physiological traits and growth forms affect communities of associated invertebrates.

    PubMed

    Bokhorst, Stef; Asplund, Johan; Kardol, Paul; Wardle, David A

    2015-09-01

    While there has been much interest in the relationships between traits of primary producers and composition of associated invertebrate consumer communities, our knowledge is largely based on studies from vascular plants, while other types of functionally important producers, such as lichens, have rarely been considered. To address how physiological traits of lichens drive community composition of invertebrates, we collected thalli from 27 lichen species from southern Norway and quantified the communities of associated springtails, mites, and nematodes. For each lichen species, we measured key physiological thallus traits and determined whether invertebrate communities were correlated with these traits. We also explored whether invertebrate communities differed among lichen groups, categorized according to nitrogen-fixing ability, growth form, and substratum. Lichen traits explained up to 39% of the variation in abundances of major invertebrate groups. For many invertebrate groups, abundance was positively correlated with lichen N and P concentrations, N:P ratio, and the percentage of water content on saturation (WC), but had few relationships with concentrations of carbon-based secondary compounds. Diversity and taxonomic richness of invertebrate groups were sometimes also correlated with lichen N and N:P ratios. Nitrogen-fixing lichens showed higher abundance and diversity of some invertebrate groups than did non-N-fixing lichens. However, this emerged in part because most N-fixing lichens have a foliose growth form that benefits invertebrates, through, improving the microclimate, independently of N concentration. Furthermore, invertebrate communities associated with terricolous lichens were determined more by their close proximity to the soil invertebrate pool than by lichen traits. Overall, our results reveal that differences between lichen species have a large impact on the invertebrate communities that live among the thalli. Different invertebrate groups show

  1. Lichen physiological traits and growth forms affect communities of associated invertebrates.

    PubMed

    Bokhorst, Stef; Asplund, Johan; Kardol, Paul; Wardle, David A

    2015-09-01

    While there has been much interest in the relationships between traits of primary producers and composition of associated invertebrate consumer communities, our knowledge is largely based on studies from vascular plants, while other types of functionally important producers, such as lichens, have rarely been considered. To address how physiological traits of lichens drive community composition of invertebrates, we collected thalli from 27 lichen species from southern Norway and quantified the communities of associated springtails, mites, and nematodes. For each lichen species, we measured key physiological thallus traits and determined whether invertebrate communities were correlated with these traits. We also explored whether invertebrate communities differed among lichen groups, categorized according to nitrogen-fixing ability, growth form, and substratum. Lichen traits explained up to 39% of the variation in abundances of major invertebrate groups. For many invertebrate groups, abundance was positively correlated with lichen N and P concentrations, N:P ratio, and the percentage of water content on saturation (WC), but had few relationships with concentrations of carbon-based secondary compounds. Diversity and taxonomic richness of invertebrate groups were sometimes also correlated with lichen N and N:P ratios. Nitrogen-fixing lichens showed higher abundance and diversity of some invertebrate groups than did non-N-fixing lichens. However, this emerged in part because most N-fixing lichens have a foliose growth form that benefits invertebrates, through, improving the microclimate, independently of N concentration. Furthermore, invertebrate communities associated with terricolous lichens were determined more by their close proximity to the soil invertebrate pool than by lichen traits. Overall, our results reveal that differences between lichen species have a large impact on the invertebrate communities that live among the thalli. Different invertebrate groups show

  2. The Invertebrate Life of New Zealand: A Phylogeographic Approach

    PubMed Central

    Trewick, Steven A.; Wallis, Graham P.; Morgan-Richards, Mary

    2011-01-01

    Phylogeography contributes to our knowledge of regional biotas by integrating spatial and genetic information. In New Zealand, comprising two main islands and hundreds of smaller ones, phylogeography has transformed the way we view our biology and allowed comparison with other parts of the world. Here we review studies on New Zealand terrestrial and freshwater invertebrates. We find little evidence of congruence among studies of different taxa; instead there are signatures of partitioning in many different regions and expansion in different directions. A number of studies have revealed unusually high genetic distances within putative species, and in those where other data confirm this taxonomy, the revealed phylogeographic structure contrasts with northern hemisphere continental systems. Some taxa show a signature indicative of Pliocene tectonic events encompassing land extension and mountain building, whereas others are consistent with range expansion following the last glacial maximum (LGM) of the Pleistocene. There is some indication that montane taxa are more partitioned than lowland ones, but this observation is obscured by a broad range of patterns within the sample of lowland/forest taxa. We note that several geophysical processes make similar phylogeographic predictions for the same landscape, rendering confirmation of the drivers of partitioning difficult. Future multi-gene analyses where applied to testable alternative hypotheses may help resolve further the rich evolutionary history of New Zealand's invertebrates. PMID:26467729

  3. Hidden treasures in stem cells of indeterminately growing bilaterian invertebrates.

    PubMed

    Vogt, Günter

    2012-06-01

    Indeterminate growth, the life-long growth without fixed limits, is typical of some evolutionarily very successful aquatic invertebrate groups such as the decapod crustaceans, bivalve molluscs and echinoderms. These animals enlarge their organs also in the adult life period and can regenerate lost appendages and organs, which is in sharp contrast to mammals and most insects. Interestingly, decapods, bivalves and echinoderms develop only rarely neoplastic and age-related diseases, although some species reach ages exceeding 100 years. Their stem cell systems must have co-evolved with these successful life histories suggesting possession of unknown and beneficial features that might open up new vistas in stem cell biology. Research of the last decade has identified several adult stem cell systems in these groups and also some mature cell types that are capable to dedifferentiate into multipotent progenitor cells. Investigation of stem and progenitor cells in indeterminately growing bilaterian invertebrates is assumed beneficial for basic stem cell biology, aquaculture, biotechnology and perhaps medicine. The biggest treasure that could be recovered in these animal taxa concerns maintenance of stem cell niches and fidelity of stem cell division for decades without undesirable side effects such as tumour formation. Uncovering of the underlying molecular and regulatory mechanisms might evoke new ideas for the development of anti-ageing and anti-cancer interventions in humans.

  4. Multifaceted roles of Furry proteins in invertebrates and vertebrates.

    PubMed

    Nagai, Tomoaki; Mizuno, Kensaku

    2014-03-01

    Furry (Fry) is a large protein that is evolutionarily conserved from yeast to human. Fry and its orthologues in invertebrates (termed Tao3p in budding yeast, Mor2p in fission yeast, Sax-2 in nematode and Fry in fruit fly) genetically and physically interact with nuclear Dbf2-related (NDR) kinases (termed Cbk1p in budding yeast, Orb6p in fission yeast, Sax-1 in nematode and Trc in fruitfly), and function as activators or scaffolds of these kinases. Fry-NDR kinase signals are implicated in the control of polarized cell growth and morphogenesis in yeast, neurite outgrowth in nematode, and epidermal morphogenesis and dendritic tiling in fruit fly. Recent studies revealed that mammalian Fry is a microtubule-associated protein that is involved in the control of chromosome alignment, spindle organization and Polo-like kinase-1 activation in mitosis, and promotes microtubule acetylation in mitotic spindles via inhibiting the tubulin deacetylase Sirtuin 2. Here, we review current knowledge about the diverse cellular functions and regulation of Fry proteins in invertebrates and vertebrates.

  5. Antimicrobial peptides in marine invertebrate health and disease.

    PubMed

    Destoumieux-Garzón, Delphine; Rosa, Rafael Diego; Schmitt, Paulina; Barreto, Cairé; Vidal-Dupiol, Jeremie; Mitta, Guillaume; Gueguen, Yannick; Bachère, Evelyne

    2016-05-26

    Aquaculture contributes more than one-third of the animal protein from marine sources worldwide. A significant proportion of aquaculture products are derived from marine protostomes that are commonly referred to as 'marine invertebrates'. Among them, penaeid shrimp (Ecdysozosoa, Arthropoda) and bivalve molluscs (Lophotrochozoa, Mollusca) are economically important. Mass rearing of arthropods and molluscs causes problems with pathogens in aquatic ecosystems that are exploited by humans. Remarkably, species of corals (Cnidaria) living in non-exploited ecosystems also suffer from devastating infectious diseases that display intriguing similarities with those affecting farmed animals. Infectious diseases affecting wild and farmed animals that are present in marine environments are predicted to increase in the future. This paper summarizes the role of the main pathogens and their interaction with host immunity, with a specific focus on antimicrobial peptides (AMPs) and pathogen resistance against AMPs. We provide a detailed review of penaeid shrimp AMPs and their role at the interface between the host and its resident/pathogenic microbiota. We also briefly describe the relevance of marine invertebrate AMPs in an applied context.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.

  6. Trophic transfer of pyrene metabolites between aquatic invertebrates.

    PubMed

    Carrasco Navarro, V; Leppänen, M T; Kukkonen, J V K; Godoy Olmos, S

    2013-02-01

    The trophic transfer of pyrene metabolites was studied using Gammarus setosus as a predator and the invertebrates Lumbriculus variegatus and Chironomus riparius as prey. The results obtained by liquid scintillation counting confirmed that the pyrene metabolites produced by the aquatic invertebrates L. variegatus and C. riparius were transferred to G. setosus through the diet. More detailed analyses by liquid chromatography discovered that two of the metabolites produced by C. riparius appeared in the chromatograms of G. setosus tissue extracts, proving their trophic transfer. These metabolites were not present in chromatograms of G. setosus exclusively exposed to pyrene. The present study supports the trophic transfer of PAH metabolites between benthic macroinvertebrates and common species of an arctic amphipod. As some PAH metabolites are more toxic than the parent compounds, the present study raises concerns about the consequences of their trophic transfer and the fate and effects of PAHs in natural environments. PMID:23202283

  7. Hydrologic variability enhances stream biofilm grazing by invertebrates

    NASA Astrophysics Data System (ADS)

    Ceola, S.; Hödl, I.; Adlboller, M.; Singer, G.; Bertuzzo, E.; Mari, L.; Botter, G.; Battin, T. J.; Gatto, M.; Rinaldo, A.

    2012-12-01

    The temporal variability of streamflows is a key feature structuring and controlling ecological communities and ecosystem processes. The magnitude, frequency and predictability of streamflows, and thus of velocity and near-bed shear stress fields, control structure and function of benthic invertebrates and biofilms - attached and matrix-enclosed microbial communities at the base of the food chain. Although alterations of streamflow regime due to climate change, habitat fragmentation or other anthropogenic factors are ubiquitous, their ecological implications remain poorly understood. Here, by experimenting with two contrasting flow regimes in stream microcosms, we show how flow variability affects invertebrate grazing of phototrophic biofilms (i.e. periphyton). In both flow regimes, we manipulated light availability as a key control on biofilm algal productivity and grazer activity, thereby allowing the test of flow regime effects across various biofilm biomass to grazing activity ratios. Average grazing rates were significantly enhanced under variable flow conditions and highest at intermediate light availability. Our results suggest that stochastic flow regime offers increased opportunity for grazing under more favorable shear stress conditions, with implications for trophic carbon transfer in stream food webs.

  8. Antimicrobial peptides in marine invertebrate health and disease.

    PubMed

    Destoumieux-Garzón, Delphine; Rosa, Rafael Diego; Schmitt, Paulina; Barreto, Cairé; Vidal-Dupiol, Jeremie; Mitta, Guillaume; Gueguen, Yannick; Bachère, Evelyne

    2016-05-26

    Aquaculture contributes more than one-third of the animal protein from marine sources worldwide. A significant proportion of aquaculture products are derived from marine protostomes that are commonly referred to as 'marine invertebrates'. Among them, penaeid shrimp (Ecdysozosoa, Arthropoda) and bivalve molluscs (Lophotrochozoa, Mollusca) are economically important. Mass rearing of arthropods and molluscs causes problems with pathogens in aquatic ecosystems that are exploited by humans. Remarkably, species of corals (Cnidaria) living in non-exploited ecosystems also suffer from devastating infectious diseases that display intriguing similarities with those affecting farmed animals. Infectious diseases affecting wild and farmed animals that are present in marine environments are predicted to increase in the future. This paper summarizes the role of the main pathogens and their interaction with host immunity, with a specific focus on antimicrobial peptides (AMPs) and pathogen resistance against AMPs. We provide a detailed review of penaeid shrimp AMPs and their role at the interface between the host and its resident/pathogenic microbiota. We also briefly describe the relevance of marine invertebrate AMPs in an applied context.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'. PMID:27160602

  9. Effects of copper on invertebrate-sediment interactions.

    PubMed

    Hunting, E R; Mulder, C; Kraak, M H S; Breure, A M; Admiraal, W

    2013-09-01

    Toxicants potentially decouple links between biodiversity and ecosystem processes. This study aimed to evaluate how toxicants affect invertebrate bioturbation and decomposition. Effects of copper on functionally distinct macrofaunal species (Asellus aquaticus and Tubifex spp.), decomposition (release of dissolved organic carbon, DOC) and Average Metabolic Response (AMR) and Community Metabolic Diversity (CMD) of bacteria were determined in 5-day microcosm experiments. Bioturbation was assessed as sediment redox potential (Eh) profiles. Concentration-response curves of the functional parameters DOC, and the faunal mediated AMR and CMD in the presence of Tubifex spp. depended on Tubifex spp. survival, i.e. similar EC50 values for both endpoints. In contrast, functional parameters in the presence of A. aquaticus were more sensitive than survival. Sediment Eh-profiles showed that reduced decomposition was caused by reduced sediment reworking by A. aquaticus at sub-lethal copper concentrations. These observations hint at a decoupling of invertebrate community structure and ecosystem functioning upon stress. PMID:23747821

  10. Toxicity of carbon nanotubes to freshwater aquatic invertebrates.

    PubMed

    Mwangi, Joseph N; Wang, Ning; Ingersoll, Christopher G; Hardesty, Doug K; Brunson, Eric L; Li, Hao; Deng, Baolin

    2012-08-01

    Carbon nanotubes (CNTs) are hydrophobic in nature and thus tend to accumulate in sediments if released into aquatic environments. As part of our overall effort to examine the toxicity of carbon-based nanomaterials to sediment-dwelling invertebrates, we have evaluated the toxicity of different types of CNTs in 14-d water-only exposures to an amphipod (Hyalella azteca), a midge (Chironomus dilutus), an oligochaete (Lumbriculus variegatus), and a mussel (Villosa iris) in advance of conducting whole-sediment toxicity tests with CNTs. The results of these toxicity tests conducted with CNTs added to water showed that 1.00 g/L (dry wt) of commercial sources of CNTs significantly reduced the survival or growth of the invertebrates. Toxicity was influenced by the type and source of the CNTs, by whether the materials were precleaned by acid, by whether sonication was used to disperse the materials, and by species of the test organisms. Light and electron microscope imaging of the surviving test organisms showed the presence of CNTs in the gut as well as on the outer surface of the test organisms, although no evidence was observed to show penetration of CNTs through cell membranes. The present study demonstrated that both the metals solubilized from CNTs such as nickel and the "metal-free" CNTs contributed to the toxicity.

  11. Homology and Convergence in Vertebrate and Invertebrate Nervous Systems

    NASA Astrophysics Data System (ADS)

    Sandeman, David

    Each year the meeting of the American Neuroscience Society attracts over 20,000 members, reflecting the explosion of interest in this field that has occurred over the past few decades. Researchers from many disciplines are focusing their skills on the investigation of every aspect of nervous systems, and neuroscience now encompasses the entire range of endeavour from the study of the single molecules that make up neural membranes to the non-invasive observation of neural function in animals behaving in their natural environments. Advances over the past three decades in our understanding of nervous systems are impressive and come from a multifaceted approach to the study of both vertebrate and invertebrate animals. An almost unexpected by-product of the parallel investigation of vertebrate and invertebrate nervous systems that is explored in this article is the emergent view of an intricate web of evolutionary homology and convergence exhibited in the structure and function of the nervous systems of these two large, paraphyletic groups of animals.

  12. Comparative ecotoxicity of chlorantraniliprole to non-target soil invertebrates.

    PubMed

    Lavtižar, Vesna; Berggren, Kristina; Trebše, Polonca; Kraak, Michiel H S; Verweij, Rudo A; van Gestel, Cornelis A M

    2016-09-01

    The insecticide chlorantraniliprole (CAP) is gaining importance in agricultural practice, but data on its possible negative effects on non-target organisms is severely deficient. This study therefore determined CAP toxicity to non-target soil invertebrates playing a crucial role in ecosystem functioning, including springtails (Folsomia candida), isopods (Porcellio scaber), enchytraeids (Enchytraeus crypticus) and oribatid mites (Oppia nitens). In sublethal toxicity tests in Lufa 2.2 soil, chronic exposure to CAP concentrations up to 1000 mg/kgdw did not affect the survival and reproduction of E. crypticus and O. nitens nor the survival, body weight and consumption of P. scaber. In contrast, the survival and reproduction of F. candida was severely affected, with an EC50 for effects on reproduction of 0.14 mg CAP/kgdw. The toxicity of CAP to the reproduction of F. candida was tested in four different soils following OECD guideline 232, and additionally in an avoidance test according to ISO guideline 17512-2. A significantly lower toxicity in soils rich in organic matter was observed, compared to low organic soils. Observations in the avoidance test with F. candida suggest that CAP acted in a prompt way, by affecting collembolan locomotor abilities thus preventing them from escaping contaminated soil. This study shows that CAP may especially pose a risk to non-target soil arthropods closely related to insects, while other soil invertebrates seem rather insensitive.

  13. Public versus personal information for mate copying in an invertebrate.

    PubMed

    Mery, Frédéric; Varela, Susana A M; Danchin, Etienne; Blanchet, Simon; Parejo, Deseada; Coolen, Isabelle; Wagner, Richard H

    2009-05-12

    Organisms require information to make decisions about fitness-affecting resources, such as mates. Animals may extract "personal information" about potential mates by observing their physical characteristics or extract additional "public information" by observing their mating performance [1]. Mate copying by females [2-6] is a form of public information use that may reduce uncertainty about male quality, allowing more adaptive choices [2]. Experimental studies have produced evidence that female mate copying occurs in several species of fish [3], birds [5-7], and mammals [8], including humans [9]. We report the first evidence that a female invertebrate can exploit public information to select mates. In a first experiment, Drosophila melanogaster female prospectors increased their time in the attraction zones of poor-condition males, but not of good-condition males, after having observed them with a model female. This suggests that females appraised prospective mates by exploiting public information and did so mainly when it contrasted with personal information. In a second experiment, prospector females preferably mated with males of the color type they had previously observed copulating over males of the rejected color type, suggesting that female Drosophila can generalize socially learned information. The complexity of Drosophila decision-making suggests an unprecedented level of cognition in invertebrates. Our findings have implications for evolution given that socially learned mate preferences may lead to reproductive isolation, setting the stage for speciation [10]. PMID:19361993

  14. Fertilization success in marine invertebrates: the influence of gamete age.

    PubMed

    Williams, Mark Elliott; Bentley, Matthew Graeme

    2002-02-01

    Gamete age has been postulated to be unimportant to the fertilization ecology of marine invertebrates. However, recent research suggests that, for some species at least, it may have a direct impact upon fertilization success. We present comparative data on the influence of gamete age on fertilization and development success in several marine invertebrates: the polychaetes Arenicola marina and Nereis virens and the asteroid echinoderm Asterias rubens. Oocytes are much longer lived in the polychaetes than in the echinoderm, with A. marina oocytes still capable of fertilizing and developing normally 96 h post-spawning. Developmental abnormalities and failure to reach blastula tend to occur well before the fertilizable life of the oocytes has expired. Sperm are similarly longer lived in the polychaetes; however, fertilizing capacity is markedly reduced following incubation in conspecific egg-conditioned seawater. These results are discussed in terms of the fertilization strategies of the three species. We further suggest that, for A. marina at least, longer-lived sperm and eggs are central to the fertilization strategy of this species.

  15. Comparative ecotoxicity of chlorantraniliprole to non-target soil invertebrates.

    PubMed

    Lavtižar, Vesna; Berggren, Kristina; Trebše, Polonca; Kraak, Michiel H S; Verweij, Rudo A; van Gestel, Cornelis A M

    2016-09-01

    The insecticide chlorantraniliprole (CAP) is gaining importance in agricultural practice, but data on its possible negative effects on non-target organisms is severely deficient. This study therefore determined CAP toxicity to non-target soil invertebrates playing a crucial role in ecosystem functioning, including springtails (Folsomia candida), isopods (Porcellio scaber), enchytraeids (Enchytraeus crypticus) and oribatid mites (Oppia nitens). In sublethal toxicity tests in Lufa 2.2 soil, chronic exposure to CAP concentrations up to 1000 mg/kgdw did not affect the survival and reproduction of E. crypticus and O. nitens nor the survival, body weight and consumption of P. scaber. In contrast, the survival and reproduction of F. candida was severely affected, with an EC50 for effects on reproduction of 0.14 mg CAP/kgdw. The toxicity of CAP to the reproduction of F. candida was tested in four different soils following OECD guideline 232, and additionally in an avoidance test according to ISO guideline 17512-2. A significantly lower toxicity in soils rich in organic matter was observed, compared to low organic soils. Observations in the avoidance test with F. candida suggest that CAP acted in a prompt way, by affecting collembolan locomotor abilities thus preventing them from escaping contaminated soil. This study shows that CAP may especially pose a risk to non-target soil arthropods closely related to insects, while other soil invertebrates seem rather insensitive. PMID:27337437

  16. Toxicity of carbon nanotubes to freshwater aquatic invertebrates

    USGS Publications Warehouse

    Mwangi, Joseph N.; Wang, Ning; Ingersoll, Christopher G.; Hardesty, Doug K.; Brunson, Eric L.; Li, Hao; Deng, Baolin

    2012-01-01

    Carbon nanotubes (CNTs) are hydrophobic in nature and thus tend to accumulate in sediments if released into aquatic environments. As part of our overall effort to examine the toxicity of carbon-based nanomaterials to sediment-dwelling invertebrates, we have evaluated the toxicity of different types of CNTs in 14-d water-only exposures to an amphipod (Hyalella azteca), a midge (Chironomus dilutus), an oligochaete (Lumbriculus variegatus), and a mussel (Villosa iris) in advance of conducting whole-sediment toxicity tests with CNTs. The results of these toxicity tests conducted with CNTs added to water showed that 1.00g/L (dry wt) of commercial sources of CNTs significantly reduced the survival or growth of the invertebrates. Toxicity was influenced by the type and source of the CNTs, by whether the materials were precleaned by acid, by whether sonication was used to disperse the materials, and by species of the test organisms. Light and electron microscope imaging of the surviving test organisms showed the presence of CNTs in the gut as well as on the outer surface of the test organisms, although no evidence was observed to show penetration of CNTs through cell membranes. The present study demonstrated that both the metals solubilized from CNTs such as nickel and the "metal-free" CNTs contributed to the toxicity.

  17. Stream invertebrate community functional responses to deposited sediment

    USGS Publications Warehouse

    Rabeni, C.F.; Doisy, K.E.; Zweig, L.D.

    2005-01-01

    We investigated functional responses of benthic invertebrates to deposited sediment in four Missouri USA streams. In each stream, invertebrates were sampled along continuums of deposited sediment (particles <2 mm in size) from 0 to 100% surface cover in reaches of fairly homogeneous substrate composition, current velocity, and water depths. Correlations, graphical representations, and the cumulative response curves of feeding and habit groups provided strong empirical support for distinct community functional changes due to deposited sediment. Feeding groups were more sensitive to deposited sediment than habit groups. Densities of all the feeding groups decreased significantly with increasing deposited sediment, while relative densities of gatherers increased significantly. Taxa richness also decreased significantly for all the feeding groups except for the shredders. Increases in deposited sediment were related to significant density decreases for only the clingers and sprawlers in the habit group, resulting in significant increases in the relative densities of both burrowers and climbers. Clingers, sprawlers, and swimmers also showed significant decreases in taxa richness. ?? Eawag, 2005.

  18. Lessons from Digestive-Tract Symbioses Between Bacteria and Invertebrates.

    PubMed

    Graf, Joerg

    2016-09-01

    In most animals, digestive tracts harbor the greatest number of bacteria in the animal that contribute to its health: by aiding in the digestion of nutrients, provisioning essential nutrients and protecting against colonization by pathogens. Invertebrates have been used to enhance our understanding of metabolic processes and microbe-host interactions owing to experimental advantages. This review describes how advances in DNA sequencing technologies have dramatically altered how researchers investigate microbe-host interactions, including 16S rRNA gene surveys, metagenome experiments, and metatranscriptome studies. Advantages and challenges of each of these approaches are described herein. Hypotheses generated through omics studies can be directly tested using site-directed mutagenesis, and findings from transposon studies and site-directed experiments are presented. Finally, unique structural aspects of invertebrate digestive tracts that contribute to symbiont specificity are presented. The combination of omics approaches with genetics and microscopy allows researchers to move beyond correlations to identify conserved mechanisms of microbe-host interactions. PMID:27482740

  19. Homology and convergence in vertebrate and invertebrate nervous systems.

    PubMed

    Sandeman, D

    1999-08-01

    Each year the meeting of the American Neuroscience Society attracts over 20,000 members, reflecting the explosion of interest in this field that has occurred over the past few decades. Researchers from many disciplines are focusing their skills on the investigation of every aspect of nervous systems, and neuroscience now encompasses the entire range of endeavour from the study of the single molecules that make up neural membranes to the non-invasive observation of neural function in animals behaving in their natural environments. Advances over the past three decades in our understanding of nervous systems are impressive and come from a multifaceted approach to the study of both vertebrate and invertebrate animals. An almost unexpected by-product of the parallel investigation of vertebrate and invertebrate nervous systems that is explored in this article is the emergent view of an intricate web of evolutionary homology and convergence exhibited in the structure and function of the nervous systems of these two large, paraphyletic groups of animals.

  20. Seasonal changes in the invertebrate community of granular activated carbon filters and control technologies.

    PubMed

    Wang, Qing; You, Wei; Li, Xiaowei; Yang, Yufeng; Liu, Lijun

    2014-03-15

    Invertebrate colonization of granular activated carbon (GAC) filters in the waterworks is one of the most frequently occurring and least studied biological problems of water processing in China. A survey of invertebrate colonization of GAC filters was carried out weekly from October 2010 to December 2011 at a reservoir water treatment works in South China. Twenty-six kinds of invertebrates were observed. The abundance was as high as 5600ind.m(-3) with a mean of 860ind.m(-3). Large variations in abundance were observed among different seasons and before and after GAC filtration. The dominant organisms were rotifers and copepods. The average invertebrate abundance in the filtrate was 12-18.7 times of that in the pre-filtered water. Results showed that the GAC filters were colonized by invertebrates which may lead to a higher output of organisms in the filtrate than in the pre-filtered water. The invertebrate abundance in the GAC filters was statistically correlated with the water temperature. Seasonal patterns were observed. The invertebrate abundance grew faster in the spring and summer. Copepods were dominant in the summer while rotifers dominated in all other seasons of the year. There was a transition of small invertebrates (rotifers) gradually being substituted by larger invertebrates (copepods) from spring to summer. Control measures such as backwashing with chloric water, drying filter beds and soaking with saliferous water were implemented in the waterworks to reduce invertebrate abundances in the GAC filters. The results showed that soaking with saliferous water (99%, reduction in percent) was best but drying the filter beds (84%) was more economical. Soaking filter beds with 20g/L saliferous water for one day can be implemented in case of emergency. In order to keep invertebrate abundance in the acceptable range, some of these measures should be adopted.

  1. Soil nutrient additions increase invertebrate herbivore abundances, but not herbivory, across three grassland systems.

    PubMed

    La Pierre, Kimberly J; Smith, Melinda D

    2016-02-01

    Resource availability may influence invertebrate communities, with important consequences for ecosystem function, such as biomass production. We assessed: (1) the effects of experimental soil nutrient additions on invertebrate abundances and feeding rates and (2) the resultant changes in the effects of invertebrates on aboveground plant biomass at three grassland sites spanning the North American Central Plains, across which plant tissue chemistry and biomass vary. Invertebrate communities and rates of herbivory were sampled within a long-term nutrient-addition experiment established at each site along the broad Central Plains precipitation gradient. Additionally, the effects of invertebrates on aboveground plant biomass were determined under ambient and elevated nutrient conditions. At the more mesic sites, invertebrate herbivore abundances increased and their per capita rate of herbivory decreased with nutrient additions. In contrast, at the semi-arid site where plant biomass is low and plant nutrient concentrations are high, invertebrate herbivore abundances did not vary and per capita rates of herbivory increased with nutrient additions. No change in the effect of invertebrate herbivores on aboveground plant biomass was observed at any of the sites. In sum, nutrient additions induced shifts in both plant biomass and leaf nutrient content, which altered invertebrate abundances and feeding rate. However, due to the inverse relationship between changes in herbivore abundance and per capita rates of herbivory, nutrient additions did not alter the effect of invertebrates on aboveground biomass. Overall, we suggest that this inverse response of herbivore abundance and per capita feeding rate may buffer ecosystems against changes in invertebrate damage in response to fluctuations in nutrient levels.

  2. Draft Genome Sequences of the Fish Pathogen Vibrio harveyi Strains VH2 and VH5.

    PubMed

    Castillo, Daniel; D'Alvise, Paul; Middelboe, Mathias; Gram, Lone; Liu, Siyang; Kalatzis, Panos G; Kokkari, Constantina; Katharios, Pantelis

    2015-01-01

    Vibrio harveyi is an important marine pathogen that is responsible for vibriosis outbreaks in cultured fish and invertebrates worldwide. Here, we announce the draft genome sequences of V. harveyi strains VH2 and VH5, isolated from farmed juvenile Seriola dumerili during outbreaks of vibriosis in Crete, Greece. PMID:26383670

  3. Draft Genome Sequences of the Fish Pathogen Vibrio harveyi Strains VH2 and VH5

    PubMed Central

    Castillo, Daniel; D’Alvise, Paul; Middelboe, Mathias; Gram, Lone; Liu, Siyang; Kalatzis, Panos G.; Kokkari, Constantina

    2015-01-01

    Vibrio harveyi is an important marine pathogen that is responsible for vibriosis outbreaks in cultured fish and invertebrates worldwide. Here, we announce the draft genome sequences of V. harveyi strains VH2 and VH5, isolated from farmed juvenile Seriola dumerili during outbreaks of vibriosis in Crete, Greece. PMID:26383670

  4. The closterovirus-derived gene expression and RNA interference vectors as tools for research and plant biotechnology

    PubMed Central

    Dolja, Valerian V.; Koonin, Eugene V.

    2013-01-01

    Important progress in understanding replication, interactions with host plants, and evolution of closteroviruses enabled engineering of several vectors for gene expression and virus-induced gene silencing. Due to the broad host range of closteroviruses, these vectors expanded vector applicability to include important woody plants such as citrus and grapevine. Furthermore, large closterovirus genomes offer genetic capacity and stability unrivaled by other plant viral vectors. These features provided immense opportunities for using closterovirus vectors for the functional genomics studies and pathogen control in economically valuable crops. This review briefly summarizes advances in closterovirus research during the last decade, explores the relationships between virus biology and vector design, and outlines the most promising directions for future application of closterovirus vectors. PMID:23596441

  5. Pond and Stream Safari: A Guide to the Ecology of Aquatic Invertebrates.

    ERIC Educational Resources Information Center

    Edelstein, Karen

    This packet includes a leader's guide, a quick reference guide to aquatic invertebrates, a checklist of common aquatic invertebrates, and activity sheets. The leader's guide includes four sections on background information and seven activities. Background sections include: Understanding Aquatic Insects; Growing Up: Aquatic Insect Forms; Adapting…

  6. Slovakian and Turkish Students' Fear, Disgust and Perceived Danger of Invertebrates

    ERIC Educational Resources Information Center

    Prokop, Pavol; Usak, Muhammet; Erdogan, Mehmet; Fancovicova, Jana; Bahar, Mehmet

    2011-01-01

    Human perceives invertebrates less positively than vertebrates because they are small and behaviourally and morphologically unfamiliar. This cross-cultural research focused on Slovakian (n=150) and Turkish (n=164) students' fear, disgust and perceived danger regarding 25 invertebrates [including 5 disease relevant adult insects, 5 ectoparasites, 5…

  7. Streamflow characteristics and benthic invertebrate assemblages in streams across the western United States

    USGS Publications Warehouse

    Brasher, Anne M.D.; Konrad, Chris P.; May, Jason T.; Edmiston, C. Scott; Close, Rebecca N.

    2010-01-01

    Hydrographic characteristics of streamflow, such as high-flow pulses, base flow (background discharge between floods), extreme low flows, and floods, significantly influence aquatic organisms. Streamflow can be described in terms of magnitude, timing, duration, frequency, and variation (hydrologic regime). These characteristics have broad effects on ecosystem productivity, habitat structure, and ultimately on resident fish, invertebrate, and algae communities. Increasing human use of limited water resources has modified hydrologic regimes worldwide. Identifying the most ecologically significant hydrographic characteristics would facilitate the development of water-management strategies. Benthic invertebrates include insects, mollusks (snails and clams), worms, and crustaceans (shrimp) that live on the streambed. Invertebrates play an important role in the food web, consuming other invertebrates and algae and being consumed by fish and birds. Hydrologic alteration associated with land and water use can change the natural hydrologic regime and may affect benthic invertebrate assemblage composition and structure through changes in density of invertebrates or taxa richness (number of different species). This study examined associations between the hydrologic regime and characteristics of benthic invertebrate assemblages across the western United States and developed tools to identify streamflow characteristics that are likely to affect benthic invertebrate assemblages.

  8. Big Fleas Have Little Fleas: How discoveries of invertebrate diseases are advancing modern science.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Review of: “Big Fleas Have Little Fleas: How discoveries of invertebrate diseases are advancing modern science”. Elizabeth W. Davdison. 2006. The University of Arizona Press, Tucson, AZ. 208 pp. Dr. Davidson links many of the accomplishments in invertebrate pathology to subsequent successes in the l...

  9. Influence of antifouling paint on freshwater invertebrates (Mytilidae, Chironomidae and Naididae): density, richness and composition.

    PubMed

    Fujita, D S; Takeda, A M; Coutinho, R; Fernandes, F C

    2015-11-01

    We conducted a study about invertebrates on artificial substrates with different antifouling paints in order to answer the following questions 1) is there lower accumulation of organic matter on substrates with antifouling paints, 2) is invertebrate colonization influenced by the release of biocides from antifouling paints, 3) is the colonization of aquatic invertebrates positively influenced by the material accumulated upon the substrate surface and 4) is the assemblage composition of invertebrates similar among the different antifouling paints? To answer these questions, four structures were installed in the Baía River in February 1st, 2007. Each structure was composed of 7 wood boards: 5 boards painted with each type of antifouling paints (T1, T2, T3, T4 and T5), one painted only with the primer (Pr) and the other without any paint (Cn). After 365 days, we observed a greater accumulation of organic matter in the substrates with T2 and T3 paint coatings. Limnoperna fortunei was recorded in all tested paints, with higher densities in the control, primer, T2 and T3. The colonization of Chironomidae and Naididae on the substrate was positively influenced by L. fortunei density. The non-metric multidimensional scaling (NMDS) of the invertebrate community provided evidence of the clear distinction of invertebrate assemblages among the paints. Paints T2 and T3 were the most similar to the control and primer. Our results suggest that antifouling paints applied on substrates hinder invertebrate colonization by decreasing the density and richness of invertebrates.

  10. The Influence of Flood Disturbances on Interspecific Competition Between Stream Invertebrates

    NASA Astrophysics Data System (ADS)

    Effenberger, M.; Diehl, S.; Matthaei, C. D.

    2005-05-01

    We investigated the influence of repeated abiotic disturbances on interspecific competition between stream invertebrates. Artificial substrates (tiles) were exposed in 2 German streams with different flow regimes (floodprone versus stable). Half the tiles were disturbed (once every 2 weeks) by scrubbing to simulate a bed-moving flood, the other half remained undisturbed. We also manipulated densities of 2 of the most common invertebrate taxa in each stream (floodprone: Baetis and Heptageniidae; stable: Simulium and Brachycentrus montanus). Three invertebrate removal treatments (removal of taxon 1, removal of taxon 2, and unmanipulated controls) were applied, and invertebrates were removed every 3 days. After 2, 4 and 6 weeks each, we sampled 8 tiles from each treatment and determined invertebrate faunal composition, epilithic algal biomass (Chl a) and biofilm biomass (AFDM) for each sample. Both disturbance and invertebrate removal affected the stream biota. Disturbance reduced algal and biofilm biomasses in both streams, and invertebrate density in the floodprone stream. Brachycentrus removal resulted in higher flatworm density. Disturbance and invertebrate removal also interacted with each other. Density of the "non-target" mayfly Baetis in the stable stream was highest in Simulium removal treatments on disturbed tiles, but lowest in Simulium removal treatments on undisturbed tiles.

  11. An overview on genome organization of marine organisms.

    PubMed

    Costantini, Maria

    2015-12-01

    In this review we will concentrate on some general genome features of marine organisms and their evolution, ranging from vertebrate to invertebrates until unicellular organisms. Before genome sequencing, the ultracentrifugation in CsCl led to high resolution of mammalian DNA (without seeing at the sequence). The analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong in a small number of families characterized by different GC levels. The recent availability of a number of fully sequenced genomes allowed mapping very precisely the isochores, based on DNA sequences. Since isochores are tightly linked to biological properties such as gene density, replication timing and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function and evolution. This led the current level of knowledge and to further insights.

  12. [Vector control and malaria control].

    PubMed

    Carnevale, P; Mouchet, J

    1990-01-01

    Vector control is an integral part of malaria control. Limiting parasite transmission vector control must be considered as one of the main preventive measure. Indeed it prevents transmission of Plasmodium from man to vector and from vector to man. But vector control must be adapted to local situation to be efficient and feasible. Targets of vector control can be larval and/or adults stages. In both cases 3 main methods are currently available: physical (source reduction), chemical (insecticides) and biological tolls. Antilarval control is useful only in some particular circumstances (unstable malaria, island, oasis...) Antiadult control is mainly based upon house-spraying while pyrethroid treated bed nets is advocated regarding efficiency, simple technique and cheap price. Vector control measures could seem restricted but can be very efficient if political will is added to a right choice of adapted measures, a good training of involved personal and a large information of the population concerned with vector control.

  13. Herpes simplex virus type 1-derived recombinant and amplicon vectors.

    PubMed

    Fraefel, Cornel; Marconi, Peggy; Epstein, Alberto L

    2011-01-01

    Herpes simplex virus type 1 (HSV-1) is a human pathogen whose lifestyle is based on a long-term dual interaction with the infected host, being able to establish both lytic and latent infections. The virus genome is a 153 kbp double-stranded DNA molecule encoding more than 80 genes. The interest of HSV-1 as gene transfer vector stems from its ability to infect many different cell types, both quiescent and proliferating cells, the very high packaging capacity of the virus capsid, the outstanding neurotropic adaptations that this virus has evolved, and the fact that it never integrates into the cellular chromosomes, thus avoiding the risk of insertional mutagenesis. Two types of vectors can be derived from HSV-1, recombinant vectors and amplicon vectors, and different methodologies have been developed to prepare large stocks of each type of vector. This chapter summarizes (1) the two approaches most commonly used to prepare recombinant vectors through homologous recombination, either in eukaryotic cells or in bacteria, and (2) the two methodologies currently used to generate helper-free amplicon vectors, either using a bacterial artificial chromosome (BAC)-based approach or a Cre/loxP site-specific recombination strategy.

  14. Modular evolution of glutathione peroxidase genes in association with different biochemical properties of their encoded proteins in invertebrate animals

    PubMed Central

    Bae, Young-An; Cai, Guo-Bin; Kim, Seon-Hee; Zo, Young-Gun; Kong, Yoon

    2009-01-01

    Background Phospholipid hydroperoxide glutathione peroxidases (PHGPx), the most abundant isoforms of GPx families, interfere directly with hydroperoxidation of lipids. Biochemical properties of these proteins vary along with their donor organisms, which has complicated the phylogenetic classification of diverse PHGPx-like proteins. Despite efforts for comprehensive analyses, the evolutionary aspects of GPx genes in invertebrates remain largely unknown. Results We isolated GPx homologs via in silico screening of genomic and/or expressed sequence tag databases of eukaryotic organisms including protostomian species. Genes showing strong similarity to the mammalian PHGPx genes were commonly found in all genomes examined. GPx3- and GPx7-like genes were additionally detected from nematodes and platyhelminths, respectively. The overall distribution of the PHGPx-like proteins with different biochemical properties was biased across taxa; selenium- and glutathione (GSH)-dependent proteins were exclusively detected in platyhelminth and deuterostomian species, whereas selenium-independent and thioredoxin (Trx)-dependent enzymes were isolated in the other taxa. In comparison of genomic organization, the GSH-dependent PHGPx genes showed a conserved architectural pattern, while their Trx-dependent counterparts displayed complex exon-intron structures. A codon for the resolving Cys engaged in reductant binding was found to be substituted in a series of genes. Selection pressure to maintain the selenocysteine codon in GSH-dependent genes also appeared to be relaxed during their evolution. With the dichotomized fashion in genomic organizations, a highly polytomic topology of their phylogenetic trees implied that the GPx genes have multiple evolutionary intermediate forms. Conclusion Comparative analysis of invertebrate GPx genes provides informative evidence to support the modular pathways of GPx evolution, which have been accompanied with sporadic expansion/deletion and exon

  15. An invertebrate stomach's view on vertebrate ecology: certain invertebrates could be used as "vertebrate samplers" and deliver DNA-based information on many aspects of vertebrate ecology.

    PubMed

    Calvignac-Spencer, Sébastien; Leendertz, Fabian H; Gilbert, M Thomas P; Schubert, Grit

    2013-11-01

    Recent studies suggest that vertebrate genetic material ingested by invertebrates (iDNA) can be used to investigate vertebrate ecology. Given the ubiquity of invertebrates that feed on vertebrates across the globe, iDNA might qualify as a very powerful tool for 21st century population and conservation biologists. Here, we identify some invertebrate characteristics that will likely influence iDNA retrieval and elaborate on the potential uses of invertebrate-derived information. We hypothesize that beyond inventorying local faunal diversity, iDNA should allow for more profound insights into wildlife population density, size, mortality, and infectious agents. Based on the similarities of iDNA with other low-quality sources of DNA, a general technical framework for iDNA analyses is proposed. As it is likely that no such thing as a single ideal iDNA sampler exists, forthcoming research efforts should aim at cataloguing invertebrate properties relevant to iDNA retrieval so as to guide future usage of the invertebrate tool box.

  16. Functional traits of soil invertebrates as indicators for exposure to soil disturbance.

    PubMed

    Hedde, Mickaël; van Oort, Folkert; Lamy, Isabelle

    2012-05-01

    We tested a trait-based approach to link a soil disturbance to changes in invertebrate communities. Soils and macro-invertebrates were sampled in sandy soils contaminated by long-term wastewater irrigation, adding notably organic matter and trace metals (TM). We hypothesized that functional traits of invertebrates depict ways of exposure and that exposure routes relate to specific TM pools. Geophages and soft-body invertebrates were chosen to inform on exposure by ingestion or contact, respectively. Trait-based indices depicted more accurately effects of pollution than community density and diversity did. Exposure by ingestion had more deleterious effects than by contact. Both types of exposed invertebrates were influenced by TM, but geophages mainly responded to changes in soil organic matter contents. The trait-based approach requires to be applied in various conditions to uncorrelate specific TM impacts from those of other environmental factors.

  17. Effects of fish predation on invertebrates associated with a macrophyte in Lake Onalaska, Wisconsin

    USGS Publications Warehouse

    Chilton, E.W., II; Margraf, F.J.

    1990-01-01

    We tested the effects of fish predation on the macroinvertebrates associated with Vallisneria americana (Michx) by using enclosure/exclosure experiments in lake Onalaska, Wisconsin. Four treatments were used: open water (cageless) controls, cage-effect controls (partially enclosed cages), exclosures (all fish removed), and enclosures (cages stocked with a known density of bluegills Lepomis macrochirus, Rafinesque). Bluegill predation at the density tested (one 70 mm fish per 0.37m2) did not depress Vallisneria associated invertebrate density. Mean invertebrate abundance and biomass (number and dry weight of invertebrates per g dry plant weight) increased in both exclosures and enclosures relative to open water controls. The most likely explanation is that the cages excluded some vertebrate predator(s) from those two treatments and decreased predation pressure within the cages. Large invertebrates, such as Hyalella azteca, Enallagma sp., Gyraulus sp., and Physa sp., increased in abundance within cages, whereas, small invertebrates such as chironomid larvae decreased in abundance.

  18. Isolation, Electron Microscopy and 3D Reconstruction of Invertebrate Muscle Myofilaments

    PubMed Central

    Craig, Roger

    2011-01-01

    Understanding the molecular mechanism of muscle contraction and its regulation has been greatly influenced and aided by studies of myofilament structure in invertebrate muscles. Invertebrates are easily obtained and cover a broad spectrum of species and functional specializations. The thick (myosin-containing) filaments from some invertebrates are especially stable and simple in structure and thus much more amenable to structural analysis than those of vertebrates. Comparative studies of invertebrate filaments by electron microscopy and image processing have provided important generalizations of muscle molecular structure and function. This article reviews methods for preparing thick and thin filaments from invertebrate muscle, for imaging filaments by electron microscopy, and for determining their three dimensional structure by image processing. It also highlights some of the key insights into filament function that have come from these studies. PMID:22155190

  19. Construction and characterization of novel fowlpox virus shuttle vectors.

    PubMed

    Du, Shouwen; Liu, Cunxia; Zhu, Yilong; Wang, Yuhang; Ren, Dayong; Wang, Maopeng; Tan, Peng; Li, Xiao; Tian, Mingyao; Zhang, Yanfang; Li, Jinze; Zhao, Fei; Li, Chang; Jin, Ningyi

    2015-02-01

    Viral vectors are important vehicles in vaccine research. Avipoxviruses including fowlpox virus (FPV) play major roles in viral vaccine vector development for the prevention and therapy of human and other veterinary diseases due to their immunomodulatory effects and safety profile. Recently, we analyzed the genomic and proteomic backgrounds of the Chinese FPV282E4 strain. Based on analysis of the whole genome of FPV282E4, the FPV150 and FPV193 loci were chosen as insertion sites for foreign genes, and two shuttle vectors with a triple-gene expression cassette were designed and constructed. Homologous recombination between the FPV virus genome and sequences within the shuttle plasmids in infected cells was confirmed. The recombinants were obtained through several rounds of plaque purification using enhanced green fluorescent protein as a reporter and evaluated for the correct expression of foreign genes in vitro using RT-PCR, real-time PCR and Western blotting. Morphogenesis and growth kinetics were assayed via transmission electron microscopy and viral titering, respectively. Results showed that recombinant viruses were generated and correctly expressed foreign genes in CEF, BHK-21 and 293T cells. At least three different exogenous genes could be expressed simultaneously and stably over multiple passages. Additionally, the FPV150 mutation, FPV193 deletion and insertion of foreign genes did not affect the morphogenesis, replication and proliferation of recombinant viruses in cells. Our study contributes to the improvement of FPV vectors for multivalent vaccines.

  20. Application of Multiple Index Development Approaches to Benthic Invertebrate Data from the Virginian Biogeographic Province (SETAC NA)

    EPA Science Inventory

    Benthic invertebrate indices have commonly been utilized to assess benthic invertebrate communities. These indices have been constructed using different techniques, but have shown different levels of application success. For example, the EMAP Virginian Province Index did not pe...

  1. Elusive vector glueball

    SciTech Connect

    Suzuki, Mahiko

    2002-05-01

    If the vector glueball {Omicron} exists in the mass range that theory suggests, its resonant production cross section can be detected in e{sup +}e{sup -} annihilation only if the decay width is very narrow ({le} a few MeV). Otherwise {Omicron} will be observed only indirectly through its mixing with {psi}{prime}. We propose a few tests of the {Omicron}-{psi}{prime} mixing for future charm factories.

  2. Vector soliton fission.

    PubMed

    Lu, F; Lin, Q; Knox, W H; Agrawal, Govind P

    2004-10-29

    We investigate the vectorial nature of soliton fission in an isotropic nonlinear medium both theoretically and experimentally. As a specific example, we show that supercontinuum generation in a tapered fiber is extremely sensitive to the input state of polarization. Multiple vector solitons generated through soliton fission exhibit different states of elliptical polarization while emitting nonsolitonic radiation with complicated polarization features. Experiments performed with a tapered fiber agree with our theoretical description.

  3. Vector Magnetograph Design

    NASA Technical Reports Server (NTRS)

    Chipman, Russell A.

    1996-01-01

    This report covers work performed during the period of November 1994 through March 1996 on the design of a Space-borne Solar Vector Magnetograph. This work has been performed as part of a design team under the supervision of Dr. Mona Hagyard and Dr. Alan Gary of the Space Science Laboratory. Many tasks were performed and this report documents the results from some of those tasks, each contained in the corresponding appendix. Appendices are organized in chronological order.

  4. Environmental hazards of aluminum to plants, invertebrates, fish, and wildlife

    USGS Publications Warehouse

    Sparling, D.W.; Lowe, T.P.

    1996-01-01

    Aluminum is extremely common throughout the world and is innocuous under circumneutral or alkaline conditions. However, in acidic environments, it can be a maJor limiting factor to many plants and aquatic organisms. The greatest concern for toxicity in North America occurs in areas that are affected by wet and dry acid deposition, such as eastern Canada and the northeastern U.S. Acid mine drainage, logging, and water treatment plant effluents containing alum can be other maJor sources of Al. In solution, the metal can combine with several different agents to affect toxicity. In general, Al hydroxides and monomeric Al are the most toxic forms. Dissolved organic carbons, F, PO(3)3- and SO(4)2- ameliorate toxicity by reducing bioavailability. Elevated metal levels in water and soil can cause serious problems for some plants. Algae tend to be both acid- and Al tolerant and, although some species may disappear with reduced pH, overall algae productivity and biomass are seldom affected if pH is above 3.0. Aluminum and acid toxicity tend to be additive to some algae when pH is less than 4.5. Because the metal binds with inorganic P, it may reduce P availability and reduce productivity. Forest die-backs in North America involving red spruce, Fraser fir, balsam fir, loblolly pine, slash pine, and sugar maples have been ascribed to Al toxicity, and extensive areas of European forests have died because of the combination of high soil Al and low pH. Extensive research on crops has produced Al-resistant cultivars and considerable knowledge about mechanisms of and defenses against toxicity. Very low Al levels may benefit some plants, although the metal is not recognized as an essential nutrient. Hyperaccumulator species of plants may concentrate Al to levels that are toxic to herbivores. Toxicity in aquatic invertebrates is also acid dependent. Taxa such as Ephemeroptera, Plecoptera, and Cladocera are sensitive and may perish when Al is less than 1 mg.L-1 whereas dipterans

  5. Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation.

    PubMed

    Yoshida, Masa-aki; Ishikura, Yukiko; Moritaki, Takeya; Shoguchi, Eiichi; Shimizu, Kentaro K; Sese, Jun; Ogura, Atsushi

    2011-09-01

    Comparative genome structure analysis allows us to identify novel genes, repetitive sequences and gene duplications. To explore lineage-specific genomic changes of the molluscs that is good model for development of nervous system in invertebrate, we conducted comparative genome structure analyses of three molluscs, pygmy squid, nautilus and scallops using partial genome shotgun sequencing. Most effective elements on the genome structural changes are repetitive elements (REs) causing expansion of genome size and whole genome duplication producing large amount of novel functional genes. Therefore, we investigated variation and proportion of REs and whole genome duplication. We, first, identified variations of REs in the three molluscan genomes by homology-based and de novo RE detection. Proportion of REs were 9.2%, 4.0%, and 3.8% in the pygmy squid, nautilus and scallop, respectively. We, then, estimated genome size of the species as 2.1, 4.2 and 1.8 Gb, respectively, with 2× coverage frequency and DNA sequencing theory. We also performed a gene duplication assay based on coding genes, and found that large-scale duplication events occurred after divergence from the limpet Lottia, an out-group of the three molluscan species. Comparison of all the results suggested that RE expansion did not relate to the increase in genome size of nautilus. Despite close relationships to nautilus, the squid has the largest portion of REs and smaller genome size than nautilus. We also identified lineage-specific RE and gene-family expansions, possibly relate to acquisition of the most complicated eye and brain systems in the three species.

  6. Recurrent Horizontal Transfers of Chapaev Transposons in Diverse Invertebrate and Vertebrate Animals

    PubMed Central

    Zhang, Hua-Hao; Feschotte, Cédric; Han, Min-Jin; Zhang, Ze

    2014-01-01

    Horizontal transfer (HT) of a transposable element (TE) into a new genome is regarded as an important force to drive genome variation and biological innovation. In addition, HT also plays an important role in the persistence of TEs in eukaryotic genomes. Here, we provide the first documented example for the repeated HT of three families of Chapaev transposons in a wide range of animal species, including mammals, reptiles, jawed fishes, lampreys, insects, and in an insect bracovirus. Multiple alignments of the Chapaev transposons identified in these species revealed extremely high levels of nucleotide sequence identity (79–99%), which are inconsistent with vertical evolution given the deep divergence time separating these host species. Rather, the discontinuous distribution amongst species and lack of purifying selection acting on these transposons strongly suggest that they were independently and horizontally transferred into these species lineages. The detection of Chapaev transposons in an insect bracovirus indicated that these viruses might act as a possible vector for the horizontal spread of Chapaev transposons. One of the Chapaev families was also shared by lampreys and some of their common hosts (such as sturgeon and paddlefish), which suggested that parasite–host interaction might facilitate HTs. PMID:24868016

  7. Vector-Borne Bacterial Plant Pathogens: Interactions with Hemipteran Insects and Plants

    PubMed Central

    Perilla-Henao, Laura M.; Casteel, Clare L.

    2016-01-01

    Hemipteran insects are devastating pests of crops due to their wide host range, rapid reproduction, and ability to transmit numerous plant-infecting pathogens as vectors. While the field of plant–virus–vector interactions has flourished in recent years, plant–bacteria–vector interactions remain poorly understood. Leafhoppers and psyllids are by far the most important vectors of bacterial pathogens, yet there are still significant gaps in our understanding of their feeding behavior, salivary secretions, and plant responses as compared to important viral vectors, such as whiteflies and aphids. Even with an incomplete understanding of plant–bacteria–vector interactions, some common themes have emerged: (1) all known vector-borne bacteria share the ability to propagate in the plant and insect host; (2) particular hemipteran families appear to be incapable of transmitting vector-borne bacteria; (3) all known vector-borne bacteria have highly reduced genomes and coding capacity, resulting in host-dependence; and (4) vector-borne bacteria encode proteins that are essential for colonization of specific hosts, though only a few types of proteins have been investigated. Here, we review the current knowledge on important vector-borne bacterial pathogens, including Xylella fastidiosa, Spiroplasma spp., Liberibacter spp., and ‘Candidatus Phytoplasma spp.’. We then highlight recent approaches used in the study of vector-borne bacteria. Finally, we discuss the application of this knowledge for control and future directions that will need to be addressed in the field of vector–plant–bacteria interactions. PMID:27555855

  8. New vectors for epitope tagging and gene disruption in Schizosaccharomyces pombe

    PubMed Central

    Gadaleta, Mariana C.; Iwasaki, Osamu; Noguchi, Chiaki; Noma, Ken-ichi; Noguchi, Eishi

    2013-01-01

    We describe a series of new vectors for PCR-based epitope tagging and gene disruption in the fission yeast Schizosaccharomyces pombe, an exceptional model organism for the study of cellular processes. The vectors are designed for amplification of gene-targeting DNA cassettes and integration into specific genetic loci, allowing expression of proteins fused to 12 tandem copies of the Pk (V5) epitope or 5 tandem copies of the FLAG epitope with a glycine linker. These vectors are available with various antibiotic or nutritional markers and are useful for protein studies using biochemical and cell biological methods. We also describe new vectors for fluorescent protein-tagging and gene disruption using ura4MX6, LEU2MX6, and his3MX6 selection markers, allowing researchers in the S. pombe community to disrupt genes and manipulate genomic loci using primer sets already available for the widely used pFA6a-MX6 system. Our new vectors may also be useful for gene manipulation in Saccharomyces cerevisiae. Method Summary Our 12Pk-tagging vectors for genomic integration significantly improve the sensitivity of protein detection by Western blotting. We also describe genomic 5FLAG-tagging vectors with a glycine linker, which allows flexibility between the epitope and the protein, enhancing immunoprecipitation efficiency. This report also describes vectors for fluorescent-tagging and gene deletion useful in S. pombe. PMID:24215641

  9. Decoding the ubiquitin-mediated pathway of arthropod disease vectors.

    PubMed

    Choy, Anthony; Severo, Maiara S; Sun, Ruobai; Girke, Thomas; Gillespie, Joseph J; Pedra, Joao H F

    2013-01-01

    Protein regulation by ubiquitin has been extensively described in model organisms. However, characterization of the ubiquitin machinery in disease vectors remains mostly unknown. This fundamental gap in knowledge presents a concern because new therapeutics are needed to control vector-borne diseases, and targeting the ubiquitin machinery as a means for disease intervention has been already adopted in the clinic. In this study, we employed a bioinformatics approach to uncover the ubiquitin-mediated pathway in the genomes of Anopheles gambiae, Aedes aegypti, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus and Rhodnius prolixus. We observed that (1) disease vectors encode a lower percentage of ubiquitin-related genes when compared to Drosophila melanogaster, Mus musculus and Homo sapiens but not Saccharomyces cerevisiae; (2) overall, there are more proteins categorized as E3 ubiquitin ligases when compared to E2-conjugating or E1-activating enzymes; (3) the ubiquitin machinery within the three mosquito genomes is highly similar; (4) ubiquitin genes are more than doubled in the Chagas disease vector (R. prolixus) when compared to other arthropod vectors; (5) the deer tick I. scapularis and the body louse (P. humanus) genomes carry low numbers of E1-activating enzymes and HECT-type E3 ubiquitin ligases; (6) R. prolixus have low numbers of RING-type E3 ubiquitin ligases; and (7) C. quinquefasciatus present elevated numbers of predicted F-box E3 ubiquitin ligases, JAB and UCH deubiquitinases. Taken together, these findings provide novel opportunities to study the interaction between a pathogen and an arthropod vector. PMID:24205097

  10. DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

    PubMed

    Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

    2016-01-01

    The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

  11. DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

    PubMed

    Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

    2016-01-01

    The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects. PMID:27460368

  12. Trisoxazole macrolides from Hexabranchus nudibranchs and other marine invertebrates.

    PubMed

    Matsunaga, S

    2006-01-01

    Trisoxazole macrolides are cytotoxic and antifungal metabolites initially isolated from the egg-ribbons of the Hexabranchus nudibranch and later found in other marine invertebrates. They possess a characteristic macrolide portion, in which three contiguous oxazole units are integrated, and a side-chain with an N-methyl-vinylformamide terminus. The planar structures of the first members of this group, ulapualides and kabiramide C, were determined by interpretation of spectral data in conjunction with chemical degradation. Following these studies, the structures of approximately 35 congeners have been reported, including mycalolides from a marine sponge Mycale sp. The absolute stereochemistry of mycalolides was determined by chemical methods. Trisoxazole macrolides depolymerize F-actin and form a 1:1 complex with G-actin, thereby exhibiting potent toxicity toward eukaryotic cells. X-ray crystallography established the mode of binding of some of the members to G-actin and their absolute stereochemistry. PMID:17153346

  13. Interdependence of specialization and biodiversity in Phanerozoic marine invertebrates.

    PubMed

    Nürnberg, Sabine; Aberhan, Martin

    2015-03-17

    Studies of the dynamics of biodiversity often suggest that diversity has upper limits, but the complex interplay between ecological and evolutionary processes and the relative role of biotic and abiotic factors that set upper limits to diversity are poorly understood. Here we statistically assess the relationship between global biodiversity and the degree of habitat specialization of benthic marine invertebrates over the Phanerozoic eon. We show that variation in habitat specialization correlates positively with changes in global diversity, that is, times of high diversity coincide with more specialized faunas. We identify the diversity dynamics of specialists but not generalists, and origination rates but not extinction rates, as the main drivers of this ecological interdependence. Abiotic factors fail to show any significant relationship with specialization. Our findings suggest that the overall level of specialization and its fluctuations over evolutionary timescales are controlled by diversity-dependent processes--driven by interactions between organisms competing for finite resources.

  14. Selected recent in vivo studies on chemical measurements in invertebrates.

    PubMed

    Majdi, S; Ren, L; Fathali, H; Li, X; Ewing, A G

    2015-06-01

    In vivo measurements of neurotransmitters and related compounds have provided a better understanding of the chemical interactions that are a major part in functioning of brains. In addition, a great deal of technology has been developed to measure chemical species in other areas of living organisms. A key part of this work has been sampling technologies as well as direct measurements in vivo. This is extremely important when sampling from the smallest animal systems. Yet, very small invertebrate systems are excellent models and often have better defined and more easily manipulated genetics. This review focuses on in vivo measurements, electrochemical methods, fluorescence techniques, and sampling and is further narrowed to work over approximately the last three years. Rapid developments of in vivo studies in these model systems should aid in finding solutions to biological and bioanalytical challenges related to human physiological functions and neurodegenerative diseases.

  15. The colloid osmotic pressures of invertebrate body fluids.

    PubMed

    Mangum, C P; Johansen, K

    1975-12-01

    Colloid osmotic pressures of the body fluids of twenty invertebrate species were measured directly. The results, which are generally lower than predicted values for the same species, pertain to several physiological questions: (1) they do not quantitatively explain the frequently observed hyperosmoticity of body fluids in species believed to be osmoconformers, indicating that the condition cannot be merely a consequence of a Gibbs-Donnan equilibrium; (2) the excess of hydrostatic over colloid osmotic pressure is very small. This result supports the hypothesis that the oxygen transport function of bloods with extracellular haemocyanins and haem proteins is limited by their colligative properties; (3) the pressure relationships and the absence of colloid osmotic activity in urine indicates that filtration contributes to urine formation in several species.

  16. The physics of broadcast spawning in benthic invertebrates.

    PubMed

    Crimaldi, John P; Zimmer, Richard K

    2014-01-01

    Most benthic invertebrates broadcast their gametes into the sea, whereupon successful fertilization relies on the complex interaction between the physics of the surrounding fluid flow and the biological properties and behavior of eggs and sperm. We present a holistic overview of the impact of instantaneous flow processes on fertilization across a range of scales. At large scales, transport and stirring by the flow control the distribution of gametes. Although mean dilution of gametes by turbulence is deleterious to fertilization, a variety of instantaneous flow phenomena can aggregate gametes before dilution occurs. We argue that these instantaneous flow processes are key to fertilization efficiency. At small scales, sperm motility and taxis enhance contact rates between sperm and chemoattractant-releasing eggs. We argue that sperm motility is a biological adaptation that replaces molecular diffusion in conventional mixing processes and enables gametes to bridge the gap that remains after aggregation by the flow.

  17. Effects of Microgravity and Hypergravity on Invertebrate Development

    NASA Technical Reports Server (NTRS)

    Miquel, J.

    1985-01-01

    Data suggest that abnormal gravity loads do not increase the rate of mutations in lower animals. Insects such as Drosophila melanogaster and Tribolium confusum have been able to reproduce aboard unmanned and manned space satellites, though no precise quantitative data have been obtained on mating competence and various aspects of development. Research with Drosophila flown on Cosmos spacecraft suggests that flight behavior is seriously disturbed in insects exposed to microgravity, which is reflected in increased oxygen utilization and concomitant life shortening. The decrease in longevity was less striking when the flies were enclosed in space, which suggests that they could adapt to the altered gravitational environment when maturation of flight behavior took place in microgravity. The reviewed data suggest that further research on the development of invertebrates in space is in order for clarification of the metabolic and behavioral effects of microgravity and of the development and function of the orientation and gravity sensing mechanisms of lower animals.

  18. Impact theory of mass extinctions and the invertebrate fossil record

    SciTech Connect

    Alvarez, W.; Kauffman, E.G.; Surlyk, F.; Alvarez, L.W.; Asaro, F.; Michel, H.V.

    1984-03-16

    There is much evidence that the Cretaceous-Tertiary boundary was marked by a massive meteorite impact. Theoretical consideration of the consequences of such an impact predicts sharp extinctions in many groups of animals precisely at the boundary. Paleontological data clearly show gradual declines in diversity over the last 1 to 10 million years in various invertebrate groups. Reexamination of data from careful studies of the best sections shows that, in addition to undergoing the decline, four groups (ammonites, cheilostomate bryozoans, brachiopods, and bivalves) were affected by sudden truncations precisely at the iridium anomaly that marks the boundary. The paleontological record thus bears witness to terminal-Cretaceous extinctions on two time scales: a slow decline unrelated to the impact and a sharp truncation synchronous with and probably caused by the impact. 50 references, 4 figures.

  19. Production ecology of invertebrates in small experimental ponds

    SciTech Connect

    Cushman, R.M.; Franco, P.J.; Goyert, J.C.; Lesslie, P.A.

    1986-07-01

    Production of invertebrates is estimated for a series of small experimental ponds in Tennessee. Annual dry weight production of predator insects is about 4.5 g/m/sup 2/ and of herbivore-detritivore insects about 3.8 g/m/sup 2/; insects whose trophic position could not be classified account for an annual dry weight production of about 0.3 g/m/sup 2/. Annual dry weight production of zooplankton is about 14.5 t/m/sup 2/, of annelids 25.4 g/m/sup 2/ and of snails 3.1 g/m/sup 2/. The data are consistent with published information that the predator insects probably depend on a variety of energy sources to support their estimated production rate.

  20. An investigation into the chemical composition of alternative invertebrate prey.

    PubMed

    Oonincx, D G A B; Dierenfeld, E S

    2012-01-01

    The aim of this study was to determine the chemical composition of eight invertebrate species and evaluate their suitability as alternative prey. The species selected were rusty red cockroaches (Blatta lateralis), six-spotted cockroaches (Eublaberus distanti), Madagascar hissing cockroaches (Gromphadorhina portentosa), fruit flies (Drosophila melanogaster), false katydids (Microcentrum rhombifolium), beetles of the mealworm (Tenebrio molitor), and superworm beetles (Zophobas morio), as well as woodlice (Porcellio scaber). Dry matter (DM), crude protein, crude fat, neutral detergent fiber, acid detergent fiber, ash, macro and trace minerals, vitamins A and E, and carotenoid concentrations were quantified. Significant differences were found between species. Crude protein content ranged from 38 to 76% DM, fat from14 to 54% DM, and ash from 2 to 8% DM. In most species, calcium:phosphorus was low (0.08-0.30:1); however, P. scaber was an exception (12:1) and might prove useful as a dietary source of calcium for insectivores. Vitamin E content was low for most species (6-16 mg/kg DM), except for D. melanogaster and M. rhombifolium (112 and 110 mg/kg DM). The retinol content, as a measure of vitamin A activity, was low in all specimens, but varied greatly among samples (0.670-886 mg/kg DM). The data presented can be used to alter diets to better suit the estimated requirements of insectivores in captivity. Future research on the topic of composition of invertebrate prey species should focus on determination of nutrient differences owing to species, developmental stage, and diet.