Molecular Analysis of Vector Genome Structures After Liver Transduction by Conventional and Self-Complementary Adeno-Associated Viral Serotype Vectors in Murine and Nonhuman Primate Models

PubMed Central

Sun, Xun; Lu, You; Bish, Lawrence T.; Calcedo, Roberto; Wilson, James M.

2010-01-01

Abstract Vectors based on several new adeno-associated viral (AAV) serotypes demonstrated strong hepatocyte tropism and transduction efficiency in both small- and large-animal models for liver-directed gene transfer. Efficiency of liver transduction by AAV vectors can be further improved in both murine and nonhuman primate (NHP) animals when the vector genomes are packaged in a self-complementary (sc) format. In an attempt to understand potential molecular mechanism(s) responsible for enhanced transduction efficiency of the sc vector in liver, we performed extensive molecular studies of genome structures of conventional single-stranded (ss) and sc AAV vectors from liver after AAV gene transfer in both mice and NHPs. These included treatment with exonucleases with specific substrate preferences, single-cutter restriction enzyme digestion and polarity-specific hybridization-based vector genome mapping, and bacteriophage ϕ29 DNA polymerase-mediated and double-stranded circular template-specific rescue of persisted circular genomes. In mouse liver, vector genomes of both genome formats seemed to persist primarily as episomal circular forms, but sc vectors converted into circular forms more rapidly and efficiently. However, the overall differences in vector genome abundance and structure in the liver between ss and sc vectors could not account for the remarkable differences in transduction. Molecular structures of persistent genomes of both ss and sc vectors were significantly more heterogeneous in macaque liver, with noticeable structural rearrangements that warrant further characterizations. PMID:20113166

Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts.

PubMed

Alex, Anoop; Antunes, Agostinho

2018-01-01

Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.

Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts

PubMed Central

Alex, Anoop

2018-01-01

Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts. PMID:29775460

Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary.

PubMed

Keller, Thomas E; Han, Priscilla; Yi, Soojin V

2016-04-01

Genomes of invertebrates and vertebrates exhibit highly divergent patterns of DNA methylation. Invertebrate genomes tend to be sparsely methylated, and DNA methylation is mostly targeted to a subset of transcription units (gene bodies). In a drastic contrast, vertebrate genomes are generally globally and heavily methylated, punctuated by the limited local hypo-methylation of putative regulatory regions such as promoters. These genomic differences also translate into functional differences in DNA methylation and gene regulation. Although promoter DNA methylation is an important regulatory component of vertebrate gene expression, its role in invertebrate gene regulation has been little explored. Instead, gene body DNA methylation is associated with expression of invertebrate genes. However, the evolutionary steps leading to the differentiation of invertebrate and vertebrate genomic DNA methylation remain unresolved. Here we analyzed experimentally determined DNA methylation maps of several species across the invertebrate-vertebrate boundary, to elucidate how vertebrate gene methylation has evolved. We show that, in contrast to the prevailing idea, a substantial number of promoters in an invertebrate basal chordate Ciona intestinalis are methylated. Moreover, gene expression data indicate significant, epigenomic context-dependent associations between promoter methylation and expression in C. intestinalis. However, there is no evidence that promoter methylation in invertebrate chordate has been evolutionarily maintained across the invertebrate-vertebrate boundary. Rather, body-methylated invertebrate genes preferentially obtain hypo-methylated promoters among vertebrates. Conversely, promoter methylation is preferentially found in lineage- and tissue-specific vertebrate genes. These results provide important insights into the evolutionary origin of epigenetic regulation of vertebrate gene expression. © The Author(s) 2015. Published by Oxford University Press on behalf

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

PubMed Central

Dugan, Vivien G.; Emrich, Scott J.; Giraldo-Calderón, Gloria I.; Harb, Omar S.; Newman, Ruchi M.; Pickett, Brett E.; Schriml, Lynn M.; Stockwell, Timothy B.; Stoeckert, Christian J.; Sullivan, Dan E.; Singh, Indresh; Ward, Doyle V.; Yao, Alison; Zheng, Jie; Barrett, Tanya; Birren, Bruce; Brinkac, Lauren; Bruno, Vincent M.; Caler, Elizabet; Chapman, Sinéad; Collins, Frank H.; Cuomo, Christina A.; Di Francesco, Valentina; Durkin, Scott; Eppinger, Mark; Feldgarden, Michael; Fraser, Claire; Fricke, W. Florian; Giovanni, Maria; Henn, Matthew R.; Hine, Erin; Hotopp, Julie Dunning; Karsch-Mizrachi, Ilene; Kissinger, Jessica C.; Lee, Eun Mi; Mathur, Punam; Mongodin, Emmanuel F.; Murphy, Cheryl I.; Myers, Garry; Neafsey, Daniel E.; Nelson, Karen E.; Nierman, William C.; Puzak, Julia; Rasko, David; Roos, David S.; Sadzewicz, Lisa; Silva, Joana C.; Sobral, Bruno; Squires, R. Burke; Stevens, Rick L.; Tallon, Luke; Tettelin, Herve; Wentworth, David; White, Owen; Will, Rebecca; Wortman, Jennifer; Zhang, Yun; Scheuermann, Richard H.

2014-01-01

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a

Standardized metadata for human pathogen/vector genomic sequences.

PubMed

Dugan, Vivien G; Emrich, Scott J; Giraldo-Calderón, Gloria I; Harb, Omar S; Newman, Ruchi M; Pickett, Brett E; Schriml, Lynn M; Stockwell, Timothy B; Stoeckert, Christian J; Sullivan, Dan E; Singh, Indresh; Ward, Doyle V; Yao, Alison; Zheng, Jie; Barrett, Tanya; Birren, Bruce; Brinkac, Lauren; Bruno, Vincent M; Caler, Elizabet; Chapman, Sinéad; Collins, Frank H; Cuomo, Christina A; Di Francesco, Valentina; Durkin, Scott; Eppinger, Mark; Feldgarden, Michael; Fraser, Claire; Fricke, W Florian; Giovanni, Maria; Henn, Matthew R; Hine, Erin; Hotopp, Julie Dunning; Karsch-Mizrachi, Ilene; Kissinger, Jessica C; Lee, Eun Mi; Mathur, Punam; Mongodin, Emmanuel F; Murphy, Cheryl I; Myers, Garry; Neafsey, Daniel E; Nelson, Karen E; Nierman, William C; Puzak, Julia; Rasko, David; Roos, David S; Sadzewicz, Lisa; Silva, Joana C; Sobral, Bruno; Squires, R Burke; Stevens, Rick L; Tallon, Luke; Tettelin, Herve; Wentworth, David; White, Owen; Will, Rebecca; Wortman, Jennifer; Zhang, Yun; Scheuermann, Richard H

2014-01-01

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a

Genome Investigations of Vector Competence in Aedes aegypti to Inform Novel Arbovirus Disease Control Approaches

PubMed Central

Severson, David W.; Behura, Susanta K.

2016-01-01

Dengue (DENV), yellow fever, chikungunya, and Zika virus transmission to humans by a mosquito host is confounded by both intrinsic and extrinsic variables. Besides virulence factors of the individual arboviruses, likelihood of virus transmission is subject to variability in the genome of the primary mosquito vector, Aedes aegypti. The “vectorial capacity” of A. aegypti varies depending upon its density, biting rate, and survival rate, as well as its intrinsic ability to acquire, host and transmit a given arbovirus. This intrinsic ability is known as “vector competence”. Based on whole transcriptome analysis, several genes and pathways have been predicated to have an association with a susceptible or refractory response in A. aegypti to DENV infection. However, the functional genomics of vector competence of A. aegypti is not well understood, primarily due to lack of integrative approaches in genomic or transcriptomic studies. In this review, we focus on the present status of genomics studies of DENV vector competence in A. aegypti as limited information is available relative to the other arboviruses. We propose future areas of research needed to facilitate the integration of vector and virus genomics and environmental factors to work towards better understanding of vector competence and vectorial capacity in natural conditions. PMID:27809220

Diversity of large DNA viruses of invertebrates.

PubMed

Williams, Trevor; Bergoin, Max; van Oers, Monique M

2017-07-01

In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for invertebrates. We present their taxonomical classification and describe the evolutionary relationships among various groups of invertebrate-infecting viruses. We also indicate the relationships of the invertebrate viruses to viruses infecting mammals or other vertebrates. The shared characteristics of the viruses within the various families are described, including the structure of the virus particle, genome properties, and gene expression strategies. Finally, we explain the transmission and mode of infection of the most important viruses in these families and indicate, which orders of invertebrates are susceptible to these pathogens. Copyright © 2016 Elsevier Inc. All rights reserved.

Invertebrate Iridoviruses: A Glance over the Last Decade

PubMed Central

Özcan, Orhan; Ilter-Akulke, Ayca Zeynep; Scully, Erin D.; Özgen, Arzu

2018-01-01

Members of the family Iridoviridae (iridovirids) are large dsDNA viruses that infect both invertebrate and vertebrate ectotherms and whose symptoms range in severity from minor reductions in host fitness to systemic disease and large-scale mortality. Several characteristics have been useful for classifying iridoviruses; however, novel strains are continuously being discovered and, in many cases, reliable classification has been challenging. Further impeding classification, invertebrate iridoviruses (IIVs) can occasionally infect vertebrates; thus, host range is often not a useful criterion for classification. In this review, we discuss the current classification of iridovirids, focusing on genomic and structural features that distinguish vertebrate and invertebrate iridovirids and viral factors linked to host interactions in IIV6 (Invertebrate iridescent virus 6). In addition, we show for the first time how complete genome sequences of viral isolates can be leveraged to improve classification of new iridovirid isolates and resolve ambiguous relations. Improved classification of the iridoviruses may facilitate the identification of genus-specific virulence factors linked with diverse host phenotypes and host interactions. PMID:29601483

Invertebrate Iridoviruses: A Glance over the Last Decade.

PubMed

İnce, İkbal Agah; Özcan, Orhan; Ilter-Akulke, Ayca Zeynep; Scully, Erin D; Özgen, Arzu

2018-03-30

Members of the family Iridoviridae (iridovirids) are large dsDNA viruses that infect both invertebrate and vertebrate ectotherms and whose symptoms range in severity from minor reductions in host fitness to systemic disease and large-scale mortality. Several characteristics have been useful for classifying iridoviruses; however, novel strains are continuously being discovered and, in many cases, reliable classification has been challenging. Further impeding classification, invertebrate iridoviruses (IIVs) can occasionally infect vertebrates; thus, host range is often not a useful criterion for classification. In this review, we discuss the current classification of iridovirids, focusing on genomic and structural features that distinguish vertebrate and invertebrate iridovirids and viral factors linked to host interactions in IIV6 (Invertebrate iridescent virus 6). In addition, we show for the first time how complete genome sequences of viral isolates can be leveraged to improve classification of new iridovirid isolates and resolve ambiguous relations. Improved classification of the iridoviruses may facilitate the identification of genus-specific virulence factors linked with diverse host phenotypes and host interactions.

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

2015-01-02

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. Copyright © 2015, American Association for the Advancement of Science.

CRISPR/Cas9-Advancing Orthopoxvirus Genome Editing for Vaccine and Vector Development.

PubMed

Okoli, Arinze; Okeke, Malachy I; Tryland, Morten; Moens, Ugo

2018-01-22

The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) technology is revolutionizing genome editing approaches. Its high efficiency, specificity, versatility, flexibility, simplicity and low cost have made the CRISPR/Cas9 system preferable to other guided site-specific nuclease-based systems such as TALENs (Transcription Activator-like Effector Nucleases) and ZFNs (Zinc Finger Nucleases) in genome editing of viruses. CRISPR/Cas9 is presently being applied in constructing viral mutants, preventing virus infections, eradicating proviral DNA, and inhibiting viral replication in infected cells. The successful adaptation of CRISPR/Cas9 to editing the genome of Vaccinia virus paves the way for its application in editing other vaccine/vector-relevant orthopoxvirus (OPXV) strains. Thus, CRISPR/Cas9 can be used to resolve some of the major hindrances to the development of OPXV-based recombinant vaccines and vectors, including sub-optimal immunogenicity; transgene and genome instability; reversion of attenuation; potential of spread of transgenes to wildtype strains and close contacts, which are important biosafety and risk assessment considerations. In this article, we review the published literature on the application of CRISPR/Cas9 in virus genome editing and discuss the potentials of CRISPR/Cas9 in advancing OPXV-based recombinant vaccines and vectors. We also discuss the application of CRISPR/Cas9 in combating viruses of clinical relevance, the limitations of CRISPR/Cas9 and the current strategies to overcome them.

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.

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

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.

CRISPR/Cas9—Advancing Orthopoxvirus Genome Editing for Vaccine and Vector Development

PubMed Central

Okoli, Arinze; Okeke, Malachy I.; Tryland, Morten; Moens, Ugo

2018-01-01

The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) technology is revolutionizing genome editing approaches. Its high efficiency, specificity, versatility, flexibility, simplicity and low cost have made the CRISPR/Cas9 system preferable to other guided site-specific nuclease-based systems such as TALENs (Transcription Activator-like Effector Nucleases) and ZFNs (Zinc Finger Nucleases) in genome editing of viruses. CRISPR/Cas9 is presently being applied in constructing viral mutants, preventing virus infections, eradicating proviral DNA, and inhibiting viral replication in infected cells. The successful adaptation of CRISPR/Cas9 to editing the genome of Vaccinia virus paves the way for its application in editing other vaccine/vector-relevant orthopoxvirus (OPXV) strains. Thus, CRISPR/Cas9 can be used to resolve some of the major hindrances to the development of OPXV-based recombinant vaccines and vectors, including sub-optimal immunogenicity; transgene and genome instability; reversion of attenuation; potential of spread of transgenes to wildtype strains and close contacts, which are important biosafety and risk assessment considerations. In this article, we review the published literature on the application of CRISPR/Cas9 in virus genome editing and discuss the potentials of CRISPR/Cas9 in advancing OPXV-based recombinant vaccines and vectors. We also discuss the application of CRISPR/Cas9 in combating viruses of clinical relevance, the limitations of CRISPR/Cas9 and the current strategies to overcome them. PMID:29361752

Genome-wide association between DNA methylation and alternative splicing in an invertebrate

PubMed Central

2012-01-01

Background Gene bodies are the most evolutionarily conserved targets of DNA methylation in eukaryotes. However, the regulatory functions of gene body DNA methylation remain largely unknown. DNA methylation in insects appears to be primarily confined to exons. Two recent studies in Apis mellifera (honeybee) and Nasonia vitripennis (jewel wasp) analyzed transcription and DNA methylation data for one gene in each species to demonstrate that exon-specific DNA methylation may be associated with alternative splicing events. In this study we investigated the relationship between DNA methylation, alternative splicing, and cross-species gene conservation on a genome-wide scale using genome-wide transcription and DNA methylation data. Results We generated RNA deep sequencing data (RNA-seq) to measure genome-wide mRNA expression at the exon- and gene-level. We produced a de novo transcriptome from this RNA-seq data and computationally predicted splice variants for the honeybee genome. We found that exons that are included in transcription are higher methylated than exons that are skipped during transcription. We detected enrichment for alternative splicing among methylated genes compared to unmethylated genes using fisher’s exact test. We performed a statistical analysis to reveal that the presence of DNA methylation or alternative splicing are both factors associated with a longer gene length and a greater number of exons in genes. In concordance with this observation, a conservation analysis using BLAST revealed that each of these factors is also associated with higher cross-species gene conservation. Conclusions This study constitutes the first genome-wide analysis exhibiting a positive relationship between exon-level DNA methylation and mRNA expression in the honeybee. Our finding that methylated genes are enriched for alternative splicing suggests that, in invertebrates, exon-level DNA methylation may play a role in the construction of splice variants by positively

The Primary Role of Fibrinogen-Related Proteins in Invertebrates Is Defense, Not Coagulation

PubMed Central

Hanington, Patrick C.; Zhang, Si-Ming

2010-01-01

In vertebrates, the conversion of fibrinogen into fibrin is an essential process that underlies the establishment of the supporting protein framework required for coagulation. In invertebrates, fibrinogen-domain-containing proteins play a role in the defense response generated against pathogens; however, they do not function in coagulation, suggesting that this role has been recently acquired. Molecules containing fibrinogen motifs have been identified in numerous invertebrate organisms, and most of these molecules known to date have been linked to defense. Moreover, recent genome projects of invertebrate animals have revealed surprisingly high numbers of fibrinogen-like loci in their genomes, suggesting important and perhaps diverse functions of fibrinogen-like proteins in invertebrates. The ancestral role of molecules containing fibrinogen-related domains (FReDs) with immunity is the focus of this review, with emphasis on specific FReDs called fibrinogen-related proteins (FREPs) identified from the schistosome-transmitting mollusc Biomphalaria glabrata. Herein, we outline the range of invertebrate organisms FREPs can be found in, and detail the roles these molecules play in defense and protection against infection. PMID:21063081

Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing.

PubMed

Cramaro, Wibke J; Hunewald, Oliver E; Bell-Sakyi, Lesley; Muller, Claude P

2017-02-08

Global warming and other ecological changes have facilitated the expansion of Ixodes ricinus tick populations. Ixodes ricinus is the most important carrier of vector-borne pathogens in Europe, transmitting viruses, protozoa and bacteria, in particular Borrelia burgdorferi (sensu lato), the causative agent of Lyme borreliosis, the most prevalent vector-borne disease in humans in the Northern hemisphere. To faster control this disease vector, a better understanding of the I. ricinus tick is necessary. To facilitate such studies, we recently published the first reference genome of this highly prevalent pathogen vector. Here, we further extend these studies by scaffolding and annotating the first reference genome by using ultra-long sequencing reads from third generation single molecule sequencing. In addition, we present the first genome size estimation for I. ricinus ticks and the embryo-derived cell line IRE/CTVM19. 235,953 contigs were integrated into 204,904 scaffolds, extending the currently known genome lengths by more than 30% from 393 to 516 Mb and the N50 contig value by 87% from 1643 bp to a N50 scaffold value of 3067 bp. In addition, 25,263 sequences were annotated by comparison to the tick's North American relative Ixodes scapularis. After (conserved) hypothetical proteins, zinc finger proteins, secreted proteins and P450 coding proteins were the most prevalent protein categories annotated. Interestingly, more than 50% of the amino acid sequences matching the homology threshold had 95-100% identity to the corresponding I. scapularis gene models. The sequence information was complemented by the first genome size estimation for this species. Flow cytometry-based genome size analysis revealed a haploid genome size of 2.65Gb for I. ricinus ticks and 3.80 Gb for the cell line. We present a first draft sequence map of the I. ricinus genome based on a PacBio-Illumina assembly. The I. ricinus genome was shown to be 26% (500 Mb) larger than the genome of its

2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.

PubMed

Hernandez-Castro, Luis E; Paterno, Marta; Villacís, Anita G; Andersson, Björn; Costales, Jaime A; De Noia, Michele; Ocaña-Mayorga, Sofía; Yumiseva, Cesar A; Grijalva, Mario J; Llewellyn, Martin S

2017-07-01

Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses. The 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area. Our findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment.

2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador

PubMed Central

Villacís, Anita G.; Andersson, Björn; Costales, Jaime A.; De Noia, Michele; Ocaña-Mayorga, Sofía; Yumiseva, Cesar A.; Grijalva, Mario J.; Llewellyn, Martin S.

2017-01-01

Background Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses. Methodology/Principal findings The 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area. Conclusions/Significance Our findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment. PMID:28723901

Cre/lox-Recombinase-Mediated Cassette Exchange for Reversible Site-Specific Genomic Targeting of the Disease Vector, Aedes aegypti.

PubMed

Häcker, Irina; Harrell Ii, Robert A; Eichner, Gerrit; Pilitt, Kristina L; O'Brochta, David A; Handler, Alfred M; Schetelig, Marc F

2017-03-07

Site-specific genome modification (SSM) is an important tool for mosquito functional genomics and comparative gene expression studies, which contribute to a better understanding of mosquito biology and are thus a key to finding new strategies to eliminate vector-borne diseases. Moreover, it allows for the creation of advanced transgenic strains for vector control programs. SSM circumvents the drawbacks of transposon-mediated transgenesis, where random transgene integration into the host genome results in insertional mutagenesis and variable position effects. We applied the Cre/lox recombinase-mediated cassette exchange (RMCE) system to Aedes aegypti, the vector of dengue, chikungunya, and Zika viruses. In this context we created four target site lines for RMCE and evaluated their fitness costs. Cre-RMCE is functional in a two-step mechanism and with good efficiency in Ae. aegypti. The advantages of Cre-RMCE over existing site-specific modification systems for Ae. aegypti, phiC31-RMCE and CRISPR, originate in the preservation of the recombination sites, which 1) allows successive modifications and rapid expansion or adaptation of existing systems by repeated targeting of the same site; and 2) provides reversibility, thus allowing the excision of undesired sequences. Thereby, Cre-RMCE complements existing genomic modification tools, adding flexibility and versatility to vector genome targeting.

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

“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

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

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.

A pair of new BAC and BIBAC vectors that facilitate BAC/BIBAC library construction and intact large genomic DNA insert exchange.

PubMed

Shi, Xue; Zeng, Haiyang; Xue, Yadong; Luo, Meizhong

2011-10-11

Large-insert BAC and BIBAC libraries are important tools for structural and functional genomics studies of eukaryotic genomes. To facilitate the construction of BAC and BIBAC libraries and the transfer of complete large BAC inserts into BIBAC vectors, which is desired in positional cloning, we developed a pair of new BAC and BIBAC vectors. The new BAC vector pIndigoBAC536-S and the new BIBAC vector BIBAC-S have the following features: 1) both contain two 18-bp non-palindromic I-SceI sites in an inverted orientation at positions that flank an identical DNA fragment containing the lacZ selection marker and the cloning site. Large DNA inserts can be excised from the vectors as single fragments by cutting with I-SceI, allowing the inserts to be easily sized. More importantly, because the two vectors contain different antibiotic resistance genes for transformant selection and produce the same non-complementary 3' protruding ATAA ends by I-SceI that suppress self- and inter-ligations, the exchange of intact large genomic DNA inserts between the BAC and BIBAC vectors is straightforward; 2) both were constructed as high-copy composite vectors. Reliable linearized and dephosphorylated original low-copy pIndigoBAC536-S and BIBAC-S vectors that are ready for library construction can be prepared from the high-copy composite vectors pHZAUBAC1 and pHZAUBIBAC1, respectively, without the need for additional preparation steps or special reagents, thus simplifying the construction of BAC and BIBAC libraries. BIBAC clones constructed with the new BIBAC-S vector are stable in both E. coli and Agrobacterium. The vectors can be accessed through our website http://GResource.hzau.edu.cn. The two new vectors and their respective high-copy composite vectors can largely facilitate the construction and characterization of BAC and BIBAC libraries. The transfer of complete large genomic DNA inserts from one vector to the other is made straightforward.

Applying Genomic and Bioinformatic Resources to Human Adenovirus Genomes for Use in Vaccine Development and for Applications in Vector Development for Gene Delivery

PubMed Central

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. PMID:21994597

Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors.

PubMed

Oppenheim, Sara J; Rosenfeld, Jeffrey A; DeSalle, Rob

2017-02-27

The persistent and growing gap between the availability of sequenced genomes and the ability to assign functions to sequenced genes led us to explore ways to maximize the information content of automated annotation for studies of anopheline mosquitos. Specifically, we use genome content analysis of a large number of previously sequenced anopheline mosquitos to follow the loss and gain of protein families over the evolutionary history of this group. The importance of this endeavor lies in the potential for comparative genomic studies between Anopheles and closely related non-vector species to reveal ancestral genome content dynamics involved in vector competence. In addition, comparisons within Anopheles could identify genome content changes responsible for variation in the vectorial capacity of this family of important parasite vectors. The competence and capacity of P. falciparum vectors do not appear to be phylogenetically constrained within the Anophelinae. Instead, using ancestral reconstruction methods, we suggest that a previously unexamined component of vector biology, anopheline nucleotide metabolism, may contribute to the unique status of anophelines as P. falciparum vectors. While the fitness effects of nucleotide co-option by P. falciparum parasites on their anopheline hosts are not yet known, our results suggest that anopheline genome content may be responding to selection pressure from P. falciparum. Whether this response is defensive, in an attempt to redress improper nucleotide balance resulting from P. falciparum infection, or perhaps symbiotic, resulting from an as-yet-unknown mutualism between anophelines and P. falciparum, is an open question that deserves further study. Clearly, there is a wealth of functional information to be gained from detailed manual genome annotation, yet the rapid increase in the number of available sequences means that most researchers will not have the time or resources to manually annotate all the sequence data they

Getting genetic access to natural adenovirus genomes to explore vector diversity.

PubMed

Zhang, Wenli; Ehrhardt, Anja

2017-10-01

Recombinant vectors based on the human adenovirus type 5 (HAdV5) have been developed and extensively used in preclinical and clinical studies for over 30 years. However, certain restrictions of HAdV5-based vectors have limited their clinical applications because they are rather inefficient in specifically transducing cells of therapeutic interest that lack the coxsackievirus and adenovirus receptor (CAR). Moreover, enhanced vector-associated toxicity and widespread preexisting immunity have been shown to significantly hamper the effectiveness of HAdV-5-mediated gene transfer. However, evolution of adenoviruses in the natural host is driving the generation of novel types with altered virulence, enhanced transmission, and altered tissue tropism. As a consequence, an increasing number of alternative adenovirus types were identified, which may represent a valuable resource for the development of novel vector types. Thus, researchers are focusing on the other naturally occurring adenovirus types, which are structurally similar but functionally different from HAdV5. To this end, several strategies have been devised for getting genetic access to adenovirus genomes, resulting in a new panel of adenoviral vectors. Importantly, these vectors were shown to have a host range different from HAdV5 and to escape the anti-HAdV5 immune response, thus underlining the great potential of this approach. In summary, this review provides a state-of-the-art overview of one essential step in adenoviral vector development.

Diversity of small, single-stranded DNA viruses of invertebrates and their chaotic evolutionary past.

PubMed

Tijssen, Peter; Pénzes, Judit J; Yu, Qian; Pham, Hanh T; Bergoin, Max

2016-10-01

A wide spectrum of invertebrates is susceptible to various single-stranded DNA viruses. Their relative simplicity of replication and dependence on actively dividing cells makes them highly pathogenic for many invertebrates (Hexapoda, Decapoda, etc.). We present their taxonomical classification and describe the evolutionary relationships between various groups of invertebrate-infecting viruses, their high degree of recombination, and their relationship to viruses infecting mammals or other vertebrates. They share characteristics of the viruses within the various families, including structure of the virus particle, genome properties, and gene expression strategy. Copyright © 2016. Published by Elsevier Inc.

Stable integration of recombinant adeno-associated virus vector genomes after transduction of murine hematopoietic stem cells.

PubMed

Han, Zongchao; Zhong, Li; Maina, Njeri; Hu, Zhongbo; Li, Xiaomiao; Chouthai, Nitin S; Bischof, Daniela; Weigel-Van Aken, Kirsten A; Slayton, William B; Yoder, Mervin C; Srivastava, Arun

2008-03-01

We previously reported that among single-stranded adeno-associated virus (ssAAV) vectors, serotypes 1 through 5, ssAAV1 is the most efficient in transducing murine hematopoietic stem cells (HSCs), but viral second-strand DNA synthesis remains a rate-limiting step. Subsequently, using double-stranded, self-complementary AAV (scAAV) vectors, serotypes 7 through 10, we observed that scAAV7 vectors also transduce murine HSCs efficiently. In the present study, we used scAAV1 and scAAV7 shuttle vectors to transduce HSCs in a murine bone marrow serial transplant model in vivo, which allowed examination of the AAV proviral integration pattern in the mouse genome, as well as recovery and nucleotide sequence analyses of AAV-HSC DNA junction fragments. The proviral genomes were stably integrated, and integration sites were localized to different mouse chromosomes. None of the integration sites was found to be in a transcribed gene, or near a cellular oncogene. None of the animals, monitored for up to 1 year, exhibited pathological abnormalities. Thus, AAV proviral integration-induced risk of oncogenesis was not found in our study, which provides functional confirmation of stable transduction of self-renewing multipotential HSCs by scAAV vectors as well as promise for the use of these vectors in the potential treatment of disorders of the hematopoietic system.

An adaptable chromosome preparation methodology for use in invertebrate research organisms.

PubMed

Guo, Longhua; Accorsi, Alice; He, Shuonan; Guerrero-Hernández, Carlos; Sivagnanam, Shamilene; McKinney, Sean; Gibson, Matthew; Sánchez Alvarado, Alejandro

2018-02-26

The ability to efficiently visualize and manipulate chromosomes is fundamental to understanding the genome architecture of organisms. Conventional chromosome preparation protocols developed for mammalian cells and those relying on species-specific conditions are not suitable for many invertebrates. Hence, a simple and inexpensive chromosome preparation protocol, adaptable to multiple invertebrate species, is needed. We optimized a chromosome preparation protocol and applied it to several planarian species (phylum Platyhelminthes), the freshwater apple snail Pomacea canaliculata (phylum Mollusca), and the starlet sea anemone Nematostella vectensis (phylum Cnidaria). We demonstrated that both mitotically active adult tissues and embryos can be used as sources of metaphase chromosomes, expanding the potential use of this technique to invertebrates lacking cell lines and/or with limited access to the complete life cycle. Simple hypotonic treatment with deionized water was sufficient for karyotyping; growing cells in culture was not necessary. The obtained karyotypes allowed the identification of differences in ploidy and chromosome architecture among otherwise morphologically indistinguishable organisms, as in the case of a mixed population of planarians collected in the wild. Furthermore, we showed that in all tested organisms representing three different phyla this protocol could be effectively coupled with downstream applications, such as chromosome fluorescent in situ hybridization. Our simple and inexpensive chromosome preparation protocol can be readily adapted to new invertebrate research organisms to accelerate the discovery of novel genomic patterns across the branches of the tree of life.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2014-01-01

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

Genomic Footprints of Selective Sweeps from Metabolic Resistance to Pyrethroids in African Malaria Vectors Are Driven by Scale up of Insecticide-Based Vector Control.

PubMed

Barnes, Kayla G; Weedall, Gareth D; Ndula, Miranda; Irving, Helen; Mzihalowa, Themba; Hemingway, Janet; Wondji, Charles S

2017-02-01

Insecticide resistance in mosquito populations threatens recent successes in malaria prevention. Elucidating patterns of genetic structure in malaria vectors to predict the speed and direction of the spread of resistance is essential to get ahead of the 'resistance curve' and to avert a public health catastrophe. Here, applying a combination of microsatellite analysis, whole genome sequencing and targeted sequencing of a resistance locus, we elucidated the continent-wide population structure of a major African malaria vector, Anopheles funestus. We identified a major selective sweep in a genomic region controlling cytochrome P450-based metabolic resistance conferring high resistance to pyrethroids. This selective sweep occurred since 2002, likely as a direct consequence of scaled up vector control as revealed by whole genome and fine-scale sequencing of pre- and post-intervention populations. Fine-scaled analysis of the pyrethroid resistance locus revealed that a resistance-associated allele of the cytochrome P450 monooxygenase CYP6P9a has swept through southern Africa to near fixation, in contrast to high polymorphism levels before interventions, conferring high levels of pyrethroid resistance linked to control failure. Population structure analysis revealed a barrier to gene flow between southern Africa and other areas, which may prevent or slow the spread of the southern mechanism of pyrethroid resistance to other regions. By identifying a genetic signature of pyrethroid-based interventions, we have demonstrated the intense selective pressure that control interventions exert on mosquito populations. If this level of selection and spread of resistance continues unabated, our ability to control malaria with current interventions will be compromised.

Torix group Rickettsia are widespread in Culicoides biting midges (Diptera: Ceratopogonidae), reach high frequency and carry unique genomic features

PubMed Central

Pilgrim, Jack; Ander, Mats; Garros, Claire; Baylis, Matthew; Hurst, Gregory D. D.

2017-01-01

Summary There is increasing interest in the heritable bacteria of invertebrate vectors of disease as they present novel targets for control initiatives. Previous studies on biting midges (Culicoides spp.), known to transmit several RNA viruses of veterinary importance, have revealed infections with the endosymbiotic bacteria, Wolbachia and Cardinium. However, rickettsial symbionts in these vectors are underexplored. Here, we present the genome of a previously uncharacterized Rickettsia endosymbiont from Culicoides newsteadi (RiCNE). This genome presents unique features potentially associated with host invasion and adaptation, including genes for the complete non‐oxidative phase of the pentose phosphate pathway, and others predicted to mediate lipopolysaccharides and cell wall modification. Screening of 414 Culicoides individuals from 29 Palearctic or Afrotropical species revealed that Rickettsia represent a widespread but previously overlooked association, reaching high frequencies in midge populations and present in 38% of the species tested. Sequence typing clusters the Rickettsia within the Torix group of the genus, a group known to infect several aquatic and hematophagous taxa. FISH analysis indicated the presence of Rickettsia bacteria in ovary tissue, indicating their maternal inheritance. Given the importance of biting midges as vectors, a key area of future research is to establish the impact of this endosymbiont on vector competence. PMID:28805302

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

In vivo Assembly in Escherichia coli of Transformation Vectors for Plastid Genome Engineering.

PubMed

Wu, Yuyong; You, Lili; Li, Shengchun; Ma, Meiqi; Wu, Mengting; Ma, Lixin; Bock, Ralph; Chang, Ling; Zhang, Jiang

2017-01-01

Plastid transformation for the expression of recombinant proteins and entire metabolic pathways has become a promising tool for plant biotechnology. However, large-scale application of this technology has been hindered by some technical bottlenecks, including lack of routine transformation protocols for agronomically important crop plants like rice or maize. Currently, there are no standard or commercial plastid transformation vectors available for the scientific community. Construction of a plastid transformation vector usually requires tedious and time-consuming cloning steps. In this study, we describe the adoption of an in vivo Escherichia coli cloning (iVEC) technology to quickly assemble a plastid transformation vector. The method enables simple and seamless build-up of a complete plastid transformation vector from five DNA fragments in a single step. The vector assembled for demonstration purposes contains an enhanced green fluorescent protein (GFP) expression cassette, in which the gfp transgene is driven by the tobacco plastid ribosomal RNA operon promoter fused to the 5' untranslated region (UTR) from gene10 of bacteriophage T7 and the transcript-stabilizing 3'UTR from the E. coli ribosomal RNA operon rrnB . Successful transformation of the tobacco plastid genome was verified by Southern blot analysis and seed assays. High-level expression of the GFP reporter in the transplastomic plants was visualized by confocal microscopy and Coomassie staining, and GFP accumulation was ~9% of the total soluble protein. The iVEC method represents a simple and efficient approach for construction of plastid transformation vector, and offers great potential for the assembly of increasingly complex vectors for synthetic biology applications in plastids.

Efficient genome editing of wild strawberry genes, vector development and validation.

PubMed

Zhou, Junhui; Wang, Guoming; Liu, Zhongchi

2018-03-25

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system is an effective genome editing tool for plant and animal genomes. However, there are still few reports on the successful application of CRISPR-Cas9 to horticultural plants, especially with regard to germ-line transmission of targeted mutations. Here, we report high-efficiency genome editing in the wild strawberry Fragaria vesca and its successful application to mutate the auxin biosynthesis gene TAA1 and auxin response factor 8 (ARF8). In our CRISPR system, the Arabidopsis U6 promoter AtU6-26 and the wild strawberry U6 promoter FveU6-2 were each used to drive the expression of sgRNA, and both promoters were shown to lead to high-efficiency genome editing in strawberry. To test germ-line transmission of the edited mutations and new mutations induced in the next generation, the progeny of the primary (T0) transgenic plants carrying the CRISPR construct was analysed. New mutations were detected in the progeny plants at a high efficiency, including large deletions between the two PAM sites. Further, T1 plants harbouring arf8 homozygous knockout mutations grew considerably faster than wild-type plants. The results indicate that our CRISPR vectors can be used to edit the wild strawberry genome at a high efficiency and that both sgRNA design and appropriate U6 promoters contribute to the success of genomic editing. Our results open up exciting opportunities for engineering strawberry and related horticultural crops to improve traits of economic importance. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Vectors of invasions in freshwater invertebrates and fishes

USGS Publications Warehouse

Fuller, Pamela 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).

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

USDA-ARS?s Scientific Manuscript database

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...

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.

Ecological approaches to informing public health policy and risk assessments on emerging vector-borne zoonoses

PubMed Central

Medlock, JM; Jameson, LJ

2010-01-01

Pathogens associated with vector-borne zoonoses occur in enzootic cycles within nature. They are driven by a combination of vertebrate host and invertebrate vector population dynamics, which in turn respond to changes in environmental stimuli. Human involvement in these cycles, and hence the occurrence of human disease, is often to act as incidental host. From a public health perspective our ability to better predict human outbreaks of these diseases and prepare intervention and mitigation strategies relies on understanding the natural cycle of pathogen transmission. This requires consideration of, for example, invertebrate and vertebrate ecology and biology, climatology, land use and habitat change. Collectively, these can be referred to as medical entomology and medical ecology. This article reviews the importance for inclusion of such disciplines when assessing the public health risk from vector-borne zoonoses and summarizes the possible future challenges and driving forces for changes in vector status and vector-borne zoonoses emergence, with a particular focus on a UK and European context. PMID:22460391

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.

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.

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. © 2013 John Wiley & Sons Ltd.

In vivo Assembly in Escherichia coli of Transformation Vectors for Plastid Genome Engineering

PubMed Central

Wu, Yuyong; You, Lili; Li, Shengchun; Ma, Meiqi; Wu, Mengting; Ma, Lixin; Bock, Ralph; Chang, Ling; Zhang, Jiang

2017-01-01

Plastid transformation for the expression of recombinant proteins and entire metabolic pathways has become a promising tool for plant biotechnology. However, large-scale application of this technology has been hindered by some technical bottlenecks, including lack of routine transformation protocols for agronomically important crop plants like rice or maize. Currently, there are no standard or commercial plastid transformation vectors available for the scientific community. Construction of a plastid transformation vector usually requires tedious and time-consuming cloning steps. In this study, we describe the adoption of an in vivo Escherichia coli cloning (iVEC) technology to quickly assemble a plastid transformation vector. The method enables simple and seamless build-up of a complete plastid transformation vector from five DNA fragments in a single step. The vector assembled for demonstration purposes contains an enhanced green fluorescent protein (GFP) expression cassette, in which the gfp transgene is driven by the tobacco plastid ribosomal RNA operon promoter fused to the 5′ untranslated region (UTR) from gene10 of bacteriophage T7 and the transcript-stabilizing 3′UTR from the E. coli ribosomal RNA operon rrnB. Successful transformation of the tobacco plastid genome was verified by Southern blot analysis and seed assays. High-level expression of the GFP reporter in the transplastomic plants was visualized by confocal microscopy and Coomassie staining, and GFP accumulation was ~9% of the total soluble protein. The iVEC method represents a simple and efficient approach for construction of plastid transformation vector, and offers great potential for the assembly of increasingly complex vectors for synthetic biology applications in plastids. PMID:28871270

Invertebrate biomechanics.

PubMed

Patek, S N; Summers, A P

2017-05-22

Invertebrate biomechanics focuses on mechanical analyses of non-vertebrate animals, which at root is no different in aim and technique from vertebrate biomechanics, or for that matter the biomechanics of plants and fungi. But invertebrates are special - they are fabulously diverse in form, habitat, and ecology and manage this without the use of hard, internal skeletons. They are also numerous and, in many cases, tractable in an experimental and field setting. In this Primer, we will probe three axes of invertebrate diversity: worms (Phylum Annelida), spiders (Class Arachnida) and insects (Class Insecta); three habitats: subterranean, terrestrial and airborne; and three integrations with other fields: ecology, engineering and evolution. Our goal is to capture the field of invertebrate biomechanics, which has blossomed from having a primary focus on discoveries at the interface of physics and biology to being inextricably linked with integrative challenges that span biology, physics, mathematics and engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

PubMed Central

Hosmani, Prashant S.; Villalobos-Ayala, Krystal; Miller, Sherry; Shippy, Teresa; Flores, Mirella; Rosendale, Andrew; Cordola, Chris; Bell, Tracey; Mann, Hannah; DeAvila, Gabe; DeAvila, Daniel; Moore, Zachary; Buller, Kyle; Ciolkevich, Kathryn; Nandyal, Samantha; Mahoney, Robert; Van Voorhis, Joshua; Dunlevy, Megan; Farrow, David; Hunter, David; Morgan, Taylar; Shore, Kayla; Guzman, Victoria; Izsak, Allison; Dixon, Danielle E.; Cridge, Andrew; Cano, Liliana; Cao, Xiaolong; Jiang, Haobo; Leng, Nan; Johnson, Shannon; Cantarel, Brandi L.; Richards, Stephen; English, Adam; Shatters, Robert G.; Childers, Chris; Chen, Mei-Ju; Hunter, Wayne; Cilia, Michelle; Mueller, Lukas A.; Munoz-Torres, Monica; Nelson, David; Poelchau, Monica F.; Benoit, Joshua B.; Wiersma-Koch, Helen; D’Elia, Tom; Brown, Susan J.

2017-01-01

Abstract The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. Database URL: https://citrusgreening.org/ PMID:29220441

CRISPR-Cas9 vectors for genome editing and host engineering in the baculovirus-insect cell system.

PubMed

Mabashi-Asazuma, Hideaki; Jarvis, Donald L

2017-08-22

The baculovirus-insect cell system (BICS) has been widely used to produce many different recombinant proteins for basic research and is being used to produce several biologics approved for use in human or veterinary medicine. Early BICS were technically complex and constrained by the relatively primordial nature of insect cell protein glycosylation pathways. Since then, recombination has been used to modify baculovirus vectors-which has simplified the system-and transform insect cells, which has enhanced its protein glycosylation capabilities. Now, CRISPR-Cas9 tools for site-specific genome editing are needed to facilitate further improvements in the BICS. Thus, in this study, we used various insect U6 promoters to construct CRISPR-Cas9 vectors and assessed their utility for site-specific genome editing in two insect cell lines commonly used as hosts in the BICS. We demonstrate the use of CRISPR-Cas9 to edit an endogenous insect cell gene and alter protein glycosylation in the BICS.

Introduction: Invertebrate Neuropeptides XIV

USDA-ARS?s Scientific Manuscript database

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...

Introduction: Invertebrate Neuropeptides XVI

USDA-ARS?s Scientific Manuscript database

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...

Introduction: Invertebrate Neuropeptides XV

USDA-ARS?s Scientific Manuscript database

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...

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.

All-in-One CRISPR-Cas9/FokI-dCas9 Vector-Mediated Multiplex Genome Engineering in Cultured Cells.

PubMed

Sakuma, Tetsushi; Sakamoto, Takuya; Yamamoto, Takashi

2017-01-01

CRISPR-Cas9 enables highly convenient multiplex genome engineering in cultured cells, because it utilizes generic Cas9 nuclease and an easily customizable single-guide RNA (sgRNA) for site-specific DNA double-strand break induction. We previously established a multiplex CRISPR-Cas9 assembly system for constructing an all-in-one vector simultaneously expressing multiple sgRNAs and Cas9 nuclease or other Cas9 variants including FokI-dCas9, which supersedes the wild-type Cas9 with regard to high specificity. In this chapter, we describe a streamlined protocol to design and construct multiplex CRISPR-Cas9 or FokI-dCas9 vectors, to introduce them into cultured cells by lipofection or electroporation, to enrich the genomically edited cells with a transient puromycin selection, to validate the mutation efficiency by Surveyor nuclease assay, and to perform off-target analyses. We show that our protocol enables highly efficient multiplex genome engineering even in hard-to-transfect HepG2 cells.

Torix group Rickettsia are widespread in Culicoides biting midges (Diptera: Ceratopogonidae), reach high frequency and carry unique genomic features.

PubMed

Pilgrim, Jack; Ander, Mats; Garros, Claire; Baylis, Matthew; Hurst, Gregory D D; Siozios, Stefanos

2017-10-01

There is increasing interest in the heritable bacteria of invertebrate vectors of disease as they present novel targets for control initiatives. Previous studies on biting midges (Culicoides spp.), known to transmit several RNA viruses of veterinary importance, have revealed infections with the endosymbiotic bacteria, Wolbachia and Cardinium. However, rickettsial symbionts in these vectors are underexplored. Here, we present the genome of a previously uncharacterized Rickettsia endosymbiont from Culicoides newsteadi (RiCNE). This genome presents unique features potentially associated with host invasion and adaptation, including genes for the complete non-oxidative phase of the pentose phosphate pathway, and others predicted to mediate lipopolysaccharides and cell wall modification. Screening of 414 Culicoides individuals from 29 Palearctic or Afrotropical species revealed that Rickettsia represent a widespread but previously overlooked association, reaching high frequencies in midge populations and present in 38% of the species tested. Sequence typing clusters the Rickettsia within the Torix group of the genus, a group known to infect several aquatic and hematophagous taxa. FISH analysis indicated the presence of Rickettsia bacteria in ovary tissue, indicating their maternal inheritance. Given the importance of biting midges as vectors, a key area of future research is to establish the impact of this endosymbiont on vector competence. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Reflections on the Anopheles gambiae genome sequence, transgenic mosquitoes and the prospect for controlling malaria and other vector borne diseases.

PubMed

Tabachnick, Walter J

2003-09-01

The completion of the Anopheles gambiae Giles genome sequencing project is a milestone toward developing more effective strategies in reducing the impact of malaria and other vector borne diseases. The successes in developing transgenic approaches using mosquitoes have provided another essential new tool for further progress in basic vector genetics and the goal of disease control. The use of transgenic approaches to develop refractory mosquitoes is also possible. The ability to use genome sequence to identify genes, and transgenic approaches to construct refractory mosquitoes, has provided the opportunity that with the future development of an appropriate genetic drive system, refractory transgenes can be released into vector populations leading to nontransmitting mosquitoes. An. gambiae populations incapable of transmitting malaria. This compelling strategy will be very difficult to achieve and will require a broad substantial research program for success. The fundamental information that is required on genome structure, gene function and environmental effects on genetic expression are largely unknown. The ability to predict gene effects on phenotype is rudimentary, particularly in natural populations. As a result, the release of a refractory transgene into natural mosquito populations is imprecise and there is little ability to predict unintended consequences. The new genetic tools at hand provide opportunities to address an array of important issues, many of which can have immediate impact on the effectiveness of a host of strategies to control vector borne disease. Transgenic release approaches represent only one strategy that should be pursued. A balanced research program is required.

Ocean acidification reduces sperm flagellar motility in broadcast spawning reef invertebrates.

PubMed

Morita, Masaya; Suwa, Ryota; Iguchi, Akira; Nakamura, Masako; Shimada, Kazuaki; Sakai, Kazuhiko; Suzuki, Atsushi

2010-05-01

Ocean acidification is now recognized as a threat to marine ecosystems; however, the effect of ocean acidification on fertilization in marine organisms is still largely unknown. In this study, we focused on sperm flagellar motility in broadcast spawning reef invertebrates (a coral and a sea cucumber). Below pH 7.7, the pH predicted to occur within the next 100 years, sperm flagellar motility was seriously impaired in these organisms. Considering that sperm flagellar motility is indispensable for transporting the paternal haploid genome for fertilization, fertilization taking place in seawater may decline in the not too distant future. Urgent surveys are necessary for a better understanding of the physiological consequences of ocean acidification on sperm flagellar motility in a wide range of marine invertebrates.

Germline incorporation of a replication-defective adenoviral vector in mice does not alter immune responses to adenoviral vectors.

PubMed

Camargo, F D; Huey-Louie, D A; Finn, A V; Sassani, A B; Cozen, A E; Moriwaki, H; Schneider, D B; Agah, R; Dichek, D A

2000-11-01

The utility of adenoviral vectors is limited by immune responses to adenoviral antigens. We sought to develop immune-competent mice in which the immune response to adenoviral antigens was selectively absent. To do so, we generated mice that were transgenic for a replication-defective vector. Adenoviral antigens might be seen as self-antigens by these mice, and the mice could exhibit immunologic tolerance after postnatal exposure to adenoviral vectors. In addition, characterization of these mice could reveal potential consequences of germline transmission of an adenoviral vector, as might occur in a gene therapy trial. Injection of a "null" (not containing a transgene) E1, E3-deleted vector genome into mouse zygotes yielded five founders that were capable of transmitting the vector genome. Among offspring of these mice, transgenic pups were significantly underrepresented: 108 of 255 pups (42%) were transgenic (P<0.02 versus expected frequency of 50%). Postnatal transgenic mice, however, had no apparent abnormalities. Persistence of an adenoviral vector after intravenous injection was equivalent in livers of transgenic mice and their nontransgenic littermates. Transgenic and nontransgenic mice also had equivalent humoral and cellular immune responses to adenoviral vector injection. Mice that are transgenic for an E1, E3-deleted adenoviral genome can be easily generated; however, they are not tolerant of adenovirus. Moreover, germline transmission of an adenoviral vector genome does not prevent generation of a robust immune response after exposure to adenoviral antigens.

Can plastic bag derived-microplastics act as vectors for metal exposure in terrestrial invertebrates?

NASA Astrophysics Data System (ADS)

E Hodson, Mark; Duffus-Hodson, Calum A.; Prendergast-Miller, Miranda; Thorpe, Karen

2017-04-01

Microplastics are widely reported contaminants in marine and freshwater ecosystems and studies have shown that they can be ingested by aquatic organisms and lead to potential negative effects on health. The effects can arise from the physical effects of the plastics (e.g. food displacement and blockages of the digestive tract) and from their potential to adsorb contaminants, primarily organic compounds, resulting in an increased exposure of the organism to toxic contaminants. Studies are beginning to emerge that also show a high abundance of microplastics in the terrestrial environment but there remains a lack of data on the impacts of these terrestrial microplastics or their interaction with other terrestrial pollutants. We conducted Zn adsorption experiments using HDPE microplastics, derived from plastic bags. Zinc adsorption to microplastics was similar to that observed in soils, but in the presence of both soil and microplastics, preferential adsorption onto the soil was observed. In desorption experiments, desorption of Zn from microplastics and soils was minimal (< 10 %) in 0.01 M CaCl2 solution, but in synthetic earthworm guts desorption of 40 - 60% was observed for the microplastics compared to 2 - 15 % for the soils. In earthworm exposure experiments Lumbricus terrestris earthworms cultivated in soils containing 0.35% by mass of Zn-bearing plastic (236 - 4505 mg kg-1) ingested the microplastics with no evidence for either preferential feeding or avoidance. There was no evidence for an accumulation of the microplastics in the earthworm gut or for signs of toxicity. Our experiments demonstrate that earthworms will ingest microplastics and that microplastics can adsorb metals and act as vectors for metal exposure in soil invertebrates. However, for Zn, the risk associated with this exposure appears to be minimal.

[Sendai virus vector: vector development and its application to health care and biotechnology].

PubMed

Iida, Akihiro

2007-06-01

Sendai virus (SeV) is an enveloped virus with a nonsegmented negative-strand RNA genome and a member of the paramyxovirus family. We have developed SeV vector which has shown a high efficiently of gene transfer and expression of foreign genes to a wide range of dividing and non-dividing mammalian cells and tissues. One of the characteristics of the vector is that the genome is located exclusively in the cytoplasm of infected cells and does not go through a DNA phase; thus there is no concern about unwanted integration of foreign sequences into chromosomal DNA. Therefore, this new class of "cytoplasmic RNA vector", an RNA vector with cytoplasmic expression, is expected to be a safer and more efficient viral vector than existing vectors for application to human therapy in various fields including gene therapy and vaccination. In this review, I describe development of Sendai virus vector, its application in the field of biotechnology and clinical application aiming to treat for a large number of diseases including cancer, cardiovascular disease, infectious diseases and neurologic disorders.

Chromosomal integration of adenoviral vector DNA in vivo.

PubMed

Stephen, Sam Laurel; Montini, Eugenio; Sivanandam, Vijayshankar Ganesh; Al-Dhalimy, Muhseen; Kestler, Hans A; Finegold, Milton; Grompe, Markus; Kochanek, Stefan

2010-10-01

So far there has been no report of any clinical or preclinical evidence for chromosomal vector integration following adenovirus (Ad) vector-mediated gene transfer in vivo. We used liver gene transfer with high-capacity Ad vectors in the FAH(Deltaexon5) mouse model to analyze homologous and heterologous recombination events between vector and chromosomal DNA. Intravenous injection of Ad vectors either expressing a fumarylacetoacetate hydrolase (FAH) cDNA or carrying part of the FAH genomic locus resulted in liver nodules of FAH-expressing hepatocytes, demonstrating chromosomal vector integration. Analysis of junctions between vector and chromosomal DNA following heterologous recombination indicated integration of the vector genome through its termini. Heterologous recombination occurred with a median frequency of 6.72 x 10(-5) per transduced hepatocyte, while homologous recombination occurred more rarely with a median frequency of 3.88 x 10(-7). This study has established quantitative and qualitative data on recombination of adenoviral vector DNA with genomic DNA in vivo, contributing to a risk-benefit assessment of the biosafety of Ad vector-mediated gene transfer.

*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...

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.

Genomic Confirmation of Hybridisation and Recent Inbreeding in a Vector-Isolated Leishmania Population

PubMed Central

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. PMID:24453988

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.

Conserved Genes Act as Modifiers of Invertebrate SMN Loss of Function Defects

PubMed Central

Chang, Howard C.; Sen, Anindya; Kalloo, Geetika; Harris, Jevede; Barsby, Tom; Walsh, Melissa B.; Satterlee, John S.; Li, Chris; Van Vactor, David; Artavanis-Tsakonas, Spyros; Hart, Anne C.

2010-01-01

Spinal Muscular Atrophy (SMA) is caused by diminished function of the Survival of Motor Neuron (SMN) protein, but the molecular pathways critical for SMA pathology remain elusive. We have used genetic approaches in invertebrate models to identify conserved SMN loss of function modifier genes. Drosophila melanogaster and Caenorhabditis elegans each have a single gene encoding a protein orthologous to human SMN; diminished function of these invertebrate genes causes lethality and neuromuscular defects. To find genes that modulate SMN function defects across species, two approaches were used. First, a genome-wide RNAi screen for C. elegans SMN modifier genes was undertaken, yielding four genes. Second, we tested the conservation of modifier gene function across species; genes identified in one invertebrate model were tested for function in the other invertebrate model. Drosophila orthologs of two genes, which were identified originally in C. elegans, modified Drosophila SMN loss of function defects. C. elegans orthologs of twelve genes, which were originally identified in a previous Drosophila screen, modified C. elegans SMN loss of function defects. Bioinformatic analysis of the conserved, cross-species, modifier genes suggests that conserved cellular pathways, specifically endocytosis and mRNA regulation, act as critical genetic modifiers of SMN loss of function defects across species. PMID:21124729

SVGenes: a library for rendering genomic features in scalable vector graphic format.

PubMed

Etherington, Graham J; MacLean, Daniel

2013-08-01

Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image. These features make SVG a potentially useful format for the preparation of publication quality figures including genomic objects such as genes or sequencing coverage and for web applications that require rich user-interaction with the graphical elements. SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface. The library implements a simple Page object that spaces and contains horizontal Track objects that in turn style, colour and positions features within them. Tracks are the level at which visual information is supplied providing the full styling capability of the SVG standard. Genomic entities like genes, transcripts and histograms are modelled in Glyph objects that are attached to a track and take advantage of SVG primitives to render the genomic features in a track as any of a selection of defined glyphs. The feature model within SVGenes is simple but flexible and not dependent on particular existing gene feature formats meaning graphics for any existing datasets can easily be created without need for conversion. The library is provided as a Ruby Gem from https://rubygems.org/gems/bio-svgenes under the MIT license, and open source code is available at https://github.com/danmaclean/bioruby-svgenes also under the MIT License. dan.maclean@tsl.ac.uk.

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

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.

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

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.

A CGMMV genome-replicon vector with partial sequences of coat protein gene efficiently expresses GFP in Nicotiana benthamiana.

PubMed

Jailani, A Abdul Kader; Solanki, Vikas; Roy, Anirban; Sivasudha, T; Mandal, Bikash

2017-04-02

A highly infectious clone of Cucumber green mottle mosaic virus (CGMMV), a cucurbit-infecting tobamovirus was utilized for designing of gene expression vectors. Two versions of vector were examined for their efficacy in expressing the green fluorescent protein (GFP) in Nicotiana benthamiana. When the GFP gene was inserted at the stop codon of coat protein (CP) gene of the CGMMV genome without any read-through codon, systemic expression of GFP, as well as virion formation and systemic symptoms expression were obtained in N. benthamiana. The qRT-PCR analysis showed 23 fold increase of GFP over actin at 10days post inoculation (dpi), which increased to 45 fold at 14dpi and thereafter the GFP expression was significantly declined. Further, we show that when the most of the CP sequence is deleted retaining only the first 105 nucleotides, the shortened vector containing GFP in frame of original CP open reading frame (ORF) resulted in 234 fold increase of GFP expression over actin at 5dpi in N. benthamiana without the formation of virions and disease symptoms. Our study demonstrated that a simple manipulation of CP gene in the CGMMV genome while preserving the translational frame of CP resulted in developing a virus-free, rapid and efficient foreign protein expression system in the plant. The CGMMV based vectors developed in this study may be potentially useful for the production of edible vaccines in cucurbits. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Evolutionary genomics: transdomain gene transfers.

PubMed

Bordenstein, Seth R

2007-11-06

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.

An improved host-vector system for Candida maltosa using a gene isolated from its genome that complements the his5 mutation of Saccharomyces cerevisiae.

PubMed

Hikiji, T; Ohkuma, M; Takagi, M; Yano, K

1989-10-01

The host-vector system of an n-alkane-assimilating-yeast, Candida maltosa, which we previously constructed using an autonomously replicating sequence (ARS) region isolated from the genome of this yeast, utilizes C. maltosa J288 (leu2-) as a host. As this host had a serious growth defect on n-alkane, we developed an improved host-vector system using C. maltosa CH1 (his-) as host. The vectors were constructed with the Candida ARS region and a DNA fragment isolated from the genome of C. maltosa. Since this DNA fragment could complement histidine auxotrophy of both C. maltosa CH1 and S. cerevisiae (his5-), we termed the gene contained in this DNA fragment C-HIS5. The vectors were characterized in terms of transformation frequency and stability, and the nucleotide sequence of C-HIS5 was determined. The deduced amino acid sequence (389 residues) shared 51% homology with that of HIS5 of S. cerevisiae (384 residues; Nishiwaki et al. 1987).

Ensembl Genomes 2016: more genomes, more complexity.

PubMed

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

2016-01-04

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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Complete mitochondrial genome of Lutzomyia (Nyssomyia) umbratilis (Diptera: Psychodidae), the main vector of Leishmania guyanensis.

PubMed

Kocher, Arthur; Gantier, Jean-Charles; Holota, Hélène; Jeziorski, Céline; Coissac, Eric; Bañuls, Anne-Laure; Girod, Romain; Gaborit, Pascal; Murienne, Jérôme

2016-11-01

The nearly complete mitochondrial genome of Lutzomyia umbratilis Ward & Fraiha, 1977 (Psychodidae: Phlebotominae), considered as the main vector of Leishmania guyanensis, is presented. The sequencing has been performed on an Illumina Hiseq 2500 platform, with a genome skimming strategy. The full nuclear ribosomal RNA segment was also assembled. The mitogenome of L. umbratilis was determined to be at least 15,717 bp-long and presents an architecture found in many mitogenomes of insect (13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one non-coding region also referred as the control region). The control region contains a large repeated element of c. 370 bp and a poly-AT region of unknown length. This is the first mitogenome of Psychodidae to be described.

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. Copyright © 2016 Elsevier Ltd. All rights reserved.

Vector systems for prenatal gene therapy: principles of retrovirus vector design and production.

PubMed

Howe, Steven J; Chandrashekran, Anil

2012-01-01

Vectors derived from the Retroviridae family have several attributes required for successful gene delivery. Retroviral vectors have an adequate payload size for the coding regions of most genes; they are safe to handle and simple to produce. These vectors can be manipulated to target different cell types with low immunogenicity and can permanently insert genetic information into the host cells' genome. Retroviral vectors have been used in gene therapy clinical trials and successfully applied experimentally in vitro, in vivo, and in utero.

Introduction: Invertebrate Neuropeptides XI

USDA-ARS?s Scientific Manuscript database

This publication represents an introduction to the eleventh 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 characterization of new biologic...

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. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

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.

Parasite-mediated interactions within the insect vector: Trypanosoma rangeli strategies.

PubMed

Garcia, Eloi S; Castro, Daniele P; Figueiredo, Marcela B; Azambuja, Patrícia

2012-05-30

Trypanosoma rangeli is a protozoan that is non-pathogenic for humans and other mammals but causes pathology in the genus Rhodnius. T. rangeli and R. prolixus is an excellent model for studying the parasite-vector interaction, but its cycle in invertebrates remains unclear. The vector becomes infected on ingesting blood containing parasites, which subsequently develop in the gut, hemolymph and salivary glands producing short and large epimastigotes and metacyclic trypomastigotes, which are the infective forms. The importance of the T. rangeli cycle is the flagellate penetration into the gut cells and invasion of the salivary glands. The establishment of the parasite depends on the alteration of some vector defense mechanisms. Herein, we present our understanding of T. rangeli infection on the vector physiology, including gut and salivary gland invasions, hemolymph reactions and behavior alteration.

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. Copyright © 2011 Elsevier Inc. All rights reserved.

The Calyptogena magnifica chemoautotrophic symbiont genome

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

Newton, I.L.; Woyke, T.; Auchtung, T.A.

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.

Influence of sequence and size of DNA on packaging efficiency of parvovirus MVM-based vectors.

PubMed

Brandenburger, A; Coessens, E; El Bakkouri, K; Velu, T

1999-05-01

We have derived a vector from the autonomous parvovirus MVM(p), which expresses human IL-2 specifically in transformed cells (Russell et al., J. Virol 1992;66:2821-2828). Testing the therapeutic potential of these vectors in vivo requires high-titer stocks. Stocks with a titer of 10(9) can be obtained after concentration and purification (Avalosse et al., J. Virol. Methods 1996;62:179-183), but this method requires large culture volumes and cannot easily be scaled up. We wanted to increase the production of recombinant virus at the initial transfection step. Poor vector titers could be due to inadequate genome amplification or to inefficient packaging. Here we show that intracellular amplification of MVM vector genomes is not the limiting factor for vector production. Several vector genomes of different size and/or structure were amplified to an equal extent. Their amplification was also equivalent to that of a cotransfected wild-type genome. We did not observe any interference between vector and wild-type genomes at the level of DNA amplification. Despite equivalent genome amplification, vector titers varied greatly between the different genomes, presumably owing to differences in packaging efficiency. Genomes with a size close to 100% that of wild type were packaged most efficiently with loss of efficiency at lower and higher sizes. However, certain genomes of identical size showed different packaging efficiencies, illustrating the importance of the DNA sequence, and probably its structure.

AAV Vectorization of DSB-mediated Gene Editing Technologies.

PubMed

Moser, Rachel J; Hirsch, Matthew L

2016-01-01

Recent work both at the bench and the bedside demonstrate zinc-finger nucleases (ZFNs), CRISPR/Cas9, and other programmable site-specific endonuclease technologies are being successfully utilized within and alongside AAV vectors to induce therapeutically relevant levels of directed gene editing within the human chromosome. Studies from past decades acknowledge that AAV vector genomes are enhanced substrates for homology-directed repair in the presence or absence of targeted DNA damage within the host genome. Additionally, AAV vectors are currently the most efficient format for in vivo gene delivery with no vector related complications in >100 clinical trials for diverse diseases. At the same time, advancements in the design of custom-engineered site-specific endonucleases and the utilization of elucidated endonuclease formats have resulted in efficient and facile genetic engineering for basic science and for clinical therapies. AAV vectors and gene editing technologies are an obvious marriage, using AAV for the delivery of repair substrate and/or a gene encoding a designer endonuclease; however, while efficient delivery and enhanced gene targeting by vector genomes are advantageous, other attributes of AAV vectors are less desirable for gene editing technologies. This review summarizes the various roles that AAV vectors play in gene editing technologies and provides insight into its trending applications for the treatment of genetic diseases.

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.

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

Differential endozoochory of aquatic invertebrates by two duck species in shallow lakes

NASA Astrophysics Data System (ADS)

Valls, Luis; Castillo-Escrivà, Andreu; Barrera, Luis; Gómez, Eulalia; Gil-Delgado, José Antonio; Mesquita-Joanes, Francesc; Armengol, Xavier

2017-04-01

Animal vectors are essential for the movement of invertebrate resting eggs between water bodies. However, differences in habitat preferences and feeding behaviour between bird species may result in variations in the dispersal of invertebrates via these birds, even if the different bird species live in the same lake. To test such effects, faecal samples from Anas platyrhynchos (collected in autumn and spring) and Tadorna tadorna (collected in spring) were cultured in water at 20° C and 12 L: 12 D conditions in order to quantify the resting eggs which could be internally transported by these birds. One half of each faecal sample was initially cultured at a conductivity of 0.6 mS cm-1 and the other half at 6 mS cm-1. 1054 invertebrates hatched from a total of 60 faecal samples, including cladocerans, copepods, ostracods, rotifers and ciliates, with a wide variability among faeces. Autumn yielded a low proportion of samples with hatchlings (12.5%) compared to spring (90%). Significant differences were observed between birds, but not between conductivity treatments. Thus, our results imply different hatching dynamics affected by disperser and season, but most species transported as resting eggs by birds seem to have a wide tolerance to hatch under variable salinity conditions. These differences may largery influence the metacommunity dynamics of lake networks, and could be a key factor to consider in wetland conservation planning.

Antifouling Compounds from Marine Invertebrates.

PubMed

Qi, Shu-Hua; Ma, Xuan

2017-08-28

In this review, a comprehensive overview about the antifouling compounds from marine invertebrates is described. In total, more than 198 antifouling compounds have been obtained from marine invertebrates, specifically, sponges, gorgonian and soft corals.

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)

Antifouling Compounds from Marine Invertebrates

PubMed Central

Qi, Shu-Hua; Ma, Xuan

2017-01-01

In this review, a comprehensive overview about the antifouling compounds from marine invertebrates is described. In total, more than 198 antifouling compounds have been obtained from marine invertebrates, specifically, sponges, gorgonian and soft corals. PMID:28846623

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

Arsenic Speciation of Terrestrial Invertebrates

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

Moriarty, M.M.; Koch, I.; Gordon, R.A.

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 absorptionmore » 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.« less

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

Predation scars may influence host susceptibility to pathogens: evaluating the role of corallivores as vectors of coral disease.

PubMed

Nicolet, K J; Chong-Seng, K M; Pratchett, M S; Willis, B L; Hoogenboom, M O

2018-03-27

Infectious diseases not regulated by host density, such as vector-borne diseases, have the potential to drive population declines and extinctions. Here we test the vector potential of the snail Drupella sp. and butterflyfish Chaetodon plebeius for two coral diseases, black band (BBD) and brown band (BrB) disease. Drupella transmitted BrB to healthy corals in 40% of cases immediately following feeding on infected corals, and even in 12% of cases 12 and 24 hours following feeding. However, Drupella was unable to transmit BBD in either transmission treatment. In a field experiment testing the vector potential of naturally-occurring fish assemblages, equivalent numbers of caged and uncaged coral fragments became infected with either BrB, BBD or skeletal eroding band, indicating that corallivorous fish were unlikely to have caused transmission. In aquaria, C. plebeius did not transmit either BBD or BrB, even following extended feeding on both infected and healthy nubbins. A literature review confirmed only four known coral disease vectors, all invertebrates, corroborating our conclusion that polyp-feeding fishes are unlikely to be vectors of coral diseases. This potentially because polyp-feeding fishes produce shallow lesions, not allowing pathogens to invade coral tissues. In contrast, corallivorous invertebrates that create deeper feeding scars increase pathogens transmission.

Uncoupling proteins of invertebrates: A review.

PubMed

Slocinska, Malgorzata; Barylski, Jakub; Jarmuszkiewicz, Wieslawa

2016-09-01

Uncoupling proteins (UCPs) mediate inducible proton conductance in the mitochondrial inner membrane. Herein, we summarize our knowledge regarding UCPs in invertebrates. Since 2001, the presence of UCPs has been demonstrated in nematodes, mollusks, amphioxi, and insects. We discuss the following important issues concerning invertebrate UCPs: their evolutionary relationships, molecular and functional properties, and physiological impact. Evolutionary analysis indicates that the branch of vertebrate and invertebrate UCP4-5 diverged early in the evolutionary process prior to the divergence of the animal groups. Several proposed physiological roles of invertebrate UCPs are energy control, metabolic balance, and preventive action against oxidative stress. © 2016 IUBMB Life, 68(9):691-699, 2016. © 2016 International Union of Biochemistry and Molecular Biology.

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

Genome-Wide RNAi Screen Identifies Broadly-Acting Host Factors That Inhibit Arbovirus Infection

PubMed Central

Yasunaga, Ari; Hanna, Sheri L.; Li, Jianqing; Cho, Hyelim; Rose, Patrick P.; Spiridigliozzi, Anna; Gold, Beth; Diamond, Michael S.; Cherry, Sara

2014-01-01

Vector-borne viruses are an important class of emerging and re-emerging pathogens; thus, an improved understanding of the cellular factors that modulate infection in their respective vertebrate and insect hosts may aid control efforts. In particular, cell-intrinsic antiviral pathways restrict vector-borne viruses including the type I interferon response in vertebrates and the RNA interference (RNAi) pathway in insects. However, it is likely that additional cell-intrinsic mechanisms exist to limit these viruses. Since insects rely on innate immune mechanisms to inhibit virus infections, we used Drosophila as a model insect to identify cellular factors that restrict West Nile virus (WNV), a flavivirus with a broad and expanding geographical host range. Our genome-wide RNAi screen identified 50 genes that inhibited WNV infection. Further screening revealed that 17 of these genes were antiviral against additional flaviviruses, and seven of these were antiviral against other vector-borne viruses, expanding our knowledge of invertebrate cell-intrinsic immunity. Investigation of two newly identified factors that restrict diverse viruses, dXPO1 and dRUVBL1, in the Tip60 complex, demonstrated they contributed to antiviral defense at the organismal level in adult flies, in mosquito cells, and in mammalian cells. These data suggest the existence of broadly acting and functionally conserved antiviral genes and pathways that restrict virus infections in evolutionarily divergent hosts. PMID:24550726

Habitat Variation in Wetland Invertebrate Communities With Varying Mosquito Larviciding Strategies

NASA Astrophysics Data System (ADS)

Marcus, M. A.; Bailey, R. C.

2005-05-01

Monitoring, surveillance, and vector control of West Nile virus have received much attention and public resources in North America following the occurrence of human cases in 1999. With increased frequency of mosquito prevention and control programs, investigation of long-term ecological effects of larvicides used on wetland invertebrate communities is necessary. Before these effects can be examined, the variation among ponds and wetlands in features other than larviciding history needs to be examined. In a study on Bacillus thuringienisis israelensis (Bti), in the Township of East Gwillimbury and surrounding area, located in Southern Ontario, Canada, 18 wetlands were repeatedly sampled over a 5 month period. Physical habitat features, water chemistry (i.e. temperature, pH, conductivity, and dissolved oxygen), and metal and ion concentrations were measured and Principal Component Analysis was used to determine how ecosystem descriptors varied and covaried among ponds. Results showed sites with high sodium and chloride concentrations were positively correlated with both submerged and herbaceous plants in sandy environments and relatively high pHs. Based on these results, we predict weak effects of larvicide treatment on pond invertebrate communities relative to other natural and anthropogenic factors.

An efficient viral vector for functional genomic studies of Prunus fruit trees and its induced resistance to Plum pox virus via silencing of a host factor gene.

PubMed

Cui, Hongguang; Wang, Aiming

2017-03-01

RNA silencing is a powerful technology for molecular characterization of gene functions in plants. A commonly used approach to the induction of RNA silencing is through genetic transformation. A potent alternative is to use a modified viral vector for virus-induced gene silencing (VIGS) to degrade RNA molecules sharing similar nucleotide sequence. Unfortunately, genomic studies in many allogamous woody perennials such as peach are severely hindered because they have a long juvenile period and are recalcitrant to genetic transformation. Here, we report the development of a viral vector derived from Prunus necrotic ringspot virus (PNRSV), a widespread fruit tree virus that is endemic in all Prunus fruit production countries and regions in the world. We show that the modified PNRSV vector, harbouring the sense-orientated target gene sequence of 100-200 bp in length in genomic RNA3, could efficiently trigger the silencing of a transgene or an endogenous gene in the model plant Nicotiana benthamiana. We further demonstrate that the PNRSV-based vector could be manipulated to silence endogenous genes in peach such as eukaryotic translation initiation factor 4E isoform (eIF(iso)4E), a host factor of many potyviruses including Plum pox virus (PPV). Moreover, the eIF(iso)4E-knocked down peach plants were resistant to PPV. This work opens a potential avenue for the control of virus diseases in perennial trees via viral vector-mediated silencing of host factors, and the PNRSV vector may serve as a powerful molecular tool for functional genomic studies of Prunus fruit trees. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes.

PubMed

Singh, Param Priya; Arora, Jatin; Isambert, Hervé

2015-07-01

Whole genome duplications (WGD) have now been firmly established in all major eukaryotic kingdoms. In particular, all vertebrates descend from two rounds of WGDs, that occurred in their jawless ancestor some 500 MY ago. Paralogs retained from WGD, also coined 'ohnologs' after Susumu Ohno, have been shown to be typically associated with development, signaling and gene regulation. Ohnologs, which amount to about 20 to 35% of genes in the human genome, have also been shown to be prone to dominant deleterious mutations and frequently implicated in cancer and genetic diseases. Hence, identifying ohnologs is central to better understand the evolution of vertebrates and their susceptibility to genetic diseases. Early computational analyses to identify vertebrate ohnologs relied on content-based synteny comparisons between the human genome and a single invertebrate outgroup genome or within the human genome itself. These approaches are thus limited by lineage specific rearrangements in individual genomes. We report, in this study, the identification of vertebrate ohnologs based on the quantitative assessment and integration of synteny conservation between six amniote vertebrates and six invertebrate outgroups. Such a synteny comparison across multiple genomes is shown to enhance the statistical power of ohnolog identification in vertebrates compared to earlier approaches, by overcoming lineage specific genome rearrangements. Ohnolog gene families can be browsed and downloaded for three statistical confidence levels or recompiled for specific, user-defined, significance criteria at http://ohnologs.curie.fr/. In the light of the importance of WGD on the genetic makeup of vertebrates, our analysis provides a useful resource for researchers interested in gaining further insights on vertebrate evolution and genetic diseases.

Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes

PubMed Central

Singh, Param Priya; Arora, Jatin; Isambert, Hervé

2015-01-01

Whole genome duplications (WGD) have now been firmly established in all major eukaryotic kingdoms. In particular, all vertebrates descend from two rounds of WGDs, that occurred in their jawless ancestor some 500 MY ago. Paralogs retained from WGD, also coined ‘ohnologs’ after Susumu Ohno, have been shown to be typically associated with development, signaling and gene regulation. Ohnologs, which amount to about 20 to 35% of genes in the human genome, have also been shown to be prone to dominant deleterious mutations and frequently implicated in cancer and genetic diseases. Hence, identifying ohnologs is central to better understand the evolution of vertebrates and their susceptibility to genetic diseases. Early computational analyses to identify vertebrate ohnologs relied on content-based synteny comparisons between the human genome and a single invertebrate outgroup genome or within the human genome itself. These approaches are thus limited by lineage specific rearrangements in individual genomes. We report, in this study, the identification of vertebrate ohnologs based on the quantitative assessment and integration of synteny conservation between six amniote vertebrates and six invertebrate outgroups. Such a synteny comparison across multiple genomes is shown to enhance the statistical power of ohnolog identification in vertebrates compared to earlier approaches, by overcoming lineage specific genome rearrangements. Ohnolog gene families can be browsed and downloaded for three statistical confidence levels or recompiled for specific, user-defined, significance criteria at http://ohnologs.curie.fr/. In the light of the importance of WGD on the genetic makeup of vertebrates, our analysis provides a useful resource for researchers interested in gaining further insights on vertebrate evolution and genetic diseases. PMID:26181593

Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates.

PubMed

Nakatani, Yoichiro; Takeda, Hiroyuki; Kohara, Yuji; Morishita, Shinichi

2007-09-01

Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as the two rounds of whole-genome duplications (2R WGD) affected evolutionary complexity and novelty in vertebrates. Reconstructing the ancestral vertebrate genome is highly nontrivial because of the difficulty in identifying traces originating from the 2R WGD. To resolve this problem, we developed a novel method capable of pinning down remains of the 2R WGD in the human and medaka fish genomes using invertebrate tunicate and sea urchin genes to define ohnologs, i.e., paralogs produced by the 2R WGD. We validated the reconstruction using the chicken genome, which was not considered in the reconstruction step, and observed that many ancestral proto-chromosomes were retained in the chicken genome and had one-to-one correspondence to chicken microchromosomes, thereby confirming the reconstructed ancestral genomes. Our reconstruction revealed a contrast between the slow karyotype evolution after the second WGD and the rapid, lineage-specific genome reorganizations that occurred in the ancestral lineages of major taxonomic groups such as teleost fishes, amphibians, reptiles, and marsupials.

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.

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.

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. © 2016 International Society for Neurochemistry.

Gene therapy using retrovirus vectors: vector development and biosafety at clinical trials.

PubMed

Doi, Knayo; Takeuchi, Yasuhiro

2015-01-01

Retrovirus vectors (gammaretroviral and lentiviral vectors) have been considered as promising tools to transfer therapeutic genes into patient cells because they can permanently integrate into host cellular genome. To treat monogenic, inherited diseases, retroviral vectors have been used to add correct genes into patient cells. Conventional gammaretroviral vectors achieved successful results in clinical trials: treated patients had therapeutic gene expression in target cells and had improved symptoms of diseases. However, serious side-effects of leukemia occurred, caused by retroviral insertional mutagenesis (IM). These incidences stressed the importance of monitoring vector integration sites in patient cells as well as of re-consideration on safer vectors. More recently lentiviral vectors which can deliver genes into non-dividing cells started to be used in clinical trials including neurological disorders, showing their efficacy. Vector integration site analysis revealed that lentiviruses integrate less likely to near promoter regions of oncogenes than gammaretroviruses and no adverse events have been reported in lentiviral vector-mediated gene therapy clinical trials. Therefore lentiviral vectors have promises to be applied to a wide range of common diseases in near future. For example, T cells from cancer patients were transduced to express chimeric T cell receptors recognizing their tumour cells enhancing patients' anti-cancer immunity.

Vector-virus interactions and transmission dynamics of West Nile virus.

PubMed

Ciota, Alexander T; Kramer, Laura D

2013-12-09

West Nile virus (WNV; Flavivirus; Flaviviridae) is the cause of the most widespread arthropod-borne viral disease in the world and the largest outbreak of neuroinvasive disease ever observed. Mosquito-borne outbreaks are influenced by intrinsic (e.g., vector and viral genetics, vector and host competence, vector life-history traits) and extrinsic (e.g., temperature, rainfall, human land use) factors that affect virus activity and mosquito biology in complex ways. The concept of vectorial capacity integrates these factors to address interactions of the virus with the arthropod host, leading to a clearer understanding of their complex interrelationships, how they affect transmission of vector-borne disease, and how they impact human health. Vertebrate factors including host competence, population dynamics, and immune status also affect transmission dynamics. The complexity of these interactions are further exacerbated by the fact that not only can divergent hosts differentially alter the virus, but the virus also can affect both vertebrate and invertebrate hosts in ways that significantly alter patterns of virus transmission. This chapter concentrates on selected components of the virus-vector-vertebrate interrelationship, focusing specifically on how interactions between vector, virus, and environment shape the patterns and intensity of WNV transmission.

Vector-Virus Interactions and Transmission Dynamics of West Nile Virus

PubMed Central

Ciota, Alexander T.; Kramer, Laura D.

2013-01-01

West Nile virus (WNV; Flavivirus; Flaviviridae) is the cause of the most widespread arthropod-borne viral disease in the world and the largest outbreak of neuroinvasive disease ever observed. Mosquito-borne outbreaks are influenced by intrinsic (e.g., vector and viral genetics, vector and host competence, vector life-history traits) and extrinsic (e.g., temperature, rainfall, human land use) factors that affect virus activity and mosquito biology in complex ways. The concept of vectorial capacity integrates these factors to address interactions of the virus with the arthropod host, leading to a clearer understanding of their complex interrelationships, how they affect transmission of vector-borne disease, and how they impact human health. Vertebrate factors including host competence, population dynamics, and immune status also affect transmission dynamics. The complexity of these interactions are further exacerbated by the fact that not only can divergent hosts differentially alter the virus, but the virus also can affect both vertebrate and invertebrate hosts in ways that significantly alter patterns of virus transmission. This chapter concentrates on selected components of the virus-vector-vertebrate interrelationship, focusing specifically on how interactions between vector, virus, and environment shape the patterns and intensity of WNV transmission. PMID:24351794

Visualization for genomics: the Microbial Genome Viewer.

PubMed

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

(New hosts and vectors for genome cloning)

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

Not Available

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.

Targeted transgene insertion into the CHO cell genome using Cre recombinase-incorporating integrase-defective retroviral vectors.

PubMed

Kawabe, Yoshinori; Shimomura, Takuya; Huang, Shuohao; Imanishi, Suguru; Ito, Akira; Kamihira, Masamichi

2016-07-01

Retroviral vectors have served as efficient gene delivery tools in various biotechnology fields. However, viral DNA is randomly inserted into the genome, which can cause problems, such as insertional mutagenesis and gene silencing. Previously, we reported a site-specific gene integration system, in which a transgene is integrated into a predetermined chromosomal locus of Chinese hamster ovary (CHO) cells using integrase-defective retroviral vectors (IDRVs) and Cre recombinase. In this system, a Cre expression plasmid is transfected into founder cells before retroviral transduction. In practical applications of site-specific gene modification such as for hard-to-transfect cells or for in vivo gene delivery, both the transgene and the Cre protein into retroviral virions should be encapsulate. Here, we generated novel hybrid IDRVs in which viral genome and enzymatically active Cre can be delivered (Cre-IDRVs). Cre-IDRVs encoding marker genes, neomycin resistance and enhanced green fluorescent protein (EGFP), flanked by wild-type and mutated loxP sites were produced using an expression plasmid for a chimeric protein of Cre and retroviral gag-pol. After analyzing the incorporation of the Cre protein into retroviral virions by Western blotting, the Cre-IDRV was infected into founder CHO cells, in which marker genes (hygromycin resistance and red fluorescent protein) flanked with corresponding loxP sites are introduced into the genome. G418-resistant colonies expressing GFP appeared and the site-specific integration of the transgene into the expected chromosomal site was confirmed by PCR and sequencing of amplicons. Moreover, when Cre-IDRV carried a gene expression unit for a recombinant antibody, the recombinant cells in which the antibody expression cassette was integrated in a site-specific manner were generated and the cells produced the recombinant antibody. This method may provide a promising tool to perform site-specific gene modification according to Cre

Development of versatile non-homologous end joining-based knock-in module for genome editing.

PubMed

Sawatsubashi, Shun; Joko, Yudai; Fukumoto, Seiji; Matsumoto, Toshio; Sugano, Shigeo S

2018-01-12

CRISPR/Cas9-based genome editing has dramatically accelerated genome engineering. An important aspect of genome engineering is efficient knock-in technology. For improved knock-in efficiency, the non-homologous end joining (NHEJ) repair pathway has been used over the homology-dependent repair pathway, but there remains a need to reduce the complexity of the preparation of donor vectors. We developed the versatile NHEJ-based knock-in module for genome editing (VIKING). Using the consensus sequence of the time-honored pUC vector to cut donor vectors, any vector with a pUC backbone could be used as the donor vector without customization. Conditions required to minimize random integration rates of the donor vector were also investigated. We attempted to isolate null lines of the VDR gene in human HaCaT keratinocytes using knock-in/knock-out with a selection marker cassette, and found 75% of clones isolated were successfully knocked-in. Although HaCaT cells have hypotetraploid genome composition, the results suggest multiple clones have VDR null phenotypes. VIKING modules enabled highly efficient knock-in of any vectors harboring pUC vectors. Users now can insert various existing vectors into an arbitrary locus in the genome. VIKING will contribute to low-cost genome engineering.

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

The Adenovirus Genome Contributes to the Structural Stability of the Virion

PubMed Central

Saha, Bratati; Wong, Carmen M.; Parks, Robin J.

2014-01-01

Adenovirus (Ad) vectors are currently the most commonly used platform for therapeutic gene delivery in human gene therapy clinical trials. Although these vectors are effective, many researchers seek to further improve the safety and efficacy of Ad-based vectors through detailed characterization of basic Ad biology relevant to its function as a vector system. Most Ad vectors are deleted of key, or all, viral protein coding sequences, which functions to not only prevent virus replication but also increase the cloning capacity of the vector for foreign DNA. However, radical modifications to the genome size significantly decreases virion stability, suggesting that the virus genome plays a role in maintaining the physical stability of the Ad virion. Indeed, a similar relationship between genome size and virion stability has been noted for many viruses. This review discusses the impact of the genome size on Ad virion stability and emphasizes the need to consider this aspect of virus biology in Ad-based vector design. PMID:25254384

Targeting vector construction through recombineering.

PubMed

Malureanu, Liviu A

2011-01-01

Gene targeting in mouse embryonic stem cells is an essential, yet still very expensive and highly time-consuming, tool and method to study gene function at the organismal level or to create mouse models of human diseases. Conventional cloning-based methods have been largely used for generating targeting vectors, but are hampered by a number of limiting factors, including the variety and location of restriction enzymes in the gene locus of interest, the specific PCR amplification of repetitive DNA sequences, and cloning of large DNA fragments. Recombineering is a technique that exploits the highly efficient homologous recombination function encoded by λ phage in Escherichia coli. Bacteriophage-based recombination can recombine homologous sequences as short as 30-50 bases, allowing manipulations such as insertion, deletion, or mutation of virtually any genomic region. The large availability of mouse genomic bacterial artificial chromosome (BAC) libraries covering most of the genome facilitates the retrieval of genomic DNA sequences from the bacterial chromosomes through recombineering. This chapter describes a successfully applied protocol and aims to be a detailed guide through the steps of generation of targeting vectors through recombineering.

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.

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)

Germline Cas9 expression yields highly efficient genome engineering in a major worldwide disease vector, Aedes aegypti

PubMed Central

Li, Ming; Bui, Michelle; Yang, Ting; Bowman, Christian S.; White, Bradley J.; Akbari, Omar S.

2017-01-01

The development of CRISPR/Cas9 technologies has dramatically increased the accessibility and efficiency of genome editing in many organisms. In general, in vivo germline expression of Cas9 results in substantially higher activity than embryonic injection. However, no transgenic lines expressing Cas9 have been developed for the major mosquito disease vector Aedes aegypti. Here, we describe the generation of multiple stable, transgenic Ae. aegypti strains expressing Cas9 in the germline, resulting in dramatic improvements in both the consistency and efficiency of genome modifications using CRISPR. Using these strains, we disrupted numerous genes important for normal morphological development, and even generated triple mutants from a single injection. We have also managed to increase the rates of homology-directed repair by more than an order of magnitude. Given the exceptional mutagenic efficiency and specificity of the Cas9 strains we engineered, they can be used for high-throughput reverse genetic screens to help functionally annotate the Ae. aegypti genome. Additionally, these strains represent a step toward the development of novel population control technologies targeting Ae. aegypti that rely on Cas9-based gene drives. PMID:29138316

Germline Cas9 expression yields highly efficient genome engineering in a major worldwide disease vector, Aedes aegypti.

PubMed

Li, Ming; Bui, Michelle; Yang, Ting; Bowman, Christian S; White, Bradley J; Akbari, Omar S

2017-12-05

The development of CRISPR/Cas9 technologies has dramatically increased the accessibility and efficiency of genome editing in many organisms. In general, in vivo germline expression of Cas9 results in substantially higher activity than embryonic injection. However, no transgenic lines expressing Cas9 have been developed for the major mosquito disease vector Aedes aegypti Here, we describe the generation of multiple stable, transgenic Ae. aegypti strains expressing Cas9 in the germline, resulting in dramatic improvements in both the consistency and efficiency of genome modifications using CRISPR. Using these strains, we disrupted numerous genes important for normal morphological development, and even generated triple mutants from a single injection. We have also managed to increase the rates of homology-directed repair by more than an order of magnitude. Given the exceptional mutagenic efficiency and specificity of the Cas9 strains we engineered, they can be used for high-throughput reverse genetic screens to help functionally annotate the Ae. aegypti genome. Additionally, these strains represent a step toward the development of novel population control technologies targeting Ae. aegypti that rely on Cas9-based gene drives. Copyright © 2017 the Author(s). Published by PNAS.

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.

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

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. Copyright © 2016 Elsevier Inc. All rights reserved.

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…

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)

Transcriptome of the adult female malaria mosquito vector Anopheles albimanus.

PubMed

Martínez-Barnetche, Jesús; Gómez-Barreto, Rosa E; Ovilla-Muñoz, Marbella; Téllez-Sosa, Juan; García López, David E; Dinglasan, Rhoel R; Ubaida Mohien, Ceereena; MacCallum, Robert M; Redmond, Seth N; Gibbons, John G; Rokas, Antonis; Machado, Carlos A; Cazares-Raga, Febe E; González-Cerón, Lilia; Hernández-Martínez, Salvador; Rodríguez López, Mario H

2012-05-30

Human Malaria is transmitted by mosquitoes of the genus Anopheles. Transmission is a complex phenomenon involving biological and environmental factors of humans, parasites and mosquitoes. Among more than 500 anopheline species, only a few species from different branches of the mosquito evolutionary tree transmit malaria, suggesting that their vectorial capacity has evolved independently. Anopheles albimanus (subgenus Nyssorhynchus) is an important malaria vector in the Americas. The divergence time between Anopheles gambiae, the main malaria vector in Africa, and the Neotropical vectors has been estimated to be 100 My. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to explore the mosquito biology beyond the An. gambiae complex. We sequenced the transcriptome of the An. albimanus adult female. By combining Sanger, 454 and Illumina sequences from cDNA libraries derived from the midgut, cuticular fat body, dorsal vessel, salivary gland and whole body, we generated a single, high-quality assembly containing 16,669 transcripts, 92% of which mapped to the An. darlingi genome and covered 90% of the core eukaryotic genome. Bidirectional comparisons between the An. gambiae, An. darlingi and An. albimanus predicted proteomes allowed the identification of 3,772 putative orthologs. More than half of the transcripts had a match to proteins in other insect vectors and had an InterPro annotation. We identified several protein families that may be relevant to the study of Plasmodium-mosquito interaction. An open source transcript annotation browser called GDAV (Genome-Delinked Annotation Viewer) was developed to facilitate public access to the data generated by this and future transcriptome projects. We have explored the adult female transcriptome of one important New World malaria vector, An. albimanus. We identified protein-coding transcripts involved in biological processes that may

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. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

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

Studying the genetic basis of speciation in high gene flow marine invertebrates

PubMed Central

2016-01-01

A growing number of genes responsible for reproductive incompatibilities between species (barrier loci) exhibit the signals of positive selection. However, the possibility that genes experiencing positive selection diverge early in speciation and commonly cause reproductive incompatibilities has not been systematically investigated on a genome-wide scale. Here, I outline a research program for studying the genetic basis of speciation in broadcast spawning marine invertebrates that uses a priori genome-wide information on a large, unbiased sample of genes tested for positive selection. A targeted sequence capture approach is proposed that scores single-nucleotide polymorphisms (SNPs) in widely separated species populations at an early stage of allopatric divergence. The targeted capture of both coding and non-coding sequences enables SNPs to be characterized at known locations across the genome and at genes with known selective or neutral histories. The neutral coding and non-coding SNPs provide robust background distributions for identifying FST-outliers within genes that can, in principle, identify specific mutations experiencing diversifying selection. If natural hybridization occurs between species, the neutral coding and non-coding SNPs can provide a neutral admixture model for genomic clines analyses aimed at finding genes exhibiting strong blocks to introgression. Strongylocentrotid sea urchins are used as a model system to outline the approach but it can be used for any group that has a complete reference genome available. PMID:29491951

Controlled Chaos of Polymorphic Mucins in a Metazoan Parasite (Schistosoma mansoni) Interacting with Its Invertebrate Host (Biomphalaria glabrata)

PubMed Central

Roger, Emmanuel; Grunau, Christoph; Pierce, Raymond J.; Hirai, Hirohisa; Gourbal, Benjamin; Galinier, Richard; Emans, Rémi; Cesari, Italo M.; Cosseau, Céline; Mitta, Guillaume

2008-01-01

Invertebrates were long thought to possess only a simple, effective and hence non-adaptive defence system against microbial and parasitic attacks. However, recent studies have shown that invertebrate immunity also relies on immune receptors that diversify (e.g. in echinoderms, insects and mollusks (Biomphalaria glabrata)). Apparently, individual or population-based polymorphism-generating mechanisms exists that permit the survival of invertebrate species exposed to parasites. Consequently, the generally accepted arms race hypothesis predicts that molecular diversity and polymorphism also exist in parasites of invertebrates. We investigated the diversity and polymorphism of parasite molecules (Schistosoma mansoni Polymorphic Mucins, SmPoMucs) that are key factors for the compatibility of schistosomes interacting with their host, the mollusc Biomphalaria glabrata. We have elucidated the complex cascade of mechanisms acting both at the genomic level and during expression that confer polymorphism to SmPoMuc. We show that SmPoMuc is coded by a multi-gene family whose members frequently recombine. We show that these genes are transcribed in an individual-specific manner, and that for each gene, multiple splice variants exist. Finally, we reveal the impact of this polymorphism on the SmPoMuc glycosylation status. Our data support the view that S. mansoni has evolved a complex hierarchical system that efficiently generates a high degree of polymorphism—a “controlled chaos”—based on a relatively low number of genes. This contrasts with protozoan parasites that generate antigenic variation from large sets of genes such as Trypanosoma cruzi, Trypanosoma brucei and Plasmodium falciparum. Our data support the view that the interaction between parasites and their invertebrate hosts are far more complex than previously thought. While most studies in this matter have focused on invertebrate host diversification, we clearly show that diversifying mechanisms also exist on

Characteristics of Minimally Oversized Adeno-Associated Virus Vectors Encoding Human Factor VIII Generated Using Producer Cell Lines and Triple Transfection.

PubMed

Nambiar, Bindu; Cornell Sookdeo, Cathleen; Berthelette, Patricia; Jackson, Robert; Piraino, Susan; Burnham, Brenda; Nass, Shelley; Souza, David; O'Riordan, Catherine R; Vincent, Karen A; Cheng, Seng H; Armentano, Donna; Kyostio-Moore, Sirkka

2017-02-01

Several ongoing clinical studies are evaluating recombinant adeno-associated virus (rAAV) vectors as gene delivery vehicles for a variety of diseases. However, the production of vectors with genomes >4.7 kb is challenging, with vector preparations frequently containing truncated genomes. To determine whether the generation of oversized rAAVs can be improved using a producer cell-line (PCL) process, HeLaS3-cell lines harboring either a 5.1 or 5.4 kb rAAV vector genome encoding codon-optimized cDNA for human B-domain deleted Factor VIII (FVIII) were isolated. High-producing "masterwells" (MWs), defined as producing >50,000 vg/cell, were identified for each oversized vector. These MWs provided stable vector production for >20 passages. The quality and potency of the AAVrh8R/FVIII-5.1 and AAVrh8R/FVIII-5.4 vectors generated by the PCL method were then compared to those prepared via transient transfection (TXN). Southern and dot blot analyses demonstrated that both production methods resulted in packaging of heterogeneously sized genomes. However, the PCL-derived rAAV vector preparations contained some genomes >4.7 kb, whereas the majority of genomes generated by the TXN method were ≤4.7 kb. The PCL process reduced packaging of non-vector DNA for both the AAVrh8R/FVIII-5.1 and the AAVrh8R/FVIII-5.4 kb vector preparations. Furthermore, more DNA-containing viral particles were obtained for the AAVrh8R/FVIII-5.1 vector. In a mouse model of hemophilia A, animals administered a PCL-derived rAAV vector exhibited twofold higher plasma FVIII activity and increased levels of vector genomes in the liver than mice treated with vector produced via TXN did. Hence, the quality of oversized vectors prepared using the PCL method is greater than that of vectors generated using the TXN process, and importantly this improvement translates to enhanced performance in vivo.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

PubMed

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes

PubMed Central

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

Virus Database and Online Inquiry System Based on Natural Vectors.

PubMed

Dong, Rui; Zheng, Hui; Tian, Kun; Yau, Shek-Chung; Mao, Weiguang; Yu, Wenping; Yin, Changchuan; Yu, Chenglong; He, Rong Lucy; Yang, Jie; Yau, Stephen St

2017-01-01

We construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research.

Top-down control of invertebrates by Ninespine Stickleback in Arctic ponds

USGS Publications Warehouse

Laske, Sarah M.; Rosenberger, Amanda E.; Kane, William J.; Wipfli, Mark S.; Zimmerman, Christian E.

2017-01-01

Despite their widespread presence in northern-latitude ecosystems, the ecological role of Ninespine Stickleback Pungitius pungitius is not well understood. Ninespine Stickleback can occupy both top and intermediate trophic levels in freshwater ecosystems, so their role in food webs as a predator on invertebrates and as a forage fish for upper level consumers probably is substantial. We introduced Ninespine Sticklebacks to fishless ponds to elucidate their potential effects as a predator on invertebrate communities in Arctic lentic freshwaters. We hypothesized that Ninespine Stickleback would affect freshwater invertebrate communities in a top-down manner. We predicted that the addition of Ninespine Sticklebacks to fishless ponds would: 1) reduce invertebrate taxonomic richness, 2) decrease overall invertebrate abundance, 3) reduce invertebrate biomass, and 4) decrease average invertebrate body size. We tested our hypothesis at 2 locations by adding Ninespine Stickleback to isolated ponds and compared invertebrate communities over time between fish-addition and fishless control ponds. Ninespine Sticklebacks exerted strong top-down pressure on invertebrate communities mainly by changing invertebrate taxonomic richness and biomass and, to a lesser extent, abundance and average invertebrate size. Our results supported the hypothesis that Ninespine Stickleback may help shape lentic food webs in the Arctic.

Antimicrobial Compounds from Marine Invertebrates-Derived Microorganisms.

PubMed

Liu, Juan; Jung, Jee H; Liu, Yonghong

2016-01-01

It is known that marine invertebrates, including sponges, tunicates, cnidaria or mollusks, host affluent and various communities of symbiotic microorganisms. The microorganisms associated with the invertebrates metabolized various biologically active compounds, which could be an important resource for the discovery and development of potentially novel drugs. In this review, the new compounds with antimicrobial activity isolated from marine invertebrate-derived microorganisms in the last decade (2004-2014) will be presented, with focus on the relevant antimicrobial activities, origin of isolation, and information of strain species. New compounds without antimicrobial activity were not revealed.

Wood decomposition as influenced by invertebrates

Treesearch

Michael D. Ulyshen

2014-01-01

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...

Avian Paramyxovirus Type-3 as a Vaccine Vector: Identification of a Genome Location for High Level Expression of a Foreign Gene.

PubMed

Yoshida, Asuka; Samal, Siba K

2017-01-01

Avian paramyxovirus serotype 3 (APMV-3) causes infection in a wide variety of avian species, but it does not cause apparent diseases in chickens. On the contrary, APMV-1, also known as Newcastle disease virus (NDV), can cause severe disease in chickens. Currently, natural low virulence strains of NDV are used as live-attenuated vaccines throughout the world. NDV is also being evaluated as a vaccine vector against poultry pathogens. However, due to routine vaccination programs, chickens often possess pre-existing antibodies against NDV, which may cause the chickens to be less sensitive to recombinant NDV vaccines expressing antigens of other avian pathogens. Therefore, it may be possible for an APMV-3 vector vaccine to circumvent this issue. In this study, we determined the optimal insertion site in the genome of APMV-3 for high level expression of a foreign gene. We generated recombinant APMV-3 viruses expressing the green fluorescent protein (GFP) by inserting the GFP gene at five different intergenic regions in the genome. The levels of GFP transcription and translation were evaluated. Interestingly, the levels of GFP transcription and translation did not follow the 3'-to-5' attenuation mechanism of non-segmented, negative-sense RNA viruses. The insertion of GFP gene into the P-M gene junction resulted in higher level of expression of GFP than when the gene was inserted into the upstream N-P gene junction. Unlike NDV, insertion of GFP did not attenuate the growth efficiency of AMPV-3. Thus, APMV-3 could be a more useful vaccine vector for avian pathogens than NDV.

Integration of narrow-host-range vectors from Escherichia coli into the genomes of amino acid-producing corynebacteria after intergeneric conjugation.

PubMed

Mateos, L M; Schäfer, A; Kalinowski, J; Martin, J F; Pühler, A

1996-10-01

Conjugative transfer of mobilizable derivatives of the Escherichia coli narrow-host-range plasmids pBR322, pBR325, pACYC177, and pACYC184 from E. coli to species of the gram-positive genera Corynebacterium and Brevibacterium resulted in the integration of the plasmids into the genomes of the recipient bacteria. Transconjugants appeared at low frequencies and reproducibly with a delay of 2 to 3 days compared with matings with replicative vectors. Southern analysis of corynebacterial transconjugants and nucleotide sequences from insertion sites revealed that integration occurs at different locations and that different parts of the vector are involved in the process. Integration is not dependent on indigenous insertion sequence elements but results from recombination between very short homologous DNA segments (8 to 12 bp) present in the vector and in the host DNA. In the majority of the cases (90%), integration led to cointegrate formation, and in some cases, deletions or rearrangements occurred during the recombination event. Insertions were found to be quite stable even in the absence of selective pressure.

Integration of narrow-host-range vectors from Escherichia coli into the genomes of amino acid-producing corynebacteria after intergeneric conjugation.

PubMed Central

Mateos, L M; Schäfer, A; Kalinowski, J; Martin, J F; Pühler, A

1996-01-01

Conjugative transfer of mobilizable derivatives of the Escherichia coli narrow-host-range plasmids pBR322, pBR325, pACYC177, and pACYC184 from E. coli to species of the gram-positive genera Corynebacterium and Brevibacterium resulted in the integration of the plasmids into the genomes of the recipient bacteria. Transconjugants appeared at low frequencies and reproducibly with a delay of 2 to 3 days compared with matings with replicative vectors. Southern analysis of corynebacterial transconjugants and nucleotide sequences from insertion sites revealed that integration occurs at different locations and that different parts of the vector are involved in the process. Integration is not dependent on indigenous insertion sequence elements but results from recombination between very short homologous DNA segments (8 to 12 bp) present in the vector and in the host DNA. In the majority of the cases (90%), integration led to cointegrate formation, and in some cases, deletions or rearrangements occurred during the recombination event. Insertions were found to be quite stable even in the absence of selective pressure. PMID:8824624

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

Complete mitochondrial genome of Platevindex sp. (Gastropoda: Pulmonata: Systellommatophora: Onchidiidae).

PubMed

Liu, Chen; Shen, He Ding; Zhou, Na

2016-01-01

The complete mitochondrial genome sequence of Platevindex sp. is firstly described in the article. The mitogenome (13,908 bp) contains 22 tRNA genes, 2 ribosomal RNA genes and 13 protein-coding genes, and 1 putative control region (CR). CR is not well characterized due to lack of discrete conserved sequence blocks. This characteristic is similar with CRs of other invertebrate mitochondrial genomes. The characteristic is the typical bivalvia mitochondrial gene composition.

A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.

PubMed

Tsirigos, Aristotelis; Rigoutsos, Isidore

2005-01-01

In earlier work, we introduced and discussed a generalized computational framework for identifying horizontal transfers. This framework relied on a gene's nucleotide composition, obviated the need for knowledge of codon boundaries and database searches, and was shown to perform very well across a wide range of archaeal and bacterial genomes when compared with previously published approaches, such as Codon Adaptation Index and C + G content. Nonetheless, two considerations remained outstanding: we wanted to further increase the sensitivity of detecting horizontal transfers and also to be able to apply the method to increasingly smaller genomes. In the discussion that follows, we present such a method, Wn-SVM, and show that it exhibits a very significant improvement in sensitivity compared with earlier approaches. Wn-SVM uses a one-class support-vector machine and can learn using rather small training sets. This property makes Wn-SVM particularly suitable for studying small-size genomes, similar to those of viruses, as well as the typically larger archaeal and bacterial genomes. We show experimentally that the new method results in a superior performance across a wide range of organisms and that it improves even upon our own earlier method by an average of 10% across all examined genomes. As a small-genome case study, we analyze the genome of the human cytomegalovirus and demonstrate that Wn-SVM correctly identifies regions that are known to be conserved and prototypical of all beta-herpesvirinae, regions that are known to have been acquired horizontally from the human host and, finally, regions that had not up to now been suspected to be horizontally transferred. Atypical region predictions for many eukaryotic viruses, including the alpha-, beta- and gamma-herpesvirinae, and 123 archaeal and bacterial genomes, have been made available online at http://cbcsrv.watson.ibm.com/HGT_SVM/.

Wood decomposition as influenced by invertebrates

Treesearch

Michael D. Ulyshen

2016-01-01

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...

Decoding the Ubiquitin-Mediated Pathway of Arthropod Disease Vectors

PubMed Central

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

A novel packaging system for the generation of helper-free oncolytic MVM vector stocks.

PubMed

Brandenburger, A; Russell, S

1996-10-01

MVM-based autonomous parvoviral vectors have been shown to target the expression of heterologous genes in neoplastic cells and are therefore of interest for cancer gene therapy. The traditional method for production of parvoviral vectors requires the cotransfection of vector and helper plasmids into MVM-permissive cell lines, but recombination between the cotransfected plasmids invariably gives rise to vector stocks that are heavily contaminated with wild-type MVM. Therefore, to minimise recombination between the vector and helper genomes we have utilised a cell line in which the MVM helper functions are expressed inducibly from a modified MVM genome that is stably integrated into the host cell chromosome. Using this MVM packaging cell line, we could reproducibly generate MVM vector stocks that contained no detectable helper virus.

Hairpin structures with conserved sequence motifs determine the 3' ends of non-polyadenylated invertebrate iridovirus transcripts.

PubMed

İnce, İkbal Agah; Pijlman, Gorben P; Vlak, Just M; van Oers, Monique M

2017-11-01

Previously, we observed that the transcripts of Invertebrate iridescent virus 6 (IIV6) are not polyadenylated, in line with the absence of canonical poly(A) motifs (AATAAA) downstream of the open reading frames (ORFs) in the genome. Here, we determined the 3' ends of the transcripts of fifty-four IIV6 virion protein genes in infected Drosophila Schneider 2 (S2) cells. By using ligation-based amplification of cDNA ends (LACE) it was shown that the IIV6 mRNAs often ended with a CAUUA motif. In silico analysis showed that the 3'-untranslated regions of IIV6 genes have the ability to form hairpin structures (22-56 nt in length) and that for about half of all IIV6 genes these 3' sequences contained complementary TAATG and CATTA motifs. We also show that a hairpin in the 3' flanking region with conserved sequence motifs is a conserved feature in invertebrate-infecting iridoviruses (genus Iridovirus and Chloriridovirus). Copyright © 2017 Elsevier Inc. All rights reserved.

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 the...

Full-Genome Characterisation of Orungo, Lebombo and Changuinola Viruses Provides Evidence for Co-Evolution of Orbiviruses with Their Arthropod Vectors

PubMed Central

Mohd Jaafar, Fauziah; Belhouchet, Mourad; Belaganahalli, Manjunatha; Tesh, Robert B.; Mertens, Peter P. C.; Attoui, Houssam

2014-01-01

The complete genomes of Orungo virus (ORUV), Lebombo virus (LEBV) and Changuinola virus (CGLV) were sequenced, confirming that they each encode 11 distinct proteins (VP1-VP7 and NS1-NS4). Phylogenetic analyses of cell-attachment protein ‘outer-capsid protein 1′ (OC1), show that orbiviruses fall into three large groups, identified as: VP2(OC1), in which OC1 is the 2nd largest protein, including the Culicoides transmitted orbiviruses; VP3(OC1), which includes the mosquito transmitted orbiviruses; and VP4(OC1) which includes the tick transmitted viruses. Differences in the size of OC1 between these groups, places the T2 ‘subcore-shell protein’ as the third largest protein ‘VP3(T2)’ in the first of these groups, but the second largest protein ‘VP3(T2)’ in the other two groups. ORUV, LEBV and CGLV all group with the Culicoides-borne VP2(OC1)/VP3(T2) viruses. The G+C content of the ORUV, LEBV and CGLV genomes is also similar to that of the Culicoides-borne, rather than the mosquito-borne, or tick borne orbiviruses. These data suggest that ORUV and LEBV are Culicoides- rather than mosquito-borne. Multiple isolations of CGLV from sand flies suggest that they are its primary vector. OC1 of the insect-borne orbiviruses is approximately twice the size of the equivalent protein of the tick borne viruses. Together with internal sequence similarities, this suggests its origin by duplication (concatermerisation) of a smaller OC1 from an ancestral tick-borne orbivirus. Phylogenetic comparisons showing linear relationships between the dates of evolutionary-separation of their vector species, and genetic-distances between tick-, mosquito- or Culicoides-borne virus-groups, provide evidence for co-evolution of the orbiviruses with their arthropod vectors. PMID:24475112

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

Advances in Non-Viral DNA Vectors for Gene Therapy

PubMed Central

Hardee, Cinnamon L.; Arévalo-Soliz, Lirio Milenka; Hornstein, Benjamin D.; Zechiedrich, Lynn

2017-01-01

Uses of viral vectors have thus far eclipsed uses of non-viral vectors for gene therapy delivery in the clinic. Viral vectors, however, have certain issues involving genome integration, the inability to be delivered repeatedly, and possible host rejection. Fortunately, development of non-viral DNA vectors has progressed steadily, especially in plasmid vector length reduction, now allowing these tools to fill in specifically where viral or other non-viral vectors may not be the best options. In this review, we examine the improvements made to non-viral DNA gene therapy vectors, highlight opportunities for their further development, address therapeutic needs for which their use is the logical choice, and discuss their future expansion into the clinic. PMID:28208635

Avian Paramyxovirus Type-3 as a Vaccine Vector: Identification of a Genome Location for High Level Expression of a Foreign Gene

PubMed Central

Yoshida, Asuka; Samal, Siba K.

2017-01-01

Avian paramyxovirus serotype 3 (APMV-3) causes infection in a wide variety of avian species, but it does not cause apparent diseases in chickens. On the contrary, APMV-1, also known as Newcastle disease virus (NDV), can cause severe disease in chickens. Currently, natural low virulence strains of NDV are used as live-attenuated vaccines throughout the world. NDV is also being evaluated as a vaccine vector against poultry pathogens. However, due to routine vaccination programs, chickens often possess pre-existing antibodies against NDV, which may cause the chickens to be less sensitive to recombinant NDV vaccines expressing antigens of other avian pathogens. Therefore, it may be possible for an APMV-3 vector vaccine to circumvent this issue. In this study, we determined the optimal insertion site in the genome of APMV-3 for high level expression of a foreign gene. We generated recombinant APMV-3 viruses expressing the green fluorescent protein (GFP) by inserting the GFP gene at five different intergenic regions in the genome. The levels of GFP transcription and translation were evaluated. Interestingly, the levels of GFP transcription and translation did not follow the 3′-to-5′ attenuation mechanism of non-segmented, negative-sense RNA viruses. The insertion of GFP gene into the P-M gene junction resulted in higher level of expression of GFP than when the gene was inserted into the upstream N-P gene junction. Unlike NDV, insertion of GFP did not attenuate the growth efficiency of AMPV-3. Thus, APMV-3 could be a more useful vaccine vector for avian pathogens than NDV. PMID:28473820

Design and construction of functional AAV vectors.

PubMed

Gray, John T; Zolotukhin, Serge

2011-01-01

Using the basic principles of molecular biology and laboratory techniques presented in this chapter, researchers should be able to create a wide variety of AAV vectors for both clinical and basic research applications. Basic vector design concepts are covered for both protein coding gene expression and small non-coding RNA gene expression cassettes. AAV plasmid vector backbones (available via AddGene) are described, along with critical sequence details for a variety of modular expression components that can be inserted as needed for specific applications. Protocols are provided for assembling the various DNA components into AAV vector plasmids in Escherichia coli, as well as for transferring these vector sequences into baculovirus genomes for large-scale production of AAV in the insect cell production system.

Vectors, hosts, and control measures for Zika virus in the Americas

USGS Publications Warehouse

Thompson, Sarah J.; Pearce, John; Ramey, Andy M.

2017-01-01

We examine Zika virus (ZIKV) from an ecological perspective and with a focus on the Americas. We assess (1) the role of wildlife in ZIKV disease ecology, (2) how mosquito behavior and biology influence disease dynamics, and (3) how nontarget species and ecosystems may be impacted by vector control programs. Our review suggests that free-ranging, non-human primates may be involved in ZIKV transmission in the Old World; however, other wildlife species likely play a limited role in maintaining or transmitting ZIKV. In the Americas, a zoonotic cycle has not yet been definitively established. Understanding behaviors and habitat tolerances of Aedes aegypti and Aedes albopictus, two ZIKV competent vectors in the Americas, will allow more accurate modeling of disease spread and facilitate targeted and effective control efforts. Vector control efforts may have direct and indirect impacts to wildlife, particularly invertebrate feeding species; however, strategies could be implemented to limit detrimental ecological effects.

Invertebrate response to snow goose herbivory on moist-soil vegetation

USGS Publications Warehouse

Sherfy, M.H.; Kirkpatrick, R.L.

2003-01-01

Foraging activity by snow geese (Chen caerulescens) often creates large areas devoid of vegetation ("eat-outs") in moist-soil impoundments and coastal wetlands. Open-water habitats that result from eat-outs may be valuable foraging areas for other wetland-dependent birds (i.e., waterfowl and shorebirds). However, few studies have examined the effects of goose-induced habitat changes on invertebrates, an important food source for both waterfowl and shorebirds. We quantified changes in abundance and composition of benthic invertebrates in response to snow goose herbivory in moist-soil impoundments at Prime Hook National Wildlife Refuge, Delaware, USA. We found invertebrate taxon richness and diversity and abundance of Chironomidae, Coleoptera, and Total Invertebrates to be higher in goose-excluded sites than in adjacent eat-outs. These effects were most pronounced during January, February, and early April. We also measured invertebrate abundance in shorebird exclosures in eat-outs but found few detectable effects of shorebird predation on invertebrates. Our study demonstrated that abundant snow geese may negatively influence availability of invertebrates for other nonbreeding waterbirds, suggesting that management actions to reduce local goose populations or deter feeding in impoundments may be warranted.

Amphioxus: beginning of vertebrate and end of invertebrate type GnRH receptor lineage.

PubMed

Tello, Javier A; Sherwood, Nancy M

2009-06-01

In vertebrates, activation of the GnRH receptor is necessary to initiate the reproductive cascade. However, little is known about the characteristics of GnRH receptors before the vertebrates evolved. Recently genome sequencing was completed for amphioxus, Branchiostoma floridae. To understand the GnRH receptors (GnRHR) from this most basal chordate, which is also classified as an invertebrate, we cloned and characterized four GnRHR cDNAs encoded in the amphioxus genome. We found that incubation of GnRH1 (mammalian GnRH) and GnRH2 (chicken GnRH II) with COS7 cells heterologously expressing the amphioxus GnRHRs caused potent intracellular inositol phosphate turnover in two of the receptors. One of the two receptors displayed a clear preference for GnRH1 over GnRH2, a characteristic not previously seen outside the type I mammalian GnRHRs. Phylogenetic analysis grouped the four receptors into two paralogous pairs, with one pair grouping basally with the vertebrate GnRH receptors and the other grouping with the octopus GnRHR-like sequence and the related receptor for insect adipokinetic hormone. Pharmacological studies showed that octopus GnRH-like peptide and adipokinetic hormone induced potent inositol phosphate turnover in one of these other two amphioxus receptors. These data demonstrate the functional conservation of two distinct types of GnRH receptors at the base of chordates. We propose that one receptor type led to vertebrate GnRHRs, whereas the other type, related to the mollusk GnRHR-like receptor, was lost in the vertebrate lineage. This is the first report to suggest that distinct invertebrate and vertebrate GnRHRs are present simultaneously in a basal chordate, amphioxus.

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.

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., ...

Significance of bacteria associated with invertebrates in drinking water distribution networks.

PubMed

Wolmarans, E; du Preez, H H; de Wet, C M E; Venter, S N

2005-01-01

The implication of invertebrates found in drinking water distribution networks to public health is of concern to water utilities. Previous studies have shown that the bacteria associated with the invertebrates could be potentially pathogenic to humans. This study investigated the level and identity of bacteria commonly associated with invertebrates collected from the drinking water treatment systems as well as from the main pipelines leaving the treatment works. On all sampling occasions bacteria were isolated from the invertebrate samples collected. The highest bacterial counts were observed for the samples taken before filtration as was expected. There were, however, indications that optimal removal of invertebrates from water did not always occur. During the investigation, 116 colonies were sampled for further identification. The isolates represent several bacterial genera and species that are pathogenic or opportunistic pathogens of humans. Diarrhoea, meningitis, septicaemia and skin infections are among the diseases associated with these organisms. The estimated number of bacteria that could be associated with a single invertebrate (as based on average invertebrate numbers) could range from 10 to 4000 bacteria per organism. It can, therefore, be concluded that bacteria associated with invertebrates might under the worst case scenario pose a potential health risk to water users. In the light of the above findings it is clear that invertebrates in drinking water should be controlled at levels as low as technically and economically feasible.

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

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

Dcode.org anthology of comparative genomic tools.

PubMed

Loots, Gabriela G; Ovcharenko, Ivan

2005-07-01

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical application of comparative sequence analysis to genetics and genomics, we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools, zPicture and Mulan; a phylogenetic shadowing tool, eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools, rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, Creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ website.

Recombinase-Mediated Cassette Exchange Using Adenoviral Vectors.

PubMed

Kolb, Andreas F; Knowles, Christopher; Pultinevicius, Patrikas; Harbottle, Jennifer A; Petrie, Linda; Robinson, Claire; Sorrell, David A

2017-01-01

Site-specific recombinases are important tools for the modification of mammalian genomes. In conjunction with viral vectors, they can be utilized to mediate site-specific gene insertions in animals and in cell lines which are difficult to transfect. Here we describe a method for the generation and analysis of an adenovirus vector supporting a recombinase-mediated cassette exchange reaction and discuss the advantages and limitations of this approach.

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

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

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.

Sleeping Beauty-baculovirus hybrid vectors for long-term gene expression in the eye.

PubMed

Turunen, Tytteli Anni Kaarina; Laakkonen, Johanna Päivikki; Alasaarela, Laura; Airenne, Kari Juhani; Ylä-Herttuala, Seppo

2014-01-01

A baculovirus vector is capable of efficiently transducing many nondiving and diving cell types. However, the potential of baculovirus is restricted for many gene delivery applications as a result of the transient gene expression that it mediates. The plasmid-based Sleeping Beauty (SB) transposon system integrates transgenes into target cell genome efficiently with a genomic integration pattern that is generally considered safer than the integration of many other integrating vectors; yet efficient delivery of therapeutic genes into cells of target tissues in vivo is a major challenge for nonviral gene therapy. In the present study, SB was introduced into baculovirus to obtain novel hybrid vectors that would combine the best features of the two vector systems (i.e. effective gene delivery and efficient integration into the genome), thus circumventing the major limitations of these vectors. We constructed and optimized SB-baculovirus hybrid vectors that bear either SB100x transposase or SB transposon in the forward or reverse orientations with respect to the viral backbone The functionality of the novel hybrid vectors was investigated in cell cultures and in a proof-of-concept study in the mouse eye. The hybrid vectors showed high and sustained transgene expression that remained stable and demonstrated no signs of decline during the 2 months follow-up in vitro. These results were verified in the mouse eye where persistent transgene expression was detected two months after intravitreal injection. Our results confirm that (i) SB-baculovirus hybrid vectors mediate long-term gene expression in vitro and in vivo, and (ii) the hybrid vectors are potential new tools for the treatment of ocular diseases. Copyright © 2014 John Wiley & Sons, Ltd.

Rapid adaptation of invertebrate pests to climatic stress?

PubMed

Hoffmann, Ary A

2017-06-01

There is surprisingly little information on adaptive responses of pests and disease vectors to climatic stresses even though the short generation times and large population sizes associated with pests make rapid adaptation likely. Most evidence of adaptive differentiation has been obtained from geographic comparisons and these can directly or indirectly indicate rates of adaptation where historical data on invasions are available. There is very little information on adaptive shifts in pests detected through molecular comparisons even though the genomes of many pests are now available and can help to identify markers underlying adaptation. While the limited evidence available points to frequent rapid adaptation that can affect pest and disease vector control, constraints to adaptation are also evident and a predictive framework around the likelihood and limits of rapid adaptation is required. Copyright © 2017 Elsevier Inc. All rights reserved.

Reverse Genetics for Newcastle Disease Virus as a Vaccine Vector.

PubMed

Kim, Shin-Hee; Samal, Siba K

2018-02-22

Newcastle disease virus (NDV) is an economically important pathogen in the poultry industry worldwide. Recovery of infectious NDV from cDNA using reverse genetics has made it possible to manipulate the genome of NDV. This has greatly contributed to our understanding of the molecular biology and pathogenesis of NDV. Furthermore, NDV has modular genome and accommodates insertion of a foreign gene as a transcriptional unit, thus enabling NDV as a vaccine vector against diseases of humans and animals. Avirulent NDV strains (e.g., LaSota and B1) have been commonly used as vaccine vectors. In this protocol, we have described reverse genetics of NDV to be used as a vaccine vector by exemplifying the recovery of NDV vectored avian influenza virus vaccine. Specifically, cloning and recovery of NDV expressing the hemagglutinin protein of highly pathogenic influenza virus were explained. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

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.

Chironomid midges (Diptera, chironomidae) show extremely small genome sizes.

PubMed

Cornette, Richard; Gusev, Oleg; Nakahara, Yuichi; Shimura, Sachiko; Kikawada, Takahiro; Okuda, Takashi

2015-06-01

Chironomid midges (Diptera; Chironomidae) are found in various environments from the high Arctic to the Antarctic, including temperate and tropical regions. In many freshwater habitats, members of this family are among the most abundant invertebrates. In the present study, the genome sizes of 25 chironomid species were determined by flow cytometry and the resulting C-values ranged from 0.07 to 0.20 pg DNA (i.e. from about 68 to 195 Mbp). These genome sizes were uniformly very small and included, to our knowledge, the smallest genome sizes recorded to date among insects. Small proportion of transposable elements and short intron sizes were suggested to contribute to the reduction of genome sizes in chironomids. We discuss about the possible developmental and physiological advantages of having a small genome size and about putative implications for the ecological success of the family Chironomidae.

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…

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. © 2013 WILEY Periodicals, Inc.

Draft Genome Sequence of a Picorna-Like Virus Associated with Gill Tissue in Clinically Normal Brook Trout, Salvelinus fontinalis.

PubMed

Iwanowicz, Luke R; Iwanowicz, Deborah D; Adams, Cynthia R; Galbraith, Heather; Aunins, Aaron; Cornman, Robert S

2017-10-12

Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis , gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.

Draft genome sequence of a picorna-like virus associated with gill tissue in clinically normal brook trout, Salvelinus fontinalis

USGS Publications Warehouse

Iwanowicz, Luke R.; Iwanowicz, Deborah; Adams, Cynthia; Galbraith, Heather S.; Aunins, Aaron W.; Cornman, Robert S.

2017-01-01

Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis, gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.

DCODE.ORG Anthology of Comparative Genomic Tools

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

Loots, G G; Ovcharenko, I

2005-01-11

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the noncoding encryption of gene regulation across genomes. To facilitate the use of comparative genomics to practical applications in genetics and genomics we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools: zPicture and Mulan; a phylogenetic shadowing tool: eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools: rVista and multiTF; a toolmore » for extracting cis-regulatory modules governing the expression of co-regulated genes, CREME; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ web site.« less

Invertebrates of the Columbia River basin assessment area.

Treesearch

Christine G. Niwa; Roger E. Sandquist; Rod Crawford; et al.

2001-01-01

A general background on functional groups of invertebrates in the Columbia River basin and how they affect sustainability and productivity of their ecological communities is presented. The functional groups include detritivores, predators, pollinators, and grassland and forest herbivores. Invertebrate biodiversity and species of conservation interest are discussed....

Oxytocin mediated behavior in invertebrates: An evolutionary perspective.

PubMed

Lockard, Meghan A; Ebert, Margaret S; Bargmann, Cornelia I

2017-02-01

The molecular and functional conservation of oxytocin-related neuropeptides in behavior is striking. In animals separated by at least 600 million years of evolution, from roundworms to humans, oxytocin homologs play critical roles in the modulation of reproductive behavior and other biological functions. Here, we review the roles of oxytocin in invertebrate behavior from an evolutionary perspective. We begin by tracing the evolution of oxytocin through the invertebrate animal lineages, and then describe common themes in invertebrate behaviors that are mediated by oxytocin-related peptides, including reproductive behavior, learning and memory, food arousal, and predator/prey relationships. Finally, we discuss interesting future directions that have recently become experimentally tractable. Studying oxytocin in invertebrates offers precise insights into the activity of neuropeptides on well-defined neural circuits; the principles that emerge may also be represented in the more complex vertebrate brain. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 128-142, 2017. © 2016 Wiley Periodicals, Inc.

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.

Feeding live invertebrate prey in zoos and aquaria: Are there welfare concerns?

PubMed

Keller, Martha

2017-09-01

Invertebrates constitute more than 90% of all species on earth, however, as a rule, humans do not regard invertebrates as creatures that can suffer and they are generally seen as creatures that should be eliminated. As a result, the importance of their welfare may be grossly unappreciated. For instance, the feeding of live food is often viewed as a good method of enrichment and invertebrates are commonly used as live prey in many zoological facilities. As a result, zoos may send mixed messages to their patrons in that welfare is considered only for the invertebrates that are part of their zoological collection and not necessarily for the invertebrates used as feed. Research indicates that many invertebrates possess nociceptors, opioid receptors, and demonstrate behavioral responses indicative of pain sensation. In addition, in some taxa, there may be evidence of higher cognitive functions such as emotions and learning, although studies in this area of research are preliminary and sparse. Therefore, the possibility for suffering exists in many invertebrate species and as such, zoological facilities have an ethical responsibility to take their welfare into consideration. This paper discusses the current research regarding invertebrates' capacity for suffering and discusses methods facilities can use to improve the welfare of their invertebrate live prey. © 2017 Wiley Periodicals, Inc.

Disentangling Vector-Borne Transmission Networks: A Universal DNA Barcoding Method to Identify Vertebrate Hosts from Arthropod Bloodmeals

PubMed Central

Alcaide, Miguel; Rico, Ciro; Ruiz, Santiago; Soriguer, Ramón; Muñoz, Joaquín; Figuerola, Jordi

2009-01-01

Emerging infectious diseases represent a challenge for global economies and public health. About one fourth of the last pandemics have been originated by the spread of vector-borne pathogens. In this sense, the advent of modern molecular techniques has enhanced our capabilities to understand vector-host interactions and disease ecology. However, host identification protocols have poorly profited of international DNA barcoding initiatives and/or have focused exclusively on a limited array of vector species. Therefore, ascertaining the potential afforded by DNA barcoding tools in other vector-host systems of human and veterinary importance would represent a major advance in tracking pathogen life cycles and hosts. Here, we show the applicability of a novel and efficient molecular method for the identification of the vertebrate host's DNA contained in the midgut of blood-feeding arthropods. To this end, we designed a eukaryote-universal forward primer and a vertebrate-specific reverse primer to selectively amplify 758 base pairs (bp) of the vertebrate mitochondrial Cytochrome c Oxidase Subunit I (COI) gene. Our method was validated using both extensive sequence surveys from the public domain and Polymerase Chain Reaction (PCR) experiments carried out over specimens from different Classes of vertebrates (Mammalia, Aves, Reptilia and Amphibia) and invertebrate ectoparasites (Arachnida and Insecta). The analysis of mosquito, culicoid, phlebotomie, sucking bugs, and tick bloodmeals revealed up to 40 vertebrate hosts, including 23 avian, 16 mammalian and one reptilian species. Importantly, the inspection and analysis of direct sequencing electropherograms also assisted the resolving of mixed bloodmeals. We therefore provide a universal and high-throughput diagnostic tool for the study of the ecology of haematophagous invertebrates in relation to their vertebrate hosts. Such information is crucial to support the efficient management of initiatives aimed at reducing

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.

Monoclonal antibodies expression improvement in CHO cells by PiggyBac transposition regarding vectors ratios and design.

PubMed

Ahmadi, Samira; Davami, Fatemeh; Davoudi, Noushin; Nematpour, Fatemeh; Ahmadi, Maryam; Ebadat, Saeedeh; Azadmanesh, Kayhan; Barkhordari, Farzaneh; Mahboudi, Fereidoun

2017-01-01

Establishing stable Chinese Hamster Ovary (CHO) cells producing monoclonal antibodies (mAbs) usually pass through the random integration of vectors to the cell genome, which is sensitive to gene silencing. One approach to overcome this issue is to target a highly transcribed region in the genome. Transposons are useful devices to target active parts of genomes, and PiggyBac (PB) transposon can be considered as a good option. In the present study, three PB transposon donor vectors containing both heavy and light chains were constructed, one contained independent expression cassettes while the others utilized either an Internal Ribosome Entry Site (IRES) or 2A element to express mAb. Conventional cell pools were created by transferring donor vectors into the CHO cells, whereas transposon-based cells were generated by transfecting the cells with donor vectors with a companion of a transposase-encoding helper vector, with 1:2.5 helper/donor vectors ratio. To evaluate the influence of helper/donor vectors ratio on expression, the second transposon-based cell pools were generated with 1:5 helper/donor ratio. Expression levels in the transposon-based cells were two to five -folds more than those created by conventional method except for the IRES-mediated ones, in which the observed difference increased more than 100-fold. The results were dependent on both donor vector design and vectors ratios.

Monoclonal antibodies expression improvement in CHO cells by PiggyBac transposition regarding vectors ratios and design

PubMed Central

Ahmadi, Samira; Davami, Fatemeh; Davoudi, Noushin; Nematpour, Fatemeh; Ahmadi, Maryam; Ebadat, Saeedeh; Azadmanesh, Kayhan; Barkhordari, Farzaneh

2017-01-01

Establishing stable Chinese Hamster Ovary (CHO) cells producing monoclonal antibodies (mAbs) usually pass through the random integration of vectors to the cell genome, which is sensitive to gene silencing. One approach to overcome this issue is to target a highly transcribed region in the genome. Transposons are useful devices to target active parts of genomes, and PiggyBac (PB) transposon can be considered as a good option. In the present study, three PB transposon donor vectors containing both heavy and light chains were constructed, one contained independent expression cassettes while the others utilized either an Internal Ribosome Entry Site (IRES) or 2A element to express mAb. Conventional cell pools were created by transferring donor vectors into the CHO cells, whereas transposon-based cells were generated by transfecting the cells with donor vectors with a companion of a transposase-encoding helper vector, with 1:2.5 helper/donor vectors ratio. To evaluate the influence of helper/donor vectors ratio on expression, the second transposon-based cell pools were generated with 1:5 helper/donor ratio. Expression levels in the transposon-based cells were two to five -folds more than those created by conventional method except for the IRES-mediated ones, in which the observed difference increased more than 100-fold. The results were dependent on both donor vector design and vectors ratios. PMID:28662065

Adeno-Associated Virus Type 6 (AAV6) Vectors Mediate Efficient Transduction of Airway Epithelial Cells in Mouse Lungs Compared to That of AAV2 Vectors

PubMed Central

Halbert, Christine L.; Allen, James M.; Miller, A. Dusty

2001-01-01

Although vectors derived from adeno-associated virus type 2 (AAV2) promote gene transfer and expression in many somatic tissues, studies with animal models and cultured cells show that the apical surface of airway epithelia is resistant to transduction by AAV2 vectors. Approaches to increase transduction rates include increasing the amount of vector and perturbing the integrity of the epithelia. In this study, we explored the use of vectors based on AAV6 to increase transduction rates in airways. AAV vectors were made using combinations of rep, cap, and packaged genomes from AAV2 or AAV6. The packaged genomes encoded human placental alkaline phosphatase and contained terminal repeat sequences from AAV2 or AAV6. We found that transduction efficiency was primarily dependent on the source of Cap protein, defined here as the vector pseudotype. The AAV6 and AAV2 pseudotype vectors exhibited different tropisms in tissue-cultured cells, and cell transduction by AAV6 vectors was not inhibited by heparin, nor did they compete for entry in a transduction assay, indicating that AAV6 and AAV2 capsid bind different receptors. In vivo analysis of vectors showed that AAV2 pseudotype vectors gave high transduction rates in alveolar cells but much lower rates in the airway epithelium. In contrast, the AAV6 pseudotype vectors exhibited much more efficient transduction of epithelial cells in large and small airways, showing up to 80% transduction in some airways. These results, combined with our previous results showing lower immunogenicity of AAV6 than of AAV2 vectors, indicate that AAV6 vectors may provide significant advantages over AAV2 for gene therapy of lung diseases like cystic fibrosis. PMID:11413329

Environmental characteristics and benthic invertebrate assemblages in Colorado mountain lakes

USGS Publications Warehouse

LaFrancois, B.M.; Carlisle, D.M.; Nydick, K.R.; Johnson, B.M.; Baron, Jill S.

2003-01-01

Twenty-two high-elevation lakes (>3000 m) in Rocky Mountain National Park and Indian Peaks Wilderness Area, Colorado, were surveyed during summer 1998 to explore relationships among benthic invertebrates, water chemistry (particularly nitrate concentrations), and other environmental variables. Water samples were collected from the deepest portion of each lake and analyzed for ions and other water chemistry parameters. Benthic invertebrates were collected from the littoral zone using both a sweep net and Hess sampler. Physical and geographical measurements were derived from maps. Relationships among benthic invertebrate assemblages and environmental variables were examined using canonical correspondence analysis, and the importance of sampling methodology and taxonomie resolution on these relationships was evaluated. Choice of sampling methodology strongly influenced the outcome of statistical analyses, whereas taxonomie resolution did not. Presence/absence of benthic invertebrate taxa among the study lakes was best explained by elevation and presence of fish. Relative abundance and density of benthic invertebrate taxa were more strongly influenced by sampling date and water chemistry. Nitrate (NO₃⁻) concentration, potentially on the rise due to regional nitrogen deposition, was unrelated to benthic invertebrate distribution regardless of sampling method or taxonomie resolution.

Rapid construction of capsid-modified adenoviral vectors through bacteriophage lambda Red recombination.

PubMed

Campos, Samuel K; Barry, Michael A

2004-11-01

There are extensive efforts to develop cell-targeting adenoviral vectors for gene therapy wherein endogenous cell-binding ligands are ablated and exogenous ligands are introduced by genetic means. Although current approaches can genetically manipulate the capsid genes of adenoviral vectors, these approaches can be time-consuming and require multiple steps to produce a modified viral genome. We present here the use of the bacteriophage lambda Red recombination system as a valuable tool for the easy and rapid construction of capsid-modified adenoviral genomes.

Draft Genome Sequence of a Picorna-Like Virus Associated with Gill Tissue in Clinically Normal Brook Trout, Salvelinus fontinalis

PubMed Central

2017-01-01

ABSTRACT Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis, gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates. PMID:29025930

Insulated piggyBac vectors for insect transgenesis

PubMed Central

Sarkar, Abhimanyu; Atapattu, Asela; Belikoff, Esther J; Heinrich, Jörg C; Li, Xuelei; Horn, Carsten; Wimmer, Ernst A; Scott, Maxwell J

2006-01-01

Background Germ-line transformation of insects is now a widely used method for analyzing gene function and for the development of genetically modified strains suitable for pest control programs. The most widely used transposable element for the germ-line transformation of insects is piggyBac. The site of integration of the transgene can influence gene expression due to the effects of nearby transcription enhancers or silent heterochromatic regions. Position effects can be minimized by flanking a transgene with insulator elements. The scs/scs' and gypsy insulators from Drosophila melanogaster as well as the chicken β-globin HS4 insulator function in both Drosophila and mammalian cells. Results To minimize position effects we have created a set of piggyBac transformation vectors that contain either the scs/scs', gypsy or chicken β-globin HS4 insulators. The vectors contain either fluorescent protein or eye color marker genes and have been successfully used for germ-line transformation of Drosophila melanogaster. A set of the scs/scs' vectors contains the coral reef fluorescent protein marker genes AmCyan, ZsGreen and DsRed that have not been optimized for translation in human cells. These marker genes are controlled by a combined GMR-3xP3 enhancer/promoter that gives particularly strong expression in the eyes. This is also the first report of the use of the ZsGreen and AmCyan reef fluorescent proteins as transformation markers in insects. Conclusion The insulated piggyBac vectors should protect transgenes against position effects and thus facilitate fine control of gene expression in a wide spectrum of insect species. These vectors may also be used for transgenesis in other invertebrate species. PMID:16776846

Viral Determinants of Integration Site Preferences of Simian Immunodeficiency Virus-Based Vectors

PubMed Central

Monse, Hella; Laufs, Stephanie; Kuate, Seraphin; Zeller, W. Jens; Fruehauf, Stefan; Überla, Klaus

2006-01-01

Preferential integration into transcriptionally active regions of genomes has been observed for retroviral vectors based on gamma-retroviruses and lentiviruses. However, differences in the integration site preferences were detected, which might be explained by differences in viral components of the preintegration complexes. Viral determinants of integration site preferences have not been defined. Therefore, integration sites of simian immunodeficiency virus (SIV)-based vectors produced in the absence of accessory genes or lacking promoter and enhancer elements were compared. Similar integration patterns for the different SIV vectors indicate that vif, vpr, vpx, nef, env, and promoter or enhancer elements are not required for preferential integration of SIV into transcriptionally active regions of genomes. PMID:16873270

The genome sequence of the colonial chordate, Botryllus schlosseri

PubMed Central

Voskoboynik, Ayelet; Neff, Norma F; Sahoo, Debashis; Newman, Aaron M; Pushkarev, Dmitry; Koh, Winston; Passarelli, Benedetto; Fan, H Christina; Mantalas, Gary L; Palmeri, Karla J; Ishizuka, Katherine J; Gissi, Carmela; Griggio, Francesca; Ben-Shlomo, Rachel; Corey, Daniel M; Penland, Lolita; White, Richard A; Weissman, Irving L; Quake, Stephen R

2013-01-01

Botryllus schlosseri is a colonial urochordate that follows the chordate plan of development following sexual reproduction, but invokes a stem cell-mediated budding program during subsequent rounds of asexual reproduction. As urochordates are considered to be the closest living invertebrate relatives of vertebrates, they are ideal subjects for whole genome sequence analyses. Using a novel method for high-throughput sequencing of eukaryotic genomes, we sequenced and assembled 580 Mbp of the B. schlosseri genome. The genome assembly is comprised of nearly 14,000 intron-containing predicted genes, and 13,500 intron-less predicted genes, 40% of which could be confidently parceled into 13 (of 16 haploid) chromosomes. A comparison of homologous genes between B. schlosseri and other diverse taxonomic groups revealed genomic events underlying the evolution of vertebrates and lymphoid-mediated immunity. The B. schlosseri genome is a community resource for studying alternative modes of reproduction, natural transplantation reactions, and stem cell-mediated regeneration. DOI: http://dx.doi.org/10.7554/eLife.00569.001 PMID:23840927

The Ciona intestinalis genome: when the constraints are off

NASA Technical Reports Server (NTRS)

Holland, Linda Z.; Gibson-Brown, Jeremy J.

2003-01-01

The recent genome sequencing of a non-vertebrate deuterostome, the ascidian tunicate Ciona intestinalis, makes a substantial contribution to the fields of evolutionary and developmental biology.1 Tunicates have some of the smallest bilaterian genomes, embryos with relatively few cells, fixed lineages and early determination of cell fates. Initial analyses of the C. intestinalis genome indicate that it has been evolving rapidly. Comparisons with other bilaterians show that C. intestinalis has lost a number of genes, and that many genes linked together in most other bilaterians have become uncoupled. In addition, a number of independent, lineage-specific gene duplications have been detected. These new results, although interesting in themselves, will take on a deeper significance once the genomes of additional invertebrate deuterostomes (e.g. echinoderms, hemichordates and amphioxus) have been sequenced. With such a broadened database, comparative genomics can begin to ask pointed questions about the relationship between the evolution of genomes and the evolution of body plans. Copyright 2003 Wiley Periodicals, Inc.

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. Copyright © 2015. Published by Elsevier B.V.

Development of recombinant adeno-associated virus vectors carrying small interfering RNA (shHec1)-mediated depletion of kinetochore Hec1 protein in tumor cells.

PubMed

Li, L; Yang, L; Scudiero, D A; Miller, S A; Yu, Z-X; Stukenberg, P T; Shoemaker, R H; Kotin, R M

2007-05-01

Transcript depletion using small interfering RNA (siRNA) technology represents a potentially valuable technique for the treatment of cancer. However, delivering therapeutic quantities of siRNA into solid tumors by chemical transfection is not feasible, whereas viral vectors efficiently transduce many human tumor cell lines. Yet producing sufficient quantities of viral vectors that elicit acute and selective cytotoxicity remains a major obstacle for preclinical and clinical trials. Using the invertebrate Spodoptera frugiperda (Sf9) cell line, we were able to produce high titer stocks of cytotoxic recombinant adeno-associated virus (rAAV) that express short hairpin RNA (shRNA) and that efficiently deplete Hec1 (highly expressed in cancer 1), or Kntc2 (kinetochore-associated protein 2), a kinetochore protein directly involved in kinetochore microtubule interactions, chromosome congression and spindle checkpoint signaling. Depletion of Hec1 protein results in persistent spindle checkpoint activation followed by cell death. Because Hec1 expression and activity are only present in mitotic cells, non-dividing cells were not affected by rAAV treatment. On the basis of the results of screening 56 human tumor cell lines with three different serotype vectors, we used a tumor xenograft model to test the effects in vivo. The effects of the shHec1 vector were evident in sectioned and stained tumors. The experiments with rAAV-shRNA vectors demonstrate the utility of producing vectors in invertebrate cells to obtain sufficient concentrations and quantities for solid tumor therapy. This addresses an important requirement for cancer gene therapy, to produce cytotoxic vectors in sufficient quantities and concentrations to enable quantitative transduction and selective killing of solid tumor cells.

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

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

Not Available

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.

The UCSC Genome Browser database: extensions and updates 2013.

PubMed

Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; Raney, Brian J; Pohl, Andy; Malladi, Venkat S; Li, Chin H; Lee, Brian T; Learned, Katrina; Kirkup, Vanessa; Hsu, Fan; Heitner, Steve; Harte, Rachel A; Haeussler, Maximilian; Guruvadoo, Luvina; Goldman, Mary; Giardine, Belinda M; Fujita, Pauline A; Dreszer, Timothy R; Diekhans, Mark; Cline, Melissa S; Clawson, Hiram; Barber, Galt P; Haussler, David; Kent, W James

2013-01-01

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

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

Marine invertebrates: communities at risk.

PubMed

Mather, Jennifer

2013-06-10

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.

Investigations into the Settlement and Attachment of Biofouling Marine Invertebrates

DTIC Science & Technology

2015-12-17

attachment of biofouling marine invertebrates 5a. CONTRACT NUMBER N00014-12-1 -0432 5b. GRANT NUMBER n/a 5c. PROGRAM ELEMENT NUMBER n/a 6...larval settlement in a variety of marine invertebrate species, including B. neritina. Light also inhibits B. neritina larval settlement, yet the...underlying mechanisms by which light and adrenergic compounds exert their effects on larvae are largely unknown. Octopamine is considered the invertebrate

Invertebrates and Plants

Treesearch

Wendell R. Haag; Robert J. Distefano; Siobhan Fennessy; Brett D. Marshall

2013-01-01

Invertebrates and plants are among the most ubiquitous and abundant macroscopic organisms in aquatic ecosystems; they dominate most habitats in both diversity and biomass and play central roles in aquatic food webs. Plants regulate and create habitats for a wide array of organisms (Cooke et al. 2005). Snail grazing and bivalve filtering profoundly alter habitats and...

Systemic errors in quantitative polymerase chain reaction titration of self-complementary adeno-associated viral vectors and improved alternative methods.

PubMed

Fagone, Paolo; Wright, J Fraser; Nathwani, Amit C; Nienhuis, Arthur W; Davidoff, Andrew M; Gray, John T

2012-02-01

Self-complementary AAV (scAAV) vector genomes contain a covalently closed hairpin derived from a mutated inverted terminal repeat that connects the two monomer single-stranded genomes into a head-to-head or tail-to-tail dimer. We found that during quantitative PCR (qPCR) this structure inhibits the amplification of proximal amplicons and causes the systemic underreporting of copy number by as much as 10-fold. We show that cleavage of scAAV vector genomes with restriction endonuclease to liberate amplicons from the covalently closed terminal hairpin restores quantitative amplification, and we implement this procedure in a simple, modified qPCR titration method for scAAV vectors. In addition, we developed and present an AAV genome titration procedure based on gel electrophoresis that requires minimal sample processing and has low interassay variability, and as such is well suited for the rigorous quality control demands of clinical vector production facilities.

Human Induced Pluripotent Stem Cells Free of Vector and Transgene Sequences

PubMed Central

Yu, Junying; Hu, Kejin; Smuga-Otto, Kim; Tian, Shulan; Stewart, Ron; Slukvin, Igor I.; Thomson, James A.

2009-01-01

Reprogramming differentiated human cells to induced pluripotent stem (iPS) cells has applications in basic biology, drug development, and transplantation. Human iPS cell derivation previously required vectors that integrate into the genome, which can create mutations and limit the utility of the cells in both research and clinical applications. Here we describe the derivation of human iPS cells using non-integrating episomal vectors. After removal of the episome, iPS cells completely free of vector and transgene sequences are derived that are similar to human embryonic stem (ES) cells in proliferative and developmental potential. These results demonstrate that reprogramming human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors, and removes one obstacle to the clinical application of human iPS cells. PMID:19325077

Medicinal benefits of marine invertebrates: sources for discovering natural drug candidates.

PubMed

De Zoysa, Mahanama

2012-01-01

Marine invertebrates are one of the major groups of organisms, which could be diversified under the major taxonomic groups of Porifera, Cnidaria, Mollusca, Arthropoda, Echinodermata, and many other minor phyla. To date, range of medicinal benefits and a significant number of marine natural products (MNPs) have been discovered from marine invertebrates. Seafood diet from edible marine invertebrates such as mollusks and crustaceans has been linked with various medicinal benefits to improve human health. Among marine invertebrates, spongers from phylum Porifera is the most dominant group responsible for discovering large number of MNPs, which have been used as template to develop therapeutic drugs. MNPs isolated from invertebrates have shown wide range of therapeutic properties including antimicrobial, antioxidant, antihypertensive, anticoagulant, anticancer, anti-inflammatory, wound healing and immune modulator, and other medicinal effects. Therefore, marine invertebrates are rich sources of chemical diversity and health benefits for developing drug candidates, cosmetics, nutritional supplements, and molecular probes that can be supported to increase the healthy life span of human. Copyright © 2012 Elsevier Inc. All rights reserved.

Ribosomal DNA Integrating rAAV-rDNA Vectors Allow for Stable Transgene Expression

PubMed Central

Lisowski, Leszek; Lau, Ashley; Wang, Zhongya; Zhang, Yue; Zhang, Feijie; Grompe, Markus; Kay, Mark A

2012-01-01

Although recombinant adeno-associated virus (rAAV) vectors are proving to be efficacious in clinical trials, the episomal character of the delivered transgene restricts their effectiveness to use in quiescent tissues, and may not provide lifelong expression. In contrast, integrating vectors enhance the risk of insertional mutagenesis. In an attempt to overcome both of these limitations, we created new rAAV-rDNA vectors, with an expression cassette flanked by ribosomal DNA (rDNA) sequences capable of homologous recombination into genomic rDNA. We show that after in vivo delivery the rAAV-rDNA vectors integrated into the genomic rDNA locus 8–13 times more frequently than control vectors, providing an estimate that 23–39% of the integrations were specific to the rDNA locus. Moreover, a rAAV-rDNA vector containing a human factor IX (hFIX) expression cassette resulted in sustained therapeutic levels of serum hFIX even after repeated manipulations to induce liver regeneration. Because of the relative safety of integration in the rDNA locus, these vectors expand the usage of rAAV for therapeutics requiring long-term gene transfer into dividing cells. PMID:22990671

Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.

PubMed

Wang, Chao; Shi, Xue; Liu, Lin; Li, Haiyan; Ammiraju, Jetty S S; Kudrna, David A; Xiong, Wentao; Wang, Hao; Dai, Zhaozhao; Zheng, Yonglian; Lai, Jinsheng; Jin, Weiwei; Messing, Joachim; Bennetzen, Jeffrey L; Wing, Rod A; Luo, Meizhong

2013-11-01

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.

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

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.

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)

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.

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.

Shared Physiological and Molecular Responses in Marine Fish and Invertebrates to Environmental Hypoxia: Potential Biomarkers of Adverse Impacts on Marine Communities

NASA Astrophysics Data System (ADS)

Thomas, P.; Rahman, S.

2016-02-01

Knowledge of the effects of environmental exposure to hypoxia (dissolved oxygen: <2 mg/L) on critical physiological functions such as reproduction, growth and metabolism in both fish and invertebrates is essential for accurate predictions of its chronic impacts on marine communities. Marked disruption of reproduction and its endocrine control was observed in Atlantic croaker collected from the hypoxic region in the northern Gulf of Mexico. Recent research has shown that growth and its physiological upregulation is also impaired in hypoxia-exposed marine fish. Expression of insulin-like growth factor (IGF) binding protein (IGFBP), which inhibits growth, was increased in croaker livers, whereas plasma levels of IGF, the primary regulator of growth, were decreased in snapper after hypoxia exposure. In addition, hypoxia inducible factor-1 (HIF-1), which regulates changes in metabolism during adaptation to hypoxia, was upregulated in croaker collected from hypoxic environments. Interestingly, similar changes in the expression of IGFBP and HIF-1 have been found in marine crustaceans after hypoxia exposure, suggesting these responses to hypoxia are common to marine fish and invertebrates. Preliminary field studies indicate that hypoxia exposure also causes epigenetic modifications, including increases in global DNA methylation, and that these epigenetic changes can influence reproduction and growth in croaker. Epigenetic modifications can be passed to offspring and persist in future generations no longer exposed to an environmental stressor further aggravating its long-term adverse impacts on population abundance and delaying recovery. The growing availability of complete invertebrate genomes and high-throughput DNA sequencing indicates similar epigenetic studies can now be conducted with marine invertebrates. Collectively, the results indicate that environmental hypoxia exposure disrupts major physiological functions in fish and invertebrates critical for maintenance of

Phylogenetically diverse macrophyte community promotes species diversity of mobile epi-benthic invertebrates

NASA Astrophysics Data System (ADS)

Nakamoto, Kenta; Hayakawa, Jun; Kawamura, Tomohiko; Kodama, Masafumi; Yamada, Hideaki; Kitagawa, Takashi; Watanabe, Yoshiro

2018-07-01

Various aspects of plant diversity such as species diversity and phylogenetic diversity enhance the species diversity of associated animals in terrestrial systems. In marine systems, however, the effects of macrophyte diversity on the species diversity of associated animals have received little attention. Here, we sampled in a subtropical seagrass-seaweed mixed bed to elucidate the effect of the macrophyte phylogenetic diversity based on the taxonomic relatedness as well as the macrophyte species diversity on species diversity of mobile epi-benthic invertebrates. Using regression analyses for each macrophyte parameter as well as multiple regression analyses, we found that the macrophyte phylogenetic diversity (taxonomic diversity index: Delta) positively influenced the invertebrate species richness and diversity index (H‧). Although the macrophyte species richness and H‧ also positively influenced the invertebrate species richness, the best fit model for invertebrate species richness did not include them, suggesting that the macrophyte species diversity indirectly influenced invertebrate species diversity. Possible explanations of the effects of macrophyte Delta on the invertebrate species diversity were the niche complementarity effect and the selection effect. This is the first study which demonstrates that macrophyte phylogenetic diversity has a strong effect on the species diversity of mobile epi-benthic invertebrates.

Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes

PubMed Central

Smith, H A; White, B J; Kundert, P; Cheng, C; Romero-Severson, J; Andolfatto, P; Besansky, N J

2015-01-01

Although freshwater (FW) is the ancestral habitat for larval mosquitoes, multiple species independently evolved the ability to survive in saltwater (SW). Here, we use quantitative trait locus (QTL) mapping to investigate the genetic architecture of osmoregulation in Anopheles mosquitoes, vectors of human malaria. We analyzed 1134 backcross progeny from a cross between the obligate FW species An. coluzzii, and its closely related euryhaline sibling species An. merus. Tests of 2387 markers with Bayesian interval mapping and machine learning (random forests) yielded six genomic regions associated with SW tolerance. Overlap in QTL regions from both approaches enhances confidence in QTL identification. Evidence exists for synergistic as well as disruptive epistasis among loci. Intriguingly, one QTL region containing ion transporters spans the 2Rop chromosomal inversion that distinguishes these species. Rather than a simple trait controlled by one or a few loci, our data are most consistent with a complex, polygenic mode of inheritance. PMID:25920668

Evidence of secondary consumption of invertebrate prey by Double-crested Cormorants

USGS Publications Warehouse

Johnson, J. H.; Ross, R.M.; Smith, D.R.

1997-01-01

The piscivorous nature of the Double-crested Cormorant (Phalacrocorax auritus) is well documented. However, many researchers who have used regurgitated pellets to describe the diet of cormorants report that invertebrates compose a small but consistent portion of the diet. We examined the hypothesis that invertebrates found in pellets are primarily the result of secondary consumption. We used odds ratio analysis to examine associations in 2,846 individual pellets between the presence of specific invertebrate prey and the presence of fish species known to consume those invertebrate taxa. Significant (P < 0.05) relationships occurred between gastropods and pumpkinseed (Lepomis gibbosus) and ictalurids, and between decapods and rock bass (Ambloplites rupestris) and smallmouth bass (Micropterus dolomieu). Significant (P < 0.05) relationships were also found between pelecypods and pumpkinseed and ictalurids. We suggest that the invertebrate prey we observed in pellets were present in the digestive tracts of fish that were consumed by Double-crested Cormorants and hence represent secondary consumption by cormorants. We conclude that consumption of invertebrates by Double-crested Cormorants may be overestimated in the literature in instances where the diet was described using pellets.

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.

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.

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

Production of SV40-derived vectors.

PubMed

Strayer, David S; Mitchell, Christine; Maier, Dawn A; Nichols, Carmen N

2010-06-01

Recombinant simian virus 40 (rSV40)-derived vectors are particularly useful for gene delivery to bone marrow progenitor cells and their differentiated derivatives, certain types of epithelial cells (e.g., hepatocytes), and central nervous system neurons and microglia. They integrate rapidly into cellular DNA to provide long-term gene expression in vitro and in vivo in both resting and dividing cells. Here we describe a protocol for production and purification of these vectors. These procedures require only packaging cells (e.g., COS-7) and circular vector genome DNA. Amplification involves repeated infection of packaging cells with vector produced by transfection. Cotransfection is not required in any step. Viruses are purified by centrifugation using discontinuous sucrose or cesium chloride (CsCl) gradients and resulting vectors are replication-incompetent and contain no detectable wild-type SV40 revertants. These approaches are simple, give reproducible results, and may be used to generate vectors that are deleted only for large T antigen (Tag), or for all SV40-coding sequences capable of carrying up to 5 kb of foreign DNA. These vectors are best applied to long-term expression of proteins normally encoded by mammalian cells or by viruses that infect mammalian cells, or of untranslated RNAs (e.g., RNA interference). The preparative approaches described facilitate application of these vectors and allow almost any laboratory to exploit their strengths for diverse gene delivery applications.

Construction of a New Phage Integration Vector pFIV-Val for Use in Different Francisella Species

PubMed Central

Tlapák, Hana; Köppen, Kristin; Rydzewski, Kerstin; Grunow, Roland; Heuner, Klaus

2018-01-01

We recently identified and described a putative prophage on the genomic island FhaGI-1 located within the genome of Francisella hispaniensis AS02-814 (F. tularensis subsp. novicida-like 3523). In this study, we constructed two variants of a Francisella phage integration vector, called pFIV1-Val and pFIV2-Val (Francisella Integration Vector-tRNAVal-specific), using the attL/R-sites and the site-specific integrase (FN3523_1033) of FhaGI-1, a chloramphenicol resistance cassette and a sacB gene for counter selection of transformants against the vector backbone. We inserted the respective sites and genes into vector pUC57-Kana to allow for propagation in Escherichia coli. The constructs generated a circular episomal form in E. coli which could be used to transform Francisella spp. where FIV-Val stably integrated site specifically into the tRNAVal gene of the genome, whereas pUC57-Kana is lost due to counter selection. Functionality of the new vector was demonstrated by the successfully complementation of a Francisella mutant strain. The vectors were stable in vitro and during host-cell infection without selective pressure. Thus, the vectors can be applied as a further genetic tool in Francisella research, expanding the present genetic tools by an integrative element. This new element is suitable to perform long-term experiments with different Francisella species. PMID:29594068

Construction of a New Phage Integration Vector pFIV-Val for Use in Different Francisella Species.

PubMed

Tlapák, Hana; Köppen, Kristin; Rydzewski, Kerstin; Grunow, Roland; Heuner, Klaus

2018-01-01

We recently identified and described a putative prophage on the genomic island FhaGI-1 located within the genome of Francisella hispaniensis AS02-814 ( F. tularensis subsp. novicida -like 3523). In this study, we constructed two variants of a Francisella phage integration vector, called pFIV1-Val and pFIV2-Val ( Francisella Integration Vector-tRNA Val -specific), using the attL/R- sites and the site-specific integrase (FN3523_1033) of FhaGI-1, a chloramphenicol resistance cassette and a sacB gene for counter selection of transformants against the vector backbone. We inserted the respective sites and genes into vector pUC57-Kana to allow for propagation in Escherichia coli . The constructs generated a circular episomal form in E. coli which could be used to transform Francisella spp . where FIV-Val stably integrated site specifically into the tRNA Val gene of the genome, whereas pUC57-Kana is lost due to counter selection. Functionality of the new vector was demonstrated by the successfully complementation of a Francisella mutant strain. The vectors were stable in vitro and during host-cell infection without selective pressure. Thus, the vectors can be applied as a further genetic tool in Francisella research, expanding the present genetic tools by an integrative element. This new element is suitable to perform long-term experiments with different Francisella species.

Crawling to collapse: ecologically unsound ornamental invertebrate fisheries.

PubMed

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

2009-12-22

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. 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. 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.

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

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

USDA-ARS?s Scientific Manuscript database

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...

Unrestricted Hepatocyte Transduction with Adeno-Associated Virus Serotype 8 Vectors in Mice

PubMed Central

Nakai, Hiroyuki; Fuess, Sally; Storm, Theresa A.; Muramatsu, Shin-ichi; Nara, Yuko; Kay, Mark A.

2005-01-01

Recombinant adeno-associated virus (rAAV) vectors can mediate long-term stable transduction in various target tissues. However, with rAAV serotype 2 (rAAV2) vectors, liver transduction is confined to only a small portion of hepatocytes even after administration of extremely high vector doses. In order to investigate whether rAAV vectors of other serotypes exhibit similar restricted liver transduction, we performed a dose-response study by injecting mice with β-galactosidase-expressing rAAV1 and rAAV8 vectors via the portal vein. The rAAV1 vector showed a blunted dose-response similar to that of rAAV2 at high doses, while the rAAV8 vector dose-response remained unchanged at any dose and ultimately could transduce all the hepatocytes at a dose of 7.2 × 1012 vector genomes/mouse without toxicity. This indicates that all hepatocytes have the ability to process incoming single-stranded vector genomes into duplex DNA. A single tail vein injection of the rAAV8 vector was as efficient as portal vein injection at any dose. In addition, intravascular administration of the rAAV8 vector at a high dose transduced all the skeletal muscles throughout the body, including the diaphragm, the entire cardiac muscle, and substantial numbers of cells in the pancreas, smooth muscles, and brain. Thus, rAAV8 is a robust vector for gene transfer to the liver and provides a promising research tool for delivering genes to various target organs. In addition, the rAAV8 vector may offer a potential therapeutic agent for various diseases affecting nonhepatic tissues, but great caution is required for vector spillover and tight control of tissue-specific gene expression. PMID:15596817

Non-essential viral proteins of orbiviruses are essential for vector-borne spread by midges

USDA-ARS?s Scientific Manuscript database

Members of the Reoviridae family are non-enveloped multi-layered viruses with a double stranded RNA genome consisting of 9-12 genome segments. The Orbivirus genus contains vector borne virus species with 10 genome segments such as bluetongue virus (BTV) with about 30 serotypes, and African horse sic...

Surprising characteristics of visual systems of invertebrates.

PubMed

González-Martín-Moro, J; Hernández-Verdejo, J L; Jiménez-Gahete, A E

2017-01-01

To communicate relevant and striking aspects about the visual system of some close invertebrates. Review of the related literature. The capacity of snails to regenerate a complete eye, the benefit of the oval shape of the compound eye of many flying insects as a way of stabilising the image during flight, the potential advantages related to the extreme refractive error that characterises the ocelli of many insects, as well as the ability to detect polarised light as a navigation system, are some of the surprising capabilities present in the small invertebrate eyes that are described in this work. The invertebrate eyes have capabilities and sensorial modalities that are not present in the human eye. The study of the eyes of these animals can help us to improve our understanding of our visual system, and inspire the development of optical devices. Copyright © 2016 Sociedad Española de Oftalmología. Publicado por Elsevier España, S.L.U. All rights reserved.

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation.

PubMed

Petersen, Jillian M; Kemper, Anna; Gruber-Vodicka, Harald; Cardini, Ulisse; van der Geest, Matthijs; Kleiner, Manuel; Bulgheresi, Silvia; Mußmann, Marc; Herbold, Craig; Seah, Brandon K B; Antony, Chakkiath Paul; Liu, Dan; Belitz, Alexandra; Weber, Miriam

2016-10-24

Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are the primary producers, providing most of the organic carbon needed for the animal host's nutrition. We sequenced genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic symbiont was previously known to be capable of nitrogen fixation. We detected nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic habitats, where nitrogen availability often limits primary productivity.

Descriptive Statistics of the Genome: Phylogenetic Classification of Viruses.

PubMed

Hernandez, Troy; Yang, Jie

2016-10-01

The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate families with the pairwise sequence alignment tool for similar species. The submitter's judgment is then used to determine the most likely species classification. The aim of this article is to show that this process can be automated into a fast, accurate, one-step process using the proposed alignment-free method and properly implemented machine learning techniques. We present a new family of alignment-free vectorizations of the genome, the generalized vector, that maintains the speed of existing alignment-free methods while outperforming all available methods. This new alignment-free vectorization uses the frequency of genomic words (k-mers), as is done in the composition vector, and incorporates descriptive statistics of those k-mers' positional information, as inspired by the natural vector. We analyze five different characterizations of genome similarity using k-nearest neighbor classification and evaluate these on two collections of viruses totaling over 10,000 viruses. We show that our proposed method performs better than, or as well as, other methods at every level of the phylogenetic hierarchy. The data and R code is available upon request.

Pollution-tolerant invertebrates enhance greenhouse gas flux in urban wetlands.

PubMed

Mehring, Andrew S; Cook, Perran L M; Evrard, Victor; Grant, Stanley B; Levin, Lisa A

2017-09-01

One of the goals of urban ecology is to link community structure to ecosystem function in urban habitats. Pollution-tolerant wetland invertebrates have been shown to enhance greenhouse gas (GHG) flux in controlled laboratory experiments, suggesting that they may influence urban wetland roles as sources or sinks of GHG. However, it is unclear if their effects can be detected in highly variable conditions in a field setting. Here we use an extensive data set on carbon dioxide (CO 2 ), methane (CH 4 ), and nitrous oxide (N 2 O) flux in sediment cores (n = 103) collected from 10 urban wetlands in Melbourne, Australia during summer and winter in order to test for invertebrate enhancement of GHG flux. We detected significant multiplicative enhancement effects of temperature, sediment carbon content, and invertebrate density on CH 4 and CO 2 flux. Each doubling in density of oligochaete worms or large benthic invertebrates (oligochaete worms and midge larvae) corresponded to ~42% and ~15% increases in average CH 4 and CO 2 flux, respectively. However, despite exceptionally high densities, invertebrates did not appear to enhance N 2 O flux. This was likely due to fairly high organic carbon content in sediments (range 2.1-12.6%), and relatively low nitrate availability (median 1.96 μmol/L NO 3 - -N), which highlights the context-dependent nature of community structural effects on ecosystem function. The invertebrates enhancing GHG flux in this study are ubiquitous, and frequently dominate faunal communities in impaired aquatic ecosystems. Therefore, invertebrate effects on CO 2 and CH 4 flux may be common in wetlands impacted by urbanization, and urban wetlands may make greater contributions to the total GHG budgets of cities if the negative impacts of urbanization on wetlands are left unchecked. © 2017 by the Ecological Society of America.

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.

Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus.

PubMed

Yang, Jhung-Ahn; Yang, Sung-Hyun; Kim, Junghee; Kwon, Kae Kyoung; Oh, Hyun-Myung

2017-07-01

Here we report the comparative genomic analysis of strain UJ101 with 15 strains from the family Flavobacteriaceae, using the CGExplorer program. Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus, from the East Sea near Korea. The complete genome of strain UJ101 is a 3,074,209 bp, single, circular chromosome with 30.74% GC content. While the UJ101 genome contains a number of annotated genes for many metabolic pathways, such as the Embden-Meyerhof pathway, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, genes for the Entner-Douddoroff pathway are not found in the UJ101 genome. Overall, carbon fixation processes were absent but nitrate reduction and denitrification pathways were conserved. The UJ101 genome was compared to genomes from other marine animals (three invertebrate strains and 5 fish strains) and other marine animal- derived genera. Notable results by genome comparisons showed that UJ101 is capable of denitrification and nitrate reduction, and that biotin-thiamine pathway participation varies among marine bacteria; fish-dwelling bacteria, freeliving bacteria, invertebrate-dwelling bacteria, and strain UJ101. Pan-genome analysis of the 16 strains in this study included 7,220 non-redundant genes that covered 62% of the pan-genome. A core-genome of 994 genes was present and consisted of 8% of the genes from the pan-genome. Strain UJ101 is a symbiotic hetero-organotroph isolated from xanthid crab, and is a metabolic generalist with nitrate-reducing abilities but without the ability to synthesize biotin. There is a general tendency of UJ101 and some fish pathogens to prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin and thiamine auxotrophy or prototrophy may be used as important markers in microbial community studies.

Predicting subtle behavioral responses of invertebrates to soil contaminants

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

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 belowmore » 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.« less

Development of a duplex real-time RT-qPCR assay to monitor genome replication, gene expression and gene insert stability during in vivo replication of a prototype live attenuated canine distemper virus vector encoding SIV gag.

PubMed

Coleman, John W; Wright, Kevin J; Wallace, Olivia L; Sharma, Palka; Arendt, Heather; Martinez, Jennifer; DeStefano, Joanne; Zamb, Timothy P; Zhang, Xinsheng; Parks, Christopher L

2015-03-01

Advancement of new vaccines based on live viral vectors requires sensitive assays to analyze in vivo replication, gene expression and genetic stability. In this study, attenuated canine distemper virus (CDV) was used as a vaccine delivery vector and duplex 2-step quantitative real-time RT-PCR (RT-qPCR) assays specific for genomic RNA (gRNA) or mRNA have been developed that concurrently quantify coding sequences for the CDV nucleocapsid protein (N) and a foreign vaccine antigen (SIV Gag). These amplicons, which had detection limits of about 10 copies per PCR reaction, were used to show that abdominal cavity lymphoid tissues were a primary site of CDV vector replication in infected ferrets, and importantly, CDV gRNA or mRNA was undetectable in brain tissue. In addition, the gRNA duplex assay was adapted for monitoring foreign gene insert genetic stability during in vivo replication by analyzing the ratio of CDV N and SIV gag genomic RNA copies over the course of vector infection. This measurement was found to be a sensitive probe for assessing the in vivo genetic stability of the foreign gene insert. Copyright © 2014 Elsevier B.V. All rights reserved.

Packaging of HCV-RNA into lentiviral vector

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

Caval, Vincent; Piver, Eric; Service de Biochimie et Biologie Moleculaire, CHRU de Tours

2011-11-04

Highlights: Black-Right-Pointing-Pointer Description of HCV-RNA Core-D1 interactions. Black-Right-Pointing-Pointer In vivo evaluation of the packaging of HCV genome. Black-Right-Pointing-Pointer Determination of the role of the three basic sub-domains of D1. Black-Right-Pointing-Pointer Heterologous system involving HIV-1 vector particles to mobilise HCV genome. Black-Right-Pointing-Pointer Full length mobilisation of HCV genome and HCV-receptor-independent entry. -- Abstract: The advent of infectious molecular clones of Hepatitis C virus (HCV) has unlocked the understanding of HCV life cycle. However, packaging of the genomic RNA, which is crucial to generate infectious viral particles, remains poorly understood. Molecular interactions of the domain 1 (D1) of HCV Core protein andmore » HCV RNA have been described in vitro. Since compaction of genetic information within HCV genome has hampered conventional mutational approach to study packaging in vivo, we developed a novel heterologous system to evaluate the interactions between HCV RNA and Core D1. For this, we took advantage of the recruitment of Vpr fusion-proteins into HIV-1 particles. By fusing HCV Core D1 to Vpr we were able to package and transfer a HCV subgenomic replicon into a HIV-1 based lentiviral vector. We next examined how deletion mutants of basic sub-domains of Core D1 influenced HCV RNA recruitment. The results emphasized the crucial role of the first and third basic regions of D1 in packaging. Interestingly, the system described here allowed us to mobilise full-length JFH1 genome in CD81 defective cells, which are normally refractory to HCV infection. This finding paves the way to an evaluation of the replication capability of HCV in various cell types.« less

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

PubMed

Rašić, Gordana; Filipović, Igor; Weeks, Andrew R; Hoffmann, Ary A

2014-04-11

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. 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. 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. The new SNP set provided much

VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.

PubMed

Hocum, Jonah D; Battrell, Logan R; Maynard, Ryan; Adair, Jennifer E; Beard, Brian C; Rawlings, David J; Kiem, Hans-Peter; Miller, Daniel G; Trobridge, Grant D

2015-07-07

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens. We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads. VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.

Insights into bilaterian evolution from three spiralian genomes

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

Simakov, Oleg; Marletaz, Ferdinand; Cho, Sung-Jin

2012-01-07

Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those ofmore » some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.« less

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.

Integration Profile and Safety of an Adenovirus Hybrid-Vector Utilizing Hyperactive Sleeping Beauty Transposase for Somatic Integration

PubMed Central

Zhang, Wenli; Muck-Hausl, Martin; Wang, Jichang; Sun, Chuanbo; Gebbing, Maren; Miskey, Csaba; Ivics, Zoltan; Izsvak, Zsuzsanna; Ehrhardt, Anja

2013-01-01

We recently developed adenovirus/transposase hybrid-vectors utilizing the previously described hyperactive Sleeping Beauty (SB) transposase HSB5 for somatic integration and we could show stabilized transgene expression in mice and a canine model for hemophilia B. However, the safety profile of these hybrid-vectors with respect to vector dose and genotoxicity remains to be investigated. Herein, we evaluated this hybrid-vector system in C57Bl/6 mice with escalating vector dose settings. We found that in all mice which received the hyperactive SB transposase, transgene expression levels were stabilized in a dose-dependent manner and that the highest vector dose was accompanied by fatalities in mice. To analyze potential genotoxic side-effects due to somatic integration into host chromosomes, we performed a genome-wide integration site analysis using linker-mediated PCR (LM-PCR) and linear amplification-mediated PCR (LAM-PCR). Analysis of genomic DNA samples obtained from HSB5 treated female and male mice revealed a total of 1327 unique transposition events. Overall the chromosomal distribution pattern was close-to-random and we observed a random integration profile with respect to integration into gene and non-gene areas. Notably, when using the LM-PCR protocol, 27 extra-chromosomal integration events were identified, most likely caused by transposon excision and subsequent transposition into the delivered adenoviral vector genome. In total, this study provides a careful evaluation of the safety profile of adenovirus/Sleeping Beauty transposase hybrid-vectors. The obtained information will be useful when designing future preclinical studies utilizing hybrid-vectors in small and large animal models. PMID:24124483

GPCRs in invertebrate innate immunity.

PubMed

Reboul, Jerome; Ewbank, Jonathan J

2016-08-15

G-protein coupled receptors (GPCRs) represent a privileged point of contact between cells and their surrounding environment. They have been widely adopted in vertebrates as mediators of signals involved in both innate and adaptive immunity. Invertebrates rely on innate immune defences to resist infection. We review here evidence from a number of different species, principally the genetically tractable Caenorhabditis elegans and Drosophila melanogaster that points to an important role for GPCRs in modulating innate immunity in invertebrates too. In addition to examples of GPCRs involved in regulating the expression of defence genes, we discuss studies in C. elegans addressing the role of GPCR signalling in pathogen aversive behaviour. Despite the many lacunae in our current knowledge, it is clear that GPCR signalling contributes to host defence across the animal kingdom. Copyright © 2016 Elsevier Inc. All rights reserved.

Trial and error: how the unclonable human mitochondrial genome was cloned in yeast.

PubMed

Bigger, Brian W; Liao, Ai-Yin; Sergijenko, Ana; Coutelle, Charles

2011-11-01

Development of a human mitochondrial gene delivery vector is a critical step in the ability to treat diseases arising from mutations in mitochondrial DNA. Although we have previously cloned the mouse mitochondrial genome in its entirety and developed it as a mitochondrial gene therapy vector, the human mitochondrial genome has been dubbed unclonable in E. coli, due to regions of instability in the D-loop and tRNA(Thr) gene. We tested multi- and single-copy vector systems for cloning human mitochondrial DNA in E. coli and Saccharomyces cerevisiae, including transformation-associated recombination. Human mitochondrial DNA is unclonable in E. coli and cannot be retained in multi- or single-copy vectors under any conditions. It was, however, possible to clone and stably maintain the entire human mitochondrial genome in yeast as long as a single-copy centromeric plasmid was used. D-loop and tRNA(Thr) were both stable and unmutated. This is the first report of cloning the entire human mitochondrial genome and the first step in developing a gene delivery vehicle for human mitochondrial gene therapy.

The evolution of virulence of West Nile virus in a mosquito vector: implications for arbovirus adaptation and evolution.

PubMed

Ciota, Alexander T; Ehrbar, Dylan J; Matacchiero, Amy C; Van Slyke, Greta A; Kramer, Laura D

2013-03-20

Virulence is often coupled with replicative fitness of viruses in vertebrate systems, yet the relationship between virulence and fitness of arthropod-borne viruses (arboviruses) in invertebrates has not been evaluated. Although the interactions between vector-borne pathogens and their invertebrate hosts have been characterized as being largely benign, some costs of arbovirus exposure have been identified for mosquitoes. The extent to which these costs may be strain-specific and the subsequent consequences of these interactions on vector and virus evolution has not been adequately explored. Using West Nile virus (WNV) and Culex pipiens mosquitoes, we tested the hypothesis that intrahost fitness is correlated with virulence in mosquitoes by evaluating life history traits following exposure to either non-infectious bloodmeals or bloodmeals containing wildtype (WNV WT) or the high fitness, mosquito-adapted strain, WNV MP20 derived from WNV WT. Our results demonstrate strain-specific effects on mosquito survival, fecundity, and blood feeding behavior. Specifically, both resistance to and infection with WNV MP20, but not WNV WT, decreased survival of Cx. pipiens and altered fecundity and bloodfeeding such that early egg output was enhanced at a later cost. As predicted by the trade-off hypothesis of virulence, costs of infection with WNV MP20 in terms of survival were directly correlated to viral load, yet resistance to infection with this virulent strain was equally costly. Taken together, these results demonstrate that WNV MP20 infection decreases the transmission potential of Cx. pipiens populations despite the increased intrahost fitness of this strain, indicating that a virulence-transmission trade-off in invertebrates could contribute significantly to the adaptive and evolutionary constraint of arboviruses.

CASA in invertebrates.

PubMed

van der Horst, Gerhard; Bennett, Monique; Bishop, John D D

2018-04-09

Sperm movement has been described in several phyla of invertebrates. Yet, sperm motility has only been quantified using computer-aided sperm analysis (CASA-Mot) in externally fertilising species (broadcast spawners) of two phyla, molluscs and echinoderms. In the present study we quantified in detail the nature of the sperm tracks, percentage motility groupings and detailed kinematics of rapid-, medium- and slow-swimming spermatozoa in the oyster Crassostrea gigas and four species never previously studied by CASA-Mot, namely the molluscs Choromytilus meridionalis, Donax serra and Haliotis midae and the echinoderm Parechinus angulosus. A feature common to all these species are the helical tracks, the diameter of which seems to be species specific. Using CASA-Mot, the behaviour of spermatozoa was also studied over time and in the presence of egg water and Ca2+ modulators such as caffeine and procaine hydrochloride. For the first time, we show that hyperactivation can be induced in all species in the presence of egg water (sea water that was mixed with mature eggs and then centrifuged) and/or caffeine, and these hyperactivated sperm tracks were characterised using CASA-Mot. We relate the different patterns of sperm motility and behaviour to reproductive strategies such as broadcast spawning and spermcasting, and briefly review studies using CASA-Mot on other invertebrates.

Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

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

McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.

2005-08-26

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. Amore » minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.« less

Biodiversity loss in seagrass meadows due to local invertebrate fisheries and harbour activities

NASA Astrophysics Data System (ADS)

Nordlund, Lina Mtwana; Gullström, Martin

2013-12-01

Seagrass meadows provide a wide variety of ecosystem services, but their distribution and health are adversely affected by man. In the present study, we examined the influence of coastal exploitation in terms of invertebrate harvesting and harbour activity on invertebrate community composition in subtropical seagrass meadows at Inhaca Island, Mozambique, in the Western Indian Ocean. There was a fivefold higher invertebrate density and biomass, and clearly higher invertebrate species richness, in the protected (control) site compared to the two exploited sites. The causes for the clear differences between protected and exploited sites were probably a result of (1) the directional outtake of large edible or saleable invertebrates (mostly molluscs) and the absence of boat traffic in the harvested site, and (2) harbour activities. Invertebrate community composition in the two exploited sites also differed (although less clear), which was likely due to inherent distinction in type of disturbance. Our findings revealed that protection of seagrass habitat is necessary and that disturbances of different origin might require different forms of management and conservation. Designing protected areas is however a complex process due to competition for use and space with activities such as invertebrate harvesting and harbours.

Anaplasma phagocytophilum Infection Subverts Carbohydrate Metabolic Pathways in the Tick Vector, Ixodes scapularis.

PubMed

Cabezas-Cruz, Alejandro; Alberdi, Pilar; Valdés, James J; Villar, Margarita; de la Fuente, José

2017-01-01

The obligate intracellular pathogen, Anaplasma phagocytophilum , is the causative agent of human, equine, and canine granulocytic anaplasmosis and tick-borne fever (TBF) in ruminants. A. phagocytophilum has become an emerging tick-borne pathogen in the United States, Europe, Africa, and Asia, with increasing numbers of infected people and animals every year. It has been recognized that intracellular pathogens manipulate host cell metabolic pathways to increase infection and transmission in both vertebrate and invertebrate hosts. However, our current knowledge on how A. phagocytophilum affect these processes in the tick vector, Ixodes scapularis is limited. In this study, a genome-wide search for components of major carbohydrate metabolic pathways was performed in I. scapularis ticks for which the genome was recently published. The enzymes involved in the seven major carbohydrate metabolic pathways glycolysis, gluconeogenesis, pentose phosphate, tricarboxylic acid cycle (TCA), glyceroneogenesis, and mitochondrial oxidative phosphorylation and β-oxidation were identified. Then, the available transcriptomics and proteomics data was used to characterize the mRNA and protein levels of I. scapularis major carbohydrate metabolic pathway components in response to A. phagocytophilum infection of tick tissues and cultured cells. The results showed that major carbohydrate metabolic pathways are conserved in ticks. A. phagocytophilum infection inhibits gluconeogenesis and mitochondrial metabolism, but increases the expression of glycolytic genes. A model was proposed to explain how A. phagocytophilum could simultaneously control tick cell glucose metabolism and cytoskeleton organization, which may be achieved in part by up-regulating and stabilizing hypoxia inducible factor 1 alpha in a hypoxia-independent manner. The present work provides a more comprehensive view of the major carbohydrate metabolic pathways involved in the response to A. phagocytophilum infection in ticks

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Applications of lentiviral vectors in molecular imaging.

PubMed

Chatterjee, Sushmita; De, Abhijit

2014-06-01

Molecular imaging provides the ability of simultaneous visual and quantitative estimation of long term gene expression directly from living organisms. To reveal the kinetics of gene expression by imaging method, often sustained expression of the transgene is required. Lentiviral vectors have been extensively used over last fifteen years for delivery of a transgene in a wide variety of cell types. Lentiviral vectors have the well known advantages such as sustained transgene delivery through stable integration into the host genome, the capability of infecting non-dividing and dividing cells, broad tissue tropism, a reasonably large carrying capacity for delivering therapeutic and reporter gene combinations. Additionally, they do not express viral proteins during transduction, have a potentially safe integration site profile, and a relatively easy system for vector manipulation and infective viral particle production. As a result, lentiviral vector mediated therapeutic and imaging reporter gene delivery to various target organs holds promise for the future treatment. In this review, we have conducted a brief survey of important lentiviral vector developments in diverse biomedical fields including reproductive biology.

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. Copyright © 2012 Elsevier Ltd. All rights reserved.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

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.

GenomeDiagram: a python package for the visualization of large-scale genomic data.

PubMed

Pritchard, Leighton; White, Jennifer A; Birch, Paul R J; Toth, Ian K

2006-03-01

We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

How do patch quality and spatial context affect invertebrate communities in a natural moss microlandscape?

NASA Astrophysics Data System (ADS)

Trekels, Hendrik; Driesen, Mario; Vanschoenwinkel, Bram

2017-11-01

Globally, moss associated invertebrates remain poorly studied and it is largely unknown to what extent their diversity is driven by local environmental conditions or the landscape context. Here, we investigated small scale drivers of invertebrate communities in a moss landscape in a temperate forest in Western Europe. By comparing replicate quadrats of 5 different moss species in a continuous moss landscape, we found that mosses differed in invertebrate density and community composition. Although, in general, richness was similar among moss species, some invertebrate taxa were significantly linked to certain moss species. Only moss biomass and not relative moisture content could explain differences in invertebrate densities among moss species. Second, we focused on invertebrate communities associated with the locally common moss species Kindbergia praelonga in isolated moss patches on dead tree trunks to look at effects of patch size, quality, heterogeneity and connectivity on invertebrate communities. Invertebrate richness was higher in patches under closed canopies than under more open canopies, presumably due to the higher input of leaf litter and/or lower evaporation. In addition, increased numbers of other moss species in the same patch seemed to promote invertebrate richness in K. praelonga, possibly due to mass effects. Since invertebrate richness was unaffected by patch size and isolation, dispersal was probably not limiting in this system with patches separated by tens of meters, or stochastic extinctions may be uncommon. Overall, we conclude that invertebrate composition in moss patches may not only depend on local patch conditions, in a particular moss species, but also on the presence of other moss species in the direct vicinity.

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.

The octopus genome and the evolution of cephalopod neural and morphological novelties.

PubMed

Albertin, Caroline B; Simakov, Oleg; Mitros, Therese; Wang, Z Yan; Pungor, Judit R; Edsinger-Gonzales, Eric; Brenner, Sydney; Ragsdale, Clifton W; Rokhsar, Daniel S

2015-08-13

Coleoid cephalopods (octopus, squid and cuttlefish) are active, resourceful predators with a rich behavioural repertoire. They have the largest nervous systems among the invertebrates and present other striking morphological innovations including camera-like eyes, prehensile arms, a highly derived early embryogenesis and a remarkably sophisticated adaptive colouration system. To investigate the molecular bases of cephalopod brain and body innovations, we sequenced the genome and multiple transcriptomes of the California two-spot octopus, Octopus bimaculoides. We found no evidence for hypothesized whole-genome duplications in the octopus lineage. The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians, except for massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc-finger transcription factors. Extensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described, as well as in genes participating in a broad range of other cellular functions. We identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers and the nervous system. Finally, we found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions. Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems.

Bartonella quintana Deploys Host and Vector Temperature-Specific Transcriptomes

PubMed Central

Previte, Domenic; Yoon, Kyong S.; Clark, J. Marshall; DeRisi, Joseph L.; Koehler, Jane E.

2013-01-01

The bacterial pathogen Bartonella quintana is passed between humans by body lice. B. quintana has adapted to both the human host and body louse vector niches, producing persistent infection with high titer bacterial loads in both the host (up to 105 colony-forming units [CFU]/ml) and vector (more than 108 CFU/ml). Using a novel custom microarray platform, we analyzed bacterial transcription at temperatures corresponding to the host (37°C) and vector (28°C), to probe for temperature-specific and growth phase-specific transcriptomes. We observed that transcription of 7% (93 genes) of the B. quintana genome is modified in response to change in growth phase, and that 5% (68 genes) of the genome is temperature-responsive. Among these transcriptional changes in response to temperature shift and growth phase was the induction of known B. quintana virulence genes and several previously unannotated genes. Hemin binding proteins, secretion systems, response regulators, and genes for invasion and cell attachment were prominent among the differentially-regulated B. quintana genes. This study represents the first analysis of global transcriptional responses by B. quintana. In addition, the in vivo experiments provide novel insight into the B. quintana transcriptional program within the body louse environment. These data and approaches will facilitate study of the adaptation mechanisms employed by Bartonella during the transition between human host and arthropod vector. PMID:23554923

Whole-community mutualism: associated invertebrates facilitate a dominant habitat-forming seaweed.

PubMed

Bracken, Matthew E S; Gonzalez-Dorantes, Cirse A; Stachowicz, John J

2007-09-01

Many habitat-forming, or foundation, species harbor diverse assemblages of associated taxa that benefit from the refuges from predators or harsh physical conditions that foundation species provide. Growing numbers of studies show how specific taxa associated with foundation species can benefit their hosts, but the aggregate effects of the entire community of associated species remain poorly understood. Here, we evaluate the role that a diverse assemblage of invertebrates plays in mediating the dominance of a foundation species, the green filamentous seaweed Cladophora columbiana Collins, in rocky intertidal habitats. Cladophora is a fast-growing seaweed with a high nitrogen demand, and we suggest that it persists in nutrient-limited high-intertidal pools because of local-scale nitrogen excretion by the invertebrate taxa living within its filaments. Removal of associated invertebrates resulted in a fourfold increase in the rate of water-column nitrogen depletion by Cladophora, and ammonium concentrations inside Cladophora turfs with invertebrates present were seven times higher than in the adjacent tide-pool water. The ammonium excreted by invertebrate meiofauna far surpassed the nitrogen used by Cladophora, suggesting that all of Cladophora's nitrogen requirements could be met by the invertebrates associated with it. This study links host performance to the total aggregate biomass of mutualists rather than the particular traits of any one species, suggesting the potential for important feedbacks between individual hosts and the communities of associated species that they support.

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.

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

A scalable method for the production of high-titer and high-quality adeno-associated type 9 vectors using the HSV platform

PubMed Central

Adamson-Small, Laura; Potter, Mark; Falk, Darin J; Cleaver, Brian; Byrne, Barry J; Clément, Nathalie

2016-01-01

Recombinant adeno-associated vectors based on serotype 9 (rAAV9) have demonstrated highly effective gene transfer in multiple animal models of muscular dystrophies and other neurological indications. Current limitations in vector production and purification have hampered widespread implementation of clinical candidate vectors, particularly when systemic administration is considered. In this study, we describe a complete herpes simplex virus (HSV)-based production and purification process capable of generating greater than 1 × 1014 rAAV9 vector genomes per 10-layer CellSTACK of HEK 293 producer cells, or greater than 1 × 105 vector genome per cell, in a final, fully purified product. This represents a 5- to 10-fold increase over transfection-based methods. In addition, rAAV vectors produced by this method demonstrated improved biological characteristics when compared to transfection-based production, including increased infectivity as shown by higher transducing unit-to-vector genome ratios and decreased total capsid protein amounts, shown by lower empty-to-full ratios. Together, this data establishes a significant improvement in both rAAV9 yields and vector quality. Further, the method can be readily adapted to large-scale good laboratory practice (GLP) and good manufacturing practice (GMP) production of rAAV9 vectors to enable preclinical and clinical studies and provide a platform to build on toward late-phases and commercial production. PMID:27222839

Breakdown and invertebrate colonization of dead wood in wetland, upland, and river habitats

Treesearch

A Braccia; D Batzer

2010-01-01

Breakdown of woody debris in river and upland habitats as well as the interactions between wood and invertebrates have been well described. Studies of wood in wetlands are rare, and far less is known about breakdown and invertebrate use of wood in these transitional habitats. This study experimentally assessed breakdown and invertebrate colonization of wood in a...

Presence of Tube isoforms in Litopenaeus vannamei suggests various regulatory patterns of signal transduction in invertebrate NF-κB pathway.

PubMed

Li, Chaozheng; Chen, Yixiao; Weng, Shaoping; Li, Sedong; Zuo, Hongliang; Yu, Xiaoqiang; Li, Haoyang; He, Jianguo; Xu, Xiaopeng

2014-02-01

The toll-like receptor (TLR)/NF-κB signaling pathways play critical roles in the innate immune system. The intracellular signal transduction of most TLR pathways in invertebrate cells is triggered by formation of a heterotrimeric complex composed of MyD88, Tube and Pelle. In this study, we identified a Litopenaeus vannamei Pelle (LvPelle) and an isoform of L. vannamei Tube (LvTube) designated as LvTube-1. The interactions among LvPelle, LvTube/LvTube-1 and LvMyD88/LvMyD88-1 were elucidated and their functions during pathogen infections were investigated. Knockdowns of LvPelle and LvTube/LvTube-1 using RNAi strategy led to higher mortalities of shrimps during Vibrio parahemolyticus infection, and could reduce the genome copy number of white spot syndrome virus (WSSV) in the infected muscle tissue but did not affect the mortality caused by WSSV infection. The effects of LvPelle and LvTube/LvTube-1 on promoters containing NF-κB binding motifs were analyzed by dual-luciferase reporter assays and the results demonstrated that LvTube-1 could activate the NF-κB activity to significantly higher level than LvTube did. Moreover, tissue distributions of LvTube and LvTube-1 mRNAs and their expression profiles during pathogen and immune stimulant challenges were different, indicating that they could play different roles in immune responses. This is the first report of Tube isoforms in invertebrates. Together with our previous study on LvMyD88 isoforms, our results suggest that various isoforms of adaptor components may be involved in various regulatory patterns of signal transduction in invertebrate TLR/NF-κB pathway and this could be a strategy adopted by invertebrates to modulate immune responses. Copyright © 2013 Elsevier Ltd. All rights reserved.

RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates

PubMed Central

Palmer, William H.; Hadfield, Jarrod D.; Obbard, Darren J.

2018-01-01

Conflict between organisms can lead to a reciprocal adaptation that manifests as an increased evolutionary rate in genes mediating the conflict. This adaptive signature has been observed in RNA-interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked in an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species using a formal meta-analytic framework to combine data across species and by implementing a multispecies generalized linear mixed model of mutation counts. Across species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the genes most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analyzed insect species, perhaps due to concurrent parasite-mediated arms races. PMID:29437826

A Versatile Transposon-Based Activation Tag Vector System for Functional Genomics in Cereals and Other Monocot Plants1[OA

PubMed Central

Qu, Shaohong; Desai, Aparna; Wing, Rod; Sundaresan, Venkatesan

2008-01-01

Transposon insertional mutagenesis is an effective alternative to T-DNA mutagenesis when transformation through tissue culture is inefficient as is the case for many crop species. When used as activation tags, transposons can be exploited to generate novel gain-of-function phenotypes without transformation and are of particular value in the study of polyploid plants where gene knockouts will not have phenotypes. We have developed an in cis-activation-tagging Ac-Ds transposon system in which a T-DNA vector carries a Dissociation (Ds) element containing 4× cauliflower mosaic virus enhancers along with the Activator (Ac) transposase gene. Stable Ds insertions were selected using green fluorescent protein and red fluorescent protein genes driven by promoters that are functional in maize (Zea mays) and rice (Oryza sativa). The system has been tested in rice, where 638 stable Ds insertions were selected from an initial set of 26 primary transformants. By analysis of 311 flanking sequences mapped to the rice genome, we could demonstrate the wide distribution of the elements over the rice chromosomes. Enhanced expression of rice genes adjacent to Ds insertions was detected in the insertion lines using semiquantitative reverse transcription-PCR method. The in cis-two-element vector system requires minimal number of primary transformants and eliminates the need for crossing, while the use of fluorescent markers instead of antibiotic or herbicide resistance increases the applicability to other plants and eliminates problems with escapes. Because Ac-Ds has been shown to transpose widely in the plant kingdom, the activation vector system developed in this study should be of utility more generally to other monocots. PMID:17993541

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.

The family Rhabdoviridae: Mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

USGS Publications Warehouse

Dietzgen, Ralf G.; Kondo, Hideki; Goodin, Michael M.; Kurath, Gael; Vasilakis, Nikos

2017-01-01

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.

Antimycobacterial Metabolites from Marine Invertebrates.

PubMed

Daletos, Georgios; Ancheeva, Elena; Chaidir, Chaidir; Kalscheuer, Rainer; Proksch, Peter

2016-10-01

Marine organisms play an important role in natural product-based drug research due to accumulation of structurally unique and bioactive metabolites. The exploration of marine-derived compounds may significantly extend the scientific knowledge of potential scaffolds for antibiotic drug discovery. Development of novel antitubercular agents is especially significant as the emergence of drug-resistant Mycobacterium tuberculosis strains remains threateningly high. Marine invertebrates (i.e., sponges, corals, gorgonians) as a source of new chemical entities are the center of research for several scientific groups, and the wide spectrum of biological activities of marine-derived compounds encourages scientists to carry out investigations in the field of antibiotic research, including tuberculosis treatment. The present review covers published data on antitubercular natural products from marine invertebrates grouped according to their biogenetic origin. Studies on the structure-activity relationships of these important leads are highlighted as well. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparative biology of pain: What invertebrates can tell us about how nociception works.

PubMed

Burrell, Brian D

2017-04-01

The inability to adequately treat chronic pain is a worldwide health care crisis. Pain has both an emotional and a sensory component, and this latter component, nociception, refers specifically to the detection of damaging or potentially damaging stimuli. Nociception represents a critical interaction between an animal and its environment and exhibits considerable evolutionary conservation across species. Using comparative approaches to understand the basic biology of nociception could promote the development of novel therapeutic strategies to treat pain, and studies of nociception in invertebrates can provide especially useful insights toward this goal. Both vertebrates and invertebrates exhibit segregated sensory pathways for nociceptive and nonnociceptive information, injury-induced sensitization to nociceptive and nonnociceptive stimuli, and even similar antinociceptive modulatory processes. In a number of invertebrate species, the central nervous system is understood in considerable detail, and it is often possible to record from and/or manipulate single identifiable neurons through either molecular genetic or physiological approaches. Invertebrates also provide an opportunity to study nociception in an ethologically relevant context that can provide novel insights into the nature of how injury-inducing stimuli produce persistent changes in behavior. Despite these advantages, invertebrates have been underutilized in nociception research. In this review, findings from invertebrate nociception studies are summarized, and proposals for how research using invertebrates can address questions about the fundamental mechanisms of nociception are presented. Copyright © 2017 the American Physiological Society.

Comparative biology of pain: What invertebrates can tell us about how nociception works

PubMed Central

2017-01-01

The inability to adequately treat chronic pain is a worldwide health care crisis. Pain has both an emotional and a sensory component, and this latter component, nociception, refers specifically to the detection of damaging or potentially damaging stimuli. Nociception represents a critical interaction between an animal and its environment and exhibits considerable evolutionary conservation across species. Using comparative approaches to understand the basic biology of nociception could promote the development of novel therapeutic strategies to treat pain, and studies of nociception in invertebrates can provide especially useful insights toward this goal. Both vertebrates and invertebrates exhibit segregated sensory pathways for nociceptive and nonnociceptive information, injury-induced sensitization to nociceptive and nonnociceptive stimuli, and even similar antinociceptive modulatory processes. In a number of invertebrate species, the central nervous system is understood in considerable detail, and it is often possible to record from and/or manipulate single identifiable neurons through either molecular genetic or physiological approaches. Invertebrates also provide an opportunity to study nociception in an ethologically relevant context that can provide novel insights into the nature of how injury-inducing stimuli produce persistent changes in behavior. Despite these advantages, invertebrates have been underutilized in nociception research. In this review, findings from invertebrate nociception studies are summarized, and proposals for how research using invertebrates can address questions about the fundamental mechanisms of nociception are presented. PMID:28053241

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

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

Advancing Neuroscience Research in Africa: Invertebrate Species to the Rescue.

PubMed

Balogun, Wasiu Gbolahan; Cobham, Ansa Emmanuel; Amin, Abdulbasit; Seeni, Azman

2018-03-15

Neuroscience research and training in many African countries are difficult due to funding and infrastructure deficit. This has resulted in few neuroscientists within Africa. However, invertebrates such as Drosophila and Caenorhabditis elegans could provide the perfect answer to these difficulties. These organisms are cheap, easy to handle and offer a comparable advantage over vertebrates in neuroscience research modeling because they have a simple nervous system and exhibit well-defined behaviors. Studies using invertebrates have helped to understand neurosciences and the complexes associated with it. If Africa wants to catch up with the rest of the world in neuroscience research, it needs to employ this innovative cost-effective approach in its research. To improve invertebrate neuroscience within the Africa continent, the authors advocated the establishment of invertebrate research centers either at regional or national level across Africa. Finally, there is also a need to provide public funding to consolidate the gains that have been made by not-for-profit international organizations over the years. Copyright © 2018 IBRO. Published by Elsevier Ltd. All rights reserved.

Genetic Competence Drives Genome Diversity in Bacillus subtilis

PubMed Central

Chevreux, Bastien; Serra, Cláudia R; Schyns, Ghislain; Henriques, Adriano O

2018-01-01

Abstract Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them. PMID:29272410

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

USDA-ARS?s Scientific Manuscript database

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...

Characterization of bioactive peptides obtained from marine invertebrates.

PubMed

Lee, Jung Kwon; Jeon, Joong-Kyun; Kim, Se-Kwon; Byun, Hee-Guk

2012-01-01

Bioactive peptides as products of hydrolysis of diverse marine invertebrate (shellfish, crustacean, rotifer, etc.) proteins are the focus of current research. After much research on these muscles and by-products, some biologically active peptides were identified and applied to useful compounds for human utilization. This chapter reviews bioactive peptides from marine invertebrates in regarding to their bioactivities. Additionally, specific characteristics of antihypertensive, anti-Alzheimer, antioxidant, antimicrobial peptide enzymatic production, methods to evaluate bioactivity capacity, bioavailability, and safety concerns of peptides are reviewed. Copyright © 2012 Elsevier Inc. All rights reserved.

The End of a 60-year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton

PubMed Central

Toenshoff, Elena R.; Fields, Peter D.; Bourgeois, Yann X.; Ebert, Dieter

2018-01-01

The planktonic freshwater crustacean of the genus Daphnia are a model system for biomedical research and, in particular, invertebrate-parasite interactions. Up until now, no virus has been characterized for this system. Here we report the discovery of an iridovirus as the causative agent of White Fat Cell Disease (WFCD) in Daphnia. WFCD is a highly virulent disease of Daphnia that can easily be cultured under laboratory conditions. Although it has been studied from sites across Eurasia for more than 60 years, its causative agent had not been described, nor had an iridovirus been connected to WFCD before now. Here we find that an iridovirus—the Daphnia iridescent virus 1 (DIV-1)—is the causative agent of WFCD. DIV-1 has a genome sequence of about 288 kbp, with 39% G+C content and encodes 367 predicted open reading frames. DIV-1 clusters together with other invertebrate iridoviruses but has by far the largest genome among all sequenced iridoviruses. Comparative genomics reveal that DIV-1 has apparently recently lost a substantial number of unique genes but has also gained genes by horizontal gene transfer from its crustacean host. DIV-1 represents the first invertebrate iridovirus that encodes proteins to purportedly cap RNA, and it contains unique genes for a DnaJ-like protein, a membrane glycoprotein and protein of the immunoglobulin superfamily, which may mediate host–pathogen interactions and pathogenicity. Our findings end a 60-year search for the causative agent of WFCD and add to our knowledge of iridovirus genomics and invertebrate–virus interactions. PMID:29487186

Common mechanisms of synaptic plasticity in vertebrates and invertebrates

PubMed Central

Glanzman, David L.

2016-01-01

Until recently, the literature on learning-related synaptic plasticity in invertebrates has been dominated by models assuming plasticity is mediated by presynaptic changes, whereas the vertebrate literature has been dominated by models assuming it is mediated by postsynaptic changes. Here I will argue that this situation does not reflect a biological reality and that, in fact, invertebrate and vertebrate nervous systems share a common set of mechanisms of synaptic plasticity. PMID:20152143

Insects and other invertebrates

Treesearch

John R. Jones; Norbert V. DeByle; Diane M. Bowers

1985-01-01

Quaking aspen throughout its range appears to be host to several insect and other invertebrate pests (fig. 1). It is a short-lived species that is palatable to a large variety of animals. Furniss and Carolin (1977) listed 33 insect species that use aspen as a food source. Some are quite damaging and may kill otherwise healthy stands of aspen; others feed on weakened or...

The importance of invertebrates when considering the impacts of anthropogenic noise

PubMed Central

Morley, Erica L.; Jones, Gareth; Radford, Andrew N.

2014-01-01

Anthropogenic noise is now recognized as a major global pollutant. Rapidly burgeoning research has identified impacts on individual behaviour and physiology through to community disruption. To date, however, there has been an almost exclusive focus on vertebrates. Not only does their central role in food webs and in fulfilling ecosystem services make imperative our understanding of how invertebrates are impacted by all aspects of environmental change, but also many of their inherent characteristics provide opportunities to overcome common issues with the current anthropogenic noise literature. Here, we begin by explaining why invertebrates are likely to be affected by anthropogenic noise, briefly reviewing their capacity for hearing and providing evidence that they are capable of evolutionary adaptation and behavioural plasticity in response to natural noise sources. We then discuss the importance of quantifying accurately and fully both auditory ability and noise content, emphasizing considerations of direct relevance to how invertebrates detect sounds. We showcase how studying invertebrates can help with the behavioural bias in the literature, the difficulties in drawing strong, ecologically valid conclusions and the need for studies on fitness impacts. Finally, we suggest avenues of future research using invertebrates that would advance our understanding of the impact of anthropogenic noise. PMID:24335986

The importance of invertebrates when considering the impacts of anthropogenic noise.

PubMed

Morley, Erica L; Jones, Gareth; Radford, Andrew N

2014-02-07

Anthropogenic noise is now recognized as a major global pollutant. Rapidly burgeoning research has identified impacts on individual behaviour and physiology through to community disruption. To date, however, there has been an almost exclusive focus on vertebrates. Not only does their central role in food webs and in fulfilling ecosystem services make imperative our understanding of how invertebrates are impacted by all aspects of environmental change, but also many of their inherent characteristics provide opportunities to overcome common issues with the current anthropogenic noise literature. Here, we begin by explaining why invertebrates are likely to be affected by anthropogenic noise, briefly reviewing their capacity for hearing and providing evidence that they are capable of evolutionary adaptation and behavioural plasticity in response to natural noise sources. We then discuss the importance of quantifying accurately and fully both auditory ability and noise content, emphasizing considerations of direct relevance to how invertebrates detect sounds. We showcase how studying invertebrates can help with the behavioural bias in the literature, the difficulties in drawing strong, ecologically valid conclusions and the need for studies on fitness impacts. Finally, we suggest avenues of future research using invertebrates that would advance our understanding of the impact of anthropogenic noise.

Production, concentration and titration of pseudotyped HIV-1-based lentiviral vectors.

PubMed

Kutner, Robert H; Zhang, Xian-Yang; Reiser, Jakob

2009-01-01

Over the past decade, lentiviral vectors have emerged as powerful tools for transgene delivery. The use of lentiviral vectors has become commonplace and applications in the fields of neuroscience, hematology, developmental biology, stem cell biology and transgenesis are rapidly emerging. Also, lentiviral vectors are at present being explored in the context of human clinical trials. Here we describe improved protocols to generate highly concentrated lentiviral vector pseudotypes involving different envelope glycoproteins. In this protocol, vector stocks are prepared by transient transfection using standard cell culture media or serum-free media. Such stocks are then concentrated by ultracentrifugation and/or ion exchange chromatography, or by precipitation using polyethylene glycol 6000, resulting in vector titers of up to 10(10) transducing units per milliliter and above. We also provide reliable real-time PCR protocols to titrate lentiviral vectors based on proviral DNA copies present in genomic DNA extracted from transduced cells or on vector RNA. These production/concentration methods result in high-titer vector preparations that show reduced toxicity compared with lentiviral vectors produced using standard protocols involving ultracentrifugation-based methods. The vector production and titration protocol described here can be completed within 8 d.

Circadian rhythms in insect disease vectors

PubMed Central

Meireles-Filho, Antonio Carlos Alves; Kyriacou, Charalambos Panayiotis

2013-01-01

Organisms from bacteria to humans have evolved under predictable daily environmental cycles owing to the Earth’s rotation. This strong selection pressure has generated endogenous circadian clocks that regulate many aspects of behaviour, physiology and metabolism, anticipating and synchronising internal time-keeping to changes in the cyclical environment. In haematophagous insect vectors the circadian clock coordinates feeding activity, which is important for the dynamics of pathogen transmission. We have recently witnessed a substantial advance in molecular studies of circadian clocks in insect vector species that has consolidated behavioural data collected over many years, which provided insights into the regulation of the clock in the wild. Next generation sequencing technologies will facilitate the study of vector genomes/transcriptomes both among and within species and illuminate some of the species-specific patterns of adaptive circadian phenotypes that are observed in the field and in the laboratory. In this review we will explore these recent findings and attempt to identify potential areas for further investigation. PMID:24473802

Specific insertions of zinc finger domains into Gag-Pol yield engineered retroviral vectors with selective integration properties

PubMed Central

Lim, Kwang-il; Klimczak, Ryan; Yu, Julie H.; Schaffer, David V.

2010-01-01

Retroviral vectors offer benefits of efficient delivery and stable gene expression; however, their clinical use raises the concerns of insertional mutagenesis and potential oncogenesis due to genomic integration preferences in transcriptional start sites (TSS). We have shifted the integration preferences of retroviral vectors by generating a library of viral variants with a DNA-binding domain inserted at random positions throughout murine leukemia virus Gag-Pol, then selecting for variants that are viable and exhibit altered integration properties. We found seven permissive zinc finger domain (ZFD) insertion sites throughout Gag-Pol, including within p12, reverse transcriptase, and integrase. Comprehensive genome integration analysis showed that several ZFD insertions yielded retroviral vector variants with shifted integration patterns that did not favor TSS. Furthermore, integration site analysis revealed selective integration for numerous mutants. For example, two retroviral variants with a given ZFD at appropriate positions in Gag-Pol strikingly integrated primarily into four common sites out of 3.1 × 109 possible human genome locations (P = 4.6 × 10-29). Our findings demonstrate that insertion of DNA-binding motifs into multiple locations in Gag-Pol can make considerable progress toward engineering safer retroviral vectors that integrate into a significantly narrowed pool of sites on human genome and overcome the preference for TSS. PMID:20616052

Complete replication-competent adenovirus 11p vectors with E1 or E3 insertions show improved heat stability

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

Mei, Ya-Fang, E-mail: ya-fang.mei@umu.se

2016-10-15

Conventional adenovirus vectors harboring E1 or E3 deletions followed by the insertion of an exogenous gene show considerably reduced virion stability. Here, we report strategies to generate complete replication-competent Ad11p(RCAd11p) vectors that overcome the above disadvantage. A GFP cassette was successfully introduced either upstream of E1A or in the E3A region. The resulting vectors showed high expression levels of the hexon and E1genes and also strongly induced the cytopathic effect in targeted cells. When harboring oversized genomes, the RCAd11pE1 and RCAd11pE3 vectors showed significantly improved heat stability in comparison to Ad11pwt;of the three, RCAd11pE3 was the most tolerant to heatmore » treatment. Electron microscopy showed that RCAd11pE3, RCAd11pE1, Ad11pwt, and Ad11pE1 Delmanifested dominant, moderate, minimum, or no full virus particles after heat treatment at 47 °C for 5 h. Our results demonstrated that both genome size and the insertion site in the viral genome affect virion stability. -- Highlights: •Replicating adenovirus 11p GFP vectors at the E1 or E3 region were generated. •RCAd11pE3 and RCAd11pE1 vectors manifested significantly improved heat stability. •RCAd11pE3 and RCAd11pE1 showed more full viral particles than Ad11pwt after heating. •We demonstrated that both genome size and the insertion site affect virion stability.« less

Comparative genomic analysis by microbial COGs self-attraction rate.

PubMed

Santoni, Daniele; Romano-Spica, Vincenzo

2009-06-21

Whole genome analysis provides new perspectives to determine phylogenetic relationships among microorganisms. The availability of whole nucleotide sequences allows different levels of comparison among genomes by several approaches. In this work, self-attraction rates were considered for each cluster of orthologous groups of proteins (COGs) class in order to analyse gene aggregation levels in physical maps. Phylogenetic relationships among microorganisms were obtained by comparing self-attraction coefficients. Eighteen-dimensional vectors were computed for a set of 168 completely sequenced microbial genomes (19 archea, 149 bacteria). The components of the vector represent the aggregation rate of the genes belonging to each of 18 COGs classes. Genes involved in nonessential functions or related to environmental conditions showed the highest aggregation rates. On the contrary genes involved in basic cellular tasks showed a more uniform distribution along the genome, except for translation genes. Self-attraction clustering approach allowed classification of Proteobacteria, Bacilli and other species belonging to Firmicutes. Rearrangement and Lateral Gene Transfer events may influence divergences from classical taxonomy. Each set of COG classes' aggregation values represents an intrinsic property of the microbial genome. This novel approach provides a new point of view for whole genome analysis and bacterial characterization.

Uptake and elimination kinetics of metals in soil invertebrates: a review.

PubMed

Ardestani, Masoud M; van Straalen, Nico M; van Gestel, Cornelis A M

2014-10-01

Uptake and elimination kinetics of metals in soil invertebrates are a function of both soil and organism properties. This study critically reviewed metal toxicokinetics in soil invertebrates and its potential use for assessing bioavailability. Uptake and elimination rate constants of different metals are summarized. Invertebrates have different strategies for essential and non-essential metals. As a consequence, different types of models must be applied to describe metal uptake and elimination kinetics. We discuss model parameters for each metal separately and show how they are influenced by exposure concentrations and by physiological properties of the organisms. Soil pH, cation exchange capacity, clay and organic matter content significantly affect uptake rates of non-essential metals in soil invertebrates. For essential metals, kinetics is hardly influenced by soil properties, but rather prone to physiological regulation mechanisms of the organisms. Our analysis illustrates that toxicokinetics can be a valuable measurement to assess bioavailability of soil-bound metals. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont

PubMed Central

Lindsey, Amelia R. I.; Werren, John H.; Richards, Stephen; Stouthamer, Richard

2016-01-01

Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum. The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain. PMID:27194801

Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont.

PubMed

Lindsey, Amelia R I; Werren, John H; Richards, Stephen; Stouthamer, Richard

2016-07-07

Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain. Copyright © 2016 Lindsey et al.

Development of biotic ligand models for chronic manganese toxicity to fish, invertebrates, and algae.

PubMed

Peters, Adam; Lofts, Stephen; Merrington, Graham; Brown, Bruce; Stubblefield, William; Harlow, Keven

2011-11-01

Ecotoxicity tests were performed with fish, invertebrates, and algae to investigate the effect of water quality parameters on Mn toxicity. Models were developed to describe the effects of Mn as a function of water quality. Calcium (Ca) has a protective effect on Mn toxicity for both fish and invertebrates, and magnesium (Mg) also provides a protective effect for invertebrates. Protons have a protective effect on Mn toxicity to algae. The models derived are consistent with models of the toxicity of other metals to aquatic organisms in that divalent cations can act as competitors to Mn toxicity in fish and invertebrates, and protons act as competitors to Mn toxicity in algae. The selected models are able to predict Mn toxicity to the test organisms to within a factor of 2 in most cases. Under low-pH conditions invertebrates are the most sensitive taxa, and under high-pH conditions algae are most sensitive. The point at which algae become more sensitive than invertebrates depends on the Ca concentration and occurs at higher pH when Ca concentrations are low, because of the sensitivity of invertebrates under these conditions. Dissolved organic carbon concentrations have very little effect on the toxicity of Mn to aquatic organisms. Copyright © 2011 SETAC.

Global patterns in post-dispersal seed removal by invertebrates and vertebrates.

PubMed

Peco, Begoña; Laffan, Shawn W; Moles, Angela T

2014-01-01

It is commonly accepted that species interactions such as granivory are more intense in the tropics. However, this has rarely been tested. A global dataset of post-dispersal seed removal by invertebrates and vertebrates for 79 native plant species from semi-natural and natural terrestrial habitats ranging from 55° N to 45° S, was compiled from the global literature to test the hypothesis that post-dispersal seed removal by invertebrates and vertebrates is more intense at lower latitudes. We also quantified the relationship between post-dispersal seed removal by vertebrates and by invertebrates to global climatic features including temperature, actual evapotranspiration (AET) and rainfall seasonality. Linear mixed effect models were applied to describe the relationships between seed removal and latitude, hemisphere and climatic variables controlling for the effect of seed mass. Post-dispersal seed removal by invertebrates was negatively related to latitude. In contrast, post-dispersal seed removal by vertebrates was positively but weakly related to latitude. Mean annual temperature and actual evapotranspiration were positively related to post-dispersal seed removal by invertebrates, but not to post-dispersal seed removal by vertebrates, which was only marginally negatively related to rainfall seasonality. The inclusion of seed mass improved the fit of all models, but the term for seed mass was not significant in any model. Although a good climatic model for predicting post-dispersal seed predation by vertebrates at the global level was not found, our results suggest different and opposite latitudinal patterns of post-dispersal seed removal by invertebrates vs vertebrates. This is the first time that a negative relationship between post-dispersal seed removal by invertebrates and latitude, and a positive relationship with temperature and AET have been documented at a global-scale. These results have important implications for understanding global patterns in plant

Global Patterns in Post-Dispersal Seed Removal by Invertebrates and Vertebrates

PubMed Central

Peco, Begoña; Laffan, Shawn W.; Moles, Angela T.

2014-01-01

It is commonly accepted that species interactions such as granivory are more intense in the tropics. However, this has rarely been tested. A global dataset of post-dispersal seed removal by invertebrates and vertebrates for 79 native plant species from semi-natural and natural terrestrial habitats ranging from 55° N to 45° S, was compiled from the global literature to test the hypothesis that post-dispersal seed removal by invertebrates and vertebrates is more intense at lower latitudes. We also quantified the relationship between post-dispersal seed removal by vertebrates and by invertebrates to global climatic features including temperature, actual evapotranspiration (AET) and rainfall seasonality. Linear mixed effect models were applied to describe the relationships between seed removal and latitude, hemisphere and climatic variables controlling for the effect of seed mass. Post-dispersal seed removal by invertebrates was negatively related to latitude. In contrast, post-dispersal seed removal by vertebrates was positively but weakly related to latitude. Mean annual temperature and actual evapotranspiration were positively related to post-dispersal seed removal by invertebrates, but not to post-dispersal seed removal by vertebrates, which was only marginally negatively related to rainfall seasonality. The inclusion of seed mass improved the fit of all models, but the term for seed mass was not significant in any model. Although a good climatic model for predicting post-dispersal seed predation by vertebrates at the global level was not found, our results suggest different and opposite latitudinal patterns of post-dispersal seed removal by invertebrates vs vertebrates. This is the first time that a negative relationship between post-dispersal seed removal by invertebrates and latitude, and a positive relationship with temperature and AET have been documented at a global-scale. These results have important implications for understanding global patterns in plant

Molecular characterization, genomic distribution and evolutionary dynamics of Short INterspersed Elements in the termite genome.

PubMed

Luchetti, Andrea; Mantovani, Barbara

2011-02-01

Short INterspersed Elements (SINEs) in invertebrates, and especially in animal inbred genomes such that of termites, are poorly known; in this paper we characterize three new SINE families (Talub, Taluc and Talud) through the analyses of 341 sequences, either isolated from the Reticulitermes lucifugus genome or drawn from EST Genbank collection. We further add new data to the only isopteran element known so far, Talua. These SINEs are tRNA-derived elements, with an average length ranging from 258 to 372 bp. The tails are made up by poly(A) or microsatellite motifs. Their copy number varies from 7.9 × 10(3) to 10(5) copies, well within the range observed for other metazoan genomes. Species distribution, age and target site duplication analysis indicate Talud as the oldest, possibly inactive SINE originated before the onset of Isoptera (~150 Myr ago). Taluc underwent to substantial sequence changes throughout the evolution of termites and data suggest it was silenced and then re-activated in the R. lucifugus lineage. Moreover, Taluc shares a conserved sequence block with other unrelated SINEs, as observed for some vertebrate and cephalopod elements. The study of genomic environment showed that insertions are mainly surrounded by microsatellites and other SINEs, indicating a biased accumulation within non-coding regions. The evolutionary dynamics of Talu~ elements is explained through selective mechanisms acting in an inbred genome; in this respect, the study of termites' SINEs activity may provide an interesting framework to address the (co)evolution of mobile elements and the host genome.

Anterograde or Retrograde Transsynaptic Circuit Tracing in Vertebrates with Vesicular Stomatitis Virus Vectors

PubMed Central

Beier, Kevin T.; Mundell, Nathan A.; Pan, Y. Albert; Cepko, Constance L.

2016-01-01

Viruses have been used as transsynaptic tracers, allowing one to map the inputs and outputs of neuronal populations, due to their ability to replicate in neurons and transmit in vivo only across synaptically connected cells. To date, their use has been largely restricted to mammals. In order to explore the use of such viruses in an expanded host range, we tested the transsynaptic tracing ability of recombinant vesicular stomatitis virus (rVSV) vectors in a variety of organisms. Successful infection and gene expression were achieved in a wide range of organisms, including vertebrate and invertebrate model organisms. Moreover, rVSV enabled transsynaptic tracing of neural circuitry in predictable directions dictated by the viral envelope glycoprotein (G), derived from either VSV or rabies virus (RABV). Anterograde and retrograde labeling, from initial infection and/or viral replication and transmission, was observed in Old and New World monkeys, seahorses, jellyfish, zebrafish, chickens, and mice. These vectors are widely applicable for gene delivery, afferent tract tracing, and/or directional connectivity mapping. Here, we detail the use of these vectors and provide protocols for propagating virus, changing the surface glycoprotein, and infecting multiple organisms using several injection strategies. PMID:26729030

Ensembl Genomes 2013: scaling up access to genome-wide data.

PubMed

Kersey, Paul Julian; Allen, James E; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D; Maheswari, Uma; Maslen, Gareth; Nuhn, Michael; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Tuli, Mary Ann; Walts, Brandon; Williams, Gareth; Wilson, Derek; Youens-Clark, Ken; Monaco, Marcela K; Stein, Joshua; Wei, Xuehong; Ware, Doreen; Bolser, Daniel M; Howe, Kevin Lee; Kulesha, Eugene; Lawson, Daniel; Staines, Daniel Michael

2014-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

Construction of a transfer vector for a clonal isolate of LdNPV

Treesearch

Shivanand T. Hiremath; Martha Fikes; Audrey Ichida

1991-01-01

Deoxyribonucleic acid from a clonal isolate of LdNPV (CI A2-1), obtained by in vivo cloning procedures, was used to construct genomic libraries in phage (lamda Gem 11) and cosmid (pHC79) vectors. Overlapping clones were selected to generate a restriction enzyme map. The restriction enzyme map, covering about 85% of the CI A2-1 genome, was determined...

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…

[New hosts and vectors for genome cloning]. Progress report, 1990--1991

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

Not Available

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.

The Apis mellifera Filamentous Virus Genome

PubMed Central

Gauthier, Laurent; Cornman, Scott; Hartmann, Ulrike; Cousserans, François; Evans, Jay D.; de Miranda, Joachim R.; Neumann, Peter

2015-01-01

A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double stranded DNA molecule of approximately 498,500 nucleotides with a GC content of 50.8%. It encompasses 247 non-overlapping open reading frames (ORFs), equally distributed on both strands, which cover 65% of the genome. While most of the ORFs lacked threshold sequence alignments to reference protein databases, twenty-eight were found to display significant homologies with proteins present in other large double stranded DNA viruses. Remarkably, 13 ORFs had strong similarity with typical baculovirus domains such as PIFs (per os infectivity factor genes: pif-1, pif-2, pif-3 and p74) and BRO (Baculovirus Repeated Open Reading Frame). The putative AmFV DNA polymerase is of type B, but is only distantly related to those of the baculoviruses. The ORFs encoding proteins involved in nucleotide metabolism had the highest percent identity to viral proteins in GenBank. Other notable features include the presence of several collagen-like, chitin-binding, kinesin and pacifastin domains. Due to the large size of the AmFV genome and the inconsistent affiliation with other large double stranded DNA virus families infecting invertebrates, AmFV may belong to a new virus family. PMID:26184284

The Apis mellifera Filamentous Virus Genome.

PubMed

Gauthier, Laurent; Cornman, Scott; Hartmann, Ulrike; Cousserans, François; Evans, Jay D; de Miranda, Joachim R; Neumann, Peter

2015-07-09

A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double stranded DNA molecule of approximately 498,500 nucleotides with a GC content of 50.8%. It encompasses 247 non-overlapping open reading frames (ORFs), equally distributed on both strands, which cover 65% of the genome. While most of the ORFs lacked threshold sequence alignments to reference protein databases, twenty-eight were found to display significant homologies with proteins present in other large double stranded DNA viruses. Remarkably, 13 ORFs had strong similarity with typical baculovirus domains such as PIFs (per os infectivity factor genes: pif-1, pif-2, pif-3 and p74) and BRO (Baculovirus Repeated Open Reading Frame). The putative AmFV DNA polymerase is of type B, but is only distantly related to those of the baculoviruses. The ORFs encoding proteins involved in nucleotide metabolism had the highest percent identity to viral proteins in GenBank. Other notable features include the presence of several collagen-like, chitin-binding, kinesin and pacifastin domains. Due to the large size of the AmFV genome and the inconsistent affiliation with other large double stranded DNA virus families infecting invertebrates, AmFV may belong to a new virus family.

The octopus genome and the evolution of cephalopod neural and morphological novelties

PubMed Central

Albertin, Caroline B.; Simakov, Oleg; Mitros, Therese; Wang, Z. Yan; Pungor, Judit R.; Edsinger-Gonzalez, Eric; Brenner, Sydney; Ragsdale, Clifton W.; Rokhsar, Daniel S.

2016-01-01

Coleoid cephalopods (octopus, squid, and cuttlefish) are active, resourceful predators with a rich behavioral repertoire1. They have the largest nervous systems among the invertebrates2 and present other striking morphological innovations including camera-like eyes, prehensile arms, a highly derived early embryogenesis, and the most sophisticated adaptive coloration system among all animals1,3. To investigate the molecular bases of cephalopod brain and body innovations we sequenced the genome and multiple transcriptomes of the California two-spot octopus, Octopus bimaculoides. We found no evidence for hypothesized whole genome duplications in the octopus lineage4–6. The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians, except for massive expansions in two gene families formerly thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc finger transcription factors. Extensive mRNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described7, as well as in genes participating in a broad range of other cellular functions. We identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers, and the nervous system. Finally, we found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions. Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodeling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems. PMID:26268193

GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

PubMed

Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

2013-04-10

Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

Detection of betanodaviruses in apparently healthy aquarium fishes and invertebrates

PubMed Central

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

2006-01-01

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

The buzz on caffeine in invertebrates: effects on behavior and molecular mechanisms

PubMed Central

Mustard, Julie A.

2014-01-01

A number of recent studies from as diverse fields as plant-pollinator interactions, analyses of caffeine as an environmental pollutant, and the ability of caffeine to provide protection against neurodegenerative diseases have generated interest in understanding the actions of caffeine in invertebrates. This review summarizes what is currently known about the effects of caffeine on behavior and its molecular mechanisms in invertebrates. Caffeine appears to have similar effects on locomotion and sleep in both invertebrates and mammals. Furthermore, as in mammals, caffeine appears to have complex effects on learning and memory. However, the underlying mechanisms for these effects may differ between invertebrates and vertebrates. While caffeine’s ability to cause release of intracellular calcium stores via ryanodine receptors and its actions as a phosphodiesterase inhibitor have been clearly established in invertebrates, its ability to interact with invertebrate adenosine receptors remains an important open question. Initial studies in insects and mollusks suggest an interaction between caffeine and the dopamine signaling pathway; more work needs to be done to understand the mechanisms by which caffeine influences signaling via biogenic amines. As of yet, little is known about whether other actions of caffeine in vertebrates, such as its effects on GABAA and glycine receptors, are conserved. Furthermore, the pharmacokinetics of caffeine remains to be elucidated. Overall behavioral responses to caffeine appear to be conserved amongst organisms; however, we are just beginning to understand the mechanisms underlying its effects across animal phyla. PMID:24162934

The buzz on caffeine in invertebrates: effects on behavior and molecular mechanisms.

PubMed

Mustard, Julie A

2014-04-01

A number of recent studies from as diverse fields as plant-pollinator interactions, analyses of caffeine as an environmental pollutant, and the ability of caffeine to provide protection against neurodegenerative diseases have generated interest in understanding the actions of caffeine in invertebrates. This review summarizes what is currently known about the effects of caffeine on behavior and its molecular mechanisms in invertebrates. Caffeine appears to have similar effects on locomotion and sleep in both invertebrates and mammals. Furthermore, as in mammals, caffeine appears to have complex effects on learning and memory. However, the underlying mechanisms for these effects may differ between invertebrates and vertebrates. While caffeine's ability to cause release of intracellular calcium stores via ryanodine receptors and its actions as a phosphodiesterase inhibitor have been clearly established in invertebrates, its ability to interact with invertebrate adenosine receptors remains an important open question. Initial studies in insects and mollusks suggest an interaction between caffeine and the dopamine signaling pathway; more work needs to be done to understand the mechanisms by which caffeine influences signaling via biogenic amines. As of yet, little is known about whether other actions of caffeine in vertebrates, such as its effects on GABAA and glycine receptors, are conserved. Furthermore, the pharmacokinetics of caffeine remains to be elucidated. Overall behavioral responses to caffeine appear to be conserved amongst organisms; however, we are just beginning to understand the mechanisms underlying its effects across animal phyla.

Peptide-Based Technologies to Alter Adenoviral Vector Tropism: Ways and Means for Systemic Treatment of Cancer

PubMed Central

Reetz, Julia; Herchenröder, Ottmar; Pützer, Brigitte M.

2014-01-01

Due to the fundamental progress in elucidating the molecular mechanisms of human diseases and the arrival of the post-genomic era, increasing numbers of therapeutic genes and cellular targets are available for gene therapy. Meanwhile, the most important challenge is to develop gene delivery vectors with high efficiency through target cell selectivity, in particular under in situ conditions. The most widely used vector system to transduce cells is based on adenovirus (Ad). Recent endeavors in the development of selective Ad vectors that target cells or tissues of interest and spare the alteration of all others have focused on the modification of the virus broad natural tropism. A popular way of Ad targeting is achieved by directing the vector towards distinct cellular receptors. Redirecting can be accomplished by linking custom-made peptides with specific affinity to cellular surface proteins via genetic integration, chemical coupling or bridging with dual-specific adapter molecules. Ideally, targeted vectors are incapable of entering cells via their native receptors. Such altered vectors offer new opportunities to delineate functional genomics in a natural environment and may enable efficient systemic therapeutic approaches. This review provides a summary of current state-of-the-art techniques to specifically target adenovirus-based gene delivery vectors. PMID:24699364

Enzyme-Assisted Discovery of Antioxidant Peptides from Edible Marine Invertebrates: A Review

PubMed Central

Chai, Tsun-Thai; Law, Yew-Chye; Wong, Fai-Chu; Kim, Se-Kwon

2017-01-01

Marine invertebrates, such as oysters, mussels, clams, scallop, jellyfishes, squids, prawns, sea cucumbers and sea squirts, are consumed as foods. These edible marine invertebrates are sources of potent bioactive peptides. The last two decades have seen a surge of interest in the discovery of antioxidant peptides from edible marine invertebrates. Enzymatic hydrolysis is an efficient strategy commonly used for releasing antioxidant peptides from food proteins. A growing number of antioxidant peptide sequences have been identified from the enzymatic hydrolysates of edible marine invertebrates. Antioxidant peptides have potential applications in food, pharmaceuticals and cosmetics. In this review, we first give a brief overview of the current state of progress of antioxidant peptide research, with special attention to marine antioxidant peptides. We then focus on 22 investigations which identified 32 antioxidant peptides from enzymatic hydrolysates of edible marine invertebrates. Strategies adopted by various research groups in the purification and identification of the antioxidant peptides will be summarized. Structural characteristic of the peptide sequences in relation to their antioxidant activities will be reviewed. Potential applications of the peptide sequences and future research prospects will also be discussed. PMID:28212329

Enzyme-Assisted Discovery of Antioxidant Peptides from Edible Marine Invertebrates: A Review.

PubMed

Chai, Tsun-Thai; Law, Yew-Chye; Wong, Fai-Chu; Kim, Se-Kwon

2017-02-16

Marine invertebrates, such as oysters, mussels, clams, scallop, jellyfishes, squids, prawns, sea cucumbers and sea squirts, are consumed as foods. These edible marine invertebrates are sources of potent bioactive peptides. The last two decades have seen a surge of interest in the discovery of antioxidant peptides from edible marine invertebrates. Enzymatic hydrolysis is an efficient strategy commonly used for releasing antioxidant peptides from food proteins. A growing number of antioxidant peptide sequences have been identified from the enzymatic hydrolysates of edible marine invertebrates. Antioxidant peptides have potential applications in food, pharmaceuticals and cosmetics. In this review, we first give a brief overview of the current state of progress of antioxidant peptide research, with special attention to marine antioxidant peptides. We then focus on 22 investigations which identified 32 antioxidant peptides from enzymatic hydrolysates of edible marine invertebrates. Strategies adopted by various research groups in the purification and identification of the antioxidant peptides will be summarized. Structural characteristic of the peptide sequences in relation to their antioxidant activities will be reviewed. Potential applications of the peptide sequences and future research prospects will also be discussed.

Wetlands of the Prairie Pothole Region: Invertebrate species composition, ecology, and management

USGS Publications Warehouse

Euliss, N.H.; Wrubleski, D.A.; Mushet, D.M.; Batzer, D.P.; Rader, R.B.; Wissinger, S.A.

1999-01-01

The Prairie Pothole Region (PPR) of the United States and Canada is a unique area where shallow depressions created by the scouring action of Pleistocene glaciation interact with mid-continental climate variations to create and maintain a variety of wetland classes. These wetlands possess unique environmental and biotic characteristics that add to the overall regional diversity and production of aquatic invertebrates and the vertebrate wildlife that depend upon them as food. Climatic extremes in the PPR have a profound and dynamic influence on wetland hydrology, hydroperiod, chemistry, and ultimately the biota. Available knowledge of aquatic invertebrates in the PPR suggests that diversity of invertebrates within each wetland class is low. Harsh environmental conditions range from frigid winter temperatures that freeze wetlands and their sediments to hot summer temperatures and drought conditions that create steep salinity gradients and seasonally dry habitats. Consequently, the invertebrate community is composed mostly of ecological generalists that possess the necessary adaptations to tolerate environmental extremes. In this review, we describe the highly dynamic nature of prairie pothole wetlands and suggest that invertebrate studies be evaluated within a conceptual framework that considers important hydrologic, chemical, and climatic events.

The value of agricultural wetlands as invertebrate resources for wintering shorebirds

USGS Publications Warehouse

Taft, Oriane W.; Haig, Susan M.

2005-01-01

Agricultural landscapes have received little recognition for the food resources they provide to wintering waterbirds. In the Willamette Valley of Oregon, modest yet significant populations of wintering shorebirds (Charadriiformes) regularly use hundreds of dispersed wetlands on agricultural lands. Benthic invertebrates are a critical resource for the survival of overwintering shorebirds, yet the abundance of invertebrate resources in agricultural wetlands such as these has not been quantified. To evaluate the importance of agricultural wetlands to a population of wintering shorebirds, the density, biomass, and general community composition of invertebrates available to birds were quantified at a sample of Willamette Valley sites during a wet (1999–2000) and a dry winter (2000–2001). Invertebrate densities ranged among wetlands from 173 to 1925 (mean ± S.E.: 936 ± 106) individuals/m2 in the wet winter, and from 214 to 3484 (1028 ± 155) individuals/m2 in the dry winter. Total invertebrate estimated biomass among wetlands ranged from 35 to 652 (mean ± S.E.: 364 ± 35) mg/m2 in the wet winter, and from 85 to 1405 (437 ± 62) mg/m2 in the dry winter. These estimates for food abundance were comparable to that observed in some other important freshwater wintering regions in North America.

The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins.

PubMed

Dietzgen, Ralf G; Kondo, Hideki; Goodin, Michael M; Kurath, Gael; Vasilakis, Nikos

2017-01-02

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Genome editing technologies to fight infectious diseases.

PubMed

Trevisan, Marta; Palù, Giorgio; Barzon, Luisa

2017-11-01

Genome editing by programmable nucleases represents a promising tool that could be exploited to develop new therapeutic strategies to fight infectious diseases. These nucleases, such as zinc-finger nucleases, transcription activator-like effector nucleases, clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein 9 (Cas9) and homing endonucleases, are molecular scissors that can be targeted at predetermined loci in order to modify the genome sequence of an organism. Areas covered: By perturbing genomic DNA at predetermined loci, programmable nucleases can be used as antiviral and antimicrobial treatment. This approach includes targeting of essential viral genes or viral sequences able, once mutated, to inhibit viral replication; repurposing of CRISPR-Cas9 system for lethal self-targeting of bacteria; targeting antibiotic-resistance and virulence genes in bacteria, fungi, and parasites; engineering arthropod vectors to prevent vector-borne infections. Expert commentary: While progress has been done in demonstrating the feasibility of using genome editing as antimicrobial strategy, there are still many hurdles to overcome, such as the risk of off-target mutations, the raising of escape mutants, and the inefficiency of delivery methods, before translating results from preclinical studies into clinical applications.

Engineered Viruses as Genome Editing Devices

PubMed Central

Chen, Xiaoyu; Gonçalves, Manuel A F V

2016-01-01

Genome editing based on sequence-specific designer nucleases, also known as programmable nucleases, seeks to modify in a targeted and precise manner the genetic information content of living cells. Delivering into cells designer nucleases alone or together with donor DNA templates, which serve as surrogate homologous recombination (HR) substrates, can result in gene knockouts or gene knock-ins, respectively. As engineered replication-defective viruses, viral vectors are having an increasingly important role as delivery vehicles for donor DNA templates and designer nucleases, namely, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated Cas9 (CRISPR−Cas9) nucleases, also known as RNA-guided nucleases (RGNs). We review this dual role played by engineered viral particles on genome editing while focusing on their main scaffolds, consisting of lentiviruses, adeno-associated viruses, and adenoviruses. In addition, the coverage of the growing body of research on the repurposing of viral vectors as delivery systems for genome editing tools is complemented with information regarding their main characteristics, pros, and cons. Finally, this information is framed by a concise description of the chief principles, tools, and applications of the genome editing field as a whole. PMID:26336974

Engineered Viruses as Genome Editing Devices.

PubMed

Chen, Xiaoyu; Gonçalves, Manuel A F V

2016-03-01

Genome editing based on sequence-specific designer nucleases, also known as programmable nucleases, seeks to modify in a targeted and precise manner the genetic information content of living cells. Delivering into cells designer nucleases alone or together with donor DNA templates, which serve as surrogate homologous recombination (HR) substrates, can result in gene knockouts or gene knock-ins, respectively. As engineered replication-defective viruses, viral vectors are having an increasingly important role as delivery vehicles for donor DNA templates and designer nucleases, namely, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated Cas9 (CRISPR-Cas9) nucleases, also known as RNA-guided nucleases (RGNs). We review this dual role played by engineered viral particles on genome editing while focusing on their main scaffolds, consisting of lentiviruses, adeno-associated viruses, and adenoviruses. In addition, the coverage of the growing body of research on the repurposing of viral vectors as delivery systems for genome editing tools is complemented with information regarding their main characteristics, pros, and cons. Finally, this information is framed by a concise description of the chief principles, tools, and applications of the genome editing field as a whole.

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.

Phase 1 Gene Therapy for Duchenne Muscular Dystrophy Using a Translational Optimized AAV Vector

PubMed Central

Bowles, Dawn E; McPhee, Scott WJ; Li, Chengwen; Gray, Steven J; Samulski, Jade J; Camp, Angelique S; Li, Juan; Wang, Bing; Monahan, Paul E; Rabinowitz, Joseph E; Grieger, Joshua C; Govindasamy, Lakshmanan; Agbandje-McKenna, Mavis; Xiao, Xiao; Samulski, R Jude

2012-01-01

Efficient and widespread gene transfer is required for successful treatment of Duchenne muscular dystrophy (DMD). Here, we performed the first clinical trial using a chimeric adeno-associated virus (AAV) capsid variant (designated AAV2.5) derived from a rational design strategy. AAV2.5 was generated from the AAV2 capsid with five mutations from AAV1. The novel chimeric vector combines the improved muscle transduction capacity of AAV1 with reduced antigenic crossreactivity against both parental serotypes, while keeping the AAV2 receptor binding. In a randomized double-blind placebo-controlled phase I clinical study in DMD boys, AAV2.5 vector was injected into the bicep muscle in one arm, with saline control in the contralateral arm. A subset of patients received AAV empty capsid instead of saline in an effort to distinguish an immune response to vector versus minidystrophin transgene. Recombinant AAV genomes were detected in all patients with up to 2.56 vector copies per diploid genome. There was no cellular immune response to AAV2.5 capsid. This trial established that rationally designed AAV2.5 vector was safe and well tolerated, lays the foundation of customizing AAV vectors that best suit the clinical objective (e.g., limb infusion gene delivery) and should usher in the next generation of viral delivery systems for human gene transfer. PMID:22068425

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

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

2016-09-13

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.

Invertebrate biomass: Associations with lesser prairie-chicken habitat use and sand sagebrush density in southwestern Kansas

USGS Publications Warehouse

Jamison, B.E.; Robel, R.J.; Pontius, J.S.; Applegate, R.D.

2002-01-01

Invertebrates are important food sources for lesser prairie-chicken (Tympanuchus pallidicinctus) adults and broods. We compared invertebrate biomass in areas used and not used by lesser prairie-chicken adults and broods. We used radiotelemetry to determine use and non-use areas in sand sagebrush (Artemisia filifolia) prairie in southwestern Kansas and sampled invertebrate populations during summer 1998 and 1999. Sweepnet-collected biomass of short-horned grasshoppers (Acrididae) and total invertebrate biomass generally were greater in habitats used by lesser prairie-chickens than in paired non-use areas. We detected no differences in pitfall-collected biomass of Acrididae (P=0.81) or total invertebrate biomass (P=0.93) among sampling areas with sand sagebrush canopy cover of 0 to 10%, 11 to 30%, and >30%. Results of multivariate analysis and regression model selection suggested that forbs were more strongly associated with invertebrate biomass than shrubs, grasses, or bare ground. We could not separate lesser prairie-chicken selection for areas of forb cover from selection of areas with greater invertebrate biomass associated with forb cover. Regardless of whether the effects of forbs were direct or indirect, their importance in sand sagebrush habitat has management implications. Practices that maintain or increase forb cover likely will increase invertebrate biomass and habitat quality in southwestern Kansas.

Invertebrate biomass: associations with lesser prairie-chicken habitat use and sand sagebrush density in southwestern Kansas

USGS Publications Warehouse

Jamison, B.; Robel, R.J.; Pontius, J.S.; Applegate, R.D.

2002-01-01

Invertebrates are important food sources for lesser prairie-chicken (Tympanuchus pallidicinctus) adults and broods. We compared invertebrate biomass in areas used and not used by lesser prairie-chicken adults and broods. We used radiotelemetry to determine use and non-use areas in sand sagebrush (Artemisia filifolia) prairie in southwestern Kansas and sampled invertebrate populations during summer 1998 and 1999. Sweepnet-collected biomass of short-horned grasshoppers (Acrididae) and total invertebrate biomass generally were greater in habitats used by lesser prairie-chickens than in paired non-use areas. We detected no differences in pitfall-collected biomass of Acrididae (P=0.81) or total invertebrate biomass (P=0.93) among sampling areas with sand sagebrush canopy cover of 0 to 10%, 11 to 30%, and >30%. Results of multivariate analysis and regression model selection suggested that forbs were more strongly associated with invertebrate biomass than shrubs, grasses, or bare ground. We could not separate lesser prairie-chicken selection for areas of forb cover from selection of areas with greater invertebrate biomass associated with forb cover. Regardless of whether the effects of forbs were direct or indirect, their importance in sand sagebrush habitat has management implications. Practices that maintain or increase forb cover likely will increase invertebrate biomass and habitat quality in southwestern Kansas.

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)

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.

Salmon-derived nitrogen in terrestrial invertebrates from coniferous forests of the Pacific Northwest

PubMed Central

2002-01-01

Background Bi-directional flow of nutrients between marine and terrestrial ecosystems can provide essential resources that structure communities in transitional habitats. On the Pacific coast of North America, anadromous salmon (Oncorhynchus spp.) constitute a dominant nutrient subsidy to aquatic habitats and riparian vegetation, although the contribution to terrestrial habitats is not well established. We use a dual isotope approach of δ15N and δ13C to test for the contribution of salmon nutrients to multiple trophic levels of litter-based terrestrial invertebrates below and above waterfalls that act as a barrier to salmon migration on two watersheds in coastal British Columbia. Results Invertebrates varied predictably in δ15N with enrichment of 3–8‰ below the falls compared with above the falls in all trophic groups on both watersheds. We observed increasing δ15N levels in our invertebrate groups with increasing consumption of dietary protein. Invertebrates varied in δ13C but did not always vary predictably with trophic level or habitat. From 19.4 to 71.5% of invertebrate total nitrogen was originally derived from salmon depending on taxa, watershed, and degree of fractionation from the source. Conclusions Enrichment of δ15N in the invertebrate community below the falls in conjunction with the absence of δ13C enrichment suggests that enrichment in δ15N occurs primarily through salmon-derived nitrogen subsidies to litter, soil and vegetation N pools rather than from direct consumption of salmon tissue or salmon tissue consumers. Salmon nutrient subsidies to terrestrial habitats may result in shifts in invertebrate community structure, with subsequent implications for higher vertebrate consumers, particularly the passerines. PMID:11914157

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)

Chemical screening method for the rapid identification of microbial sources of marine invertebrate-associated metabolites.

PubMed

Berrue, Fabrice; Withers, Sydnor T; Haltli, Brad; Withers, Jo; Kerr, Russell G

2011-03-21

Marine invertebrates have proven to be a rich source of secondary metabolites. The growing recognition that marine microorganisms associated with invertebrate hosts are involved in the biosynthesis of secondary metabolites offers new alternatives for the discovery and development of marine natural products. However, the discovery of microorganisms producing secondary metabolites previously attributed to an invertebrate host poses a significant challenge. This study describes an efficient chemical screening method utilizing a 96-well plate-based bacterial cultivation strategy to identify and isolate microbial producers of marine invertebrate-associated metabolites.

Acute toxicity and inactivation tests of CO2 on invertebrates in drinking water treatment systems.

PubMed

Yin, Wen-Chao; Zhang, Jin-Song; Liu, Li-Jun; Zhao, Jian-Shu; Li, Tuo

2011-01-01

In addition to the esthetic problem caused by invertebrates, researchers are recently starting to be more aware of their potential importance in terms of public health. However, the inactivation methods of invertebrates which could proliferate in drinking water treatment systems are not well developed. The objective of this study is to assess the acute toxicity and inactivation effects of CO2 on familiar invertebrates in water treatment processes. The results of this study revealed that CO2 has a definite toxicity to familiar invertebrates. The values of 24-h LC50 (median lethal concentration) were calculated for each test with six groups of invertebrates. The toxicity of CO2 was higher with increasing concentrations in solution but was lower with the increase in size of the invertebrates. Above the concentration of 1,000 mg/L for the CO2 solution, the 100% inactivation time of all the invertebrates was less than 5 s, and in 15 min, the inactivation ratio showed a gradient descent with a decline in concentration. As seen for Mesocyclops thermocyclopoides, by dosing with a sodium bicarbonate solution first and adding a dilute hydrochloric acid solution 5 min later, it is possible to obtain a satisfactory inactivation effect in the GAC (granular activated carbon) filters.

A Foxtail mosaic virus Vector for Virus-Induced Gene Silencing in Maize.

PubMed

Mei, Yu; Zhang, Chunquan; Kernodle, Bliss M; Hill, John H; Whitham, Steven A

2016-06-01

Plant viruses have been widely used as vectors for foreign gene expression and virus-induced gene silencing (VIGS). A limited number of viruses have been developed into viral vectors for the purposes of gene expression or VIGS in monocotyledonous plants, and among these, the tripartite viruses Brome mosaic virus and Cucumber mosaic virus have been shown to induce VIGS in maize (Zea mays). We describe here a new DNA-based VIGS system derived from Foxtail mosaic virus (FoMV), a monopartite virus that is able to establish systemic infection and silencing of endogenous maize genes homologous to gene fragments inserted into the FoMV genome. To demonstrate VIGS applications of this FoMV vector system, four genes, phytoene desaturase (functions in carotenoid biosynthesis), lesion mimic22 (encodes a key enzyme of the porphyrin pathway), iojap (functions in plastid development), and brown midrib3 (caffeic acid O-methyltransferase), were silenced and characterized in the sweet corn line Golden × Bantam. Furthermore, we demonstrate that the FoMV infectious clone establishes systemic infection in maize inbred lines, sorghum (Sorghum bicolor), and green foxtail (Setaria viridis), indicating the potential wide applications of this viral vector system for functional genomics studies in maize and other monocots. © 2016 American Society of Plant Biologists. All Rights Reserved.

Rapid Global Expansion of Invertebrate Fisheries: Trends, Drivers, and Ecosystem Effects

PubMed Central

Anderson, Sean C.; Mills Flemming, Joanna; Watson, Reg; Lotze, Heike K.

2011-01-01

Background Worldwide, finfish fisheries are receiving increasing assessment and regulation, slowly leading to more sustainable exploitation and rebuilding. In their wake, invertebrate fisheries are rapidly expanding with little scientific scrutiny despite increasing socio-economic importance. Methods and Findings We provide the first global evaluation of the trends, drivers, and population and ecosystem consequences of invertebrate fisheries based on a global catch database in combination with taxa-specific reviews. We also develop new methodologies to quantify temporal and spatial trends in resource status and fishery development. Since 1950, global invertebrate catches have increased 6-fold with 1.5 times more countries fishing and double the taxa reported. By 2004, 34% of invertebrate fisheries were over-exploited, collapsed, or closed. New fisheries have developed increasingly rapidly, with a decrease of 6 years (3 years) in time to peak from the 1950s to 1990s. Moreover, some fisheries have expanded further and further away from their driving market, encompassing a global fishery by the 1990s. 71% of taxa (53% of catches) are harvested with habitat-destructive gear, and many provide important ecosystem functions including habitat, filtration, and grazing. Conclusions Our findings suggest that invertebrate species, which form an important component of the basis of marine food webs, are increasingly exploited with limited stock and ecosystem-impact assessments, and enhanced management attention is needed to avoid negative consequences for ocean ecosystems and human well-being. PMID:21408090

The Early Shorebird Will Catch Fewer Invertebrates on Trampled Sandy Beaches

PubMed Central

Schlacher, Thomas A.; Carracher, Lucy K.; Porch, Nicholas; Connolly, Rod M.; Olds, Andrew D.; Gilby, Ben L.; Ekanayake, Kasun B.; Maslo, Brooke; Weston, Michael A.

2016-01-01

Many species of birds breeding on ocean beaches and in coastal dunes are of global conservation concern. Most of these species rely on invertebrates (e.g. insects, small crustaceans) as an irreplaceable food source, foraging primarily around the strandline on the upper beach near the dunes. Sandy beaches are also prime sites for human recreation, which impacts these food resources via negative trampling effects. We quantified acute trampling impacts on assemblages of upper shore invertebrates in a controlled experiment over a range of foot traffic intensities (up to 56 steps per square metre) on a temperate beach in Victoria, Australia. Trampling significantly altered assemblage structure (species composition and density) and was correlated with significant declines in invertebrate abundance and species richness. Trampling effects were strongest for rare species. In heavily trafficked plots the abundance of sand hoppers (Amphipoda), a principal prey item of threatened Hooded Plovers breeding on this beach, was halved. In contrast to the consistently strong effects of trampling, natural habitat attributes (e.g. sediment grain size, compactness) were much less influential predictors. If acute suppression of invertebrates caused by trampling, as demonstrated here, is more widespread on beaches it may constitute a significant threat to endangered vertebrates reliant on these invertebrates. This calls for a re-thinking of conservation actions by considering active management of food resources, possibly through enhancement of wrack or direct augmentation of prey items to breeding territories. PMID:27564550

The Early Shorebird Will Catch Fewer Invertebrates on Trampled Sandy Beaches.

PubMed

Schlacher, Thomas A; Carracher, Lucy K; Porch, Nicholas; Connolly, Rod M; Olds, Andrew D; Gilby, Ben L; Ekanayake, Kasun B; Maslo, Brooke; Weston, Michael A

2016-01-01

Many species of birds breeding on ocean beaches and in coastal dunes are of global conservation concern. Most of these species rely on invertebrates (e.g. insects, small crustaceans) as an irreplaceable food source, foraging primarily around the strandline on the upper beach near the dunes. Sandy beaches are also prime sites for human recreation, which impacts these food resources via negative trampling effects. We quantified acute trampling impacts on assemblages of upper shore invertebrates in a controlled experiment over a range of foot traffic intensities (up to 56 steps per square metre) on a temperate beach in Victoria, Australia. Trampling significantly altered assemblage structure (species composition and density) and was correlated with significant declines in invertebrate abundance and species richness. Trampling effects were strongest for rare species. In heavily trafficked plots the abundance of sand hoppers (Amphipoda), a principal prey item of threatened Hooded Plovers breeding on this beach, was halved. In contrast to the consistently strong effects of trampling, natural habitat attributes (e.g. sediment grain size, compactness) were much less influential predictors. If acute suppression of invertebrates caused by trampling, as demonstrated here, is more widespread on beaches it may constitute a significant threat to endangered vertebrates reliant on these invertebrates. This calls for a re-thinking of conservation actions by considering active management of food resources, possibly through enhancement of wrack or direct augmentation of prey items to breeding territories.

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.

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…

Marine Invertebrate Metabolites with Anticancer Activities: Solutions to the “Supply Problem”

PubMed Central

Gomes, Nelson G. M.; Dasari, Ramesh; Chandra, Sunena; Kiss, Robert; Kornienko, Alexander

2016-01-01

Marine invertebrates provide a rich source of metabolites with anticancer activities and several marine-derived agents have been approved for the treatment of cancer. However, the limited supply of promising anticancer metabolites from their natural sources is a major hurdle to their preclinical and clinical development. Thus, the lack of a sustainable large-scale supply has been an important challenge facing chemists and biologists involved in marine-based drug discovery. In the current review we describe the main strategies aimed to overcome the supply problem. These include: marine invertebrate aquaculture, invertebrate and symbiont cell culture, culture-independent strategies, total chemical synthesis, semi-synthesis, and a number of hybrid strategies. We provide examples illustrating the application of these strategies for the supply of marine invertebrate-derived anticancer agents. Finally, we encourage the scientific community to develop scalable methods to obtain selected metabolites, which in the authors’ opinion should be pursued due to their most promising anticancer activities. PMID:27213412

Newcastle disease virus vectored vaccines as bivalent or antigen delivery vaccines

PubMed Central

2017-01-01

Recent advances in reverse genetics techniques make it possible to manipulate the genome of RNA viruses such as Newcastle disease virus (NDV). Several NDV vaccine strains have been used as vaccine vectors in poultry, mammals, and humans to express antigens of different pathogens. The safety, immunogenicity, and protective efficacy of these NDV-vectored vaccines have been evaluated in pre-clinical and clinical studies. The vaccines are safe in mammals, humans, and poultry. Bivalent NDV-vectored vaccines against pathogens of economic importance to the poultry industry have been developed. These bivalent vaccines confer solid protective immunity against NDV and other foreign antigens. In most cases, NDV-vectored vaccines induce strong local and systemic immune responses against the target foreign antigen. This review summarizes the development of NDV-vectored vaccines and their potential use as a base for designing other effective vaccines for veterinary and human use. PMID:28775971

Vertebrate hosts and phylogenetic relationships of amphibian trypanosomes from a potential invertebrate vector, Culex territans Walker (Diptera: Culicidae).

PubMed

Bartlett-Healy, Kristen; Crans, Wayne; Gaugler, Randy

2009-04-01

The blood meals of field-collected female Culex territans (Diptera: Culicidae) were concurrently assayed for the presence of trypanosomes and for vertebrate host identification. We amplified vertebrate DNA in 42 of 119 females and made positive identification to the host species level in 29 of those samples. Of the 119 field-collected Cx. territans females, 24 were infected with trypanosomes. Phylogenetic analysis placed the trypanosomes in the amphibian portion of the aquatic clade of the Trypanosomatidae. These trypanosomes were isolated from Cx. territans females that had fed on the frog species Rana clamitans, R. catesbeiana, R. virgatipes, and Rana spp. Results support a potential new lineage of dipteran-transmitted amphibian trypanosomes may occur within the aquatic clade. The frequency in which female Cx. territans acquire trypanosomes, through diverse feeding habits, indicates a new relationship between amphibian trypanosomes and mosquitoes that has not been examined previously. Combining Trypanosoma species, invertebrate, and vertebrate hosts to existing phylogenies can elucidate trypanosome and host relationships.

Dual AAV Vectors for Stargardt Disease.

PubMed

Trapani, Ivana

2018-01-01

Stargardt disease (STGD1), due to mutations in the large ABCA4 gene, is the most common inherited macular degeneration in humans. Attempts at developing gene therapy approaches for treatment of STGD1 are currently ongoing. Among all the vectors available for gene therapy of inherited retinal diseases, those based on adeno-associated viruses (AAV) are the most promising given the efficacy shown in various animal models and their excellent safety profile in humans, as confirmed in many ongoing clinical trials. However, one of the main obstacles for the use of AAV is their limited effective packaging capacity of about 5 kb. Taking advantage of the AAV genome's ability to concatemerize , others and we have recently developed dual AAV vectors to overcome this limit. We tested dual AAV vectors for ABCA4 delivery, and found that they transduce efficiently both mouse and pig photoreceptors , and rescue the Abca4-/- mouse retinal phenotype, indicating their potential for gene therapy of STGD1. This chapter details how we designed dual AAV vectors for the delivery of the ABCA4 gene and describes the techniques that can be explored to evaluate dual AAV transduction efficiency in vitro and in the retina, and their efficacy in the mouse model of STGD1.

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.

Marine nutrient contributions to tidal creeks in Virginia: spawning marine fish as nutrient vectors to freshwater ecosystems

NASA Astrophysics Data System (ADS)

Macavoy, S. E.; Garman, G. C.

2006-12-01

Coastal freshwater streams are typically viewed as conduits for the transport of sediment and nutrients to the coasts. Some coastal streams however experience seasonal migrations of anadromous fish returning to the freshwater to spawn. The fish may be vectors for the delivery of marine nutrients to nutrient poor freshwater in the form of excreted waste and post-spawning carcasses. Nutrients derived from marine sources are 13C, 15N and 34S enriched relative to nutrients in freshwater. Here we examine sediment, particulate organic matter (POM), invertebrates and fish in two tidal freshwater tributaries of the James River USA. The d15N of POM became elevated (from 3.8 to 6.5%), coincident with the arrival of anadromous river herring (Alosa sp), indicating a pulse of marine nitrogen. However, the elevated 15N was not observed in sediment samples or among invertebrates, which did not experience a seasonal isotopic shift (there were significant differences however among the guilds of invertebrate). Anadromous Alosa aestivalis captured within the tidal freshwater were 13C and 34S enriched (-19.3 and 17.2%, respectively) relative to resident freshwater fishes (-26.4 and 3.6% respectively) captured within 2 weeks of the Alosa. Although it is likely that marine derived nitrogen was detected in the tidal freshwater, it was not in sufficient abundance to change the isotope signature of most ecosystem components.

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.

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii

PubMed Central

De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A.; Smits, Theo H. M.; Venter, Stephanus N.; Coutinho, Teresa A.

2017-01-01

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range. PMID:28959245

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.

PubMed

De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A; Smits, Theo H M; Venter, Stephanus N; Coutinho, Teresa A

2017-01-01

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes , has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis . While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Gene Transfer into Rat Brain Using Adenoviral Vectors

PubMed Central

Puntel, Mariana; Kroeger, Kurt M.; Sanderson, Nicholas S.R.; Thomas, Clare E.; Castro, Maria G.; Lowenstein, Pedro R.

2010-01-01

Viral vector–mediated gene delivery is an attractive procedure for introducing genes into the brain, both for purposes of basic neuroscience research and to develop gene therapy for neurological diseases. Replication-defective adenoviruses possess many features which make them ideal vectors for this purpose—efficiently transducing terminally differentiated cells such as neurons and glial cells, resulting in high levels of transgene expression in vivo. Also, in the absence of anti-adenovirus immunity, these vectors can sustain very long-term transgene expression within the brain parenchyma. This unit provides protocols for the stereotactic injection of adenoviral vectors into the brain, followed by protocols to detect transgene expression or infiltrates of immune cells by immunocytochemistry or immunofluorescence. ELISPOT and neutralizing antibody assay methodologies are provided to quantitate the levels of cellular and humoral immune responses against adenoviruses. Quantitation of adenoviral vector genomes within the rat brain using qPCR is also described. Curr. Protoc. Neurosci. 50:4.24.1–4.24.49. © 2010 by John Wiley & Sons, Inc. PMID:20066657

Storm-event-transport of urban-use pesticides to streams likely impairs invertebrate assemblages.

PubMed

Carpenter, Kurt D; Kuivila, Kathryn M; Hladik, Michelle L; Haluska, Tana; Cole, Michael B

2016-06-01

Insecticide use in urban areas results in the detection of these compounds in streams following stormwater runoff at concentrations likely to cause toxicity for stream invertebrates. In this 2013 study, stormwater runoff and streambed sediments were analyzed for 91 pesticides dissolved in water and 118 pesticides on sediment. Detections included 33 pesticides, including insecticides, fungicides, herbicides, degradates, and a synergist. Patterns in pesticide occurrence reveal transport of dissolved and sediment-bound pesticides, including pyrethroids, from upland areas through stormwater outfalls to receiving streams. Nearly all streams contained at least one insecticide at levels exceeding an aquatic-life benchmark, most often for bifenthrin and (or) fipronil. Multiple U.S. EPA benchmark or criterion exceedances occurred in 40 % of urban streams sampled. Bed sediment concentrations of bifenthrin were highly correlated (p < 0.001) with benthic invertebrate assemblages. Non-insects and tolerant invertebrates such as amphipods, flatworms, nematodes, and oligochaetes dominated streams with relatively high concentrations of bifenthrin in bed sediments, whereas insects, sensitive invertebrates, and mayflies were much more abundant at sites with no or low bifenthrin concentrations. The abundance of sensitive invertebrates, % EPT, and select mayfly taxa were strongly negatively correlated with organic-carbon normalized bifenthrin concentrations in streambed sediments. Our findings from western Clackamas County, Oregon (USA), expand upon previous research demonstrating the transport of pesticides from urban landscapes and linking impaired benthic invertebrate assemblages in urban streams with exposure to pyrethroid insecticides.

Storm-event-transport of urban-use pesticides to streams likely impairs invertebrate assemblages

USGS Publications Warehouse

Carpenter, Kurt; Kuivila, Kathryn; Hladik, Michelle; Haluska, Tana L.; Michael B. Cole,

2016-01-01

Insecticide use in urban areas results in the detection of these compounds in streams following stormwater runoff at concentrations likely to cause toxicity for stream invertebrates. In this 2013 study, stormwater runoff and streambed sediments were analyzed for 91 pesticides dissolved in water and 118 pesticides on sediment. Detections included 33 pesticides, including insecticides, fungicides, herbicides, degradates, and a synergist. Patterns in pesticide occurrence reveal transport of dissolved and sediment-bound pesticides, including pyrethroids, from upland areas through stormwater outfalls to receiving streams. Nearly all streams contained at least one insecticide at levels exceeding an aquatic-life benchmark, most often for bifenthrin and (or) fipronil. Multiple U.S. EPA benchmark or criterion exceedances occurred in 40 % of urban streams sampled. Bed sediment concentrations of bifenthrin were highly correlated (p < 0.001) with benthic invertebrate assemblages. Non-insects and tolerant invertebrates such as amphipods, flatworms, nematodes, and oligochaetes dominated streams with relatively high concentrations of bifenthrin in bed sediments, whereas insects, sensitive invertebrates, and mayflies were much more abundant at sites with no or low bifenthrin concentrations. The abundance of sensitive invertebrates, % EPT, and select mayfly taxa were strongly negatively correlated with organic-carbon normalized bifenthrin concentrations in streambed sediments. Our findings from western Clackamas County, Oregon (USA), expand upon previous research demonstrating the transport of pesticides from urban landscapes and linking impaired benthic invertebrate assemblages in urban streams with exposure to pyrethroid insecticides.

Spatial and temporal variability in benthic invertebrate assemblages in Upper Klamath Lake, Oregon

USGS Publications Warehouse

Stauffer-Olsen, Natalie J.; Carter, James L.; Fend, Steven V.

2017-01-01

Upper Klamath Lake (UKL) in southern Oregon has experienced declines in water quality due to excessive nutrient loading. This has led to annual cyanobacterial blooms, primarily of Aphanizomenon flos-aquae (AFA). Benthic invertebrates are important food resources for benthic feeding fishes; however, they can increase autochthonous nutrient cycling in lakes and as a result might be contributing to poor water quality in UKL. This study determined the density and taxonomic richness of benthic invertebrate assemblages in three geographic regions (north, central, and south) and three habitats (littoral, open-water and trench) across UKL. Sediment composition and water quality were also characterized at each of the 21 benthic invertebrate collection sites. Three sampling trips were made from May–July 2013. Mean lake-wide invertebrate density was 12 617 ± 7506 individuals m-2 (n = 63, based on 189 Ekman grabs) with oligochaetes, chironomids, and leeches representing 97% of all individuals. Mean invertebrate richness per sample was 16 ± 4 (n = 63). Two and three-way repeated measures ANOVAs identified differences in invertebrate densities and richness among regions, habitats, and sampling periods. There were no differences in total density among sampling periods. Total density was higher in littoral compared to open-water habitats, and in the northern region, proximal to all riverine inputs to the lake, compared to the central or southern regions. Although variances were heterogeneous, the number of taxa appeared to differ between habitats and regions.

The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.

PubMed

Dehal, Paramvir; Satou, Yutaka; Campbell, Robert K; Chapman, Jarrod; Degnan, Bernard; De Tomaso, Anthony; Davidson, Brad; Di Gregorio, Anna; Gelpke, Maarten; Goodstein, David M; Harafuji, Naoe; Hastings, Kenneth E M; Ho, Isaac; Hotta, Kohji; Huang, Wayne; Kawashima, Takeshi; Lemaire, Patrick; Martinez, Diego; Meinertzhagen, Ian A; Necula, Simona; Nonaka, Masaru; Putnam, Nik; Rash, Sam; Saiga, Hidetoshi; Satake, Masanobu; Terry, Astrid; Yamada, Lixy; Wang, Hong-Gang; Awazu, Satoko; Azumi, Kaoru; Boore, Jeffrey; Branno, Margherita; Chin-Bow, Stephen; DeSantis, Rosaria; Doyle, Sharon; Francino, Pilar; Keys, David N; Haga, Shinobu; Hayashi, Hiroko; Hino, Kyosuke; Imai, Kaoru S; Inaba, Kazuo; Kano, Shungo; Kobayashi, Kenji; Kobayashi, Mari; Lee, Byung-In; Makabe, Kazuhiro W; Manohar, Chitra; Matassi, Giorgio; Medina, Monica; Mochizuki, Yasuaki; Mount, Steve; Morishita, Tomomi; Miura, Sachiko; Nakayama, Akie; Nishizaka, Satoko; Nomoto, Hisayo; Ohta, Fumiko; Oishi, Kazuko; Rigoutsos, Isidore; Sano, Masako; Sasaki, Akane; Sasakura, Yasunori; Shoguchi, Eiichi; Shin-i, Tadasu; Spagnuolo, Antoinetta; Stainier, Didier; Suzuki, Miho M; Tassy, Olivier; Takatori, Naohito; Tokuoka, Miki; Yagi, Kasumi; Yoshizaki, Fumiko; Wada, Shuichi; Zhang, Cindy; Hyatt, P Douglas; Larimer, Frank; Detter, Chris; Doggett, Norman; Glavina, Tijana; Hawkins, Trevor; Richardson, Paul; Lucas, Susan; Kohara, Yuji; Levine, Michael; Satoh, Nori; Rokhsar, Daniel S

2002-12-13

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

Using invertebrate model organisms for neuroscience research and training: an opportunity for Africa.

PubMed

Balogun, Wasiu Gbolahan; Cobham, Ansa Emmanuel; Amin, Abdulbasit; Seeni, Azman

2018-05-24

Africa is faced with an increasing underrepresentation of her research progress in many fields of science including neuroscience. This underrepresentation stems from the very low investments directed towards research by African governments as these are thought to be high-priced. Scientists and researchers within the continent are left to compete highly for the very limited research grants or choose to fund research from their personal purse. Therefore, presenting a need for all possible strategies to make science and research approaches more affordable in Africa. This paper presents one of such strategy, which advocates the use of invertebrate animal models for neuroscience research in place of the commonly used vertebrate models. Invertebrates are cheaper, more available and easy to handle options and their use is on the rise, even in the developed societies of the world. Here, we investigate the current state of invertebrate neuroscience research in Africa looking at countries and institutions conducting neuroscience research with invertebrates and their publication output. We discuss the factors which impede invertebrate neuroscience research in Africa like lack of research infrastructure and adequate expert scientists and conclude by suggesting solutions to these challenges.

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.

Molecular Architecture and Biomedical Leads of Terpenes from Red Sea Marine Invertebrates

PubMed Central

Hegazy, Mohamed Elamir F.; Mohamed, Tarik A.; Alhammady, Montaser A.; Shaheen, Alaa M.; Reda, Eman H.; Elshamy, Abdelsamed I.; Aziz, Mina; Paré, Paul W.

2015-01-01

Marine invertebrates including sponges, soft coral, tunicates, mollusks and bryozoan have proved to be a prolific source of bioactive natural products. Among marine-derived metabolites, terpenoids have provided a vast array of molecular architectures. These isoprenoid-derived metabolites also exhibit highly specialized biological activities ranging from nerve regeneration to blood-sugar regulation. As a result, intense research activity has been devoted to characterizing invertebrate terpenes from both a chemical and biological standpoint. This review focuses on the chemistry and biology of terpene metabolites isolated from the Red Sea ecosystem, a unique marine biome with one of the highest levels of biodiversity and specifically rich in invertebrate species. PMID:26006713

Molecular architecture and biomedical leads of terpenes from red sea marine invertebrates.

PubMed

Hegazy, Mohamed Elamir F; Mohamed, Tarik A; Alhammady, Montaser A; Shaheen, Alaa M; Reda, Eman H; Elshamy, Abdelsamed I; Aziz, Mina; Paré, Paul W

2015-05-20

Marine invertebrates including sponges, soft coral, tunicates, mollusks and bryozoan have proved to be a prolific source of bioactive natural products. Among marine-derived metabolites, terpenoids have provided a vast array of molecular architectures. These isoprenoid-derived metabolites also exhibit highly specialized biological activities ranging from nerve regeneration to blood-sugar regulation. As a result, intense research activity has been devoted to characterizing invertebrate terpenes from both a chemical and biological standpoint. This review focuses on the chemistry and biology of terpene metabolites isolated from the Red Sea ecosystem, a unique marine biome with one of the highest levels of biodiversity and specifically rich in invertebrate species.

Phylogenetic study of the oxytocin-like immunoreactive system in invertebrates.

PubMed

Mizuno, J; Takeda, N

1988-01-01

1. A phylogenetic study of oxytocin (OXT)-like immunoreactive cells was performed by the PAP method in the central nervous system of invertebrates. 2. The immunoreactivity was detected in the nerve cells of Hydra magnipapillata of the Coelenterata; Neanthes japonica and Pheretima communissima of the Annelida; Oncidium verrucosum, Limax marginatus and Meretrix lamarckii of the Mollusca; and Baratha brassica of the Arthropoda. 3. No immunoreactive cells were found in Bipalium sp. of the Platyhelminthes; Pomacea canaliculata, Aplysia kurodai, Bradybaena similaris and Achatina fulica of the Mollusca; and Gnorimosphaeroma rayi, Procambarus clarkii, Hemigrapsus sanguineus, Helice tridens and Gryllus bimaculatus of the Arthropoda; Asterina pectinifera of the Echinodermata; and Halocynthia roretzi of the Protochordata. 4. These results demonstrate that an OXT-immunoreactive substance is widely present not only in vertebrates but also in invertebrates. 5. OXT seems to have been introduced into these invertebrates at an early stage of their phylogenetic history.

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

Hemocitical responses to environmental stress in invertebrates: a review.

PubMed

Perez, Danielli Giuliano; Fontanetti, Carmem Silvia

2011-06-01

Although invertebrates are recognized by the great facility to accumulate pollutants present in their environment and many of them are used as sentinel species in biomonitoring studies, little is known about the impact of toxicants on the immune system of these animals. In this regard, hemocytes play a fundamental role: these cells circulate freely through the hemolymph of invertebrates and act on the recognition of foreign material to the organism, mediating and effecting the cellular defense, such as phagocytosis, nodulation, and encapsulation. Different morphological types can be recognized but still there is controversy among the researchers about the exact classification of the hemocytes due to the diversity of techniques for the preservation and observation of these cells. In the present study, a review on the main hemocyte responses to environmental stress in different invertebrate organisms is presented, emphasizing the contamination by heavy metals. It is discussed parameters such as: alteration in the number of cells involved in the defense reaction, phagocytic activity, lysosomal responses, and production of reactive oxygen species.

Unusual occurrence of a DAG motif in the Ipomovirus Cassava brown streak virus and implications for its vector transmission.

PubMed

Ateka, Elijah; Alicai, Titus; Ndunguru, Joseph; Tairo, Fred; Sseruwagi, Peter; Kiarie, Samuel; Makori, Timothy; Kehoe, Monica A; Boykin, Laura M

2017-01-01

Cassava is the main staple food for over 800 million people globally. Its production in eastern Africa is being constrained by two devastating Ipomoviruses that cause cassava brown streak disease (CBSD); Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), with up to 100% yield loss for smallholder farmers in the region. To date, vector studies have not resulted in reproducible and highly efficient transmission of CBSV and UCBSV. Most virus transmission studies have used Bemisia tabaci (whitefly), but a maximum of 41% U/CBSV transmission efficiency has been documented for this vector. With the advent of next generation sequencing, researchers are generating whole genome sequences for both CBSV and UCBSV from throughout eastern Africa. Our initial goal for this study was to characterize U/CBSV whole genomes from CBSD symptomatic cassava plants sampled in Kenya. We have generated 8 new whole genomes (3 CBSV and 5 UCBSV) from Kenya, and in the process of analyzing these genomes together with 26 previously published sequences, we uncovered the aphid transmission associated DAG motif within coat protein genes of all CBSV whole genomes at amino acid positions 52-54, but not in UCBSV. Upon further investigation, the DAG motif was also found at the same positions in two other Ipomoviruses: Squash vein yellowing virus (SqVYV), Coccinia mottle virus (CocMoV). Until this study, the highly-conserved DAG motif, which is associated with aphid transmission was only noticed once, in SqVYV but discounted as being of minimal importance. This study represents the first comprehensive look at Ipomovirus genomes to determine the extent of DAG motif presence and significance for vector relations. The presence of this motif suggests that aphids could potentially be a vector of CBSV, SqVYV and CocMov. Further transmission and ipomoviral protein evolutionary studies are needed to confirm this hypothesis.

The origin and evolution of Basigin(BSG) gene: A comparative genomic and phylogenetic analysis.

PubMed

Zhu, Xinyan; Wang, Shenglan; Shao, Mingjie; Yan, Jie; Liu, Fei

2017-07-01

Basigin (BSG), also known as extracellular matrix metalloproteinase inducer (EMMPRIN) or cluster of differentiation 147 (CD147), plays various fundamental roles in the intercellular recognition involved in immunologic phenomena, differentiation, and development. In this study, we aimed to compare the similarities and differences of BSG among organisms and explore possible evolutionary relationships based on the comparison result. We used the extensive BLAST tool to search the metazoan genomes, N-glycosylation sites, the transmembrane region and other functional sites. We then identified BSG homologs from genomic sequences and analyzed their phylogenetic relationships. We identified that BSG genes exist not only in the vertebrate metazoans but also in the invertebrate metazoans such as Amphioxus B. floridae, D. melanogaster, A. mellifera, S. japonicum, C. gigas, and T. patagoniensis. After sequence analysis, we confirmed that only vertebrate metazoans and Cephalochordate (amphioxus B. floridae) have the classic structure (a signal peptide, two Ig-like domains (IgC2 and IgI), a transmembrane region, and an intracellular domain). The invertebrate metazoans (excluding amphioxus B. floridae) lack the N-terminal signal peptides and IgC2 domain. We then generated a phylogenetic tree, genome organization comparison, and chromosomal disposition analysis based on the biological information obtained from the NCBI and Ensembl databases. Finally, we established the possible evolutionary scenario of the BSG gene, which showed the restricted exon rearrangement that has occurred during evolution, forming the present-day BSG gene. Copyright © 2017 Elsevier Ltd. All rights reserved.

Resilience vs. decline: Precipitation and atmospheric change drive contrasting responses in invertebrate communities

NASA Astrophysics Data System (ADS)

Facey, Sarah L.

Invertebrates form the foundation of terrestrial ecosystems, far outnumbering their vertebrate counterparts in terms of abundance, biomass and diversity. As such, arthropod communities play vitally important roles in ecosystem processes ranging from pollination to soil fertility. Given the importance of invertebrates in ecosystems, predicting their responses - and those of the communities they form - to global change is one of the great challenges facing contemporary ecology. Our climate is changing as a result of the anthropogenic release of greenhouse gases, including carbon dioxide (CO2), produced from burning fossil fuels and land use change. The concentration of CO2 in the atmosphere now exceeds the range the Earth has seen in the last 800,000 years. Through the effect of such gases on radiative forcing, sustained greenhouse gas emissions will continue to drive increases in global average temperatures. Additionally, precipitation patterns are likely to change across the world, with increases in the occurrence of extreme weather events, such as droughts, as well as alterations in the magnitude and frequency of rainfall events. Climate change is already causing measurable changes in the Earth's biotic environment. Past work has been heavily focused on the responses of plants to various climate change parameters, with most studies including invertebrates limited to highly controlled studies of pair-wise interactions between one arthropod species and its host plant. Relatively little work to date, however, has looked at the potential impacts of climatic and atmospheric change for invertebrate communities as a whole. The overarching goal of this project was to help remedy this research gap, specifically by investigating the effects of precipitation and atmospheric change on invertebrate communities in grassland and woodland habitat, respectively. Chapters 2 and 4 synthesised recent work on climate change-driven alterations in precipitation and atmospheric change

Anterograde or Retrograde Transsynaptic Circuit Tracing in Vertebrates with Vesicular Stomatitis Virus Vectors.

PubMed

Beier, Kevin T; Mundell, Nathan A; Pan, Y Albert; Cepko, Constance L

2016-01-04

Viruses have been used as transsynaptic tracers, allowing one to map the inputs and outputs of neuronal populations, due to their ability to replicate in neurons and transmit in vivo only across synaptically connected cells. To date, their use has been largely restricted to mammals. In order to explore the use of such viruses in an expanded host range, we tested the transsynaptic tracing ability of recombinant vesicular stomatitis virus (rVSV) vectors in a variety of organisms. Successful infection and gene expression were achieved in a wide range of organisms, including vertebrate and invertebrate model organisms. Moreover, rVSV enabled transsynaptic tracing of neural circuitry in predictable directions dictated by the viral envelope glycoprotein (G), derived from either VSV or rabies virus (RABV). Anterograde and retrograde labeling, from initial infection and/or viral replication and transmission, was observed in Old and New World monkeys, seahorses, jellyfish, zebrafish, chickens, and mice. These vectors are widely applicable for gene delivery, afferent tract tracing, and/or directional connectivity mapping. Here, we detail the use of these vectors and provide protocols for propagating virus, changing the surface glycoprotein, and infecting multiple organisms using several injection strategies. Copyright © 2016 John Wiley & Sons, Inc.

Effects of environmental stressors on lipid metabolism in aquatic invertebrates.

PubMed

Lee, Min-Chul; Park, Jun Chul; Lee, Jae-Seong

2018-07-01

Lipid metabolism is crucial for the survival and propagation of the species, since lipids are an essential cellular component across animal taxa for maintaining homeostasis in the presence of environmental stressors. This review aims to summarize information on the lipid metabolism under environmental stressors in aquatic invertebrates. Fatty acid synthesis from glucose via de novo lipogenesis (DNL) pathway is mostly well-conserved across animal taxa. The structure of free fatty acid (FFA) from both dietary and DNL pathway could be transformed by elongase and desaturase. In addition, FFA can be stored in lipid droplet as triacylglycerol, upon attachment to glycerol. However, due to the limited information on both gene and lipid composition, in-depth studies on the structural modification of FFA and their storage conformation are required. Despite previously validated evidences on the disturbance of the normal life cycle and lipid homeostasis by the environmental stressors (e.g., obesogens, salinity, temperature, pCO 2 , and nutrients) in the aquatic invertebrates, the mechanism behind these effects are still poorly understood. To overcome this limitation, omics approaches such as transcriptomic and proteomic analyses have been used, but there are still gaps in our knowledge on aquatic invertebrates as well as the lipidome. This paper provides a deeper understanding of lipid metabolism in aquatic invertebrates. Copyright © 2018 Elsevier B.V. All rights reserved.

Factors influencing soil invertebrate communities in riparian grasslands of the central platte river floodplain

USGS Publications Warehouse

Davis, C.A.; Austin, J.E.; Buhl, D.A.

2006-01-01

In the Platte River Valley of central Nebraska, USA, riparian grasslands (also known as wet meadows) have been severely impacted by a reduction in river flows, causing lower ground-water levels and altered seasonal hydroperiods. The potential impacts of these hydrologic changes, as well as the environmental factors that influence wet meadow soil invertebrate communities, are not well understood. An understanding of the ecological processes that influence these invertebrate communities is crucial for maintaining and restoring wet meadows along the Platte River. Our objectives were to describe the soil invertebrate community of wet meadows throughout the growing season and to examine the relative roles of abiotic factors in determining patterns in invertebrate community structure. We conducted the study in 12 wet meadows along the Platte River during 1999 and 2000. We identified 73 invertebrate taxa; 39 were considered soil inhabitants. Total biomass was primarily composed of earthworms, Scarabaeidae, Isopoda, and Elateridae, with earthworms and Scarabaeidae accounting for >82%. Differences in river flow and precipitation patterns influenced some soil invertebrates. Earthworms and Scarabaeidae declined dramatically from 1999 (wet year) to 2000 (dry year). The topographic gradient created by the ridge-swale complex affected several soil invertebrate taxa; Scarabaeidae, Diplopoda, and Lepidoptera biomasses were greatest on drier ridges, while Tipulidae and Isopoda biomasscs were greatest in wetter sloughs. Responses of earthworm taxa to the topographic gradient were variable, but generally, greater biomasses occurred on ridges and mid-elevations. Water-table depth and soil moisture were the most important variables influencing wet meadow soil invertebrates. Because these communities are linked to the hydrologic processes of the Platte River, future alterations of wet meadow hydrology could shift the distribution patterns of many of these invertebrates and possibly

The value of long-term stream invertebrate data collected by citizen scientists

Treesearch

Patrick M. Edwards; Stefano Goffredo

2016-01-01

The purpose of this investigation was to systematically examine the variability associated with temporally-oriented invertebrate data collected by citizen scientists and consider the value of such data for use in stream management. Variability in invertebrate data was estimated for three sources of variation: sampling, within-reach spatial and long-term temporal. Long-...

Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates

PubMed Central

Pereira, Joana; Johnson, Warren E.; O’Brien, Stephen J.; Jarvis, Erich D.; Zhang, Guojie; Gilbert, M. Thomas P.; Vasconcelos, Vitor; Antunes, Agostinho

2014-01-01

The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – Shh; Indian hedgehog – Ihh; and Desert hedgehog – Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the Hh orthologs. Our results provide new insights on the evolutionary history of the Hh gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots. PMID:25549322

Response of rocky invertebrate diversity, structure and function to the vertical layering of vegetation

NASA Astrophysics Data System (ADS)

Bustamante, María; Tajadura, Javier; Gorostiaga, José María; Saiz-Salinas, José Ignacio

2014-06-01

Macroalgae comprise a prominent part of the rocky benthos where many invertebrates develop, and are believed to be undergoing severe declines worldwide. In order to investigate how the vegetation structure (crustose, basal and canopy layers) contributes to the diversity, structure and function of benthic invertebrates, a total of 31 subtidal transects were sampled along the northeast Atlantic coast of Spain. Significant positive relationships were found between the canopy layer and faunal abundance, taxonomic diversity and functional group diversity. Canopy forming algae were also related to epiphytic invertebrates, medium size forms, colonial strategy and suspensivores. By contrast, basal algae showed negative relationships with all variables tested except for detritivores. Multivariate multiple regression analyses (DISTLM) point to crustose as well as canopy layers as the best link between seaweeds and invertebrate assemblage structure. A close relationship was found between taxonomic and functional diversities. In general, low levels of taxonomic redundancy were detected for functional groups correlated with vegetation structure. A conceptual model based on the results is proposed, describing distinct stages of invertebrate assemblages in relation to the vertical structure of vegetation.

Aquatic invertebrate ecology during a simulated botulism epizootic in a Sacramento Valley wetland

USGS Publications Warehouse

Hicks, Jane M.; Euliss, Ned H.; Harris, Stanley W.

1997-01-01

We investigated the effect of decomposing duck carcasses on aquatic invertebrate numbers, biomass, and taxonomic composition in a seasonally flooded, impounded wetland in the Sacramento Valley, California during August–November 1988 and 1989. Major invertebrate taxa were copepods (Cyclopoida, occurred in 8.3% of samples), water fleas (Daphnidae, 8.9%), water boatmen (Corisella, 10.4%), and midge larvae (Goeldichironomus, 9.3%;Chironomus, 11.5%;Tanypus, 17.2%). We found no treatment (carcass present or no carcass) by sampling day interaction for these taxa. We found a significant difference between sample plots with carcasses and those without carcasses only for Daphnidae counts andCorisella wet weights. We found significant differences among sampling days for these taxa that were probably statistical artifacts. We were unable to detect any effect of duck carcasses on aquatic invertebrate community structure and the potential availability of invertebrates as waterfowl food.

Doubling the estimate of invertebrate biomass in a rainforest canopy.

PubMed

Ellwood, Martin D F; Foster, William A

2004-06-03

Forest canopies represent the functional interface between 90% of the Earth's terrestrial biomass and the atmosphere and include some of the most threatened of all terrestrial ecosystems. However, we lack even a basic understanding of how the biomass of plants and animals is distributed throughout forest canopies, even though this information is vital for estimating energy flow, carbon cycling, resource use and the transfer of materials within this ecosystem. Here we measure the biomass of invertebrates living in a common rainforest epiphyte, describe a striking relationship between fern size and the biomass of animals within the ferns, and reveal that one large epiphyte may contain an invertebrate biomass similar to that found in the whole of the rest of the tree crown on which it is growing. Using these data, we show that including the fauna of these epiphytes--a neglected component in rainforest ecosystems--can more than double our estimate of the total invertebrate biomass in an entire rainforest canopy.

A simplified approach to construct infectious cDNA clones of a tobamovirus in a binary vector.

PubMed

Junqueira, Bruna Rayane Teodoro; Nicolini, Cícero; Lucinda, Natalia; Orílio, Anelise Franco; Nagata, Tatsuya

2014-03-01

Infectious cDNA clones of RNA viruses are important tools to study molecular processes such as replication and host-virus interactions. However, the cloning steps necessary for construction of cDNAs of viral RNA genomes in binary vectors are generally laborious. In this study, a simplified method of producing an agro-infectious Pepper mild mottle virus (PMMoV) clone is described in detail. Initially, the complete genome of PMMoV was amplified by a single-step RT-PCR, cloned, and subcloned into a small plasmid vector under the T7 RNA polymerase promoter to confirm the infectivity of the cDNA clone through transcript inoculation. The complete genome was then transferred to a binary vector using a single-step, overlap-extension PCR. The selected clones were agro-infiltrated to Nicotiana benthamiana plants and showed to be infectious, causing typical PMMoV symptoms. No differences in host responses were observed when the wild-type PMMoV isolate, the T7 RNA polymerase-derived transcripts and the agroinfiltration-derived viruses were inoculated to N. benthamiana, Capsicum chinense PI 159236 and Capsicum annuum plants. Copyright © 2013 Elsevier B.V. All rights reserved.

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

Standing crops and ecology of aquatic invertebrates in agricultural drainwater ponds in California

USGS Publications Warehouse

Euliss, N.H.; Jarvis, R.L.; Gilmer, D.S.

1991-01-01

We examined standing crops and ecology of aquatic invertebrates in agricultural drainwater evaporation ponds in California from October 1982 to March 1983 and September 1983 to March 1984. Evaporation ponds supported low diversities but high standing crops of aquatic invertebrates. A water boatman (Trichocorixa reticulata) and a midge (Tanypus grodhausi) were the most abundant invertebrates, constituting 44.9% and 51.4% of total macroinvertebrate biomass. Regression models indicated that of 6 environmental variables measured, only electrical conductivity (EC) and Julian date affected biomass and density of water boatmen. EC was the only significant correlate of midge biomass in evaporation ponds.

Production and purification of non replicative canine adenovirus type 2 derived vectors.

PubMed

Szelechowski, Marion; Bergeron, Corinne; Gonzalez-Dunia, Daniel; Klonjkowski, Bernard

2013-12-03

Adenovirus (Ad) derived vectors have been widely used for short or long-term gene transfer, both for gene therapy and vaccine applications. Because of the frequent pre-existing immunity against the classically used human adenovirus type 5, canine adenovirus type 2 (CAV2) has been proposed as an alternative vector for human gene transfer. The well-characterized biology of CAV2, together with its ease of genetic manipulation, offer major advantages, notably for gene transfer into the central nervous system, or for inducing a wide range of protective immune responses, from humoral to cellular immunity. Nowadays, CAV2 represents one of the most appealing nonhuman adenovirus for use as a vaccine vector. This protocol describes a simple method to construct, produce and titer recombinant CAV2 vectors. After cloning the expression cassette of the gene of interest into a shuttle plasmid, the recombinant genomic plasmid is obtained by homologous recombination in the E. coli BJ5183 bacterial strain. The resulting genomic plasmid is then transfected into canine kidney cells expressing the complementing CAV2-E1 genes (DK-E1). A viral amplification enables the production of a large viral stock, which is purified by ultracentrifugation through cesium chloride gradients and desalted by dialysis. The resulting viral suspension routinely has a titer of over 10(10) infectious particles per ml and can be directly administrated in vivo.

Enhancers Are Major Targets for Murine Leukemia Virus Vector Integration

PubMed Central

De Ravin, Suk See; Su, Ling; Theobald, Narda; Choi, Uimook; Macpherson, Janet L.; Poidinger, Michael; Symonds, Geoff; Pond, Susan M.; Ferris, Andrea L.; Hughes, Stephen H.

2014-01-01

ABSTRACT Retroviral vectors have been used in successful gene therapies. However, in some patients, insertional mutagenesis led to leukemia or myelodysplasia. Both the strong promoter/enhancer elements in the long terminal repeats (LTRs) of murine leukemia virus (MLV)-based vectors and the vector-specific integration site preferences played an important role in these adverse clinical events. MLV integration is known to prefer regions in or near transcription start sites (TSS). Recently, BET family proteins were shown to be the major cellular proteins responsible for targeting MLV integration. Although MLV integration sites are significantly enriched at TSS, only a small fraction of the MLV integration sites (<15%) occur in this region. To resolve this apparent discrepancy, we created a high-resolution genome-wide integration map of more than one million integration sites from CD34+ hematopoietic stem cells transduced with a clinically relevant MLV-based vector. The integration sites form ∼60,000 tight clusters. These clusters comprise ∼1.9% of the genome. The vast majority (87%) of the integration sites are located within histone H3K4me1 islands, a hallmark of enhancers. The majority of these clusters also have H3K27ac histone modifications, which mark active enhancers. The enhancers of some oncogenes, including LMO2, are highly preferred targets for integration without in vivo selection. IMPORTANCE We show that active enhancer regions are the major targets for MLV integration; this means that MLV preferentially integrates in regions that are favorable for viral gene expression in a variety of cell types. The results provide insights for MLV integration target site selection and also explain the high risk of insertional mutagenesis that is associated with gene therapy trials using MLV vectors. PMID:24501411

Studying emotion in invertebrates: what has been done, what can be measured and what they can provide.

PubMed

Perry, Clint J; Baciadonna, Luigi

2017-11-01

Until recently, whether invertebrates might exhibit emotions was unknown. This possibility has traditionally been dismissed by many as emotions are frequently defined with reference to human subjective experience, and invertebrates are often not considered to have the neural requirements for such sophisticated abilities. However, emotions are understood in humans and other vertebrates to be multifaceted brain states, comprising dissociable subjective, cognitive, behavioural and physiological components. In addition, accumulating literature is providing evidence of the impressive cognitive capacities and behavioural flexibility of invertebrates. Alongside these, within the past few years, a number of studies have adapted methods for assessing emotions in humans and other animals, to invertebrates, with intriguing results. Sea slugs, bees, crayfish, snails, crabs, flies and ants have all been shown to display various cognitive, behavioural and/or physiological phenomena that indicate internal states reminiscent of what we consider to be emotions. Given the limited neural architecture of many invertebrates, and the powerful tools available within invertebrate research, these results provide new opportunities for unveiling the neural mechanisms behind emotions and open new avenues towards the pharmacological manipulation of emotion and its genetic dissection, with advantages for disease research and therapeutic drug discovery. Here, we review the increasing evidence that invertebrates display some form of emotion, discuss the various methods used for assessing emotions in invertebrates and consider what can be garnered from further emotion research on invertebrates in terms of the evolution and underlying neural basis of emotion in a comparative context. © 2017. Published by The Company of Biologists Ltd.

Regional Patterns in Invertebrate Assemblages on Offshore Oil Platforms Along the Pacific Outer Continental Shelf

NASA Astrophysics Data System (ADS)

Zaleski, S.; Page, H. M.; Miller, R. J.; Doheny, B.; Dugan, J. E.; Schroeder, D. M.

2016-02-01

Twenty-seven oil and gas platforms are arrayed offshore California from north of Point Conception south to San Pedro Bay (a coastline distance of >300 km). To test the hypothesis that variability in the structure of sessile invertebrate communities on the platforms is associated with regional differences in sea surface temperature, we sampled space-holding invertebrate taxa photographically on 23 platforms and compared the composition and cover of invertebrates among and within regions using multivariate analyses. To explore temporal variability in invertebrate assemblages, we also compared the cover and composition of invertebrates on a subset of platforms in the Santa Barbara Channel (SBC) where data were collected over ten years previously. The composition of invertebrate assemblages differed significantly among regions, and was driven by variation in the relative abundance of certain anemone, bryozoan, tubiferous annelid, sponge, and bivalve taxa. The presence of non-native bryozoan and anemone taxa on some platforms in the south (San Pedro Bay) and southeast SBC contributed to the distinction of these assemblages from the others. Comparison of survey data on the subset of platforms in the SBC surveyed over ten years apart revealed little change in the cover of major space-holding taxa (e.g., anemones Metridium, Corynactis) across platforms, although there was an increase in cover of the non-native bryozoan Watersipora subtorquata between surveys. The existence of geographical patterns in the composition of platform invertebrate assemblages suggests that these assemblages may be useful as barometers of short and longer-term environmental change. For biogeographic transition zones, such as the SBC, monitoring of platform invertebrate assemblages could permit an evaluation of the concept that these zones are particularly susceptible to shifts in the composition of marine species driven by ocean climate.

Hybrid Adeno-Associated Viral Vectors Utilizing Transposase-Mediated Somatic Integration for Stable Transgene Expression in Human Cells

PubMed Central

Zhang, Wenli; Solanki, Manish; Müther, Nadine; Ebel, Melanie; Wang, Jichang; Sun, Chuanbo; Izsvak, Zsuzsanna; Ehrhardt, Anja

2013-01-01

Recombinant adeno-associated viral (AAV) vectors have been shown to be one of the most promising vectors for therapeutic gene delivery because they can induce efficient and long-term transduction in non-dividing cells with negligible side-effects. However, as AAV vectors mostly remain episomal, vector genomes and transgene expression are lost in dividing cells. Therefore, to stably transduce cells, we developed a novel AAV/transposase hybrid-vector. To facilitate SB-mediated transposition from the rAAV genome, we established a system in which one AAV vector contains the transposon with the gene of interest and the second vector delivers the hyperactive Sleeping Beauty (SB) transposase SB100X. Human cells were infected with the AAV-transposon vector and the transposase was provided in trans either by transient and stable plasmid transfection or by AAV vector transduction. We found that groups which received the hyperactive transposase SB100X showed significantly increased colony forming numbers indicating enhanced integration efficiencies. Furthermore, we found that transgene copy numbers in transduced cells were dose-dependent and that predominantly SB transposase-mediated transposition contributed to stabilization of the transgene. Based on a plasmid rescue strategy and a linear-amplification mediated PCR (LAM-PCR) protocol we analysed the SB100X-mediated integration profile after transposition from the AAV vector. A total of 1840 integration events were identified which revealed a close to random integration profile. In summary, we show for the first time that AAV vectors can serve as template for SB transposase mediated somatic integration. We developed the first prototype of this hybrid-vector system which with further improvements may be explored for treatment of diseases which originate from rapidly dividing cells. PMID:24116154

Multiple mating and clutch size in invertebrate brooders versus pregnant vertebrates

PubMed Central

Avise, John C.; Tatarenkov, Andrey; Liu, Jin-Xian

2011-01-01

We summarize the genetic literature on polygamy rates and sire numbers per clutch in invertebrate animals that brood their offspring and then compare findings with analogous data previously compiled for vertebrate species displaying viviparity or other pregnancy-like syndromes. As deduced from molecular parentage analyses of several thousand broods from more than 100 “pregnant” species, invertebrate brooders had significantly higher mean incidences of multiple mating than pregnant vertebrates, a finding generally consistent with the postulate that clutch size constrains successful mate numbers in species with extended parental care. However, we uncovered no significant correlation in invertebrates between brood size and genetically deduced rates of multiple mating by the incubating sex. Instead, in embryo-gestating animals otherwise as different as mammals and mollusks, polygamy rates and histograms of successful mates per brooder proved to be strikingly similar. Most previous studies have sought to understand why gestating parents have so many mates and such high incidences of successful multiple mating; an alternative perspective based on logistical constraints turns the issue on its head by asking why mate numbers and polygamy rates are much lower than they theoretically could be, given the parentage-resolving power of molecular markers and the huge sizes of many invertebrate broods. PMID:21709247

Invertebrate muscles: thin and thick filament structure; molecular basis of contraction and its regulation, catch and asynchronous muscle

PubMed Central

Hooper, Scott L.; Hobbs, Kevin H.; Thuma, Jeffrey B.

2008-01-01

This is the second in a series of canonical reviews on invertebrate muscle. We cover here thin and thick filament structure, the molecular basis of force generation and its regulation, and two special properties of some invertebrate muscle, catch and asynchronous muscle. Invertebrate thin filaments resemble vertebrate thin filaments, although helix structure and tropomyosin arrangement show small differences. Invertebrate thick filaments, alternatively, are very different from vertebrate striated thick filaments and show great variation within invertebrates. Part of this diversity stems from variation in paramyosin content, which is greatly increased in very large diameter invertebrate thick filaments. Other of it arises from relatively small changes in filament backbone structure, which results in filaments with grossly similar myosin head placements (rotating crowns of heads every 14.5 nm) but large changes in detail (distances between heads in azimuthal registration varying from three to thousands of crowns). The lever arm basis of force generation is common to both vetebrates and invertebrates, and in some invertebrates this process is understood on the near atomic level. Invertebrate actomyosin is both thin (tropomyosin:troponin) and thick (primarily via direct Ca++ binding to myosin) filament regulated, and most invertebrate muscles are dually regulated. These mechanisms are well understood on the molecular level, but the behavioral utility of dual regulation is less so. The phosphorylation state of the thick filament associated giant protein, twitchin, has been recently shown to be the molecular basis of catch. The molecular basis of the stretch activation underlying asynchronous muscle activity, however, remains unresolved. PMID:18616971

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…

Functional characterization on invertebrate and vertebrate tissues of tachykinin peptides from octopus venoms.

PubMed

Ruder, Tim; Ali, Syed Abid; Ormerod, Kiel; Brust, Andreas; Roymanchadi, Mary-Louise; Ventura, Sabatino; Undheim, Eivind A B; Jackson, Timothy N W; Mercier, A Joffre; King, Glenn F; Alewood, Paul F; Fry, Bryan G

2013-09-01

It has been previously shown that octopus venoms contain novel tachykinin peptides that despite being isolated from an invertebrate, contain the motifs characteristic of vertebrate tachykinin peptides rather than being more like conventional invertebrate tachykinin peptides. Therefore, in this study we examined the effect of three variants of octopus venom tachykinin peptides on invertebrate and vertebrate tissues. While there were differential potencies between the three peptides, their relative effects were uniquely consistent between invertebrate and vertebrae tissue assays. The most potent form (OCT-TK-III) was not only the most anionically charged but also was the most structurally stable. These results not only reveal that the interaction of tachykinin peptides is more complex than previous structure-function theories envisioned, but also reinforce the fundamental premise that animal venoms are rich resources of novel bioactive molecules, which are useful investigational ligands and some of which may be useful as lead compounds for drug design and development. Copyright © 2013 Elsevier Inc. All rights reserved.

Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis

PubMed Central

Facey, Paul D.; Méric, Guillaume; Hitchings, Matthew D.; Pachebat, Justin A.; Hegarty, Matt J.; Chen, Xiaorui; Morgan, Laura V.A.; Hoeppner, James E.; Whitten, Miranda M.A.; Kirk, William D.J.; Dyson, Paul J.; Sheppard, Sam K.; Sol, Ricardo Del

2015-01-01

Obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. Increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. Here we take a comparative genomics approach to investigate two prominent bacterial symbionts (BFo1 and BFo2) isolated from geographically separated populations of western flower thrips, Frankliniella occidentalis. Our multifaceted approach to classifying these symbionts includes concatenated multilocus sequence analysis (MLSA) phylogenies, ribosomal multilocus sequence typing (rMLST), construction of whole-genome phylogenies, and in-depth genomic comparisons. We showed that the BFo1 genome clusters more closely to species in the genus Erwinia, and is a putative close relative to Erwinia aphidicola. BFo1 is also likely to have shared a common ancestor with Erwinia pyrifoliae/Erwinia amylovora and the nonpathogenic Erwinia tasmaniensis and genetic traits similar to Erwinia billingiae. The BFo1 genome contained virulence factors found in the genus Erwinia but represented a divergent lineage. In contrast, we showed that BFo2 belongs within the Enterobacteriales but does not group closely with any currently known bacterial species. Concatenated MLSA phylogenies indicate that it may have shared a common ancestor to the Erwinia and Pantoea genera, and based on the clustering of rMLST genes, it was most closely related to Pantoea ananatis but represented a divergent lineage. We reconstructed a core genome of a putative common ancestor of Erwinia and Pantoea and compared this with the genomes of BFo bacteria. BFo2 possessed none of the virulence determinants that were omnipresent in the Erwinia and Pantoea genera. Taken together, these data are consistent with BFo2 representing a highly novel species that maybe related to known Pantoea. PMID:26185096

The inland water macro-invertebrate occurrences in Flanders, Belgium.

PubMed

Vannevel, Rudy; Brosens, Dimitri; Cooman, Ward De; Gabriels, Wim; Frank Lavens; Mertens, Joost; Vervaeke, Bart

2018-01-01

The Flanders Environment Agency (VMM) has been performing biological water quality assessments on inland waters in Flanders (Belgium) since 1989 and sediment quality assessments since 2000. The water quality monitoring network is a combined physico-chemical and biological network, the biological component focusing on macro-invertebrates. The sediment monitoring programme produces biological data to assess the sediment quality. Both monitoring programmes aim to provide index values, applying a similar conceptual methodology based on the presence of macro-invertebrates. The biological data obtained from both monitoring networks are consolidated in the VMM macro-invertebrates database and include identifications at family and genus level of the freshwater phyla Coelenterata, Platyhelminthes, Annelida, Mollusca, and Arthropoda. This paper discusses the content of this database, and the dataset published thereof: 282,309 records of 210 observed taxa from 4,140 monitoring sites located on 657 different water bodies, collected during 22,663 events. This paper provides some background information on the methodology, temporal and spatial coverage, and taxonomy, and describes the content of the dataset. The data are distributed as open data under the Creative Commons CC-BY license.

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.

Aboveground vertebrate and invertebrate herbivore impacts on net N mineralization in subalpine grasslands

Treesearch

Anita C. Risch; Martin Schutz; Martijn L. Vandegehuchte; Wim H. van der Putten; Henk Duyts; Ursina Raschein; Dariusz J. Gwiazdowicz; Matt D. Busse; Deborah S. Page-Dumroese; Stephan Zimmerman

2015-01-01

Aboveground herbivores have strong effects on grassland nitrogen (N) cycling. They can accelerate or slow down soil net N mineralization depending on ecosystem productivity and grazing intensity. Yet, most studies only consider either ungulates or invertebrate herbivores, but not the combined effect of several functionally different vertebrate and invertebrate...

The effect of the lamprey larvicide, 3-trifluormethyl-4-nitrophenol, on selected aquatic invertebrates

USGS Publications Warehouse

Smith, Allen J.

1967-01-01

The chemical compound 3-trifluoromethyl-4-nitrophenol (TFM) is used to control the sea lamprey (Petromyzon marinus) in the upper Great Lakes. It is introduced into streams in which sea lampreys have spawned, to kill the larvae. These 'treatments' are carried out at intervals shorter than the larval phase of the sea lamprey's life cycle (about 4 to 7 years) to prevent movement of the metamorphosed parasitic lampreys into the lakes. Most of the streams which contain sea lamprey larvae also have valuable resident fish or serve as spawning and nursery areas for fish of the Great Lakes. These species must be protected from both the direct toxic effects of the control method and from indirect effects such as destruction of food supplies. Studies have shown that TFM is nontoxic to most species of fish when used at the concentrations that kill larval lampreys. Information on the effect of TFM on aquatic invertebrates is meager. Applegate et al. reported that TFM was not harmful to selected invertebrates which they included in simulated stream tests. They also stated that no harmful effects to invertebrates were observed during actual stream application. The variety of invertebrate species used in simulated stream tests was limited, and close observation of invertebrates under stream conditions is difficult. Therefore, the present laboratory bioassays were conducted to determine the toxicity of TFM to representatives of a number of groups of invertebrates.

Antibody-mediated targeting of replication-competent retroviral vectors.

PubMed

Tai, Chien-Kuo; Logg, Christopher R; Park, Jinha M; Anderson, W French; Press, Michael F; Kasahara, Noriyuki

2003-05-20

Replication-competent murine leukemia virus (MLV) vectors can be engineered to achieve high efficiency gene transfer to solid tumors in vivo and tumor-restricted replication, however their safety can be further enhanced by redirecting tropism of the virus envelope. We have therefore tested the targeting capability and replicative stability of ecotropic and amphotropic replication-competent retrovirus (RCR) vectors containing two tandem repeats from the immunoglobulin G-binding domain of Staphylococcal protein A inserted into the proline-rich "hinge" region of the envelope, which enables modular use of antibodies of various specificities for vector targeting. The modified envelopes were efficiently expressed and incorporated into virions, were capable of capturing monoclonal anti-HER2 antibodies, and mediated efficient binding of the virus-antibody complex to HER2-positive target cells. While infectivity was markedly reduced by pseudotyping with targeted envelopes alone, coexpression of wild-type envelope rescued efficient cellular entry. Both ecotropic and amphotropic RCR vector/anti-HER2 antibody complexes achieved significant enhancement of transduction on murine target cells overexpressing HER2, which could be competed by preincubation with excess free antibodies. Interestingly, HER2-expressing human breast cancer cells did not show enhancement of transduction despite efficient antibody-mediated cell surface binding, suggesting that target cell-specific parameters markedly affect the efficiency of post-binding entry processes. Serial replication of targeted vectors resulted in selection of Z domain deletion variants, but reduction of the overall size of the vector genome enhanced its stability. Application of antibody-mediated targeting to the initial localization of replication-competent virus vectors to tumor sites will thus require optimized target selection and vector design.

Spatial and temporal variability in the structure of invertebrate assemblages in control stream mesocosms.

PubMed

Wong, Diana C L; Maltby, Lorraine; Whittle, Don; Warren, Philip; Dorn, Philip B

2004-01-01

Outdoor stream mesocosm studies conducted between 1992 and 1996 at two facilities enabled the investigation of structural variability in invertebrate assemblages within and between studies. Temporal variability of benthic invertebrate assemblages between eight replicate streams within a study was assessed in a 28-day mesocosm study without chemical treatment. Cluster analysis, non-metric multidimensional scaling, and principal component analysis each showed the untreated assemblages as structurally distinct groups on the three sampling days. The assemblages between the eight replicate streams showed >88% Bray-Curtis similarity at any one time during the study. In addition, pre-treatment data from a series of four studies conducted at one facility were used to examine structural variability in the starting benthic invertebrate assemblages between studies. Invertebrate assemblages were structurally distinct at the start of each mesocosm study conducted in different years at the same facility and the taxa responsible for differences in the assemblages were also different each year. The implications of temporal and spatial variability in benthic invertebrate assemblages within and between mesocosm studies with regards to species sensitivity and study repeatability should be considered when results of such studies are used in risk assessment.

Integration event induced changes in recombinant protein productivity in Pichia pastoris discovered by whole genome sequencing and derived vector optimization.

PubMed

Schwarzhans, Jan-Philipp; Wibberg, Daniel; Winkler, Anika; Luttermann, Tobias; Kalinowski, Jörn; Friehs, Karl

2016-05-20

The classic AOX1 replacement approach is still one of the most often used techniques for expression of recombinant proteins in the methylotrophic yeast Pichia pastoris. Although this approach is largely successful, it frequently delivers clones with unpredicted production characteristics and a work-intense screening process is required to find the strain with desired productivity. In this project 845 P. pastoris clones, transformed with a GFP expression cassette, were analyzed for their methanol-utilization (Mut)-phenotypes, GFP gene expression levels and gene copy numbers. Several groups of strains with irregular features were identified. Such features include GFP expression that is markedly higher or lower than expected based on gene copy number as well as strains that grew under selective conditions but where the GFP gene cassette and its expression could not be detected. From these classes of strains 31 characteristic clones were selected and their genomes sequenced. By correlating the assembled genome data with the experimental phenotypes novel insights were obtained. These comprise a clear connection between productivity and cassette-to-cassette orientation in the genome, the occurrence of false-positive clones due to a secondary recombination event, and lower total productivity due to the presence of untransformed cells within the isolates were discovered. To cope with some of these problems, the original vector was optimized by replacing the AOX1 terminator, preventing the occurrence of false-positive clones due to the secondary recombination event. Standard methods for transformation of P. pastoris led to a multitude of unintended and sometimes detrimental integration events, lowering total productivity. By documenting the connections between productivity and integration event we obtained a deeper understanding of the genetics of mutation in P. pastoris. These findings and the derived improved mutagenesis and transformation procedures and tools will help

Recent Advances in Preclinical Developments Using Adenovirus Hybrid Vectors.

PubMed

Ehrke-Schulz, Eric; Zhang, Wenli; Gao, Jian; Ehrhardt, Anja

2017-10-01

Adenovirus (Ad)-based vectors are efficient gene-transfer vehicles to deliver foreign DNA into living organisms, offering large cargo capacity and low immunogenicity and genotoxicity. As Ad shows low integration rates of their genomes into host chromosomes, vector-derived gene expression decreases due to continuous cell cycling in regenerating tissues and dividing cell populations. To overcome this hurdle, adenoviral delivery can be combined with mechanisms leading to maintenance of therapeutic DNA and long-term effects of the desired treatment. Several hybrid Ad vectors (AdV) exploiting various strategies for long-term treatment have been developed and characterized. This review summarizes recent developments of preclinical approaches using hybrid AdVs utilizing either the Sleeping Beauty transposase system for somatic integration into host chromosomes or designer nucleases, including transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease for permanent gene editing. Further options on how to optimize these vectors further are discussed, which may lead to future clinical applications of these versatile gene-therapy tools.

Genome structure of bdelloid rotifers: shaped by asexuality or desiccation?

PubMed

Gladyshev, Eugene A; Arkhipova, Irina R

2010-01-01

Bdelloid rotifers are microscopic invertebrate animals best known for their ancient asexuality and the ability to survive desiccation at any life stage. Both factors are expected to have a profound influence on their genome structure. Recent molecular studies demonstrated that, although the gene-rich regions of bdelloid genomes are organized as colinear pairs of closely related sequences and depleted in repetitive DNA, subtelomeric regions harbor diverse transposable elements and horizontally acquired genes of foreign origin. Although asexuality is expected to result in depletion of deleterious transposons, only desiccation appears to have the power to produce all the uncovered genomic peculiarities. Repair of desiccation-induced DNA damage would require the presence of a homologous template, maintaining colinear pairs in gene-rich regions and selecting against insertion of repetitive DNA that might cause chromosomal rearrangements. Desiccation may also induce a transient state of competence in recovering animals, allowing them to acquire environmental DNA. Even if bdelloids engage in rare or obscure forms of sexual reproduction, all these features could still be present. The relative contribution of asexuality and desiccation to genome organization may be clarified by analyzing whole-genome sequences and comparing foreign gene and transposon content in species which lost the ability to survive desiccation.

GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome.

PubMed

Lu, Bingxin; Leong, Hon Wai

2016-02-01

Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial genomes. GIs are extremely important for bacterial research, because they not only promote genome evolution but also contain genes that enhance adaption and enable antibiotic resistance. Many methods have been proposed to predict GI. But most of them rely on either annotations or comparisons with other closely related genomes. Hence these methods cannot be easily applied to new genomes. As the number of newly sequenced bacterial genomes rapidly increases, there is a need for methods to detect GI based solely on sequences of a single genome. In this paper, we propose a novel method, GI-SVM, to predict GIs given only the unannotated genome sequence. GI-SVM is based on one-class support vector machine (SVM), utilizing composition bias in terms of k-mer content. From our evaluations on three real genomes, GI-SVM can achieve higher recall compared with current methods, without much loss of precision. Besides, GI-SVM allows flexible parameter tuning to get optimal results for each genome. In short, GI-SVM provides a more sensitive method for researchers interested in a first-pass detection of GI in newly sequenced genomes.

Large inserts for big data: artificial chromosomes in the genomic era.

PubMed

Tocchetti, Arianna; Donadio, Stefano; Sosio, Margherita

2018-05-01

The exponential increase in available microbial genome sequences coupled with predictive bioinformatic tools is underscoring the genetic capacity of bacteria to produce an unexpected large number of specialized bioactive compounds. Since most of the biosynthetic gene clusters (BGCs) present in microbial genomes are cryptic, i.e. not expressed under laboratory conditions, a variety of cloning systems and vectors have been devised to harbor DNA fragments large enough to carry entire BGCs and to allow their transfer in suitable heterologous hosts. This minireview provides an overview of the vectors and approaches that have been developed for cloning large BGCs, and successful examples of heterologous expression.

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...

A Foxtail mosaic virus Vector for Virus-Induced Gene Silencing in Maize1[OPEN

PubMed Central

Mei, Yu; Kernodle, Bliss M.; Hill, John H.

2016-01-01

Plant viruses have been widely used as vectors for foreign gene expression and virus-induced gene silencing (VIGS). A limited number of viruses have been developed into viral vectors for the purposes of gene expression or VIGS in monocotyledonous plants, and among these, the tripartite viruses Brome mosaic virus and Cucumber mosaic virus have been shown to induce VIGS in maize (Zea mays). We describe here a new DNA-based VIGS system derived from Foxtail mosaic virus (FoMV), a monopartite virus that is able to establish systemic infection and silencing of endogenous maize genes homologous to gene fragments inserted into the FoMV genome. To demonstrate VIGS applications of this FoMV vector system, four genes, phytoene desaturase (functions in carotenoid biosynthesis), lesion mimic22 (encodes a key enzyme of the porphyrin pathway), iojap (functions in plastid development), and brown midrib3 (caffeic acid O-methyltransferase), were silenced and characterized in the sweet corn line Golden × Bantam. Furthermore, we demonstrate that the FoMV infectious clone establishes systemic infection in maize inbred lines, sorghum (Sorghum bicolor), and green foxtail (Setaria viridis), indicating the potential wide applications of this viral vector system for functional genomics studies in maize and other monocots. PMID:27208311

Species Profiles: Life Histories and Environmental Requirements of Coastal Fishes and Invertebrates (Pacific Northwest), Pacific Oyster

DTIC Science & Technology

1988-09-01

Requirements of Coastal Fishes o and Invertebrates (Pacific Northwest) LEICT o PACIFIC OYSTER E2I 8 Coastal Ecology Group Fish and Wildlife Service Waterways...Profiles-: Life Histories and Environmental Requirements of Coastal Fishes and Invertebrates (Pacific N rthwest) PACIFIC OYSTER by Gilbert B. Pauley...Fish and Wildlife Service. 1983-19. Species profiles: life histories and environmental requirements of coastal fishes and invertebrates . U.S. Fish

Nucleic acid-induced antiviral immunity in invertebrates: an evolutionary perspective.

PubMed

Wang, Pei-Hui; Weng, Shao-Ping; He, Jian-Guo

2015-02-01

Nucleic acids derived from viral pathogens are typical pathogen associated molecular patterns (PAMPs). In mammals, the recognition of viral nucleic acids by pattern recognition receptors (PRRs), which include Toll-like receptors (TLRs) and retinoic acid-inducible gene (RIG)-I-like receptors (RLRs), induces the release of inflammatory cytokines and type I interferons (IFNs) through the activation of nuclear factor κB (NF-κB) and interferon regulatory factor (IRF) 3/7 pathways, triggering the host antiviral state. However, whether nucleic acids can induce similar antiviral immunity in invertebrates remains ambiguous. Several studies have reported that nucleic acid mimics, especially dsRNA mimic poly(I:C), can strongly induce non-specific antiviral immune responses in insects, shrimp, and oyster. This behavior shows multiple similarities to the hallmarks of mammalian IFN responses. In this review, we highlight the current understanding of nucleic acid-induced antiviral immunity in invertebrates. We also discuss the potential recognition and regulatory mechanisms that confer non-specific antiviral immunity on invertebrate hosts. Copyright © 2014 Elsevier Ltd. All rights reserved.

Will Invertebrates Require Increasingly Carbon-Rich Food in a Warming World?

PubMed

Anderson, Thomas R; Hessen, Dag O; Boersma, Maarten; Urabe, Jotaro; Mayor, Daniel J

2017-12-01

Elevated temperature causes metabolism and respiration to increase in poikilothermic organisms. We hypothesized that invertebrate consumers will therefore require increasingly carbon-rich diets in a warming environment because the increased energetic demands are primarily met using compounds rich in carbon, that is, carbohydrates and lipids. Here, we test this hypothesis using a new stoichiometric model that has carbon (C) and nitrogen (N) as currencies. Model predictions did not support the hypothesis, indicating instead that the nutritional requirements of invertebrates, at least in terms of food quality expressed as C∶N ratio, may change little, if at all, at elevated temperature. Two factors contribute to this conclusion. First, invertebrates facing limitation by nutrient elements such as N have, by default, excess C in their food that can be used to meet the increased demand for energy in a warming environment, without recourse to extra dietary C. Second, increased feeding at elevated temperature compensates for the extra demands of metabolism to the extent that, when metabolism and intake scale equally with temperature (have the same Q 10 ), the relative requirement for dietary C and N remains unaltered. Our analysis demonstrates that future climate-driven increases in the C∶N ratios of autotroph biomass will likely exacerbate the stoichiometric mismatch between nutrient-limited invertebrate grazers and their food, with important consequences for C sequestration and nutrient cycling in ecosystems.

Enzyme Histochemistry for Functional Histology in Invertebrates.

PubMed

Cima, Francesca

2017-01-01

In invertebrates, enzyme histochemistry has recently found a renaissance regarding its applications in morphology and ecology. Many enzyme activities are useful for the morphofunctional characterization of cells, as biomarkers of biological and pathologic processes, and as markers of the response to environmental stressors. Here, the adjustments to classic techniques, including the most common enzymes used for digestion, absorption, transport, and oxidation, as well as techniques for azo-coupling, metal salt substitution and oxidative coupling polymerization, are presented in detail for various terrestrial and aquatic invertebrates. This chapter also provides strategies to solve the problems regarding anesthesia, small body size, the presence of an exo- or endoskeleton and the search for the best fixative in relation to the internal fluid osmolarity. These techniques have the aim of obtaining good results for both the pre- and post-embedding labeling of specimens, tissue blocks, sections, and hemolymph smears using both light and transmission electron microscopy.

Transstadial Transmission and Long-term Association of Crimean-Congo Hemorrhagic Fever Virus in Ticks Shapes Genome Plasticity

PubMed Central

Xia, Han; Beck, Andrew S.; Gargili, Aysen; Forrester, Naomi; Barrett, Alan D. T.; Bente, Dennis A.

2016-01-01

The trade-off hypothesis, the current paradigm of arbovirus evolution, proposes that cycling between vertebrate and invertebrate hosts presents significant constraints on genetic change of arboviruses. Studying these constraints in mosquito-borne viruses has led to a new understanding of epizootics. The trade-off hypothesis is assumed to be applicable to tick-borne viruses too, although studies are lacking. Tick-borne Crimean-Congo hemorrhagic fever virus (CCHFV), a member of the family Bunyaviridae, is a major cause of severe human disease worldwide and shows an extraordinary amount of genetic diversity compared to other arboviruses, which has been linked to increased virulence and emergence in new environments. Using a transmission model for CCHFV, utilizing the main vector tick species and mice plus next generation sequencing, we detected a substantial number of consensus-level mutations in CCHFV recovered from ticks after only a single transstadial transmission, whereas none were detected in CCHFV obtained from the mammalian host. Furthermore, greater viral intra-host diversity was detected in the tick compared to the vertebrate host. Long-term association of CCHFV with its tick host for 1 year demonstrated mutations in the viral genome become fixed over time. These findings suggest that the trade-off hypothesis may not be accurate for all arboviruses. PMID:27775001

Transstadial Transmission and Long-term Association of Crimean-Congo Hemorrhagic Fever Virus in Ticks Shapes Genome Plasticity.

PubMed

Xia, Han; Beck, Andrew S; Gargili, Aysen; Forrester, Naomi; Barrett, Alan D T; Bente, Dennis A

2016-10-24

The trade-off hypothesis, the current paradigm of arbovirus evolution, proposes that cycling between vertebrate and invertebrate hosts presents significant constraints on genetic change of arboviruses. Studying these constraints in mosquito-borne viruses has led to a new understanding of epizootics. The trade-off hypothesis is assumed to be applicable to tick-borne viruses too, although studies are lacking. Tick-borne Crimean-Congo hemorrhagic fever virus (CCHFV), a member of the family Bunyaviridae, is a major cause of severe human disease worldwide and shows an extraordinary amount of genetic diversity compared to other arboviruses, which has been linked to increased virulence and emergence in new environments. Using a transmission model for CCHFV, utilizing the main vector tick species and mice plus next generation sequencing, we detected a substantial number of consensus-level mutations in CCHFV recovered from ticks after only a single transstadial transmission, whereas none were detected in CCHFV obtained from the mammalian host. Furthermore, greater viral intra-host diversity was detected in the tick compared to the vertebrate host. Long-term association of CCHFV with its tick host for 1 year demonstrated mutations in the viral genome become fixed over time. These findings suggest that the trade-off hypothesis may not be accurate for all arboviruses.

Biosafety challenges for use of lentiviral vectors in gene therapy.

PubMed

Rothe, Michael; Modlich, Ute; Schambach, Axel

2013-12-01

Lentiviral vectors are promising tools for the genetic modification of cells in biomedical research and gene therapy. Their use in recent clinical trials for the treatment of adrenoleukodystrophy, β-thalassemia, Wiskott-Aldrich- Syndrome and metachromatic leukodystrophy underlined their efficacy for therapies especially in case of hereditary diseases. In comparison to gammaretroviral LTR-driven vectors, which were employed in the first clinical trials, lentiviral vectors present with some favorable features like the ability to transduce also non-dividing cells and a potentially safer insertion profile. However, genetic modification with viral vectors in general and stable integration of the therapeutic gene into the host cell genome bear concerns with respect to different levels of personal or environmental safety. Among them, insertional mutagenesis by enhancer mediated dysregulation of neighboring genes or aberrant splicing is still the biggest concern. However, also risks like immunogenicity of vector particles, the phenotoxicity of the transgene and potential vertical or horizontal transmission by replication competent retroviruses need to be taken into account. This review will give an overview on biosafety aspects that are relevant to the use of lentiviral vectors for genetic modification and gene therapy. Furthermore, assay systems aiming at evaluating biosafety in preclinical settings and recent promising clinical trials including efforts of monitoring of patients after gene therapy will be discussed.

Field trials to evaluate effects of continuously planted transgenic insect-resistant cottons on soil invertebrates.

PubMed

Li, Xiaogang; Liu, Biao; Wang, Xingxiang; Han, Zhengmin; Cui, Jinjie; Luo, Junyu

2012-03-01

Impacts on soil invertebrates are an important aspect of environmental risk assessment and post-release monitoring of transgenic insect-resistant plants. The purpose of this study was to research and survey the effects of transgenic insect-resistant cottons that had been planted over 10 years on the abundance and community structure of soil invertebrates under field conditions. During 3 consecutive years (2006-2008), eight common taxa (orders) of soil invertebrates belonging to the phylum Arthropoda were investigated in two different transgenic cotton fields and one non-transgenic cotton field (control). Each year, soil samples were taken at four different growth stages of cotton (seedling, budding, boll forming and boll opening). Animals were extracted from the samples using the improved Tullgren method, counted and determined to the order level. The diversity of the soil fauna communities in the different fields was compared using the Simpson's, Shannon's diversity indices and evenness index. The results showed a significant sampling time variation in the abundance of soil invertebrates monitored in the different fields. However, no difference in soil invertebrate abundance was found between the transgenic cotton fields and the control field. Both sampling time and cotton treatment had a significant effect on the Simpson's, Shannon's diversity indices and evenness index. They were higher in the transgenic fields than the control field at the growth stages of cotton. Long-term cultivation of transgenic insect-resistant cottons had no significant effect on the abundance of soil invertebrates. Collembola, Acarina and Araneae could act as the indicators of soil invertebrate in this region to monitor the environmental impacts of transgenic plants in the future. This journal is © The Royal Society of Chemistry 2012

Predicting invertebrate assemblage composition from harvesting pressure and environmental characteristics on tropical reef flats

NASA Astrophysics Data System (ADS)

Jimenez, H.; Dumas, P.; Ponton, D.; Ferraris, J.

2012-03-01

Invertebrates represent an essential component of coral reef ecosystems; they are ecologically important and a major resource, but their assemblages remain largely unknown, particularly on Pacific islands. Understanding their distribution and building predictive models of community composition as a function of environmental variables therefore constitutes a key issue for resource management. The goal of this study was to define and classify the main environmental factors influencing tropical invertebrate distributions in New Caledonian reef flats and to test the resulting predictive model. Invertebrate assemblages were sampled by visual counting during 2 years and 2 seasons, then coupled to different environmental conditions (habitat composition, hydrodynamics and sediment characteristics) and harvesting status (MPA vs. non-MPA and islets vs. coastal flats). Environmental conditions were described by a principal component analysis (PCA), and contributing variables were selected. Permutational analysis of variance (PERMANOVA) was used to test the effects of different factors (status, flat, year and season) on the invertebrate assemblage composition. Multivariate regression trees (MRT) were then used to hierarchically classify the effects of environmental and harvesting variables. MRT model explained at least 60% of the variation in structure of invertebrate communities. Results highlighted the influence of status (MPA vs. non-MPA) and location (islet vs. coastal flat), followed by habitat composition, organic matter content, hydrodynamics and sampling year. Predicted assemblages defined by indicator families were very different for each environment-exploitation scenario and correctly matched a calibration data matrix. Predictions from MRT including both environmental variables and harvesting pressure can be useful for management of invertebrates in coral reef environments.

Quantifying invertebrate resistance to floods: a global-scale meta-analysis.

PubMed

McMullen, Laura E; Lytle, David A

2012-12-01

Floods are a key component of the ecology and management of riverine ecosystems around the globe, but it is not clear whether floods have predictable effects on organisms that can allow us to generalize across regions and continents. To address this, we conducted a global-scale meta-analysis to investigate effects of natural and managed floods on invertebrate resistance, the ability of invertebrates to survive flood events. We considered 994 studies for inclusion in the analysis, and after evaluation based on a priori criteria, narrowed our analysis to 41 studies spanning six of the seven continents. We used the natural-log-ratio of invertebrate abundance before and within 10 days after flood events because this measure of effect size can be directly converted to estimates of percent survival. We conducted categorical and continuous analyses that examined the contribution of environmental and study design variables to effect size heterogeneity, and examined differences in effect size among taxonomic groups. We found that invertebrate abundance was lowered by at least one-half after flood events. While natural vs. managed floods were similar in their effect, effect size differed among habitat and substrate types, with pools, sand, and boulders experiencing the strongest effect. Although sample sizes were not sufficient to examine all taxonomic groups, floods had a significant, negative effect on densities of Coleoptera, Eumalacostraca, Annelida, Ephemeroptera, Diptera, Plecoptera, and Trichoptera. Results from this study provide guidance for river flow regime prescriptions that will be applicable across continents and climate types, as well as baseline expectations for future empirical studies of freshwater disturbance.

Assessing the potential for AAV vector genotoxicity in a murine model

PubMed Central

Li, Hojun; Malani, Nirav; Hamilton, Shari R.; Schlachterman, Alexander; Bussadori, Giulio; Edmonson, Shyrie E.; Shah, Rachel; Arruda, Valder R.; Mingozzi, Federico; Fraser Wright, J.; Bushman, Frederic D.

2011-01-01

Gene transfer using adeno-associated virus (AAV) vectors has great potential for treating human disease. Recently, questions have arisen about the safety of AAV vectors, specifically, whether integration of vector DNA in transduced cell genomes promotes tumor formation. This study addresses these questions with high-dose liver-directed AAV-mediated gene transfer in the adult mouse as a model (80 AAV-injected mice and 52 controls). After 18 months of follow-up, AAV-injected mice did not show a significantly higher rate of hepatocellular carcinoma compared with controls. Tumors in mice treated with AAV vectors did not have significantly different amounts of vector DNA compared with adjacent normal tissue. A novel high-throughput method for identifying AAV vector integration sites was developed and used to clone 1029 integrants. Integration patterns in tumor tissue and adjacent normal tissue were similar to each other, showing preferences for active genes, cytosine-phosphate-guanosine islands, and guanosine/cysteine-rich regions. Gene expression data showed that genes near integration sites did not show significant changes in expression patterns compared with genes more distal to integration sites. No integration events were identified as causing increased oncogene expression. Thus, we did not find evidence that AAV vectors cause insertional activation of oncogenes and subsequent tumor formation. PMID:21106988

Intensity fading MALDI-TOF mass spectrometry and functional proteomics assignments to identify protease inhibitors in marine invertebrates.

PubMed

Covaleda, Giovanni; Trejo, Sebastian A; Salas-Sarduy, Emir; Del Rivero, Maday Alonso; Chavez, Maria Angeles; Aviles, Francesc X

2017-08-08

Proteases and their inhibitors have become molecules of increasing fundamental and applicative value. Here we report an integrated strategy to identify and analyze such inhibitors from Caribbean marine invertebrates extracts by a fast and sensitive functional proteomics-like approach. The strategy works in three steps: i) multiplexed enzymatic inhibition kinetic assays, ii) Intensity Fading MALDI-TOF MS to establish a link between inhibitory molecules and the related MALDI signal(s) detected in the extract(s), and iii) ISD-CID-T 3 MS fragmentation on the parent MALDI signals selected in the previous step, enabling the partial or total top-down sequencing of the molecules. The present study has allowed validation of the whole approach, identification of a substantial number of novel protein protease inhibitors, as well as full or partial sequencing of reference molecular species and of many unknown ones, respectively. Such inhibitors correspond to six protease subfamilies (metallocarboxypeptidases-A and -B, pepsin, papain, trypsin and subtilisin), are small (1-10KDa) disulfide-rich proteins, and have been found at diverse frequencies among the invertebrates (13 to 41%). The overall procedure could be tailored to other enzyme-inhibitor and protein interacting systems, analyzing samples at medium-throughput level and leading to the functional and structural characterization of proteinaceous ligands from complex biological extracts. Invertebrate animals, and marine ones among, display a remarkable diversity of species and contained biomolecules. Many of their proteins-peptides have high biological, biotechnological and biomedical potential interest but, because of the lack of sequenced genomes behind, their structural and functional characterization constitutes a great challenge. Here, looking at the small, disulfide-rich, proteinaceous inhibitors of proteases found in them, it is shown that such problem can be significatively facilitated by integrative multiplexed

Benthic invertebrates of fixed sites in the western Lake Michigan drainages, Wisconsin and Michigan, 1993-95

USGS Publications Warehouse

Lenz, Bernard N.; Rheaume, S.J.

2000-01-01

This report describes the variability in family-level benthic-invertebrate population data and the reliability of the data as a water-quality indicator for 11 fixed surface-water sites in the Western Lake Michigan Drainages study area of the National Water-Quality Assessment Program. Benthic-invertebrate-community measures were computed for the following: number of individuals, Hilsenhoff’s Family-Level Biotic Index, number and percent EPT (Ephemeroptera, Plecoptera, and Tricoptera), Margalef’s Diversity Index, and mean tolerance value. Relations between these measures and environmental setting, habitat, and of chemical water quality are examined. Benthic-invertebrate communities varied greatly among fixed sites and within individual streams among multiple-reach and multiple-year sampling. The variations between multiple reaches and years were sometimes larger than those found between different fixed sites. Factors affecting benthic invertebrates included both habitat and chemical quality. Generally, fixed-site streams with the highest diversity, greatest number of benthic invertebrates, and those at which community measures indicated the best water quality also had the best habitat and chemical quality. Variations among reaches are most likely related to differences in habitat. Variations among years are most likely related to climatic changes, which create variations in flow and/or chemical quality. The variability in the data analyzed in this study shows how benthic invertebrates are affected by differences in both habitat and water quality, making them useful indicators of stream health; however, a single benthic-invertebrate sample alone cannot be relied upon to accurately describe water quality of the streams in this study. Benthic-invertebrate data contributed valuable information on the biological health of the 11 fixed sites when used as one of several data sources for assessing water quality.

Genetics and evolution of triatomines: from phylogeny to vector control

PubMed Central

Gourbière, S; Dorn, P; Tripet, F; Dumonteil, E

2012-01-01

Triatomines are hemipteran bugs acting as vectors of the protozoan parasite Trypanosoma cruzi. This parasite causes Chagas disease, one of the major parasitic diseases in the Americas. Studies of triatomine genetics and evolution have been particularly useful in the design of rational vector control strategies, and are reviewed here. The phylogeography of several triatomine species is now slowly emerging, and the struggle to reconcile the phenotypic, phylogenetic, ecological and epidemiological species concepts makes for a very dynamic field. Population genetic studies using different markers indicate a wide range of population structures, depending on the triatomine species, ranging from highly fragmented to mobile, interbreeding populations. Triatomines transmit T. cruzi in the context of complex interactions between the insect vectors, their bacterial symbionts and the parasites; however, an integrated view of the significance of these interactions in triatomine biology, evolution and in disease transmission is still lacking. The development of novel genetic markers, together with the ongoing sequencing of the Rhodnius prolixus genome and more integrative studies, will provide key tools to expanding our understanding of these important insect vectors and allow the design of improved vector control strategies. PMID:21897436

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.

50 CFR 17.85 - Special rules-invertebrates.

Code of Federal Regulations, 2013 CFR

2013-10-01

... regulations or in violation of the applicable State fish and wildlife laws or regulations or the Act. (iv) You... WILDLIFE AND PLANTS (CONTINUED) ENDANGERED AND THREATENED WILDLIFE AND PLANTS Experimental Populations § 17.85 Special rules—invertebrates. (a) Seventeen mollusks in the Tennessee River. The species in the...

50 CFR 17.85 - Special rules-invertebrates.

Code of Federal Regulations, 2012 CFR

2012-10-01

... regulations or in violation of the applicable State fish and wildlife laws or regulations or the Act. (iv) You... WILDLIFE AND PLANTS (CONTINUED) ENDANGERED AND THREATENED WILDLIFE AND PLANTS Experimental Populations § 17.85 Special rules—invertebrates. (a) Seventeen mollusks in the Tennessee River. The species in the...

50 CFR 17.85 - Special rules-invertebrates.

Code of Federal Regulations, 2014 CFR