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Sample records for lentiviral integration sites

  1. Integration-deficient Lentiviral Vectors: A Slow Coming of Age

    PubMed Central

    Wanisch, Klaus; Yáñez-Muñoz, Rafael J

    2009-01-01

    Lentiviral vectors are very efficient at transducing dividing and quiescent cells, which makes them highly useful tools for genetic analysis and gene therapy. Traditionally this efficiency was considered dependent on provirus integration in the host cell genome; however, recent results have challenged this view. So called integration-deficient lentiviral vectors (IDLVs) can be produced through the use of integrase mutations that specifically prevent proviral integration, resulting in the generation of increased levels of circular vector episomes in transduced cells. These lentiviral episomes lack replication signals and are gradually lost by dilution in dividing cells, but are stable in quiescent cells. Compared to integrating lentivectors, IDLVs have a greatly reduced risk of causing insertional mutagenesis and a lower risk of generating replication-competent recombinants (RCRs). IDLVs can mediate transient gene expression in proliferating cells, stable expression in nondividing cells in vitro and in vivo, specific immune responses, RNA interference, homologous recombination (gene repair, knock-in, and knock-out), site-specific recombination, and transposition. IDLVs can be converted into replicating episomes, suggesting that if a clinically applicable system can be developed they would also become highly appropriate for stable transduction of proliferating tissues in therapeutic applications. PMID:19491821

  2. Altering Entry Site Preference of Lentiviral Vectors into Neuronal Cells by Pseudotyping with Envelope Glycoproteins.

    PubMed

    Kobayashi, Kenta; Kato, Shigeki; Inoue, Ken-Ichi; Takada, Masahiko; Kobayashi, Kazuto

    2016-01-01

    A lentiviral vector system provides a powerful strategy for gene therapy trials against a variety of neurological and neurodegenerative disorders. Pseudotyping of lentiviral vectors with different envelope glycoproteins not only confers the neurotropism to the vectors, but also alters the preference of sites of vector entry into neuronal cells. One major group of lentiviral vectors is a pseudotype with vesicular stomatitis virus glycoprotein (VSV-G) that enters preferentially cell body areas (somata/dendrites) of neurons and transduces them. Another group contains lentiviral vectors pseudotyped with fusion envelope glycoproteins composed of different sets of rabies virus glycoprotein and VSV-G segments that enter predominantly axon terminals of neurons and are transported through axons retrogradely to their cell bodies, resulting in enhanced retrograde gene transfer. This retrograde gene transfer takes a considerable advantage of delivering the transgene into neuronal cell bodies situated in regions distant from the injection site of the vectors. The rational use of these two vector groups characterized by different entry mechanisms will further extend the strategy for gene therapy of neurological and neurodegenerative disorders.

  3. Towards a Safer, More Randomized Lentiviral Vector Integration Profile Exploring Artificial LEDGF Chimeras

    PubMed Central

    Vranckx, Lenard S.; Demeulemeester, Jonas; Debyser, Zeger

    2016-01-01

    The capacity to integrate transgenes into the host cell genome makes retroviral vectors an interesting tool for gene therapy. Although stable insertion resulted in successful correction of several monogenic disorders, it also accounts for insertional mutagenesis, a major setback in otherwise successful clinical gene therapy trials due to leukemia development in a subset of treated patients. Despite improvements in vector design, their use is still not risk-free. Lentiviral vector (LV) integration is directed into active transcription units by LEDGF/p75, a host-cell protein co-opted by the viral integrase. We engineered LEDGF/p75-based hybrid tethers in an effort to elicit a more random integration pattern to increase biosafety, and potentially reduce proto-oncogene activation. We therefore truncated LEDGF/p75 by deleting the N-terminal chromatin-reading PWWP-domain, and replaced this domain with alternative pan-chromatin binding peptides. Expression of these LEDGF-hybrids in LEDGF-depleted cells efficiently rescued LV transduction and resulted in LV integrations that distributed more randomly throughout the host-cell genome. In addition, when considering safe harbor criteria, LV integration sites for these LEDGF-hybrids distributed more safely compared to LEDGF/p75-mediated integration in wild-type cells. This approach should be broadly applicable to introduce therapeutic or suicide genes for cell therapy, such as patient-specific iPS cells. PMID:27788138

  4. Development of Lentiviral Vectors for Targeted Integration and Protein Delivery.

    PubMed

    Schenkwein, Diana; Ylä-Herttuala, Seppo

    2016-01-01

    The method in this chapter describes the design of human immunodeficiency virus type 1 (HIV-1) integrase (IN)-fusion proteins which we have developed to transport different proteins into the nuclei of lentiviral vector (LV)-transduced cells. The IN-fusion protein cDNA is incorporated into the LV packaging plasmid, which leads to its incorporation into vector particles as part of a large Gag-Pol polyprotein. This specific feature of protein packaging enables also the incorporation of cytotoxic and proapoptotic proteins, such as frequently cutting endonucleases and P53. The vectors can hence be used for various protein transduction needs. An outline of the necessary methods is also given to study the functionality of a chosen IN-fusion protein in a cell culture assay. PMID:27317182

  5. Whole transcriptome characterization of aberrant splicing events induced by lentiviral vector integrations

    PubMed Central

    Cesana, Daniela; Sgualdino, Jacopo; Rudilosso, Laura; Merella, Stefania; Naldini, Luigi; Montini, Eugenio

    2012-01-01

    Gamma-retroviral/lentiviral vectors (γRV/LV) with self-inactivating (SIN) long terminal repeats (LTRs) and internal moderate cellular promoters pose a reduced risk of insertional mutagenesis when compared with vectors with active LTRs. Yet, in a recent LV-based clinical trial for β-thalassemia, vector integration within the HMGA2 gene induced the formation of an aberrantly spliced mRNA form that appeared to cause clonal dominance. Using a method that we developed, cDNA linear amplification-mediated PCR, in combination with high-throughput sequencing, we conducted a whole transcriptome analysis of chimeric LV-cellular fusion transcripts in transduced human lymphoblastoid cells and primary hematopoietic stem/progenitor cells. We observed a surprising abundance of read-through transcription originating outside and inside the provirus and identified the vector sequences contributing to the aberrant splicing process. We found that SIN LV has a sharply reduced propensity to engage in aberrant splicing compared with that of vectors carrying active LTRs. Moreover, by recoding the identified vector splice sites, we reduced residual read-through transcription and demonstrated an effective strategy for improving vectors. Characterization of the mechanisms and genetic features underlying vector-induced aberrant splicing will enable the generation of safer vectors, with low impact on the cellular transcriptome. PMID:22523064

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2005-01-01

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

  8. Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells.

    PubMed

    Holkers, Maarten; Maggio, Ignazio; Liu, Jin; Janssen, Josephine M; Miselli, Francesca; Mussolino, Claudio; Recchia, Alessandra; Cathomen, Toni; Gonçalves, Manuel A F V

    2013-03-01

    The array of genome editing strategies based on targeted double-stranded DNA break formation have recently been enriched through the introduction of transcription activator-like type III effector (TALE) nucleases (TALENs). To advance the testing of TALE-based approaches, it will be crucial to deliver these custom-designed proteins not only into transformed cell types but also into more relevant, chromosomally stable, primary cells. Viral vectors are among the most effective gene transfer vehicles. Here, we investigated the capacity of human immunodeficiency virus type 1- and adenovirus-based vectors to package and deliver functional TALEN genes into various human cell types. To this end, we attempted to assemble particles of these two vector classes, each encoding a monomer of a TALEN pair targeted to a bipartite sequence within the AAVS1 'safe harbor' locus. Vector DNA analyses revealed that adenoviral vectors transferred intact TALEN genes, whereas lentiviral vectors failed to do so, as shown by their heterogeneously sized proviruses in target cells. Importantly, adenoviral vector-mediated TALEN gene delivery resulted in site-specific double-stranded DNA break formation at the intended AAVS1 target site at similarly high levels in both transformed and non-transformed cells. In conclusion, we demonstrate that adenoviral, but not lentiviral, vectors constitute a valuable TALEN gene delivery platform.

  9. Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells

    PubMed Central

    Holkers, Maarten; Maggio, Ignazio; Liu, Jin; Janssen, Josephine M.; Miselli, Francesca; Mussolino, Claudio; Recchia, Alessandra; Cathomen, Toni; Gonçalves, Manuel A. F. V.

    2013-01-01

    The array of genome editing strategies based on targeted double-stranded DNA break formation have recently been enriched through the introduction of transcription activator-like type III effector (TALE) nucleases (TALENs). To advance the testing of TALE-based approaches, it will be crucial to deliver these custom-designed proteins not only into transformed cell types but also into more relevant, chromosomally stable, primary cells. Viral vectors are among the most effective gene transfer vehicles. Here, we investigated the capacity of human immunodeficiency virus type 1- and adenovirus-based vectors to package and deliver functional TALEN genes into various human cell types. To this end, we attempted to assemble particles of these two vector classes, each encoding a monomer of a TALEN pair targeted to a bipartite sequence within the AAVS1 ‘safe harbor’ locus. Vector DNA analyses revealed that adenoviral vectors transferred intact TALEN genes, whereas lentiviral vectors failed to do so, as shown by their heterogeneously sized proviruses in target cells. Importantly, adenoviral vector-mediated TALEN gene delivery resulted in site-specific double-stranded DNA break formation at the intended AAVS1 target site at similarly high levels in both transformed and non-transformed cells. In conclusion, we demonstrate that adenoviral, but not lentiviral, vectors constitute a valuable TALEN gene delivery platform. PMID:23275534

  10. Virological and preclinical characterization of a dendritic cell targeting, integration-deficient lentiviral vector for cancer immunotherapy.

    PubMed

    Odegard, Jared M; Kelley-Clarke, Brenna; Tareen, Semih U; Campbell, David J; Flynn, Patrick A; Nicolai, Christopher J; Slough, Megan M; Vin, Chintan D; McGowan, Patrick J; Nelson, Lisa T; Ter Meulen, Jan; Dubensky, Thomas W; Robbins, Scott H

    2015-01-01

    Dendritic cells (DCs) are essential antigen-presenting cells for the initiation of cytotoxic T-cell responses and therefore attractive targets for cancer immunotherapy. We have developed an integration-deficient lentiviral vector termed ID-VP02 that is designed to deliver antigen-encoding nucleic acids selectively to human DCs in vivo. ID-VP02 utilizes a genetically and glycobiologically engineered Sindbis virus glycoprotein to target human DCs through the C-type lectin DC-SIGN (CD209) and also binds to the homologue murine receptor SIGNR1. Specificity of ID-VP02 for antigen-presenting cells in the mouse was confirmed through biodistribution studies showing that following subcutaneous administration, transgene expression was only detectable at the injection site and the draining lymph node. A single immunization with ID-VP02 induced a high level of antigen-specific, polyfunctional effector and memory CD8 T-cell responses that fully protected against vaccinia virus challenge. Upon homologous readministration, ID-VP02 induced a level of high-quality secondary effector and memory cells characterized by stable polyfunctionality and expression of IL-7Rα. Importantly, a single injection of ID-VP02 also induced robust cytotoxic responses against an endogenous rejection antigen of CT26 colon carcinoma cells and conferred both prophylactic and therapeutic antitumor efficacy. ID-VP02 is the first lentiviral vector which combines integration deficiency with DC targeting and is currently being investigated in a phase I trial in cancer patients. PMID:25658613

  11. Transgenic expression of human glial cell line-derived neurotrophic factor from integration-deficient lentiviral vectors is neuroprotective in a rodent model of Parkinson's disease.

    PubMed

    Lu-Nguyen, Ngoc B; Broadstock, Martin; Schliesser, Maximilian G; Bartholomae, Cynthia C; von Kalle, Christof; Schmidt, Manfred; Yáñez-Muñoz, Rafael J

    2014-07-01

    Standard integration-proficient lentiviral vectors (IPLVs) are effective at much lower doses than other vector systems and have shown promise for gene therapy of Parkinson's disease (PD). Their main drawback is the risk of insertional mutagenesis. The novel biosafety-enhanced integration-deficient lentiviral vectors (IDLVs) may offer a significant enhancement in biosafety, but have not been previously tested in a model of a major disease. We have assessed biosafety and transduction efficiency of IDLVs in a rat model of PD, using IPLVs as a reference. Genomic insertion of lentivectors injected into the lesioned striatum was studied by linear amplification-mediated polymerase chain reaction (PCR), followed by deep sequencing and insertion site analysis, demonstrating lack of significant IDLV integration. Reporter gene expression studies showed efficient, long-lived, and transcriptionally targeted expression from IDLVs injected ahead of lesioning in the rat striatum, although at somewhat lower expression levels than from IPLVs. Transgenic human glial cell line-derived neurotrophic factor (hGDNF) expression from IDLVs was used for a long-term investigation of lentivector-mediated, transcriptionally targeted neuroprotection in this PD rat model. Vectors were injected before striatal lesioning, and the results showed improvements in nigral dopaminergic neuron survival and behavioral tests regardless of lentiviral integration proficiency, although they confirmed lower expression levels of hGDNF from IDLVs. These data demonstrate the effectiveness of IDLVs in a model of a major disease and indicate that these vectors could provide long-term PD treatment at low dose, combining efficacy and biosafety for targeted central nervous system applications.

  12. Lentiviral vectors.

    PubMed

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

    2011-01-01

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

  13. Genomic insertion of lentiviral DNA circles directed by the yeast Flp recombinase

    PubMed Central

    Moldt, Brian; Staunstrup, Nicklas H; Jakobsen, Maria; Yáñez-Muñoz, Rafael J; Mikkelsen, Jacob G

    2008-01-01

    Background Circular forms of viral genomic DNA are generated during infection of cells with retroviruses like HIV-1. Such circles are unable to replicate and are eventually lost as a result of cell division, lending support to the prevalent notion that episomal retroviral DNA forms are dead-end products of reverse transcription. Results We demonstrate that circular DNA generated during transduction with HIV-1-based lentiviral vectors can be utilized as substrate for gene insertion directed by nonviral recombinases co-expressed in the target cells. By packaging of lentiviral genomic RNA in integrase-defective lentiviral vectors, harboring an inactive form of the viral integrase, the normal pathway for viral integration is blocked and circular vector DNA accumulates in transduced cells as a result. We find that the amount of DNA circles is increased 4-fold in cells transduced with integration-defective vectors relative to cells treated with integrase-proficient vectors. By transduction of target cells harboring engineered recognition sites for the yeast Flp recombinase with integration-defective lentiviral vectors containing an ATG-deficient hygromycin B selection gene we demonstrate precise integration of lentiviral vector-derived DNA circles in a drug-selective approach. Moreover, it is demonstrated that trans-acting Flp recombinase can be delivered by Flp-encoding transfected plasmid DNA or, alternatively, by co-transduced integrase-defective lentiviral vectors carrying a Flp expression cassette. Conclusion Our data provide proof-of-principle that nonviral recombinases, like Flp, produced by plasmid DNA or non-integrating lentiviral vectors can gain access to circular viral recombination substrates and facilitate site-directed genomic insertion of such episomal DNA forms. Replacement of the normal viral integration machinery with nonviral mediators of integration represents a new platform for creation of lentiviral vectors with an altered integration profile. PMID

  14. Retroviral integration: Site matters

    PubMed Central

    Demeulemeester, Jonas; De Rijck, Jan

    2015-01-01

    Here, we review genomic target site selection during retroviral integration as a multistep process in which specific biases are introduced at each level. The first asymmetries are introduced when the virus takes a specific route into the nucleus. Next, by co‐opting distinct host cofactors, the integration machinery is guided to particular chromatin contexts. As the viral integrase captures a local target nucleosome, specific contacts introduce fine‐grained biases in the integration site distribution. In vivo, the established population of proviruses is subject to both positive and negative selection, thereby continuously reshaping the integration site distribution. By affecting stochastic proviral expression as well as the mutagenic potential of the virus, integration site choice may be an inherent part of the evolutionary strategies used by different retroviruses to maximise reproductive success. PMID:26293289

  15. Generation of a stable packaging cell line producing high-titer PPT-deleted integration-deficient lentiviral vectors

    PubMed Central

    Hu, Peirong; Li, Yedda; Sands, Mark S; McCown, Thomas; Kafri, Tal

    2015-01-01

    The risk of insertional mutagenesis inherent to all integrating exogenous expression cassettes was the impetus for the development of various integration-defective lentiviral vector (IDLV) systems. These systems were successfully employed in a plethora of preclinical applications, underscoring their clinical potential. However, current production of IDLVs by transient plasmid transfection is not optimal for large-scale production of clinical grade vectors. Here, we describe the development of the first tetracycline-inducible stable IDLV packaging cell line comprising the D64E integrase mutant and the VSV-G envelope protein. A conditional self-inactivating (cSIN) vector and a novel polypurine tract (PPT)-deleted vector were incorporated into the newly developed stable packaging cell line by transduction and stable transfection, respectively. High-titer (~107 infectious units (IU)/ml) cSIN vectors were routinely generated. Furthermore, screening of single-cell clones stably transfected with PPT-deleted vector DNA resulted in the identification of highly efficient producer cell lines generating IDLV titers higher than 108 IU/mL, which upon concentration increased to 1010 IU/ml. IDLVs generated by stable producer lines efficiently transduce CNS tissues of rodents. Overall, the availability of high-titer IDLV lentivirus packaging cell line described here will significantly facilitate IDLV-based basic science research, as well as preclinical and clinical applications. PMID:26229972

  16. A comparison of foamy and lentiviral vector genotoxicity in SCID-repopulating cells shows foamy vectors are less prone to clonal dominance

    PubMed Central

    Everson, Elizabeth M; Olzsko, Miles E; Leap, David J; Hocum, Jonah D; Trobridge, Grant D

    2016-01-01

    Hematopoietic stem cell (HSC) gene therapy using retroviral vectors has immense potential, but vector-mediated genotoxicity limits use in the clinic. Lentiviral vectors are less genotoxic than gammaretroviral vectors and have become the vector of choice in clinical trials. Foamy retroviral vectors have a promising integration profile and are less prone to read-through transcription than gammaretroviral or lentiviral vectors. Here, we directly compared the safety and efficacy of foamy vectors to lentiviral vectors in human CD34+ repopulating cells in immunodeficient mice. To increase their genotoxic potential, foamy and lentiviral vectors with identical transgene cassettes with a known genotoxic spleen focus forming virus promoter were used. Both vectors resulted in efficient marking in vivo and a total of 825 foamy and 460 lentiviral vector unique integration sites were recovered in repopulating cells 19 weeks after transplantation. Foamy vector proviruses were observed less often near RefSeq gene and proto-oncogene transcription start sites than lentiviral vectors. The foamy vector group were also more polyclonal with fewer dominant clones (two out of six mice) than the lentiviral vector group (eight out of eight mice), and only lentiviral vectors had integrants near known proto-oncogenes in dominant clones. Our data further support the relative safety of foamy vectors for HSC gene therapy. PMID:27579335

  17. A comparison of foamy and lentiviral vector genotoxicity in SCID-repopulating cells shows foamy vectors are less prone to clonal dominance.

    PubMed

    Everson, Elizabeth M; Olzsko, Miles E; Leap, David J; Hocum, Jonah D; Trobridge, Grant D

    2016-01-01

    Hematopoietic stem cell (HSC) gene therapy using retroviral vectors has immense potential, but vector-mediated genotoxicity limits use in the clinic. Lentiviral vectors are less genotoxic than gammaretroviral vectors and have become the vector of choice in clinical trials. Foamy retroviral vectors have a promising integration profile and are less prone to read-through transcription than gammaretroviral or lentiviral vectors. Here, we directly compared the safety and efficacy of foamy vectors to lentiviral vectors in human CD34(+) repopulating cells in immunodeficient mice. To increase their genotoxic potential, foamy and lentiviral vectors with identical transgene cassettes with a known genotoxic spleen focus forming virus promoter were used. Both vectors resulted in efficient marking in vivo and a total of 825 foamy and 460 lentiviral vector unique integration sites were recovered in repopulating cells 19 weeks after transplantation. Foamy vector proviruses were observed less often near RefSeq gene and proto-oncogene transcription start sites than lentiviral vectors. The foamy vector group were also more polyclonal with fewer dominant clones (two out of six mice) than the lentiviral vector group (eight out of eight mice), and only lentiviral vectors had integrants near known proto-oncogenes in dominant clones. Our data further support the relative safety of foamy vectors for HSC gene therapy. PMID:27579335

  18. LV305, a dendritic cell-targeting integration-deficient ZVexTM-based lentiviral vector encoding NY-ESO-1, induces potent anti-tumor immune response

    PubMed Central

    Albershardt, Tina Chang; Campbell, David James; Parsons, Andrea Jean; Slough, Megan Merrill; ter Meulen, Jan; Berglund, Peter

    2016-01-01

    We have engineered an integration-deficient lentiviral vector, LV305, to deliver the tumor antigen NY-ESO-1 to human dendritic cells in vivo through pseudotyping with a modified Sindbis virus envelop protein. Mice immunized once with LV305 developed strong, dose-dependent, multifunctional, and cytotoxic NY-ESO-1-specific cluster of differentiation 8 (CD8) T cells within 14 days post-immunization and could be boosted with LV305 at least twice to recall peak-level CD8 T-cell responses. Immunization with LV305 protected mice against tumor growth in an NY-ESO-1-expressing CT26 lung metastasis model, with the protective effect abrogated upon depletion of CD8 T cells. Adoptive transfer of CD8 T cells, alone or together with CD4 T cells or natural killer cells, from LV305-immunized donor mice to tumor-bearing recipient mice conferred significant protection against metastatic tumor growth. Biodistribution of injected LV305 in mice was limited to the site of injection and the draining lymph node, and injected LV305 exhibited minimal excretion. Mice injected with LV305 developed little to no adverse effects, as evaluated by toxicology studies adherent to good laboratory practices. Taken together, these data support the development of LV305 as a clinical candidate for treatment against tumors expressing NY-ESO-1. PMID:27626061

  19. LV305, a dendritic cell-targeting integration-deficient ZVex(TM)-based lentiviral vector encoding NY-ESO-1, induces potent anti-tumor immune response.

    PubMed

    Albershardt, Tina Chang; Campbell, David James; Parsons, Andrea Jean; Slough, Megan Merrill; Ter Meulen, Jan; Berglund, Peter

    2016-01-01

    We have engineered an integration-deficient lentiviral vector, LV305, to deliver the tumor antigen NY-ESO-1 to human dendritic cells in vivo through pseudotyping with a modified Sindbis virus envelop protein. Mice immunized once with LV305 developed strong, dose-dependent, multifunctional, and cytotoxic NY-ESO-1-specific cluster of differentiation 8 (CD8) T cells within 14 days post-immunization and could be boosted with LV305 at least twice to recall peak-level CD8 T-cell responses. Immunization with LV305 protected mice against tumor growth in an NY-ESO-1-expressing CT26 lung metastasis model, with the protective effect abrogated upon depletion of CD8 T cells. Adoptive transfer of CD8 T cells, alone or together with CD4 T cells or natural killer cells, from LV305-immunized donor mice to tumor-bearing recipient mice conferred significant protection against metastatic tumor growth. Biodistribution of injected LV305 in mice was limited to the site of injection and the draining lymph node, and injected LV305 exhibited minimal excretion. Mice injected with LV305 developed little to no adverse effects, as evaluated by toxicology studies adherent to good laboratory practices. Taken together, these data support the development of LV305 as a clinical candidate for treatment against tumors expressing NY-ESO-1. PMID:27626061

  20. LV305, a dendritic cell-targeting integration-deficient ZVex(TM)-based lentiviral vector encoding NY-ESO-1, induces potent anti-tumor immune response.

    PubMed

    Albershardt, Tina Chang; Campbell, David James; Parsons, Andrea Jean; Slough, Megan Merrill; Ter Meulen, Jan; Berglund, Peter

    2016-01-01

    We have engineered an integration-deficient lentiviral vector, LV305, to deliver the tumor antigen NY-ESO-1 to human dendritic cells in vivo through pseudotyping with a modified Sindbis virus envelop protein. Mice immunized once with LV305 developed strong, dose-dependent, multifunctional, and cytotoxic NY-ESO-1-specific cluster of differentiation 8 (CD8) T cells within 14 days post-immunization and could be boosted with LV305 at least twice to recall peak-level CD8 T-cell responses. Immunization with LV305 protected mice against tumor growth in an NY-ESO-1-expressing CT26 lung metastasis model, with the protective effect abrogated upon depletion of CD8 T cells. Adoptive transfer of CD8 T cells, alone or together with CD4 T cells or natural killer cells, from LV305-immunized donor mice to tumor-bearing recipient mice conferred significant protection against metastatic tumor growth. Biodistribution of injected LV305 in mice was limited to the site of injection and the draining lymph node, and injected LV305 exhibited minimal excretion. Mice injected with LV305 developed little to no adverse effects, as evaluated by toxicology studies adherent to good laboratory practices. Taken together, these data support the development of LV305 as a clinical candidate for treatment against tumors expressing NY-ESO-1.

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

    PubMed

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

    2014-01-01

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

  2. Efficient transduction of pigtailed macaque hematopoietic repopulating cells with HIV-based lentiviral vectors

    PubMed Central

    Trobridge, Grant D.; Beard, Brian C.; Gooch, Christina; Wohlfahrt, Martin; Olsen, Philip; Fletcher, James; Malik, Punam

    2008-01-01

    Lentiviral vectors are attractive for hematopoietic stem cell (HSC) gene therapy because they do not require mitosis for nuclear entry, they efficiently transduce hematopoietic repopulating cells, and self-inactivating (SIN) designs can be produced at high titer. Experiments to evaluate HIV-derived lentiviral vectors in nonhuman primates prior to clinical trials have been hampered by low transduction frequencies due in part to host restriction by TRIM5α. We have established conditions for efficient transduction of pigtailed macaque (Macaca nemestrina) long-term repopulating cells using VSV-G–pseudotyped HIV-based lentiviral vectors. Stable, long-term, high-level gene marking was observed in 3 macaques using relatively low MOIs (5-10) in a 48-hour ex vivo transduction protocol. All animals studied had rapid neutrophil engraftment with a median of 10.3 days to a count greater than 0.5 × 109/L (500/μL). Expression was detected in all lineages, with long-term marking levels in granulocytes at approximately 20% to 30%, and in lymphocytes at approximately 12% to 23%. All animals had polyclonal engraftment as determined by analysis of vector integration sites. These data suggest that lentiviral vectors should be highly effective for HSC gene therapy, particularly for diseases in which maintaining the engraftment potential of stem cells using short-term ex vivo transduction protocols is critical. PMID:18388180

  3. Insertional transformation of hematopoietic cells by self-inactivating lentiviral and gammaretroviral vectors.

    PubMed

    Modlich, Ute; Navarro, Susana; Zychlinski, Daniela; Maetzig, Tobias; Knoess, Sabine; Brugman, Martijn H; Schambach, Axel; Charrier, Sabine; Galy, Anne; Thrasher, Adrian J; Bueren, Juan; Baum, Christopher

    2009-11-01

    Gene transfer vectors may cause clonal imbalance and even malignant cell transformation by insertional upregulation of proto-oncogenes. Lentiviral vectors (LV) with their preferred integration in transcribed genes are considered less genotoxic than gammaretroviral vectors (GV) with their preference for integration next to transcriptional start sites and regulatory gene regions. Using a sensitive cell culture assay and a series of self-inactivating (SIN) vectors, we found that the lentiviral insertion pattern was approximately threefold less likely than the gammaretroviral to trigger transformation of primary hematopoietic cells. However, lentivirally induced mutants also showed robust replating, in line with the selection for common insertion sites (CIS) in the first intron of the Evi1 proto-oncogene. This potent proto-oncogene thus represents a CIS for both GV and LV, despite major differences in their integration mechanisms. Altering the vectors' enhancer-promoter elements had a greater effect on safety than the retroviral insertion pattern. Clinical grade LV expressing the Wiskott-Aldrich syndrome (WAS) protein under control of its own promoter had no transforming potential. Mechanistic studies support the conclusion that enhancer-mediated gene activation is the major cause for insertional transformation of hematopoietic cells, opening rational strategies for risk prevention.

  4. Comparison of Lentiviral and Sleeping Beauty Mediated αβ T Cell Receptor Gene Transfer

    PubMed Central

    Field, Anne-Christine; Vink, Conrad; Gabriel, Richard; Al-Subki, Roua; Schmidt, Manfred; Goulden, Nicholas; Stauss, Hans; Thrasher, Adrian; Morris, Emma; Qasim, Waseem

    2013-01-01

    Transfer of tumour antigen-specific receptors to T cells requires efficient delivery and integration of transgenes, and currently most clinical studies are using gamma retroviral or lentiviral systems. Whilst important proof-of-principle data has been generated for both chimeric antigen receptors and αβ T cell receptors, the current platforms are costly, time-consuming and relatively inflexible. Alternative, more cost-effective, Sleeping Beauty transposon-based plasmid systems could offer a pathway to accelerated clinical testing of a more diverse repertoire of recombinant high affinity T cell receptors. Nucleofection of hyperactive SB100X transposase-mediated stable transposition of an optimised murine-human chimeric T cell receptor specific for Wilm’s tumour antigen from a Sleeping Beauty transposon plasmid. Whilst transfer efficiency was lower than that mediated by lentiviral transduction, cells could be readily enriched and expanded, and mediated effective target cells lysis in vitro and in vivo. Integration sites of transposed TCR genes in primary T cells were almost randomly distributed, contrasting the predilection of lentiviral vectors for transcriptionally active sites. The results support exploitation of the Sleeping Beauty plasmid based system as a flexible and adaptable platform for accelerated, early-phase assessment of T cell receptor gene therapies. PMID:23840834

  5. [Transfection of HL-60 cells by Venus lentiviral vector].

    PubMed

    Li, Zheng; Hu, Shao-Yan; Cen, Jian-Nong; Chen, Zi-Xing

    2013-06-01

    In order to study the potential of Venus, lentiviral vector, applied to acute myeloid leukemia, the recombinant vector Venus-C3aR was transfected into 293T packing cells by DNA-calcium phosphate coprecipitation. All virus stocks were collected and transfected into HL-60, the GFP expression in HL-60 cells was measured by flow cytometry. The expression level of C3aR1 in transfected HL-60 cells was identified by RT-PCR and flow cytometry. The lentiviral toxicity on HL-60 was measured by using CCK-8 method and the ability of cell differentiation was observed. The results indicated that the transfection efficacy of lentiviral vector on HL-60 cells was more than 95%, which meets the needs for further study. C3aR1 expression on HL-60 cells increased after being transfected with recombinant lentiviral vector. Before and after transfection, the proliferation and differentiation of cells were not changed much. It is concluded that the lentiviral vector showed a high efficacy to transfect AML cells and can be integrated in genome of HL-60 cells to realize the stable expression of interest gene. Meanwhile, lentiviral vector can not affect HL-60 cell ability to proliferate and differentiate.

  6. Measurement of lentiviral vector titre and copy number by cross-species duplex quantitative PCR.

    PubMed

    Christodoulou, I; Patsali, P; Stephanou, C; Antoniou, M; Kleanthous, M; Lederer, C W

    2016-01-01

    Lentiviruses are the vectors of choice for many preclinical studies and clinical applications of gene therapy. Accurate measurement of biological vector titre before treatment is a prerequisite for vector dosing, and the calculation of vector integration sites per cell after treatment is as critical to the characterisation of modified cell products as it is to long-term follow-up and the assessment of risk and therapeutic efficiency in patients. These analyses are typically based on quantitative real-time PCR (qPCR), but as yet compromise accuracy and comparability between laboratories and experimental systems, the former by using separate simplex reactions for the detection of endogene and lentiviral sequences and the latter by designing different PCR assays for analyses in human cells and animal disease models. In this study, we validate in human and murine cells a qPCR system for the single-tube assessment of lentiviral vector copy numbers that is suitable for analyses in at least 33 different mammalian species, including human and other primates, mouse, pig, cat and domestic ruminants. The established assay combines the accuracy of single-tube quantitation by duplex qPCR with the convenience of one-off assay optimisation for cross-species analyses and with the direct comparability of lentiviral transduction efficiencies in different species. PMID:26202078

  7. Production of lentiviral vectors

    PubMed Central

    Merten, Otto-Wilhelm; Hebben, Matthias; Bovolenta, Chiara

    2016-01-01

    Lentiviral vectors (LV) have seen considerably increase in use as gene therapy vectors for the treatment of acquired and inherited diseases. This review presents the state of the art of the production of these vectors with particular emphasis on their large-scale production for clinical purposes. In contrast to oncoretroviral vectors, which are produced using stable producer cell lines, clinical-grade LV are in most of the cases produced by transient transfection of 293 or 293T cells grown in cell factories. However, more recent developments, also, tend to use hollow fiber reactor, suspension culture processes, and the implementation of stable producer cell lines. As is customary for the biotech industry, rather sophisticated downstream processing protocols have been established to remove any undesirable process-derived contaminant, such as plasmid or host cell DNA or host cell proteins. This review compares published large-scale production and purification processes of LV and presents their process performances. Furthermore, developments in the domain of stable cell lines and their way to the use of production vehicles of clinical material will be presented. PMID:27110581

  8. Hanford site integrated pest management plan

    SciTech Connect

    Giddings, R.F.

    1996-04-09

    The Hanford Site Integrated Pest Management Plan (HSIPMP) defines the Integrated Pest Management (IPM) decision process and subsequent strategies by which pest problems are to be solved at all Hanford Site properties per DOE-RL Site Infrastructure Division memo (WHC 9505090). The HSIPMP defines the roles that contractor organizations play in supporting the IPM process. In short the IPM process anticipates and prevents pest activity and infestation by combining several strategies to achieve long-term pest control solutions.

  9. Quantitative analysis of lentiviral transgene expression in mice over seven generations.

    PubMed

    Wang, Yong; Song, Yong-tao; Liu, Qin; Liu, Cang'e; Wang, Lu-lu; Liu, Yu; Zhou, Xiao-yang; Wu, Jun; Wei, Hong

    2010-10-01

    Lentiviral transgenesis is now recognized as an extremely efficient and cost-effective method to produce transgenic animals. Transgenes delivered by lentiviral vectors exhibited inheritable expression in many species including those which are refractory to genetic modification such as non-human primates. However, epigenetic modification was frequently observed in lentiviral integrants, and transgene expression found to be inversely correlated with methylation density. Recent data showed that about one-third lentiviral integrants exhibited hypermethylation and low expression, but did not demonstrate whether those integrants with high expression could remain constant expression and hypomethylated during long term germline transmission. In this study, using lentiviral eGFP transgenic mice as the experimental animals, lentiviral eGFP expression levels and its integrant numbers in genome were quantitatively analyzed by fluorescent quantitative polymerase-chain reaction (FQ-PCR), using the house-keeping gene ribosomal protein S18 (Rps18) and the single copy gene fatty acid binding protein of the intestine (Fabpi) as the internal controls respectively. The methylation densities of the integrants were quantitatively analyzed by bisulfite sequencing. We found that the lentiviral integrants with high expression exhibited a relative constant expression level per integrant over at least seven generations. Besides, the individuals containing these integrants exhibited eGFP expression levels which were positively and almost linearly correlated with the integrant numbers in their genomes, suggesting that no remarkable position effect on transgene expression of the integrants analyzed was observed. In addition, over seven generations the methylation density of these integrants did not increase, but rather decreased remarkably, indicating that these high expressing integrants were not subjected to de novo methylation during at least seven generations of germline transmission. Taken

  10. Titration of feline immunodeficiency virus-based lentiviral vector preparations.

    PubMed

    Saenz, Dyana T; Barraza, Román; Loewen, Nils; Teo, Wulin; Poeschla, Eric M

    2012-01-01

    Feline immunodeficiency virus (FIV)-based lentiviral vectors are useful for introducing integrated transgenes into nondividing human cells. This protocol describes methods for measuring and calculating vector titers in transducing units (TU)/mL. Alternate methods are provided for green fluorescent protein (GFP) vectors and for β-galactosidase vectors.

  11. Targeted, homology-driven gene insertion in stem cells by ZFN-loaded ‘all-in-one’ lentiviral vectors

    PubMed Central

    Cai, Yujia; Laustsen, Anders; Zhou, Yan; Sun, Chenglong; Anderson, Mads Valdemar; Li, Shengting; Uldbjerg, Niels; Luo, Yonglun; Jakobsen, Martin R; Mikkelsen, Jacob Giehm

    2016-01-01

    Biased integration remains a key challenge for gene therapy based on lentiviral vector technologies. Engineering of next-generation lentiviral vectors targeting safe genomic harbors for insertion is therefore of high relevance. In a previous paper (Cai et al., 2014a), we showed the use of integrase-defective lentiviral vectors (IDLVs) as carriers of complete gene repair kits consisting of zinc-finger nuclease (ZFN) proteins and repair sequences, allowing gene correction by homologous recombination (HR). Here, we follow this strategy to engineer ZFN-loaded IDLVs that insert transgenes by a homology-driven mechanism into safe loci. This insertion mechanism is driven by time-restricted exposure of treated cells to ZFNs. We show targeted gene integration in human stem cells, including CD34+ hematopoietic progenitors and induced pluripotent stem cells (iPSCs). Notably, targeted insertions are identified in 89% of transduced iPSCs. Our findings demonstrate the applicability of nuclease-loaded ‘all-in-one’ IDLVs for site-directed gene insertion in stem cell-based gene therapies. DOI: http://dx.doi.org/10.7554/eLife.12213.001 PMID:27278774

  12. Driving DNA transposition by lentiviral protein transduction

    PubMed Central

    Cai, Yujia; Mikkelsen, Jacob Giehm

    2014-01-01

    Gene vectors derived from DNA transposable elements have become powerful molecular tools in biomedical research and are slowly moving into the clinic as carriers of therapeutic genes. Conventional uses of DNA transposon-based gene vehicles rely on the intracellular production of the transposase protein from transfected nucleic acids. The transposase mediates mobilization of the DNA transposon, which is typically provided in the context of plasmid DNA. In recent work, we established lentiviral protein transduction from Gag precursors as a new strategy for direct delivery of the transposase protein. Inspired by the natural properties of infecting viruses to carry their own enzymes, we loaded lentivirus-derived particles not only with vector genomes carrying the DNA transposon vector but also with hundreds of transposase subunits. Such particles were found to drive efficient transposition of the piggyBac transposable element in a range of different cell types, including primary cells, and offer a new transposase delivery approach that guarantees short-term activity and limits potential cytotoxicity. DNA transposon vectors, originally developed and launched as a non-viral alternative to viral integrating vectors, have truly become viral. Here, we briefly review our findings and speculate on the perspectives and potential advantages of transposase delivery by lentiviral protein transduction. PMID:25057443

  13. The feasibility of incorporating Vpx into lentiviral gene therapy vectors

    PubMed Central

    McAllery, Samantha A; Ahlenstiel, Chantelle L; Suzuki, Kazuo; Symonds, Geoff P; Kelleher, Anthony D; Turville, Stuart G

    2016-01-01

    While current antiretroviral therapy has significantly improved, challenges still remain in life-long targeting of HIV-1 reservoirs. Lentiviral gene therapy has the potential to deliver protective genes into the HIV-1 reservoir. However, inefficient reverse transcription (RT) occurs in HIV-1 reservoirs during lentiviral gene delivery. The viral protein Vpx is capable of increasing lentiviral RT by antagonizing the restriction factor SAMHD1. Incorporating Vpx into lentiviral vectors could substantially increase gene delivery into the HIV-1 reservoir. The feasibility of this Vpx approach was tested in resting cell models utilizing macrophages and dendritic cells. Our results showed Vpx exposure led to increased permissiveness of cells over a period that exceeded 2 weeks. Consequently, significant lower potency of HIV-1 antiretrovirals inhibiting RT and integration was observed. When Vpx was incorporated with anti-HIV-1 genes inhibiting either pre-RT or post-RT stages of the viral life-cycle, transduction levels significantly increased. However, a stronger antiviral effect was only observed with constructs that inhibit pre-RT stages of the viral life cycle. In conclusion this study demonstrates a way to overcome the major delivery obstacle of gene delivery into HIV-1 reservoir cell types. Importantly, incorporating Vpx with pre-RT anti-HIV-1 genes, demonstrated the greatest protection against HIV-1 infection. PMID:27790625

  14. Launch site integration for mixed fleet operations

    NASA Technical Reports Server (NTRS)

    Scott, L. P.

    1990-01-01

    Launch site impacts and integration planning issues are presented to support launch operations for a mixed vehicle fleet (manned and cargo). Proposed ground systems and launch site configurations are described. Prelaunch processing scenarios and schedules are developed for candidate launch vehicles. Earth-to-orbit (ETO) vehicle architectures are presented to meet future launch requirements, including the Space Exploration Initiative (SEI). Flight vehicle design recommendations to enhance launch processing are discussed. The significance of operational designs for future launch vehicles is shown to be a critical factor in planning for mixed fleet launch site operations.

  15. Comprehensive, integrated, remote sensing at DOE sites

    SciTech Connect

    Lackey, J.G.; Burson, Z.G.

    1984-01-01

    The Department of Energy has established a program called Comprehensive, Integrated Remote Sensing (CIRS). The overall objective is to provide a state-of-the-art data base of remotely sensed data for all users of such information at large DOE sites. The primary types of remote sensing provided consist of the following: (1) large format aerial photography; (2) video from aerial platforms; (3) multispectral scanning; and (4) airborne nuclear radiometric surveys. Implementation of the CIRS Program began with field operations at the Savannah River Plant in 1982 and is continuing at that DOE site at a level of effort of about $1.5 m per year. Integrated remote sensing studies were subsequently extended to the West Valley Demonstration Project in the summer and fall of 1984. It is expected that the Program will eventually be extended to cover all large DOE sites on a continuing basis. 2 figures.

  16. Lentiviral vectors in cancer immunotherapy.

    PubMed

    Oldham, Robyn Aa; Berinstein, Elliot M; Medin, Jeffrey A

    2015-01-01

    Basic science advances in cancer immunotherapy have resulted in various treatments that have recently shown success in the clinic. Many of these therapies require the insertion of genes into cells to directly kill them or to redirect the host's cells to induce potent immune responses. Other analogous therapies work by modifying effector cells for improved targeting and enhanced killing of tumor cells. Initial studies done using γ-retroviruses were promising, but safety concerns centered on the potential for insertional mutagenesis have highlighted the desire to develop other options for gene delivery. Lentiviral vectors (LVs) have been identified as potentially more effective and safer alternative delivery vehicles. LVs are now in use in clinical trials for many different types of inherited and acquired disorders, including cancer. This review will discuss current knowledge of LVs and the applications of this viral vector-based delivery vehicle to cancer immunotherapy.

  17. 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.

  18. Advances in lentiviral vectors: a patent review.

    PubMed

    Picanco-Castro, Virginia; de Sousa Russo-Carbolante, Elisa Maria; Tadeu Covas, Dimas

    2012-08-01

    Lentiviral vectors are at the forefront of gene delivery systems for research and clinical applications. These vectors have the ability to efficiently transduce nondividing and dividing cells, to insert large genetic segment in the host chromatin, and to sustain stable long-term transgene expression. Most of lentiviral vectors systems in use are derived from HIV-1. Numerous modifications in the basic HIV structure have been made to ensure safety and to promote efficiency to vectors. Lentiviral vectors can be pseudotyped with distinct viral envelopes that influence vector tropism and transduction efficiency. Moreover, these vectors can be used to reprogram cells and generate induced pluripotent stem cells. This review aims to show the patents that resulted in improved safety and efficacy of lentiviral vector with important implications for clinical trials.

  19. Integrase-Deficient Lentiviral Vectors Mediate Efficient Gene Transfer to Human Vascular Smooth Muscle Cells with Minimal Genotoxic Risk

    PubMed Central

    Chick, Helen E.; Nowrouzi, Ali; Fronza, Raffaele; McDonald, Robert A.; Kane, Nicole M.; Alba, Raul; Delles, Christian; Sessa, William C.; Schmidt, Manfred; Thrasher, Adrian J.

    2012-01-01

    Abstract We have previously shown that injury-induced neointima formation was rescued by adenoviral-Nogo-B gene delivery. Integrase-competent lentiviral vectors (ICLV) are efficient at gene delivery to vascular cells but present a risk of insertional mutagenesis. Conversely, integrase-deficient lentiviral vectors (IDLV) offer additional benefits through reduced mutagenesis risk, but this has not been evaluated in the context of vascular gene transfer. Here, we have investigated the performance and genetic safety of both counterparts in primary human vascular smooth muscle cells (VSMC) and compared gene transfer efficiency and assessed the genotoxic potential of ICLVs and IDLVs based on their integration frequency and insertional profile in the human genome. Expression of enhanced green fluorescent protein (eGFP) mediated by IDLVs (IDLV-eGFP) demonstrated efficient transgene expression in VSMCs. IDLV gene transfer of Nogo-B mediated efficient overexpression of Nogo-B in VSMCs, leading to phenotypic effects on VSMC migration and proliferation, similar to its ICLV version and unlike its eGFP control and uninfected VSMCs. Large-scale integration site analyses in VSMCs indicated that IDLV-mediated gene transfer gave rise to a very low frequency of genomic integration compared to ICLVs, revealing a close-to-random genomic distribution in VSMCs. This study demonstrates for the first time the potential of IDLVs for safe and efficient vascular gene transfer. PMID:22931362

  20. Lentiviral Vectors and Cystic Fibrosis Gene Therapy

    PubMed Central

    Castellani, Stefano; Conese, Massimo

    2010-01-01

    Cystic fibrosis (CF) is a chronic autosomic recessive syndrome, caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene, a chloride channel expressed on the apical side of the airway epithelial cells. The lack of CFTR activity brings a dysregulated exchange of ions and water through the airway epithelium, one of the main aspects of CF lung disease pathophysiology. Lentiviral (LV) vectors, of the Retroviridae family, show interesting properties for CF gene therapy, since they integrate into the host genome and allow long-lasting gene expression. Proof-of-principle that LV vectors can transduce the airway epithelium and correct the basic electrophysiological defect in CF mice has been given. Initial data also demonstrate that LV vectors can be repeatedly administered to the lung and do not give rise to a gross inflammatory process, although they can elicit a T cell-mediated response to the transgene. Future studies will clarify the efficacy and safety profile of LV vectors in new complex animal models with CF, such as ferrets and pigs. PMID:21994643

  1. Lentiviral Delivery of Proteins for Genome Engineering.

    PubMed

    Cai, Yujia; Mikkelsen, Jacob Giehm

    2016-01-01

    Viruses have evolved to traverse cellular barriers and travel to the nucleus by mechanisms that involve active transport through the cytoplasm and viral quirks to resist cellular restriction factors and innate immune responses. Virus-derived vector systems exploit the capacity of viruses to ferry genetic information into cells, and now - more than three decades after the discovery of HIV - lentiviral vectors based on HIV-1 have become instrumental in biomedical research and gene therapies that require genomic insertion of transgenes. By now, the efficacy of lentiviral gene delivery to stem cells, cells of the immune system including T cells, hepatic cells, and many other therapeutically relevant cell types is well established. Along with nucleic acids, HIV-1 virions carry the enzymatic tools that are essential for early steps of infection. Such capacity to package enzymes, even proteins of nonviral origin, has unveiled new ways of exploiting cellular intrusion of HIV-1. Based on early findings demonstrating the packaging of heterologous proteins into virus particles as part of the Gag and GagPol polypeptides, we have established lentiviral protein transduction for delivery of DNA transposases and designer nucleases. This strategy for delivering genome-engineering proteins facilitates high enzymatic activity within a short time frame and may potentially improve the safety of genome editing. Exploiting the full potential of lentiviral vectors, incorporation of foreign protein can be combined with the delivery of DNA transposons or a donor sequence for homology-directed repair in so-called 'all-in-one' lentiviral vectors. Here, we briefly describe intracellular restrictions that may affect lentiviral gene and protein delivery and review the current status of lentiviral particles as carriers of tool kits for genome engineering. PMID:27228988

  2. A Large U3 Deletion Causes Increased In Vivo Expression from a Nonintegrating Lentiviral Vector

    PubMed Central

    Bayer, Matthew; Kantor, Boris; Cockrell, Adam; Ma, Hong; Zeithaml, Brian; Li, Xiangping; McCown, Thomas; Kafri, Tal

    2008-01-01

    The feasibility of employing nonintegrating lentiviral vectors has been demonstrated by recent studies showing the ability of nonintegrating lentiviral vectors to maintain transgene expression in vitro and in vivo. Furthermore, HIV-1 vectors packaged with a mutated integrase were able to correct retinal disease in a mouse model. Interestingly, these results differ from earlier studies in which first-generation nonintegrating lentiviral vectors yielded insignificant levels of transduction. However, to date a rigorous characterization of transgene expression from the currently used self-inactivating (SIN) nonintegrating lentiviral vectors has not been published. Here we characterize transgene expression from SIN nonintegrating lentiviral vectors. Overall, we found that nonintegrating vectors express transgenes at a significantly lower level than their integrating counterparts. Expression from nonintegrating vectors was improved upon introducing a longer deletion in the vector’s U3 region. A unique shuttle-vector assay indicated that the relative abundance of the different episomal forms was not altered by the longer U3 deletion. Interestingly, the longer U3 deletion did not enhance expression in the corpus callosum of the rat brain, suggesting that the extent of silencing of episomal transcription is influenced by tissue-specific factors. Finally, and for the first time, episomal expression in the mouse liver was potent and sustained. PMID:18797449

  3. Targeting lentiviral vectors for cancer immunotherapy

    PubMed Central

    Arce, Frederick; Breckpot, Karine; Collins, Mary; Escors, David

    2012-01-01

    Delivery of tumour-associated antigens (TAA) in a way that induces effective, specific immunity is a challenge in anti-cancer vaccine design. Circumventing tumour-induced tolerogenic mechanisms in vivo is also critical for effective immunotherapy. Effective immune responses are induced by professional antigen presenting cells, in particular dendritic cells (DC). This requires presentation of the antigen to both CD4+ and CD8+ T cells in the context of strong co-stimulatory signals. Lentiviral vectors have been tested as vehicles, for both ex vivo and in vivo delivery of TAA and/or activation signals to DC, and have been demonstrated to induce potent T cell mediated immune responses that can control tumour growth. This review will focus on the use of lentiviral vectors for in vivo gene delivery to DC, introducing strategies to target DC, either targeting cell entry or gene expression to improve safety of the lentiviral vaccine or targeting dendritic cell activation pathways to enhance performance of the lentiviral vaccine. In conclusion, this review highlights the potential of lentiviral vectors as a generally applicable ‘off-the-shelf’ anti-cancer immunotherapeutic. PMID:22983382

  4. Learning with two sites of synaptic integration.

    PubMed

    Körding, K P; König, P

    2000-02-01

    Since the classical work of D O Hebb 1949 The Organization of Behaviour (New York: Wiley) it is assumed that synaptic plasticity solely depends on the activity of the pre- and the postsynaptic cells. Synapses influence the plasticity of other synapses exclusively via the post-synaptic activity. This confounds effects on synaptic plasticity and neuronal activation and, thus, makes it difficult to implement networks which optimize global measures of performance. Exploring solutions to this problem, inspired by recent research on the properties of apical dendrites, we examine a network of neurons with two sites of synaptic integration. These communicate in such a way that one set of synapses mainly influences the neurons' activity; the other set gates synaptic plasticity. Analysing the system with a constant set of parameters reveals: (1) the afferents that gate plasticity act as supervisors, individual to every cell. (2) While the neurons acquire specific receptive fields the net activity remains constant for different stimuli. This ensures that all stimuli are represented and, thus, contributes to information maximization. (3) Mechanisms for maximization of coherent information can easily be implemented. Neurons with non-overlapping receptive fields learn to fire correlated and preferentially transmit information that is correlated over space. (4) We demonstrate how a new measure of performance can be implemented: cells learn to represent only the part of the input that is relevant to the processing at higher stages. This criterion is termed 'relevant infomax'.

  5. Learning with two sites of synaptic integration.

    PubMed

    Körding, K P; König, P

    2000-02-01

    Since the classical work of D O Hebb 1949 The Organization of Behaviour (New York: Wiley) it is assumed that synaptic plasticity solely depends on the activity of the pre- and the postsynaptic cells. Synapses influence the plasticity of other synapses exclusively via the post-synaptic activity. This confounds effects on synaptic plasticity and neuronal activation and, thus, makes it difficult to implement networks which optimize global measures of performance. Exploring solutions to this problem, inspired by recent research on the properties of apical dendrites, we examine a network of neurons with two sites of synaptic integration. These communicate in such a way that one set of synapses mainly influences the neurons' activity; the other set gates synaptic plasticity. Analysing the system with a constant set of parameters reveals: (1) the afferents that gate plasticity act as supervisors, individual to every cell. (2) While the neurons acquire specific receptive fields the net activity remains constant for different stimuli. This ensures that all stimuli are represented and, thus, contributes to information maximization. (3) Mechanisms for maximization of coherent information can easily be implemented. Neurons with non-overlapping receptive fields learn to fire correlated and preferentially transmit information that is correlated over space. (4) We demonstrate how a new measure of performance can be implemented: cells learn to represent only the part of the input that is relevant to the processing at higher stages. This criterion is termed 'relevant infomax'. PMID:10735527

  6. Surface modification via strain-promoted click reaction facilitates targeted lentiviral transduction.

    PubMed

    Chu, Yanjie; Oum, Yoon Hyeun; Carrico, Isaac S

    2016-01-01

    As a result of their ability to integrate into the genome of both dividing and non-dividing cells, lentiviruses have emerged as a promising vector for gene delivery. Targeted gene transduction of specific cells and tissues by lentiviral vectors has been a major goal, which has proven difficult to achieve. We report a novel targeting protocol that relies on the chemoselective attachment of cancer specific ligands to unnatural glycans on lentiviral surfaces. This strategy exhibits minimal perturbation on virus physiology and demonstrates remarkable flexibility. It allows for targeting but can be more broadly useful with applications such as vector purification and immunomodulation. PMID:26499046

  7. Surface modification via strain-promoted click reaction facilitates targeted lentiviral transduction.

    PubMed

    Chu, Yanjie; Oum, Yoon Hyeun; Carrico, Isaac S

    2016-01-01

    As a result of their ability to integrate into the genome of both dividing and non-dividing cells, lentiviruses have emerged as a promising vector for gene delivery. Targeted gene transduction of specific cells and tissues by lentiviral vectors has been a major goal, which has proven difficult to achieve. We report a novel targeting protocol that relies on the chemoselective attachment of cancer specific ligands to unnatural glycans on lentiviral surfaces. This strategy exhibits minimal perturbation on virus physiology and demonstrates remarkable flexibility. It allows for targeting but can be more broadly useful with applications such as vector purification and immunomodulation.

  8. Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin.

    PubMed Central

    Vijaya, S; Steffen, D L; Robinson, H L

    1986-01-01

    Seven cellular loci with acceptor sites for retroviral integrations have been mapped for the presence of DNase I-hypersensitive sites in chromatin. Integrations in three of these loci, chicken c-erbB, rat c-myc, and a rat locus, dsi-1, had been selected for in retrovirus-induced tumors. Of the remaining four, two, designated dsi-3 and dsi-4, harbored acceptor sites for apparently unselected integrations of Moloney murine leukemia virus in a Moloney murine leukemia virus-induced thymoma, and two, designated C and F, harbored unselected acceptor sites for Moloney murine leukemia virus integrations in a rat fibroblast cell line. Each acceptor site mapped to within 500 base pairs of a DNase I-hypersensitive site. In the analyses of the unselected integrations, six hypersensitive sites were observed in 39 kilobases of DNA. The four acceptor sites in this DNA were localized between 0.05 and 0.43 kilobases of a hypersensitive site. The probability of this close association occurring by chance was calculated to be extremely low. Hypersensitive sites were mapped in cells representing the lineage in which integration had occurred as well as in an unrelated lineage. In six of the seven acceptor loci hypersensitive sites could not be detected in the unrelated lineage. Our results indicate that retroviruses preferentially integrate close to DNase I-hypersensitive sites and that many of these sites are expressed in some but not all cells. Images PMID:3490582

  9. PBO Integrated Real-Time Observing Sites at Volcanic Sites

    NASA Astrophysics Data System (ADS)

    Mencin, D.; Jackson, M.; Borsa, A.; Feaux, K.; Smith, S.

    2009-05-01

    The Plate Boundary Observatory, an element of NSF's EarthScope program, has six integrated observatories in Yellowstone and four on Mt St Helens. These observatories consist of some combination of borehole strainmeters, borehole seismometers, GPS, tiltmeters, pore pressure, thermal measurements and meteorological data. Data from all these instruments have highly variable data rates and formats, all synchronized to GPS time which can cause significant congestion of precious communication resources. PBO has been experimenting with integrating these data streams to both maximize efficiency and minimize latency through the use of software that combines the streams, like Antelope, and VPN technologies.

  10. Design of a titering assay for lentiviral vectors utilizing direct extraction of DNA from transduced cells in microtiter plates

    PubMed Central

    Murphy, Michele E; Vin, Chintan D; Slough, Megan M; Gombotz, Wayne R; Kelley-Clarke, Brenna

    2016-01-01

    Using lentiviral vector products in clinical applications requires an accurate method for measuring transduction titer. For vectors lacking a marker gene, quantitative polymerase chain reaction is used to evaluate the number of vector DNA copies in transduced target cells, from which a transduction titer is calculated. Immune Design previously described an integration-deficient lentiviral vector pseudotyped with a modified Sindbis virus envelope for use in cancer immunotherapy (VP02, of the ZVex platform). Standard protocols for titering integration-competent lentiviral vectors employ commercial spin columns to purify vector DNA from transduced cells, but such columns are not optimized for isolation of extrachromosomal (nonintegrated) DNA. Here, we describe a 96-well transduction titer assay in which DNA extraction is performed in situ in the transduction plate, yielding quantitative recovery of extrachromosomal DNA. Vector titers measured by this method were higher than when commercial spin columns were used for DNA isolation. Evaluation of the method’s specificity, linear range, and precision demonstrate that it is suitable for use as a lot release assay to support clinical trials with VP02. Finally, the method is compatible with titering both integrating and nonintegrating lentiviral vectors, suggesting that it may be used to evaluate the transduction titer for any lentiviral vector. PMID:26942209

  11. A large U3 deletion causes increased in vivo expression from a nonintegrating lentiviral vector.

    PubMed

    Bayer, Matthew; Kantor, Boris; Cockrell, Adam; Ma, Hong; Zeithaml, Brian; Li, Xiangping; McCown, Thomas; Kafri, Tal

    2008-12-01

    The feasibility of using nonintegrating lentiviral vectors has been demonstrated by recent studies showing their ability to maintain transgene expression both in vitro and in vivo. Furthermore, human immunodeficiency virus-1 (HIV-1) vectors packaged with a mutated integrase were able to correct retinal disease in a mouse model. Interestingly, these results differ from earlier studies in which first-generation nonintegrating lentiviral vectors yielded insignificant levels of transduction. However, to date, a rigorous characterization of transgene expression from the currently used self-inactivating (SIN) nonintegrating lentiviral vectors has not been published. In this study, we characterize transgene expression from SIN nonintegrating lentiviral vectors. Overall, we found that nonintegrating vectors express transgenes at a significantly lower level than their integrating counterparts. Expression from nonintegrating vectors was improved upon introducing a longer deletion in the vector's U3 region. A unique shuttle-vector assay indicated that the relative abundance of the different episomal forms was not altered by the longer U3 deletion. Interestingly, the longer U3 deletion did not enhance expression in the corpus callosum of the rat brain, suggesting that the extent of silencing of episomal transcription is influenced by tissue-specific factors. Finally, and for the first time, episomal expression in the mouse liver was potent and sustained.

  12. Quantification of HIV-based lentiviral vectors: influence of several cell type parameters on vector infectivity.

    PubMed

    Gay, Virginie; Moreau, Karen; Hong, Saw-See; Ronfort, Corinne

    2012-02-01

    A human immunodeficiency virus type (HIV-1)-based lentiviral vector pseudotyped with the vesicular stomatitis virus envelope glycoprotein and encoding the GFP reporter gene was used to evaluate different methods of lentiviral vector titration. GFP expression, viral DNA quantification and the efficiency of vector DNA integration were assayed after infection of conventional HIV-1-permissive cell lines and human primary adult fibroblasts with the vector. We found that vector titers based on GFP expression determined by flow cytometry may vary by more than 50-fold depending on the cell type and the promoter-cell combination used. Interestingly, we observed that the viral integration process in primary HDFa cells was significantly more efficient compared to that in SupT1 or 293T cells. We propose that determination of the amount of integrated viral DNA by quantitative PCR be used in combination with the reporter gene expression assay.

  13. Conditional RNAi Using the Lentiviral GLTR System.

    PubMed

    Pfeiffenberger, Elisabeth; Sigl, Reinhard; Geley, Stephan

    2016-01-01

    RNA interference (RNAi) has become an essential technology for functional gene analysis. Its success depends on the effective expression of target gene-specific RNAi-inducing small double-stranded interfering RNA molecules (siRNAs). Here, were describe the use of a recently developed lentiviral RNAi system that allows the rapid generation of stable cell lines with inducible RNAi based on conditional expression of double-stranded short hairpin RNA (shRNA). These lentiviral vectors can be generated rapidly using the GATEWAY recombination cloning technology. Conditional cell lines can be established by using either a two-vector system in which the regulator is encoded by a separate vector or by a one-vector system. The available different lentiviral vectors for conditional shRNA expression cassette delivery co-express additional genes that allow (1) the use of fluorescent proteins for color-coded combinatorial RNAi or monitoring RNAi induction (pGLTR-FP), (2) selection of transduced cells (pGLTR-S), and (3) the generation of conditional cell lines using a one-vector system (pGLTR-X). PMID:27317178

  14. Converting Maturing Nuclear Sites to Integrated Power Production Islands

    DOE PAGESBeta

    Solbrig, Charles W.

    2011-01-01

    Nuclear islands, which are integrated power production sites, could effectively sequester and safeguard the US stockpile of plutonium. A nuclear island, an evolution of the integral fast reactor, utilizes all the Transuranics (Pu plus minor actinides) produced in power production, and it eliminates all spent fuel shipments to and from the site. This latter attribute requires that fuel reprocessing occur on each site and that fast reactors be built on-site to utilize the TRU. All commercial spent fuel shipments could be eliminated by converting all LWR nuclear power sites to nuclear islands. Existing LWR sites have the added advantage ofmore » already possessing a license to produce nuclear power. Each could contribute to an increase in the nuclear power production by adding one or more fast reactors. Both the TRU and the depleted uranium obtained in reprocessing would be used on-site for fast fuel manufacture. Only fission products would be shipped to a repository for storage. The nuclear island concept could be used to alleviate the strain of LWR plant sites currently approaching or exceeding their spent fuel pool storage capacity. Fast reactor breeding ratio could be designed to convert existing sites to all fast reactors, or keep the majority thermal.« less

  15. The Inside Out of Lentiviral Vectors

    PubMed Central

    Durand, Stéphanie; Cimarelli, Andrea

    2011-01-01

    Lentiviruses induce a wide variety of pathologies in different animal species. A common feature of the replicative cycle of these viruses is their ability to target non-dividing cells, a property that constitutes an extremely attractive asset in gene therapy. In this review, we shall describe the main basic aspects of the virology of lentiviruses that were exploited to obtain efficient gene transfer vectors. In addition, we shall discuss some of the hurdles that oppose the efficient genetic modification mediated by lentiviral vectors and the strategies that are being developed to circumvent them. PMID:22049307

  16. Immunization Delivered by Lentiviral Vectors for Cancer and Infectious Diseases

    PubMed Central

    Hu, Biliang; Tai, April; Wang, Pin

    2011-01-01

    Summary The increasing level of understanding of the lentivirus biology has been instrumental in shaping the design strategy of creating therapeutic lentiviral delivery vectors. As a result, lentiviral vectors have become one of the most powerful gene transfer vehicles. They are widely used for therapeutic purposes as well as in studies of basic biology, due to their unique characteristics. Lentiviral vectors have been successfully employed to mediate durable and efficient antigen expression and presentation in dendritic cells both in vitro and in vivo, leading to the activation of cellular immunity and humoral responses. This capability makes the lentiviral vector an ideal choice for immunizations that target a wide range of cancers and infectious diseases. Further advances into optimizing the vector system and understanding the relationship between the immune system and diseases pathogenesis will only augment the potential benefits and utility of lentiviral vaccines for human health. PMID:21198664

  17. Lentiviral delivery of short hairpin RNAs

    PubMed Central

    Manjunath, N; Haoquan, Wu; Sandesh, Subramanya; Premlata, Shankar

    2009-01-01

    In less than a decade after discovery, RNA interference-mediated gene silencing is already being tested as potential therapy in clinical trials for a number of diseases. Lentiviral vectors provide a means to express short hairpin RNA (shRNA) to induce stable and long-term gene silencing in both dividing and non-dividing cells and thus, are being intensively investigated for this purpose. However, induction of long-term shRNA expression can also cause toxicities by inducing off target effects and interference with the endogenous micro RNA (miRNA) pathway that regulates cellular gene expression. Recently, several advances have been made in the shRNA vector design to mimic cellular miRNA processing and to express multiplex siRNAs in a tightly regulated and reversible manner to overcome toxicities. In this review we describe some of these advances, focusing on the progress made in the development of lentiviral shRNA delivery strategies to combat viral infections. PMID:19341774

  18. Lentiviral Vector Gene Transfer to Porcine Airways

    PubMed Central

    Sinn, Patrick L; Cooney, Ashley L; Oakland, Mayumi; Dylla, Douglas E; Wallen, Tanner J; Pezzulo, Alejandro A; Chang, Eugene H; McCray, Paul B

    2012-01-01

    In this study, we investigated lentiviral vector development and transduction efficiencies in well-differentiated primary cultures of pig airway epithelia (PAE) and wild-type pigs in vivo. We noted gene transfer efficiencies similar to that observed for human airway epithelia (HAE). Interestingly, feline immunodeficiency virus (FIV)-based vectors transduced immortalized pig cells as well as pig primary cells more efficiently than HIV-1–based vectors. PAE express TRIM5α, a well-characterized species-specific lentiviral restriction factor. We contrasted the restrictive properties of porcine TRIM5α against FIV- and HIV-based vectors using gain and loss of function approaches. We observed no effect on HIV-1 or FIV conferred transgene expression in response to porcine TRIM5α overexpression or knockdown. To evaluate the ability of GP64-FIV to transduce porcine airways in vivo, we delivered vector expressing mCherry to the tracheal lobe of the lung and the ethmoid sinus of 4-week-old pigs. One week later, epithelial cells expressing mCherry were readily detected. Our findings indicate that pseudotyped FIV vectors confer similar tropisms in porcine epithelia as observed in human HAE and provide further support for the selection of GP64 as an appropriate envelope pseudotype for future preclinical gene therapy studies in the porcine model of cystic fibrosis (CF). PMID:23187455

  19. TECHNOLOGY INTEGRATION FOR CONTAMINATED SITE REMEDIATION: CLEANUP GOALS & PERFORMANCE CRITERIA

    EPA Science Inventory

    There is a need to develop and field-test integrated remediation technologies that operate in a synergistic manner for cost-effective treatment of contaminated sites to achieve risk-based and rational endpoints. Aggressive technologies designed for rapid source-zone remediation m...

  20. Site-specific recombinases as tools for heterologous gene integration.

    PubMed

    Hirano, Nobutaka; Muroi, Tetsurou; Takahashi, Hideo; Haruki, Mitsuru

    2011-10-01

    Site-specific recombinases are the enzymes that catalyze site-specific recombination between two specific DNA sequences to mediate DNA integration, excision, resolution, or inversion and that play a pivotal role in the life cycles of many microorganisms including bacteria and bacteriophages. These enzymes are classified as tyrosine-type or serine-type recombinases based on whether a tyrosine or serine residue mediates catalysis. All known tyrosine-type recombinases catalyze the formation of a Holliday junction intermediate, whereas the catalytic mechanism of all known serine-type recombinases includes the 180° rotation and rejoining of cleaved substrate DNAs. Both recombinase families are further subdivided into two families; the tyrosine-type recombinases are subdivided by the recombination directionality, and the serine-type recombinases are subdivided by the protein size. Over more than two decades, many different site-specific recombinases have been applied to in vivo genome engineering, and some of them have been used successfully to mediate integration, deletion, or inversion in a wide variety of heterologous genomes, including those from bacteria to higher eukaryotes. Here, we review the recombination mechanisms of the best characterized recombinases in each site-specific recombinase family and recent advances in the application of these recombinases to genomic manipulation, especially manipulations involving site-specific gene integration into heterologous genomes. PMID:21822899

  1. Modification site localization scoring integrated into a search engine.

    PubMed

    Baker, Peter R; Trinidad, Jonathan C; Chalkley, Robert J

    2011-07-01

    Large proteomic data sets identifying hundreds or thousands of modified peptides are becoming increasingly common in the literature. Several methods for assessing the reliability of peptide identifications both at the individual peptide or data set level have become established. However, tools for measuring the confidence of modification site assignments are sparse and are not often employed. A few tools for estimating phosphorylation site assignment reliabilities have been developed, but these are not integral to a search engine, so require a particular search engine output for a second step of processing. They may also require use of a particular fragmentation method and are mostly only applicable for phosphorylation analysis, rather than post-translational modifications analysis in general. In this study, we present the performance of site assignment scoring that is directly integrated into the search engine Protein Prospector, which allows site assignment reliability to be automatically reported for all modifications present in an identified peptide. It clearly indicates when a site assignment is ambiguous (and if so, between which residues), and reports an assignment score that can be translated into a reliability measure for individual site assignments.

  2. Hanford Site waste treatment/storage/disposal integration

    SciTech Connect

    MCDONALD, K.M.

    1999-02-24

    In 1998 Waste Management Federal Services of Hanford, Inc. began the integration of all low-level waste, mixed waste, and TRU waste-generating activities across the Hanford site. With seven contractors, dozens of generating units, and hundreds of waste streams, integration was necessary to provide acute waste forecasting and planning for future treatment activities. This integration effort provides disposition maps that account for waste from generation, through processing, treatment and final waste disposal. The integration effort covers generating facilities from the present through the life-cycle, including transition and deactivation. The effort is patterned after the very successful DOE Complex EM Integration effort. Although still in the preliminary stages, the comprehensive onsite integration effort has already reaped benefits. These include identifying significant waste streams that had not been forecast, identifying opportunities for consolidating activities and services to accelerate schedule or save money; and identifying waste streams which currently have no path forward in the planning baseline. Consolidation/integration of planned activities may also provide opportunities for pollution prevention and/or avoidance of secondary waste generation. A workshop was held to review the waste disposition maps, and to identify opportunities with potential cost or schedule savings. Another workshop may be held to follow up on some of the long-term integration opportunities. A change to the Hanford waste forecast data call would help to align the Solid Waste Forecast with the new disposition maps.

  3. Integrated grassland observation sites and integrated cropland observation sites at El Reno, Oklahoma

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With the financial support from the National Science Foundation and the USDA National Institute of Food and Agriculture, a team of researchers from the University of Oklahoma and the USDA ARS Grazinglands Research Laboratory have worked together and established two Integrated Grassland Observation s...

  4. Integration of Environmental Compliance at the Savannah River Site - 13024

    SciTech Connect

    Hoel, David; Griffith, Michael

    2013-07-01

    The Savannah River Site (SRS) is a large federal installation hosting diverse missions and multiple organizations with competing regulatory needs. Accordingly, there was a need to integrate environmental compliance strategies to ensure the consistent flow of information between Department of Energy-Savannah River (DOE-SR), the regulatory agencies and other interested parties. In order to meet this objective, DOE and major SRS contractors and tenants have committed to a strategy of collaboratively working together to ensure that a consistent, integrated, and fully coordinated approach to environmental compliance and regulator relationships is maintained. DOE-SR and Savannah River Nuclear Solutions, LLC, the SRS management and operations contractor, have established an environmental compliance integration process that provides for the consistent flow down of requirements to projects, facilities, SRS contractors, and subcontractors as well as the upward flow of information to assist in the early identification and resolution of environmental regulatory issues and enhancement of compliance opportunities. In addition, this process strongly fosters teamwork to collaboratively resolve complex regulatory challenges, promote pollution prevention and waste minimization opportunities to advance site missions in a manner that balances near-term actions with the long-term site vision, while being protective of human health and the environment. Communication tools are being utilized, some with enhancements, to ensure appropriate information is communicated to all levels with environmental responsibility at SRS. SRS internal regulatory integration is accomplished through a variety of informational exchange forums (e.g., Challenges, Opportunities and Resolution (COR) Team, DOE's Joint Site Regulatory Integration Team, and the Senior Environmental Managers Council (SEMC)). SRS communications and problem-solving with the regulatory agencies have been enhanced through formation of an

  5. Production and titration of lentiviral vectors.

    PubMed

    Salmon, Patrick; Trono, Didier

    2006-11-01

    Lentiviral vectors have emerged over the last decade as powerful, reliable and safe tools for stable gene transfer in a wide variety of mammalian cells. Unlike other vectors derived from oncoretroviruses, they allow for stable gene delivery into most nondividing primary cells, including neurons. This is why LVs are becoming the most useful and promising tools in the field of neuroscience, not only for research, but also for future gene and cell therapy approaches. Lentivectors (LVs) derived from HIV-1 have gradually evolved to display many desirable features aimed at increasing both their safety and their versatility. These latest designs are reviewed in this unit. This unit also describes protocols for production and titration of LVs that can be implemented in a research laboratory setting, with an emphasis on standardization to improve transposability of results between laboratories.

  6. pLR: a lentiviral backbone series to stable transduction of bicistronic genes and exchange of promoters.

    PubMed

    Vargas, José Eduardo; Salton, Gabrielle; Sodré de Castro Laino, Andressa; Pires, Tiago Dalberto; Bonamino, Martin; Lenz, Guido; Delgado-Cañedo, Andrés

    2012-11-01

    Gene transfer based on lentiviral vectors allow the integration of exogenous genes into the genome of a target cell, turning these vectors into one of the most used methods for stable transgene expression in mammalian cells, in vitro and in vivo. Currently, there are no lentivectors that allow the cloning of different genes to be regulated by different promoters. Also, there are none that permit the analysis of the expression through an IRES (internal ribosome entry site)-- reporter gene system. In this work, we have generated a series of lentivectors containing: (1) a malleable structure to allow the cloning of different target genes in a multicloning site (mcs); (2) unique site to exchange promoters, and (3) IRES followed by one of two reporter genes: eGFP or DsRed. The series of the produced vectors were named pLR (for lentivirus and RSV promoter) and were fairly efficient with a strong fluorescence of the reporter genes in direct transfection and viral transduction experiments. This being said, the pLR series have been found to be powerful biotechnological tools for stable gene transfer and expression. PMID:22728068

  7. Cellular cofactors of lentiviral integrase: from target validation to drug discovery.

    PubMed

    Taltynov, Oliver; Desimmie, Belete A; Demeulemeester, Jonas; Christ, Frauke; Debyser, Zeger

    2012-01-01

    To accomplish their life cycle, lentiviruses make use of host proteins, the so-called cellular cofactors. Interactions between host cell and viral proteins during early stages of lentiviral infection provide attractive new antiviral targets. The insertion of lentiviral cDNA in a host cell chromosome is a step of no return in the replication cycle, after which the host cell becomes a permanent carrier of the viral genome and a producer of lentiviral progeny. Integration is carried out by integrase (IN), an enzyme playing also an important role during nuclear import. Plenty of cellular cofactors of HIV-1 IN have been proposed. To date, the lens epithelium-derived growth factor (LEDGF/p75) is the best studied cofactor of HIV-1 IN. Moreover, small molecules that block the LEDGF/p75-IN interaction have recently been developed for the treatment of HIV infection. The nuclear import factor transportin-SR2 (TRN-SR2) has been proposed as another interactor of HIV IN-mediating nuclear import of the virus. Using both proteins as examples, we will describe approaches to be taken to identify and validate novel cofactors as new antiviral targets. Finally, we will highlight recent advances in the design and the development of small-molecule inhibitors binding to the LEDGF/p75-binding pocket in IN (LEDGINs).

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

    PubMed

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

    2002-05-01

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

  9. Integrated Patient Education on U.S. Hospital Web Sites.

    PubMed

    Huang, Edgar; Wu, Kerong; Edwards, Kelsey

    2016-01-01

    Based on a census of the 2015 Most Wired Hospitals, this content analysis aimed to find out how patient education has been integrated on these best IT hospitals' Web sites to serve the purposes of marketing and meeting online visitors' needs. This study will help hospitals to understand where the weaknesses are in their interactive patient education implementation and come up with a smart integration strategy. The study found that 70% of these hospitals had adopted interactive patient education contents, 76.6% of such contents were from a third-party developer, and only 20% of the hospitals linked their patient education contents to one or more of the hospital's resources while 26% cross-references such contents. The authors concluded that more hospitals should take advantage of modern information communication technology to cross-reference their patient education contents and to integrate such contents into their overall online marketing strategy to benefit patients and themselves.

  10. Integrated Patient Education on U.S. Hospital Web Sites.

    PubMed

    Huang, Edgar; Wu, Kerong; Edwards, Kelsey

    2016-01-01

    Based on a census of the 2015 Most Wired Hospitals, this content analysis aimed to find out how patient education has been integrated on these best IT hospitals' Web sites to serve the purposes of marketing and meeting online visitors' needs. This study will help hospitals to understand where the weaknesses are in their interactive patient education implementation and come up with a smart integration strategy. The study found that 70% of these hospitals had adopted interactive patient education contents, 76.6% of such contents were from a third-party developer, and only 20% of the hospitals linked their patient education contents to one or more of the hospital's resources while 26% cross-references such contents. The authors concluded that more hospitals should take advantage of modern information communication technology to cross-reference their patient education contents and to integrate such contents into their overall online marketing strategy to benefit patients and themselves. PMID:27139406

  11. Site wide integration of the Rocky Flats closure project

    SciTech Connect

    Burdge, L.F.; Golan, P.

    1998-06-01

    The prime contractor for the Rocky Flats Closure Project (RFCP), Kaiser-Hill, in concert with the Department of Energy--Rocky Flats Field Office (DOE-RFFO) has applied a fully integrated, life-cycle, critical path schedule and work planning system to manage the work that is required to close the Site. The closure of the Site is complex, in that it houses over 700 facilities, 19,600 kilograms of Special Nuclear Material (Plutonium and Uranium), and over 160,000 cubic meters of Transuranic, Low Level, and Hazardous Waste. The deactivation, decommissioning, decontaminating, and demolition of this large number of facilities, while at the same time accommodating difficult on-going activities, significantly increases the sophistication required in the planning process. The Rocky Flats team has overcome these difficulties by establishing a money oriented critical path process, to provide a least-cost avenue to supporting on-going activities and a line-of-balance process for production oriented activities. These processes, when integrated with a typical activity-based project planning system, guide the way to the shortest and most cost-effective course for the closure of the Rocky Flats Site.

  12. Host factors in retroviral integration and the selection of integration target sites

    PubMed Central

    Craigie, Robert; Bushman, Frederic D.

    2015-01-01

    In order to replicate, a retrovirus must integrate a DNA copy of the viral RNA genome into a chromosome of the host cell. The study of retroviral integration has advanced considerably in the last few years. Here we focus on host factor interactions and the linked area of integration targeting. Genome-wide screens for cellular factors affecting HIV replication have identified a series of host cell proteins that may mediate subcellular trafficking of integration complexes, nuclear import, and integration target site selection. The cell transcriptional co-activator protein LEDGF/p75 has been identified as a tethering factor important for HIV integration, and recently, BET proteins (Brd2, 4, and 4) have been identified as tethering factors for the gammaretroviruses. A new class of HIV inhibitors has been developed targeting the HIV-1 IN-LEDGF binding site, though surprisingly these inhibitors appear to block assembly late during replication and do not act at the integration step. Going forward, genome-wide studies of HIV-host interactions offer many new starting points to investigate HIV replication and identify potential new inhibitor targets. PMID:26104434

  13. Recent Advances in Lentiviral Vaccines for HIV-1 Infection.

    PubMed

    Norton, Thomas D; Miller, Elizabeth A

    2016-01-01

    The development of an effective HIV vaccine to prevent and/or cure HIV remains a global health priority. Given their central role in the initiation of adaptive immune responses, dendritic cell (DC)-based vaccines are being increasingly explored as immunotherapeutic strategies to enhance HIV-specific T cells in infected individuals and, thus, promote immune responses that may help facilitate a functional cure. HIV-1-based lentiviral (LV) vectors have inherent advantages as DC vaccine vectors due to their ability to transduce non-dividing cells and integrate into the target cell genomic DNA, allowing for expression of encoded antigens over the lifespan of the cell. Moreover, LV vectors may express additional immunostimulatory and immunoregulatory proteins that enhance DC function and direct antigen-specific T cells responses. Recent basic and clinical research efforts have broadened our understanding of LV vectors as DC-based vaccines. In this review, we provide an overview of the pre-clinical and clinical LV vector vaccine studies for treating HIV to date. We also discuss advances in LV vector designs that have enhanced DC transduction efficiency, target cell specificity, and immunogenicity, and address potential safety concerns regarding LV vector-based vaccines. PMID:27446074

  14. Recent Advances in Lentiviral Vaccines for HIV-1 Infection

    PubMed Central

    Norton, Thomas D.; Miller, Elizabeth A.

    2016-01-01

    The development of an effective HIV vaccine to prevent and/or cure HIV remains a global health priority. Given their central role in the initiation of adaptive immune responses, dendritic cell (DC)-based vaccines are being increasingly explored as immunotherapeutic strategies to enhance HIV-specific T cells in infected individuals and, thus, promote immune responses that may help facilitate a functional cure. HIV-1-based lentiviral (LV) vectors have inherent advantages as DC vaccine vectors due to their ability to transduce non-dividing cells and integrate into the target cell genomic DNA, allowing for expression of encoded antigens over the lifespan of the cell. Moreover, LV vectors may express additional immunostimulatory and immunoregulatory proteins that enhance DC function and direct antigen-specific T cells responses. Recent basic and clinical research efforts have broadened our understanding of LV vectors as DC-based vaccines. In this review, we provide an overview of the pre-clinical and clinical LV vector vaccine studies for treating HIV to date. We also discuss advances in LV vector designs that have enhanced DC transduction efficiency, target cell specificity, and immunogenicity, and address potential safety concerns regarding LV vector-based vaccines. PMID:27446074

  15. What Integration Sites Tell Us about HIV Persistence.

    PubMed

    Hughes, Stephen H; Coffin, John M

    2016-05-11

    Advances in technology have made it possible to analyze integration sites in cells from HIV-infected patients. A significant fraction of infected cells in patients on long-term therapy are clonally expanded; in some cases the integrated viral DNA contributes to the clonal expansion of the infected cells. Although the large majority (>95%) of the HIV proviruses in treated patients are defective, expanded clones can carry replication-competent proviruses, and cells from these clones can release infectious virus. As discussed in this Perspective, it is likely that cells that produce virus are strongly selected against in vivo, and cells with replication competent proviruses expand and survive because only a small fraction of the cells produce virus. These findings have implications for strategies that are intended to eliminate the reservoir of infected cells that has made it almost impossible to cure HIV-infected patients. PMID:27173927

  16. Opportunities for Launch Site Integrated System Health Engineering and Management

    NASA Technical Reports Server (NTRS)

    Waterman, Robert D.; Langwost, Patricia E.; Waterman, Susan J.

    2005-01-01

    The launch site processing flow involves operations such as functional verification, preflight servicing and launch. These operations often include hazards that must be controlled to protect human life and critical space hardware assets. Existing command and control capabilities are limited to simple limit checking durig automated monitoring. Contingency actions are highly dependent on human recognition, decision making, and execution. Many opportunities for Integrated System Health Engineering and Management (ISHEM) exist throughout the processing flow. This paper will present the current human-centered approach to health management as performed today for the shuttle and space station programs. In addition, it will address some of the more critical ISHEM needs, and provide recommendations for future implementation of ISHEM at the launch site.

  17. Hanford Site waste management and environmental restoration integration plan

    SciTech Connect

    Merrick, D.L.

    1990-04-30

    The Hanford Site Waste Management and Environmental Restoration Integration Plan'' describes major actions leading to waste disposal and site remediation. The primary purpose of this document is to provide a management tool for use by executives who need to quickly comprehend the waste management and environmental restoration programs. The Waste Management and Environmental Restoration Programs have been divided into missions. Waste Management consists of five missions: double-shell tank (DST) wastes; single-shell tank (SST) wastes (surveillance and interim storage, stabilization, and isolation); encapsulated cesium and strontium; solid wastes; and liquid effluents. Environmental Restoration consists of two missions: past practice units (PPU) (including characterization and assessment of SST wastes) and surplus facilities. For convenience, both aspects of SST wastes are discussed in one place. A general category of supporting activities is also included. 20 refs., 14 figs., 7 tabs.

  18. Characteristics of the volatile organic compounds -- Arid Integrated Demonstration Site

    SciTech Connect

    Last, G.V.; Lenhard, R.J.; Bjornstad, B.N.; Evans, J.C.; Roberson, K.R.; Spane, F.A.; Amonette, J.E.; Rockhold, M.L.

    1991-10-01

    The Volatile Organic Compounds -- Arid Integrated Demonstration Program (VOC-Arid ID) is targeted at demonstration and testing of technologies for the evaluation and cleanup of volatile organic compounds and associated contaminants at arid DOE sites. The initial demonstration site is an area of carbon tetrachloride (CCl{sub 4}) contamination located near the center of the Hanford Site. The movement of CCl{sub 4} and other volatile organic contaminants in the subsurface is very complex. The problem at the Hanford Site is further complicated by the concurrent discharge of other waste constituents including acids, lard oil, organic phosphates, and transuranic radionuclides. In addition, the subsurface environment is very complex, with large spatial variabilities in hydraulic properties. A thorough understanding of the problem is essential to the selection of appropriate containment, retrieval, and/or in situ remedial technologies. The effectiveness of remedial technologies depends on knowing where the contaminants are, how they are held up in a given physical and chemical subsurface environment; and knowing the physical, chemical, and microbiological changes that are induced by the various remedial technologies.

  19. Hanford and Savannah River Site Programmatic and Technical Integration

    SciTech Connect

    Ramsey, William Gene

    2013-08-15

    Abstract only. The Hanford Site and the Savannah River Site (SRS) were the primary plutonium production facilities within the U.S. nuclear weapons complex. Radioactive wastes were generated as part of these missions and are stored in similar fashion. The majority of radioactivity maintained by the two sites is located in underground carbon steel tanks in the physical form of supernatant, saltcake, or sludge. Disposition of SRS tank waste is ongoing by converting it into glass (pathway for sludge and radionuclides separated from supernatant or dissolved saltcake) or cement (pathway for the decontaminated supernatant and dissolved saltcake). Tank closure activity has also begun at SRS and will continue for the duration of mission. The Hanford tank waste inventory is roughly 2/3rds larger than SRS's by volume- but nominally half the radioactivity. The baseline disposition path includes high-level and low-activity waste vitrification with separate disposition of contact-handled transuranic tank waste. Retrieval of tank waste from aging single­ shell tanks (SSTs) into double-shell tanks (DSTs) is currently ongoing. As vitrification commences later this decade, Hanford will be in a similar operations mode as SRS. Site integration is increasing as the missions align. The ongoing integration is centered on key issues that impact both sites- regardless of mission timeframe. Three recent workshop exchanges have been held to improve communication with the primary intent of improving operations and technical work organization. The topics of these workshops are as follows: DST space utilization, optimization, and closure; Waste Feed Qualification; and, Cementitious Waste Forms. Key goals for these and future exchanges include aligning research and technology, preparing for joint initiatives (to maximize budgetary value for the customer), and reviewing lessons learned. Each site has played a leading role in the development of technology and operational practices that can be

  20. Research at Hanford's 300 Area Integrated Field Challenge Site

    NASA Astrophysics Data System (ADS)

    Zachara, J.; Rockhold, M.; Fredrickson, J.; Vermeul, V.; Ward, A.; Liu, C.; McKinley, J.; Bjornstad, B.; Freshley, M.; Haggerty, R.; Kent, D.; Lichtner, P.; Rubin, Y.; Versteeg, R.; Zheng, C.

    2008-12-01

    The U.S. Department of Energy - Environmental Remediation Sciences Division is supporting an Integrated Field Challenge (IFC) Site at Hanford's 300 Area. This site, immediately adjacent to the Columbia R., is the location of a groundwater uranium plume that resulted from past discharges of liquid effluent to unlined disposal ponds and trenches. Plume concentrations have persisted above the drinking water standard in spite of the cessation of all liquid discharges more than 15 years ago and significant efforts to excavate and remove contaminated sediments. The persistence of the uranium plume is postulated to be a result of a complex interplay between hydrological, geochemical, and microbiological processes, and rate-limited mass transfer in the highly heterogeneous sediments. An IFC research site has been established in the area of one of the former disposal ponds to provide the infrastructure for developing improved understanding of the mechanisms responsible for the uranium plume persistence, with an ultimate goal of providing a robust, scientific basis for future remediation decisions. Thirty-five wells were installed at the site in FY08 for subsurface characterization and monitoring of field experiments. Detailed characterization studies have been performed or are currently underway using a variety of hydrological, geophysical, geochemical, and microbiological methods. In addition to field experiments, a series of column and bench-scale transport experiments are being performed to measure process interactions at smaller scales under well-controlled laboratory conditions, and to parameterize mechanistically-based model representations of these processes. This presentation gives an overview of guiding hypotheses for the 300 Area IFC Site, the well layout and instrumentation, initial characterization results, and ongoing or planned experiments and modeling activities.

  1. Integrated Geophysical Analysis at a Legacy Test Site

    NASA Astrophysics Data System (ADS)

    Yang, X.; Mellors, R. J.; Sweeney, J. J.; Sussman, A. J.

    2015-12-01

    We integrate magnetic, electromagnetic (EM), gravity, and seismic data to develop a unified and consistent model of the subsurface at the U20ak site on Pahute Mesa at the Nevada National Nuclear Security Site (NNSS). The 1985 test, conducted in tuff at a depth of approximately 600 m did not collapse to the surface or produce a crater. The purpose of the geophysical measurements is to characterize the subsurface above and around the presumed explosion cavity. The magnetic data are used to locate steel borehole casings and pipes and are correlated with surface observations. The EM data show variation in lithology at depth and clear signatures from borehole casings and surface cables. The gravity survey detects a clear gravity low in the area of the explosion. The seismic data indicates shallow low velocity zone and indications of a deeper low velocity zones. In this study, we conduct 2D inversion of EM data for better characterization of site geology and use a common 3D density model to jointly interpret both the seismic and gravity data along with constraints on lithology boundaries from the EM. The integration of disparate geophysical datasets allows improved understanding of the non-prompt physical signatures of an underground nuclear explosion (UNE). LLNL Release Number: LLNL-ABS-675677. The authors express their gratitude to the National Nuclear Security Administration, Defense Nuclear Nonproliferation Research and Development, and the Comprehensive Inspection Technologies and UNESE working group, a multi-institutional and interdisciplinary group of scientists and engineers. This work was performed by Lawrence Livermore National Laboratory and Los Alamos National Laboratory under award number DE-AC52-06NA25946.

  2. Commercial integration and partnering at Savannah River Site

    SciTech Connect

    Steele, J.R.; Babione, R.A.; Shikashio, L.A.; Wacaster, A.J.; Paterson, A.D.

    1994-06-01

    Savannah River Site (SRS), particularly the Savannah River Technology Center (SRTC) with the experience from the first successful Integrated Technology Demonstration, can provide an excellent foundation for meeting DOE-EM`s objectives with the new DOE-EM five focus area approach. With this in mind, SRTC established an activity to pursue full commercialization of environmental technologies. This report is an assessment of the status of commercialization at SRS and provides recommendations for enhancement as well as some tools critical to implementation. A review was made of the current situation at SRS with regards to taking technology development to commercial fruition. This was done from the perspective of comparing it to known commercialization models and processes. It was found that SRTC already works through many of the steps in these processes. With integration and action-oriented efforts of the inclusion of business and market factors, SRTC could become an aggressive, successful developer of commercialized technologies. Commercial success criteria tools were developed with regards to integrating them with SRTC selection criteria to ensure that all critical factors are covered in technology commercialization project evaluations. Private investors are very clear that their interest lies in funding commercial enterprises, not merely technologies. Mobilizing private capital is critical to real job growth and long-term economic development. Also, potential industry partners were identified that are willing to be involved with SRS` technology applications and regional development efforts. As another important component to success, regional support organizations were reviewed and evaluated.

  3. Arid sites stakeholder participation in evaluating innovative technologies: VOC-Arid Site Integrated Demonstration

    SciTech Connect

    Peterson, T.S.; McCabe, G.H.; Brockbank, B.R.

    1995-05-01

    Developing and deploying innovative environmental cleanup technologies is an important goal for the U.S. Department of Energy (DOE), which faces challenging remediation problems at contaminated sites throughout the United States. Achieving meaningful, constructive stakeholder involvement in cleanup programs, with the aim of ultimate acceptance of remediation decisions, is critical to meeting those challenges. DOE`s Office of Technology Development sponsors research and demonstration of new technologies, including, in the past, the Volatile Organic Compounds Arid Site Integrated Demonstration (VOC-Arid ID), hosted at the Hanford Site in Washington State. The purpose of the VOC-Arid ID has been to develop and demonstrate new technologies for remediating carbon tetrachloride and other VOC contamination in soils and ground water. In October 1994 the VOC-Arid ID became a part of the Contaminant Plume Containment and Remediation Focus Area (Plume Focus Area). The VOC Arid ID`s purpose of involving stakeholders in evaluating innovative technologies will now be carried on in the Plume Focus Area in cooperation with Site Technology Coordination Groups and Site Specific Advisory Boards. DOE`s goal is to demonstrate promising technologies once and deploy those that are successful across the DOE complex. Achieving that goal requires that the technologies be acceptable to the groups and individuals with a stake in DOE facility cleanup. Such stakeholders include groups and individuals with an interest in cleanup, including regulatory agencies, Native American tribes, environmental and civic interest groups, public officials, environmental technology users, and private citizens. This report documents the results of the stakeholder involvement program, which is an integral part of the VOC-Arid ID.

  4. Site-Wide Integrated Water Monitoring -- Defining and Implementing Sampling Objectives to Support Site Closure

    SciTech Connect

    Wilborn, Bill; Marutzky, Sam; Knapp, Kathryn

    2013-02-24

    The Underground Test Area (UGTA) activity is responsible for assessing and evaluating the effects of the underground nuclear weapons tests on groundwater at the Nevada National Security Site (NNSS), formerly the Nevada Test Site (NTS), and implementing a corrective action closure strategy. The UGTA strategy is based on a combination of characterization, modeling studies, monitoring, and institutional controls (i.e., monitored natural attenuation). The closure strategy verifies through appropriate monitoring activities that contaminants of concern do not exceed the SDWA at the regulatory boundary and that adequate institutional controls are established and administered to ensure protection of the public. Other programs conducted at the NNSS supporting the environmental mission include the Routine Radiological Environmental Monitoring Program (RREMP), Waste Management, and the Infrastructure Program. Given the current programmatic and operational demands for various water-monitoring activities at the same locations, and the ever-increasing resource challenges, cooperative and collaborative approaches to conducting the work are necessary. For this reason, an integrated sampling plan is being developed by the UGTA activity to define sampling and analysis objectives, reduce duplication, eliminate unnecessary activities, and minimize costs. The sampling plan will ensure the right data sets are developed to support closure and efficient transition to long-term monitoring. The plan will include an integrated reporting mechanism for communicating results and integrating process improvements within the UGTA activity as well as between other U.S. Department of Energy (DOE) Programs.

  5. Demonstration of Eastman Christensen horizontal drilling system -- Integrated Demonstration Site, Savannah River Site

    SciTech Connect

    Not Available

    1992-12-01

    An innovative horizontal drilling system was used to install two horizontal wells as part of an integrated demonstration project at the Savannah River Site (SRS), Aiken, South Carolina. The SRS is located in south-central South Carolina in the upper Coastal Plain physiographic province. The demonstration site is located near the A/M Area, and is currently known as the Integated Demonstration Site. The Department of Energy's Office of Technology Development initiated an integrated demonstration of innovative technologies for cleanup of volatile organic compounds (VOCS) in soils and groundwater at the SRS in 1989. The overall goal of the program is to demonstrate, at a single location, multiple technologies in the fields of drilling, characterization, monitoring, and remediation. Innovative technologies are compared to one another and to baseline technologies in terms of technical performance and cost effectiveness. Transfer of successfully demonstrated technologies and systems to DOE environmental restoration organizations, to other government agencies, and to industry is a critical part of the program.

  6. Demonstration of Eastman Christensen horizontal drilling system -- Integrated Demonstration Site, Savannah River Site

    SciTech Connect

    Not Available

    1992-12-01

    An innovative horizontal drilling system was used to install two horizontal wells as part of an integrated demonstration project at the Savannah River Site (SRS), Aiken, South Carolina. The SRS is located in south-central South Carolina in the upper Coastal Plain physiographic province. The demonstration site is located near the A/M Area, and is currently known as the Integated Demonstration Site. The Department of Energy`s Office of Technology Development initiated an integrated demonstration of innovative technologies for cleanup of volatile organic compounds (VOCS) in soils and groundwater at the SRS in 1989. The overall goal of the program is to demonstrate, at a single location, multiple technologies in the fields of drilling, characterization, monitoring, and remediation. Innovative technologies are compared to one another and to baseline technologies in terms of technical performance and cost effectiveness. Transfer of successfully demonstrated technologies and systems to DOE environmental restoration organizations, to other government agencies, and to industry is a critical part of the program.

  7. Comparison of Lentiviral Packaging Mixes and Producer Cell Lines for RNAi Applications.

    PubMed

    Albrecht, Christian; Hosiner, Stefanie; Tichy, Brigitte; Aldrian, Silke; Hajdu, Stefan; Nürnberger, Sylvia

    2015-06-01

    Lentiviral transduction is a highly efficient DNA delivery method for RNA interference applications. However, obtaining high lentiviral titers of shRNA and miRNA encoding vectors is challenging, since shRNA and miRNA cassettes have been shown to reduce lentiviral titers. In this study, we compare four commercially available packaging mixes and two producer cell lines in order to optimize lentiviral production for gene silencing experiments. Lentiviral vectors encoding a miRNA sequence and emerald green fluorescence protein were co-transfected with ViraPower™, Lenti-X™ HTX, MISSION(®) Lentiviral or Trans-Lentiviral™ packaging mix in HEK-293T or 293FT cells. After transducing HeLa cells with virus-containing supernatant, lentiviral titers were determined by flow cytomerty. In both cell lines, the highest lentiviral titer was obtained with MISSION(®) Lentiviral packaging mix, followed by ViraPower™, Lenti-X™ HTX, and Trans-Lentiviral™. On average, HEK-293T cells produced 6.2-fold higher lentiviral titers than 293FT cells (p < 0.001). With the combination of MISSION(®) Lentiviral packaging mix and HEK-293T cells, an up to 48.5-fold higher lentiviral titer was reached compared to other packaging mixes and producer cell lines. The optimized selection of packaging mix and cell line described in this work should facilitate the production of high-titer lentiviruses for gene silencing experiments. PMID:25616840

  8. Lentiviral vector production, titration, and transduction of primary neurons.

    PubMed

    Ding, Baojin; Kilpatrick, Daniel L

    2013-01-01

    Lentiviral vectors have become very useful tools for transgene delivery. Based on their ability to transduce both dividing and nondividing cells and to produce long-term transgene expression, lentiviruses have found numerous applications in the biomedical sciences, including developmental neuroscience. This protocol describes how to prepare lentiviral vectors by calcium phosphate transfection and to concentrate viral particles by ultracentrifugation. Functional vector titers can then be determined by methods such as fluorescence-activated cell sorting or immunostaining. Effective titers in the range of 10(8)-10(9) infectious units/ml can be routinely obtained using these protocols. Finally, we describe the infection of primary neuronal cultures with lentiviral vectors resulting in 85-90 % cell transduction using appropriate multiplicities of infection.

  9. Genetic engineering of human embryonic stem cells with lentiviral vectors.

    PubMed

    Xiong, Chen; Tang, Dong-Qi; Xie, Chang-Qing; Zhang, Li; Xu, Ke-Feng; Thompson, Winston E; Chou, Wayne; Gibbons, Gary H; Chang, Lung-Ji; Yang, Li-Jun; Chen, Yuqing E

    2005-08-01

    Human embryonic stem (hES) cells present a valuable source of cells with a vast therapeutic potential. However, the low efficiency of directed differentiation of hES cells remains a major obstacle in their uses for regenerative medicine. While differentiation may be controlled by the genetic manipulation, effective and efficient gene transfer into hES cells has been an elusive goal. Here, we show stable and efficient genetic manipulations of hES cells using lentiviral vectors. This method resulted in the establishment of stable gene expression without loss of pluripotency in hES cells. In addition, lentiviral vectors were effective in conveying the expression of an U6 promoter-driven small interfering RNA (siRNA), which was effective in silencing its specific target. Taken together, our results suggest that lentiviral gene delivery holds great promise for hES cell research and application.

  10. Nevada National Security Site Integrated Groundwater Sampling Plan, Revision 0

    SciTech Connect

    Marutzky, Sam; Farnham, Irene

    2014-10-01

    The purpose of the Nevada National Security Site (NNSS) Integrated Sampling Plan (referred to herein as the Plan) is to provide a comprehensive, integrated approach for collecting and analyzing groundwater samples to meet the needs and objectives of the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Field Office (NNSA/NFO) Underground Test Area (UGTA) Activity. Implementation of this Plan will provide high-quality data required by the UGTA Activity for ensuring public protection in an efficient and cost-effective manner. The Plan is designed to ensure compliance with the UGTA Quality Assurance Plan (QAP). The Plan’s scope comprises sample collection and analysis requirements relevant to assessing the extent of groundwater contamination from underground nuclear testing. This Plan identifies locations to be sampled by corrective action unit (CAU) and location type, sampling frequencies, sample collection methodologies, and the constituents to be analyzed. In addition, the Plan defines data collection criteria such as well-purging requirements, detection levels, and accuracy requirements; identifies reporting and data management requirements; and provides a process to ensure coordination between NNSS groundwater sampling programs for sampling of interest to UGTA. This Plan does not address compliance with requirements for wells that supply the NNSS public water system or wells involved in a permitted activity.

  11. Efficient biotechnological approach for lentiviral transduction of induced pluripotent stem cells.

    PubMed

    Zare, Mehrak; Soleimani, Masoud; Mohammadian, Mozhdeh; Akbarzadeh, Abolfazl; Havasi, Parvaneh; Zarghami, Nosratollah

    2016-01-01

    Induced pluripotent stem (iPS) cells are generated from differentiated adult somatic cells by reprogramming them. Unlimited self-renewal, and the potential to differentiate into any cell type, make iPS cells very promising candidates for basic and clinical research. Furthermore, iPS cells can be genetically manipulated for use as therapeutic tools. DNA can be introduced into iPS cells, using lentiviral vectors, which represent a helpful choice for efficient transduction and stable integration of transgenes. In this study, we compare two methods of lentiviral transduction of iPS cells, namely, the suspension method and the hanging drop method. In contrast to the conventional suspension method, in the hanging drop method, embryoid body (EB) formation and transduction occur concurrently. The iPS cells were cultured to form EBs, and then transduced with lentiviruses, using the conventional suspension method and the hanging drop method, to express miR-128 and green fluorescent protein (GFP). The number of transduced cells were assessed by fluorescent microscopy and flow cytometry. MTT assay and real-time PCR were performed to determine the cell viability and transgene expression, respectively. Morphologically, GFP+ cells were more detectable in the hanging drop method, and this finding was quantified by flow cytometric analysis. According to the results of the MTT assay, cell viability was considerably higher in the hanging drop method, and real-time PCR represented a higher relative expression of miR-128 in the iPS cells introduced with lentiviruses in drops. Altogether, it seems that lentiviral transduction of challenging iPS cells using the hanging drop method offers a suitable and sufficient strategy in their gene transfer, with less toxicity than the conventional suspension method.

  12. BIOTIC INTEGRITY OF STREAMS IN THE SAVANNAH RIVER SITE INTEGRATOR OPERABLE UNITS, 1996 TO 2003

    SciTech Connect

    Paller, M; Susan Dyer, S

    2004-11-08

    The Savannah River Site (SRS) has been divided into six Integrator Operable Units (IOUs) that correspond to the watersheds of the five major streams on the SRS (Upper Three Runs, Fourmile Branch, Pen Branch, Steel Creek, and Lower Three Runs) and the portions of the Savannah River and Savannah River Swamp associated with the SRS. The streams are the primary integrators within each IOU because they potentially receive, through surface or subsurface drainage, soluble contaminants from all waste sites within their watersheds. If these contaminants reach biologically significant levels, they would be expected to effect the numbers, types, and health of stream organisms. In this study, biological sampling was conducted within each IOU as a measure of the cumulative ecological effects of the waste sites within the IOUs. The use of information from biological sampling to assess environmental quality is often termed bioassessment. The IOU bioassessment program included 38 sites in SRS streams and nine sites in the Savannah River. Sampling was conducted in 1996 to 1998, 2000, and 2003. Four bioassessment methods were used to evaluate ecological conditions in the IOU streams: the Index of Biotic Integrity, the Fish Health Assessment Index, measurement of fish tissue contaminant levels, and two benthic macroinvertebrate indices. The Index of Biotic Integrity (IBI) is an EPA supported method based on comparison of ecologically important and sensitive fish assemblage variables between potentially disturbed and reference (i.e., undisturbed) sites. It is designed to assess the ability of a stream to support a self-sustaining biological community and ecological processes typical of undisturbed, natural conditions. Since many types of contaminants can bioaccumulate, fish tissue contaminant data were used to determine the types of chemicals fish were exposed to and their relative magnitudes among IOUs. The Fish Health Assessment Index (HAI) is an EPA supported method for assessing

  13. Site Characterization of Deep Bedrock with Integrated Geophysical Survey

    NASA Astrophysics Data System (ADS)

    Son, J.; Kim, C.; Eun, S. B.

    2015-12-01

    In order to utilize the deep underground storage facility stable for a long time, precise site characterization is required before its construction. Various kinds of geophysical survey as well as drilling and geological survey should be used to know the status of deep bedrock. A research had been conducted to make the site characterization of deep bedrock for several years, and to achieve its purpose, integrated geophysical survey were applied to the test area which had gneiss bedrock. DC resistivity survey for six surficial profiles was conducted to find the appropriate location of drilling survey. Cross-hole/surface-to-hole resistivity tomography survey and borehole reflection radar survey were applied to the drill holes after its installation completed. Three bore holes of which length was 500 meter were drilled to investigate the status of deep bedrock, and cross-hole tomography survey was applied between two boreholes among these. Also borehole reflection radar survey was conducted to another two boreholes. Deep seated fracture zones which were not identified with the surficial geological and resistivity survey were found through the analysis of tomography section. Fracture zones were consisted of steep slope fault and these were also identified with the result of borehole radar section. After the basic survey was completed, one of three holes was extended to the depth of 1 km. Radar reflection survey which was only available to the deep drill-hole was applied. Because steel casing was installed to the depth of 750 m to stabilize the extended drill-hole, resistivity method was not available and borehole radar reflection method was only available among the geophysical method used in this research. Through results of radar reflection survey, several fracture zones were identified for the newly extended section of drill hole and some of those facture has relatively large size and passed through the bore hole.

  14. Lentiviral Hematopoietic Stem Cell Gene Therapy in Inherited Metabolic Disorders

    PubMed Central

    2014-01-01

    Abstract After more than 20 years of development, lentiviral hematopoietic stem cell gene therapy has entered the stage of initial clinical implementation for immune deficiencies and storage disorders. This brief review summarizes the development and applications, focusing on the lysosomal enzyme deficiencies, especially Pompe disease. PMID:25184354

  15. Repeat Hydrography at the Endeavour Integrated Study Site, 2004 - 2006

    NASA Astrophysics Data System (ADS)

    Kellogg, J. P.; McDuff, R. E.; Thomson, R. E.; Stahr, F. R.

    2006-12-01

    Significant differences exist between hydrographic transects made in the summers from 2004 to 2006 at the Endeavour Segment Integrated Study Site on the Juan de Fuca Ridge. Along and across axis sections describe the hydrographic conditions above the segment in three dimensions. The resulting sections allow for rapid evaluation of the characteristics of the neutrally buoyant plume over each of the vent fields and its location relative to the ridge axis. Results indicate heat content over the northern vent fields, Salty Dawg and Sasquatch, significantly increased between the summers of 2004 and 2005. In 2004, the plumes over these vent fields were barely discernable while in 2005 prominent plumes existed with potential temperature anomalies over 0.1°C. At the time of a rapid response cruise in March 2005, no significant change in the heat content of the water column was detected. By July 2005, dramatic changes had occurred in the overlying water column structure. The potential temperature anomaly section from 2005 is indicative of a thicker (about 75 m) neutrally buoyant plume with and substantially more heat at the north end of the valley. In 2004, the shallowest plume depth was 1900 m contrasted with 1830 m in 2005. Vent data being obtained by other RIDGE 2000 and UW Keck investigators will help constrain the underlying causes of these changes. New hydrography will be collected in August September 2006.

  16. Repeat Hydrography at the Endeavour Integrated Study Site, 2004 - 2005

    NASA Astrophysics Data System (ADS)

    Kellogg, J. P.; McDuff, R. E.; Thomson, R. E.; Stahr, F. R.

    2005-12-01

    Significant differences exist between hydrographic transects made in 2004 and 2005 at the Endeavour Segment Integrated Study Site on the Juan de Fuca Ridge. Sections that describe the conditions above the segment utilize twenty-one nearly uniformly spaced hydrographic stations from south of Mothra to north of the Sasquatch hydrothermal vent fields. Criteria used in choosing station locations included depth, ~500 m spacing from other stations, and being centrally located in the valley. The resulting sections allow for rapid evaluation of the characteristics of the neutrally buoyant plume over each of the vent fields. Preliminary results indicate heat content over the northern vent fields, Salty Dawg and Sasquatch, significantly increased between the summers of 2004 and 2005. In 2004, the plumes over these vent fields were barely discernable while in 2005 prominent plumes existed with potential temperature anomalies over 0.1°C. Vent data being obtained by other RIDGE 2000 and UW Keck investigators will help constrain the underlying causes of these changes. Isopycnals in the 2005 sections are also elevated along the entire length of the transect by approximately 50 m or more. The potential temperature anomaly section from 2005 is indicative of a thicker (about 75 m) neutrally buoyant plume and substantially more heat at the north end of the valley. In 2004, the shallowest plume depth was 1900 m contrasted with 1830 m in 2005.

  17. Current Research at the Endeavour Ridge 2000 Integrated Studies Site

    NASA Astrophysics Data System (ADS)

    Butterfield, D. A.; Kelley, D. S.; Ridge 2000 Community, R.

    2004-12-01

    Integrated geophysical, geological, chemical, and biological studies are being conducted on the Endeavour segment with primary support from NSF, the W.M. Keck Foundation, and NSERC (Canada). The research includes a seismic network, physical and chemical sensors, high-precision mapping and time-series sampling. Several research expeditions have taken place at the Endeavour ISS in the past year. In June 2003, an NSF-sponsored cruise with R.V. al T.G.Thompson/ROV al Jason2 installed microbial incubators in drill-holes in the sides of active sulfide chimneys and sampled rocks, fluids, and microbes in the Mothra and Main Endeavour Field (MEF). In July 2003, with al Thompson/Jason2, an NSF-LEXEN project at Baby Bare on Endeavour east flank conducted sampling through seafloor-penetrating probes, plus time-series sampling of fluids, microbes, and rocks at the MEF. In September 2003, with al Thompson/ROV al ROPOS, the Keck Proto-Neptune project installed a seismic network consisting of 1 broadband and 7 short-period seismometers, installation of chemical/physical sensors and time-series samplers for chemistry and microbiology in the MEF and Clam Bed sites, collection of rocks, fluids, animals, and microbes. In May/June 2004, an NSF-sponsored al Atlantis/Alvin cruise recovered sulfide incubators installed in 2003, redeployed a sulfide incubator, mapped MEF and Mothra vent fields with high-resolution Imagenix sonar, sampled fluids from MEF, Mothra, and Clam Bed, recovered year-long time-series fluid and microbial samplers from MEF and Clam Bed, recovered and installed hot vent temperature-resistivity monitors, cleaned up the MEF and deployed new markers at major sulfide structures. In August 2004, there were two MBARI/Keck-sponsored cruises with R.V. al Western Flyer/ROV al Tiburon. The first cruise completed the seismic network with addition of two more broadband seismometers and serviced all 7 short-period seismometers. al Tiburon then performed microbial and chemical

  18. Integrated Mapping and Imaging at a Legacy Test Site (Invited)

    NASA Astrophysics Data System (ADS)

    Sussman, A. J.; Schultz-Fellenz, E. S.; Kelley, R. E.; Sweeney, J. J.; Vigil, S.; DiBenedetto, J.; Chipman, V.

    2013-12-01

    A team of multi-disciplinary geoscientists was tasked to characterize and evaluate a legacy nuclear detonation site in order to develop research locations with the long-term goal of improving treaty monitoring, verification, and other national security applications. There was a test at the site of interest that was detonated on June 12, 1985 in a vertical emplacement borehole at a depth of 608m below the surface in rhyolites. With announced yield of 20-150 kt, the event did not collapse to the surface and form a crater, but rather experienced a subsurface collapse with more subtle surface expressions of deformation. This result provides the team with an opportunity to evaluate a number of surface and subsurface inspection technologies in a broad context. The team collected ground-based visual observation, ground penetrating radar, electromagnetic, ground-based and airborne LiDAR, ground-based and airborne hyperspectral, gravity and magnetics, dc and induction electrical methods, and active seismic data during field campaigns in the summers of 2012 and 2013. Detection of features was performed using various approaches that were assessed for accuracy, efficiency and diversity of target features. For example, whereas the primary target of the ground-based visual observation survey was to map the surface features, the target of the gravity survey was to attempt the detection of a possible subsurface collapse zone which might be located as little as 200 meters below the surface. The datasets from surveys described above are integrated into a geographical information system (GIS) database for analysis and visualization. Other presentations during this session provide further details as to some of the work conducted. Work by Los Alamos National Laboratory and Lawrence Livermore National Laboratory was sponsored by the National Nuclear Security Administration Award No. DE-AC52-06NA25946/NST10-NCNS-PD00. Work by National Security Technologies, LLC, was performed under

  19. Initial Characterization of Integrase-Defective Lentiviral Vectors for Pancreatic Cancer Gene Therapy.

    PubMed

    Hanoun, Naima; Gayral, Marion; Pointreau, Adeline; Buscail, Louis; Cordelier, Pierre

    2016-02-01

    The vast majority (85%) of pancreatic ductal adenocarcinomas (PDACs) are discovered at too of a late stage to allow curative surgery. In addition, PDAC is highly resistant to conventional methods of chemotherapy and radiotherapy, which only offer a marginal clinical benefit. Consequently, the prognosis of this cancer is devastating, with a 5-year survival rate of less than 5%. In this dismal context, we recently demonstrated that PDAC gene therapy using nonviral vectors is safe and feasible, with early signs of efficacy in selected patients. Our next step is to transfer to the clinic HIV-1-based lentiviral vectors (LVs) that outshine other therapeutic vectors to treat experimental models of PDAC. However, a primary safety issue presented by LVs that may delay their use in patients is the risk of oncogenesis after vector integration in the host's cell DNA. Thus, we developed a novel anticancerous approach based on integrase-defective lentiviral vectors (IDLVs) and demonstrated that IDLVs can be successfully engineered to transiently deliver therapeutic genes to inhibit pancreatic cancer cells proliferation. This work stems for the use of therapeutic IDLVs for the management of PDAC, in forthcoming early phase gene therapy clinical trial for this disease with no cure. PMID:26731312

  20. Rescue of splicing-mediated intron loss maximizes expression in lentiviral vectors containing the human ubiquitin C promoter.

    PubMed

    Cooper, Aaron R; Lill, Georgia R; Gschweng, Eric H; Kohn, Donald B

    2015-01-01

    Lentiviral vectors almost universally use heterologous internal promoters to express transgenes. One of the most commonly used promoter fragments is a 1.2-kb sequence from the human ubiquitin C (UBC) gene, encompassing the promoter, some enhancers, first exon, first intron and a small part of the second exon of UBC. Because splicing can occur after transcription of the vector genome during vector production, we investigated whether the intron within the UBC promoter fragment is faithfully transmitted to target cells. Genetic analysis revealed that more than 80% of proviral forms lack the intron of the UBC promoter. The human elongation factor 1 alpha (EEF1A1) promoter fragment intron was not lost during lentiviral packaging, and this difference between the UBC and EEF1A1 promoter introns was conferred by promoter exonic sequences. UBC promoter intron loss caused a 4-fold reduction in transgene expression. Movement of the expression cassette to the opposite strand prevented intron loss and restored full expression. This increase in expression was mostly due to non-classical enhancer activity within the intron, and movement of putative intronic enhancer sequences to multiple promoter-proximal sites actually repressed expression. Reversal of the UBC promoter also prevented intron loss and restored full expression in bidirectional lentiviral vectors.

  1. Human adipose derived mesenchymal stromal cells transduced with GFP lentiviral vectors: assessment of immunophenotype and differentiation capacity in vitro.

    PubMed

    van Vollenstee, Fiona A; Jackson, Carlo; Hoffmann, Danie; Potgieter, Marnie; Durandt, Chrisna; Pepper, Michael S

    2016-10-01

    Adipose derived mesenchymal stromal/stem cells (ASCs) are a heterogeneous population characterized by (a) their ability to adhere to plastic; (b) immunophenotypic expression of certain cell surface markers, while lacking others; and (c) the capacity to differentiate into lineages of mesodermal origin including osteocytes, chondrocytes and adipocytes. The long-term goal is to utilize these cells for clinical translation into cell-based therapies. However, preclinical safety and efficacy need to be demonstrated in animal models. ASCs can also be utilized as biological vehicles for vector-based gene delivery systems, since they are believed to home to sites of inflammation and infection in vivo. These factors motivated the development of a labelling system for ASCs using lentiviral vector-based green fluorescent protein (GFP) transduction. Human ASCs were transduced with GFP-expressing lentiviral vectors. A titration study determined the viral titer required to transduce the maximum number of ASCs. The effect of the transduced GFP lentiviral vector on ASC immunophenotypic expression of surface markers as well as their ability to differentiate into osteocytes and adipocytes were assessed in vitro. A transduction efficiency in ASC cultures of approximately 80 % was observed with an MOI of ~118. No significant immunophenotypic differences were observed between transduced and non-transduced cells and both cell types successfully differentiated into adipocytes and osteocytes in vitro. We obtained >80 % transduction of ASCs using GFP lentiviral vectors. Transduced ASCs maintained plastic adherence, demonstrated ASC immunophenotype and the ability to differentiate into cells of the mesodermal lineage. This GFP-ASC transduction technique offers a potential tracking system for future pre-clinical studies.

  2. Endogenous Lentiviral Elements in the Weasel Family (Mustelidae)

    PubMed Central

    Han, Guan-Zhu; Worobey, Michael

    2012-01-01

    Endogenous retroviruses provide molecular fossils for studying the ancient evolutionary history of retroviruses. Here, we report our independent discovery and analysis of endogenous lentiviral insertions (Mustelidae endogenous lentivirus [MELV]) within the genomes of weasel family (Mustelidae). Genome-scale screening identified MELV elements in the domestic ferret (Mustela putorius furo) genome (MELVmpf). MELVmpf exhibits a typical lentiviral genomic organization. Phylogenetic analyses position MELVmpf basal to either primate lentiviruses or feline immunodeficiency virus. Moreover, we verified the presence of MELV insertions in the genomes of several species of the Lutrinae and Mustelinae subfamilies but not the Martinae subfamily, suggesting that the invasion of MELV into the Mustelidae genomes likely took place between 8.8 and 11.8 Ma. The discovery of MELV in weasel genomes extends the host range of lentiviruses to the Caniformia (order Carnivora) and provides important insights into the prehistoric diversity of lentiviruses. PMID:22522310

  3. Endogenous lentiviral elements in the weasel family (Mustelidae).

    PubMed

    Han, Guan-Zhu; Worobey, Michael

    2012-10-01

    Endogenous retroviruses provide molecular fossils for studying the ancient evolutionary history of retroviruses. Here, we report our independent discovery and analysis of endogenous lentiviral insertions (Mustelidae endogenous lentivirus [MELV]) within the genomes of weasel family (Mustelidae). Genome-scale screening identified MELV elements in the domestic ferret (Mustela putorius furo) genome (MELVmpf). MELVmpf exhibits a typical lentiviral genomic organization. Phylogenetic analyses position MELVmpf basal to either primate lentiviruses or feline immunodeficiency virus. Moreover, we verified the presence of MELV insertions in the genomes of several species of the Lutrinae and Mustelinae subfamilies but not the Martinae subfamily, suggesting that the invasion of MELV into the Mustelidae genomes likely took place between 8.8 and 11.8 Ma. The discovery of MELV in weasel genomes extends the host range of lentiviruses to the Caniformia (order Carnivora) and provides important insights into the prehistoric diversity of lentiviruses.

  4. Pervasive supply of therapeutic lysosomal enzymes in the CNS of normal and Krabbe-affected non-human primates by intracerebral lentiviral gene therapy.

    PubMed

    Meneghini, Vasco; Lattanzi, Annalisa; Tiradani, Luigi; Bravo, Gabriele; Morena, Francesco; Sanvito, Francesca; Calabria, Andrea; Bringas, John; Fisher-Perkins, Jeanne M; Dufour, Jason P; Baker, Kate C; Doglioni, Claudio; Montini, Eugenio; Bunnell, Bruce A; Bankiewicz, Krystof; Martino, Sabata; Naldini, Luigi; Gritti, Angela

    2016-05-02

    Metachromatic leukodystrophy (MLD) and globoid cell leukodystrophy (GLD or Krabbe disease) are severe neurodegenerative lysosomal storage diseases (LSD) caused by arylsulfatase A (ARSA) and galactosylceramidase (GALC) deficiency, respectively. Our previous studies established lentiviral gene therapy (GT) as a rapid and effective intervention to provide pervasive supply of therapeutic lysosomal enzymes in CNS tissues of MLD and GLD mice. Here, we investigated whether this strategy is similarly effective in juvenile non-human primates (NHP). To provide proof of principle for tolerability and biological efficacy of the strategy, we established a comprehensive study in normal NHP delivering a clinically relevant lentiviral vector encoding for the human ARSA transgene. Then, we injected a lentiviral vector coding for the human GALC transgene in Krabbe-affected rhesus macaques, evaluating for the first time the therapeutic potential of lentiviral GT in this unique LSD model. We showed favorable safety profile and consistent pattern of LV transduction and enzyme biodistribution in the two models, supporting the robustness of the proposed GT platform. We documented moderate inflammation at the injection sites, mild immune response to vector particles in few treated animals, no indication of immune response against transgenic products, and no molecular evidence of insertional genotoxicity. Efficient gene transfer in neurons, astrocytes, and oligodendrocytes close to the injection sites resulted in robust production and extensive spreading of transgenic enzymes in the whole CNS and in CSF, leading to supraphysiological ARSA activity in normal NHP and close to physiological GALC activity in the Krabbe NHP, in which biological efficacy was associated with preliminary indication of therapeutic benefit. These results support the rationale for the clinical translation of intracerebral lentiviral GT to address CNS pathology in MLD, GLD, and other neurodegenerative LSD.

  5. Pervasive supply of therapeutic lysosomal enzymes in the CNS of normal and Krabbe-affected non-human primates by intracerebral lentiviral gene therapy.

    PubMed

    Meneghini, Vasco; Lattanzi, Annalisa; Tiradani, Luigi; Bravo, Gabriele; Morena, Francesco; Sanvito, Francesca; Calabria, Andrea; Bringas, John; Fisher-Perkins, Jeanne M; Dufour, Jason P; Baker, Kate C; Doglioni, Claudio; Montini, Eugenio; Bunnell, Bruce A; Bankiewicz, Krystof; Martino, Sabata; Naldini, Luigi; Gritti, Angela

    2016-01-01

    Metachromatic leukodystrophy (MLD) and globoid cell leukodystrophy (GLD or Krabbe disease) are severe neurodegenerative lysosomal storage diseases (LSD) caused by arylsulfatase A (ARSA) and galactosylceramidase (GALC) deficiency, respectively. Our previous studies established lentiviral gene therapy (GT) as a rapid and effective intervention to provide pervasive supply of therapeutic lysosomal enzymes in CNS tissues of MLD and GLD mice. Here, we investigated whether this strategy is similarly effective in juvenile non-human primates (NHP). To provide proof of principle for tolerability and biological efficacy of the strategy, we established a comprehensive study in normal NHP delivering a clinically relevant lentiviral vector encoding for the human ARSA transgene. Then, we injected a lentiviral vector coding for the human GALC transgene in Krabbe-affected rhesus macaques, evaluating for the first time the therapeutic potential of lentiviral GT in this unique LSD model. We showed favorable safety profile and consistent pattern of LV transduction and enzyme biodistribution in the two models, supporting the robustness of the proposed GT platform. We documented moderate inflammation at the injection sites, mild immune response to vector particles in few treated animals, no indication of immune response against transgenic products, and no molecular evidence of insertional genotoxicity. Efficient gene transfer in neurons, astrocytes, and oligodendrocytes close to the injection sites resulted in robust production and extensive spreading of transgenic enzymes in the whole CNS and in CSF, leading to supraphysiological ARSA activity in normal NHP and close to physiological GALC activity in the Krabbe NHP, in which biological efficacy was associated with preliminary indication of therapeutic benefit. These results support the rationale for the clinical translation of intracerebral lentiviral GT to address CNS pathology in MLD, GLD, and other neurodegenerative LSD. PMID

  6. Lentiviral transgenesis--a versatile tool for basic research and gene therapy.

    PubMed

    Pfeifer, Alexander

    2006-08-01

    Transgenic animals are of outstanding relevance for medical sciences, because they can be used to model human diseases and to develop gene therapy strategies. A recent development is lentiviral transgenesis: The generation of transgenic animals by lentiviral transduction of oocytes or early embryos. Lentiviral transgenesis is an efficient method to express transgenes in mice and rats as well as in biomedically relevant livestock. Thus, the applications of this technology range from the generation of disease models to gene pharming for human proteins. An important extension of viral transgenesis is the combination of lentiviral gene transfer with RNA interference. Thereby, expression of specific genes can be silenced and loss-of-function models can be generated. Finally, lentiviral transgenic animals can be used to directly evaluate gene therapy strategies that are based on lentiviral vectors prior to their use in humans.

  7. Lentiviral transgenesis--a versatile tool for basic research and gene therapy.

    PubMed

    Pfeifer, Alexander

    2006-08-01

    Transgenic animals are of outstanding relevance for medical sciences, because they can be used to model human diseases and to develop gene therapy strategies. A recent development is lentiviral transgenesis: The generation of transgenic animals by lentiviral transduction of oocytes or early embryos. Lentiviral transgenesis is an efficient method to express transgenes in mice and rats as well as in biomedically relevant livestock. Thus, the applications of this technology range from the generation of disease models to gene pharming for human proteins. An important extension of viral transgenesis is the combination of lentiviral gene transfer with RNA interference. Thereby, expression of specific genes can be silenced and loss-of-function models can be generated. Finally, lentiviral transgenic animals can be used to directly evaluate gene therapy strategies that are based on lentiviral vectors prior to their use in humans. PMID:16918338

  8. Prioritizing functional phosphorylation sites based on multiple feature integration

    PubMed Central

    Xiao, Qingyu; Miao, Benpeng; Bi, Jie; Wang, Zhen; Li, Yixue

    2016-01-01

    Protein phosphorylation is an important type of post-translational modification that is involved in a variety of biological activities. Most phosphorylation events occur on serine, threonine and tyrosine residues in eukaryotes. In recent years, many phosphorylation sites have been identified as a result of advances in mass-spectrometric techniques. However, a large percentage of phosphorylation sites may be non-functional. Systematically prioritizing functional sites from a large number of phosphorylation sites will be increasingly important for the study of their biological roles. This study focused on exploring the intrinsic features of functional phosphorylation sites to predict whether a phosphosite is likely to be functional. We found significant differences in the distribution of evolutionary conservation, kinase association, disorder score, and secondary structure between known functional and background phosphorylation datasets. We built four different types of classifiers based on the most representative features and found that their performances were similar. We also prioritized 213,837 human phosphorylation sites from a variety of phosphorylation databases, which will be helpful for subsequent functional studies. All predicted results are available for query and download on our website (Predict Functional Phosphosites, PFP, http://pfp.biosino.org/). PMID:27090940

  9. Transduction of Murine Hematopoietic Stem Cells with Tetracycline-regulated Lentiviral Vectors.

    PubMed

    Stahlhut, Maike; Schambach, Axel; Kustikova, Olga S

    2016-01-01

    Tetracycline-regulated integrating vectors allow pharmacologically controlled genetic modification of murine and human hematopoietic stem cells (HSCs). This approach combines the stable transgene insertion into a host genome with the opportunity for time- and dose-controlled reversible transgene expression in HSCs. Here, we describe the step-by-step protocol for transduction of murine stem-cell enriched populations of bone marrow cells, such as lineage negative cells (Lin(-)), with a lentiviral vector expressing the enhanced green fluorescent protein (EGFP) under the control of the tetracycline-regulated promoter. This chapter explains how to establish in vitro and in vivo systems to study transgene dose-dependent mechanisms affecting cell fate decisions of genetically modified hematopoietic cells. PMID:27317173

  10. Generation of a lentiviral vector producer cell clone for human Wiskott-Aldrich syndrome gene therapy.

    PubMed

    Wielgosz, Matthew M; Kim, Yoon-Sang; Carney, Gael G; Zhan, Jun; Reddivari, Muralidhar; Coop, Terry; Heath, Richard J; Brown, Scott A; Nienhuis, Arthur W

    2015-01-01

    We have developed a producer cell line that generates lentiviral vector particles of high titer. The vector encodes the Wiskott-Aldrich syndrome (WAS) protein. An insulator element has been added to the long terminal repeats of the integrated vector to limit proto-oncogene activation. The vector provides high-level, stable expression of WAS protein in transduced murine and human hematopoietic cells. We have also developed a monoclonal antibody specific for intracellular WAS protein. This antibody has been used to monitor expression in blood and bone marrow cells after transfer into lineage negative bone marrow cells from WAS mice and in a WAS negative human B-cell line. Persistent expression of the transgene has been observed in transduced murine cells 12-20 weeks following transplantation. The producer cell line and the specific monoclonal antibody will facilitate the development of a clinical protocol for gene transfer into WAS protein deficient stem cells. PMID:26052531

  11. Generation of a lentiviral vector producer cell clone for human Wiskott-Aldrich syndrome gene therapy.

    PubMed

    Wielgosz, Matthew M; Kim, Yoon-Sang; Carney, Gael G; Zhan, Jun; Reddivari, Muralidhar; Coop, Terry; Heath, Richard J; Brown, Scott A; Nienhuis, Arthur W

    2015-01-01

    We have developed a producer cell line that generates lentiviral vector particles of high titer. The vector encodes the Wiskott-Aldrich syndrome (WAS) protein. An insulator element has been added to the long terminal repeats of the integrated vector to limit proto-oncogene activation. The vector provides high-level, stable expression of WAS protein in transduced murine and human hematopoietic cells. We have also developed a monoclonal antibody specific for intracellular WAS protein. This antibody has been used to monitor expression in blood and bone marrow cells after transfer into lineage negative bone marrow cells from WAS mice and in a WAS negative human B-cell line. Persistent expression of the transgene has been observed in transduced murine cells 12-20 weeks following transplantation. The producer cell line and the specific monoclonal antibody will facilitate the development of a clinical protocol for gene transfer into WAS protein deficient stem cells.

  12. Surface engineering of lentiviral vectors for gene transfer into gene therapy target cells.

    PubMed

    Lévy, Camille; Verhoeyen, Els; Cosset, François-Loïc

    2015-10-01

    Since they allow gene integration into their host genome, lentiviral vectors (LVs) have strong therapeutic potentials, as emphasized by recent clinical trials. The surface-display of the pantropic vesicular stomatitis virus G glycoprotein (VSV-G) on LVs resulted in powerful tools for fundamental and clinical research. However, improved LVs are required either to genetically modify cell types not permissive to classical VSV-G-LVs or to restrict entry to specific cell types. Incorporation of heterologous viral glycoproteins (gps) on LVs often require modification of their cytoplasmic tails and ligands can be inserted into their ectodomain to target LVs to specific receptors. Recently, measles virus (MV) gps have been identified as strong candidates for LV-retargeting to multiple cell types, with the potential to evolve toward clinical applications.

  13. Therapeutic benefit of lentiviral-mediated neonatal intracerebral gene therapy in a mouse model of globoid cell leukodystrophy.

    PubMed

    Lattanzi, Annalisa; Salvagno, Camilla; Maderna, Claudio; Benedicenti, Fabrizio; Morena, Francesco; Kulik, Willem; Naldini, Luigi; Montini, Eugenio; Martino, Sabata; Gritti, Angela

    2014-06-15

    Globoid cell leukodystrophy (GLD) is an inherited lysosomal storage disease caused by β-galactocerebrosidase (GALC) deficiency. Gene therapy (GT) should provide rapid, extensive and lifetime GALC supply in central nervous system (CNS) tissues to prevent or halt irreversible neurologic progression. Here we used a lentiviral vector (LV) to transfer a functional GALC gene in the brain of Twitcher mice, a severe GLD model. A single injection of LV.GALC in the external capsule of Twitcher neonates resulted in robust transduction of neural cells with minimal and transient activation of inflammatory and immune response. Importantly, we documented a proficient transduction of proliferating and post-mitotic oligodendroglia, a relevant target cell type in GLD. GALC activity (30-50% of physiological levels) was restored in the whole CNS of treated mice as early as 8 days post-injection. The early and stable enzymatic supply ensured partial clearance of storage and reduction of psychosine levels, translating in amelioration of histopathology and enhanced lifespan. At 6 months post-injection in non-affected mice, LV genome persisted exclusively in the injected region, where transduced cells overexpressed GALC. Integration site analysis in transduced brain tissues showed no aberrant clonal expansion and preferential targeting of neural-specific genes. This study establishes neonatal LV-mediated intracerebral GT as a rapid, effective and safe therapeutic intervention to correct CNS pathology in GLD and provides a strong rationale for its application in this and similar leukodystrophies, alone or in combination with therapies targeting the somatic pathology, with the final aim of providing an effective and timely treatment of these global disorders.

  14. Enhancing Students' Thinking Skills: Exploring Model Technology-Integration Sites.

    ERIC Educational Resources Information Center

    Moersch, Christopher

    1998-01-01

    Examines ways to integrate technology into social studies, science, mathematics, and language arts. Describes model elementary and middle-school classrooms in which technology is used to investigate the concept of property, study soil porosity and the water cycle, run a student store, and promote environmental activism. (PEN)

  15. Low titer lentiviral transgenesis in rodents with simian immundeficiency virus vector.

    PubMed

    Bender, Balázs; Hoffmann, Orsolya Ivett; Negre, Didier; Kvell, Krisztián; Bősze, Zsuzsanna; Hiripi, László

    2013-09-01

    Efficient production of transgenic animals using low-titer lentiviral constructs remains challenging. Here we demonstrate that microinjection of simian immundeficiency virus-derived lentiviral constructs can produce transgenic mice and rats with high efficiency even when using low-titer virus preparations.

  16. Lentiviral vector-mediated transduction of goat undifferentiated spermatogonia.

    PubMed

    Abbasi, Hassan; Hosseini, Sayyed Morteza; Hajian, Mahdi; Nasiri, Zahra; Bahadorani, Mehrnoosh; Tahmoorespur, Mojtaba; Nasiri, Mohammad Reza; Nasr-Esfahani, Mohammad Hossein

    2015-12-01

    Recent studies show that spermatogonial stem cells (SSCs) are able to colonize and form mature spermatozoa following transplantation into germ cell depleted testes of recipient males. Therefore, efficient ways for enrichment and gene transfer into SSCs provides a powerful tool for production of transgenic animals. In order to adapt the technique to goats, three issues were addressed: (i) enrichment of the undifferentiated spermatogonia including SSCs using magnetic activated cell sorting (MACS), (ii) lentiviral vector-mediated transduction of an enhanced green fluorescent protein (EGFP) transgene into enriched cells, and (iii) transplantation of transduced undifferentiated spermatogonia into the germ cell depleted testes of immune-suppressed mice to assess for migration and colony formation ability. Enriched cells were transduced by lentiviral vectors and subsequently analyzed for expression of THY1, PLZF, VASA, UCHL1 and BCL6B genes. Cells were also analyzed for GFP and PLZF by flow cytometry. Enriched transduced cells were transplanted into germ cell depleted mice testis. Quantitative analysis of transcripts revealed that MACS-enrichment significantly increased the expression of SSC-characteristic genes THY1, PLZF, VASA, UCHL1 and BCL6B compared to non-enriched population (P≤0.05). EGFP transduction did not affect the expression levels of SSC-characteristic genes. Flow cytometry revealed that 72% of transduced-enriched cells were positive for EGFP. Finally, transduced-enriched goat SSCs could colonize within the cells into the seminiferous tubules of germ cell depleted recipient mice at higher frequency than non-enriched cells. The results indicated that enrichment of goat undifferentiated spermatogonia by magnetic-activated cell sorting for THY1 antibody combined with lentiviral vector-mediated transduction has the potential to be used for production of transgenic goats.

  17. Using Pulmozyme DNase treatment in lentiviral vector production.

    PubMed

    Shaw, Aaron; Bischof, Daniela; Jasti, Aparna; Ernstberger, Aaron; Hawkins, Troy; Cornetta, Kenneth

    2012-02-01

    In the production of lentiviral vector for clinical studies the purity of the final product is of vital importance. To remove plasmid and producer cell line DNA, investigators have incubated the vector product with Benzonase, a bacterially derived DNase. As an alternative we investigated the use of Pulmozyme, a U.S. Food and Drug Administration-approved human DNase for the treatment of cystic fibrosis, by comparing the efficiency of DNA removal from lentiviral vector preparations. A green fluorescent protein-expressing lentiviral vector was prepared by transient calcium phosphate transfection of HEK 293T cells and DNA removal was compared when treating vector after harvest or immediately after transfection. The effectiveness of DNase treatment was measured by quantitative PCR using primers for vesicular stomatitis virus glycoprotein G viral envelope plasmid. When treating the final product, 1-hr incubations (37°C) with Pulmozyme at 20 U/ml reduced plasmid DNA to undetectable levels. Longer incubations (up to 4 hr) did not improve DNA removal at lower concentrations and the effectiveness was equivalent to or better than Benzonase at 50 U/ml. Attempting to use Pulmozyme immediately after transfection, but before final medium change, as a means to decrease Pulmozyme concentration in the final product provided a 2-log reduction in DNA but was inferior to treatment at the end of production. Pulmozyme, at concentrations up to 100 U/ml, had no measurable effect on infectious titer of the final vector product. The use of Pulmozyme is likely to increase the cost of DNase treatment when preparing vector product and should be considered when generating clinical-grade vector products. PMID:22428981

  18. Sites of Retroviral DNA Integration: From Basic Research to Clinical Applications

    PubMed Central

    Serrao, Erik; Engelman, Alan N.

    2016-01-01

    One of the most crucial steps in the life cycle of a retrovirus is the integration of the viral DNA (vDNA) copy of the RNA genome into the genome of an infected host cell. Integration provides for efficient viral gene expression as well as for the segregation of the viral genomes to daughter cells upon cell division. Some integrated viruses are not well expressed, and cells latently infected with HIV-1 can resist the action of potent antiretroviral drugs and remain dormant for decades. Intensive research has been dedicated to understanding the catalytic mechanism of integration, as well as the viral and cellular determinants that influence integration site distribution throughout the host genome. In this review we summarize the evolution of techniques that have been used to recover and map retroviral integration sites, from the early days that first indicated that integration could occur in multiple cellular DNA locations, to current technologies that map upwards of millions of unique integration sites from single in vitro integration reactions or cell culture infections. We further review important insights gained from the use of such mapping techniques, including the monitoring of cell clonal expansion in patients treated with retrovirus-based gene therapy vectors, or AIDS patients on suppressive antiretroviral therapy (ART). These insights span from integrase (IN) enzyme sequence preferences within target DNA (tDNA) at the sites of integration, to the roles of host cellular proteins in mediating global integration distribution, to the potential relationship between genomic location of vDNA integration site and retroviral latency. PMID:26508664

  19. Impact of Nucleoporin-Mediated Chromatin Localization and Nuclear Architecture on HIV Integration Site Selection.

    PubMed

    Wong, Richard W; Mamede, João I; Hope, Thomas J

    2015-10-01

    It has been known for a number of years that integration sites of human immunodeficiency virus type 1 (HIV-1) DNA show a preference for actively expressed chromosomal locations. A number of viral and cellular proteins are implicated in this process, but the underlying mechanism is not clear. Two recent breakthrough publications advance our understanding of HIV integration site selection by focusing on the localization of the preferred target genes of integration. These studies reveal that knockdown of certain nucleoporins and components of nucleocytoplasmic trafficking alter integration site preference, not by altering the trafficking of the viral genome but by altering the chromatin subtype localization relative to the structure of the nucleus. Here, we describe the link between the nuclear basket nucleoporins (Tpr and Nup153) and chromatin organization and how altering the host environment by manipulating nuclear structure may have important implications for the preferential integration of HIV into actively transcribed genes, facilitating efficient viral replication. PMID:26136574

  20. Impact of Nucleoporin-Mediated Chromatin Localization and Nuclear Architecture on HIV Integration Site Selection.

    PubMed

    Wong, Richard W; Mamede, João I; Hope, Thomas J

    2015-10-01

    It has been known for a number of years that integration sites of human immunodeficiency virus type 1 (HIV-1) DNA show a preference for actively expressed chromosomal locations. A number of viral and cellular proteins are implicated in this process, but the underlying mechanism is not clear. Two recent breakthrough publications advance our understanding of HIV integration site selection by focusing on the localization of the preferred target genes of integration. These studies reveal that knockdown of certain nucleoporins and components of nucleocytoplasmic trafficking alter integration site preference, not by altering the trafficking of the viral genome but by altering the chromatin subtype localization relative to the structure of the nucleus. Here, we describe the link between the nuclear basket nucleoporins (Tpr and Nup153) and chromatin organization and how altering the host environment by manipulating nuclear structure may have important implications for the preferential integration of HIV into actively transcribed genes, facilitating efficient viral replication.

  1. Impact of Nucleoporin-Mediated Chromatin Localization and Nuclear Architecture on HIV Integration Site Selection

    PubMed Central

    Mamede, João I.

    2015-01-01

    It has been known for a number of years that integration sites of human immunodeficiency virus type 1 (HIV-1) DNA show a preference for actively expressed chromosomal locations. A number of viral and cellular proteins are implicated in this process, but the underlying mechanism is not clear. Two recent breakthrough publications advance our understanding of HIV integration site selection by focusing on the localization of the preferred target genes of integration. These studies reveal that knockdown of certain nucleoporins and components of nucleocytoplasmic trafficking alter integration site preference, not by altering the trafficking of the viral genome but by altering the chromatin subtype localization relative to the structure of the nucleus. Here, we describe the link between the nuclear basket nucleoporins (Tpr and Nup153) and chromatin organization and how altering the host environment by manipulating nuclear structure may have important implications for the preferential integration of HIV into actively transcribed genes, facilitating efficient viral replication. PMID:26136574

  2. An integrated remote sensing approach for identifying ecological range sites. [parker mountain

    NASA Technical Reports Server (NTRS)

    Jaynes, R. A.

    1983-01-01

    A model approach for identifying ecological range sites was applied to high elevation sagebrush-dominated rangelands on Parker Mountain, in south-central Utah. The approach utilizes map information derived from both high altitude color infrared photography and LANDSAT digital data, integrated with soils, geological, and precipitation maps. Identification of the ecological range site for a given area requires an evaluation of all relevant environmental factors which combine to give that site the potential to produce characteristic types and amounts of vegetation. A table is presented which allows the user to determine ecological range site based upon an integrated use of the maps which were prepared. The advantages of identifying ecological range sites through an integrated photo interpretation/LANDSAT analysis are discussed.

  3. Real-time quantitative PCR for the design of lentiviral vector analytical assays.

    PubMed

    Delenda, C; Gaillard, C

    2005-10-01

    From the recent and emerging concerns for approving lentiviral vector-mediated gene transfer in human clinical applications, several analytical methods have been applied in preclinical models to address the lentiviral vector load in batches, cells or tissues. This review points out the oldest generation methods (blots, RT activity, standard PCR) as well as a full description of the newest real-time quantitative PCR (qPCR) applications. Combinations of primer and probe sequences, which have worked in the lentiviral amplification context, have been included in the effort to dress an exhaustive list. Also, great variations have been observed from interlaboratory results, we have tempted to compare between them the different analytical methods that have been used to consider (i) the titration of lentiviral vector batches, (ii) the absence of the susceptible emerging replicative lentiviruses or (iii) the lentiviral vector biodistribution in the organism.

  4. Lentiviral Vector-Mediated RNA Silencing in the Central Nervous System

    PubMed Central

    Foster, Edmund; Moon, Lawrence D.F.

    2014-01-01

    Abstract RNA silencing is an established method for investigating gene function and has attracted particular interest because of the potential for generating RNA-based therapeutics. Using lentiviral vectors as an efficient delivery system that offers stable, long-term expression in postmitotic cells further enhances the applicability of an RNA-based gene therapy for the CNS. In this review we provide an overview of both lentiviral vectors and RNA silencing along with design considerations for generating lentiviral vectors capable of RNA silencing. We go on to describe the current preclinical data regarding lentiviral vector-mediated RNA silencing for CNS disorders and discuss the concerns of side effects associated with lentiviral vectors and small interfering RNAs and how these might be mitigated. PMID:24090197

  5. BET proteins promote efficient murine leukemia virus integration at transcription start sites

    PubMed Central

    Sharma, Amit; Larue, Ross C.; Plumb, Matthew R.; Malani, Nirav; Male, Frances; Slaughter, Alison; Kessl, Jacques J.; Shkriabai, Nikolozi; Coward, Elizabeth; Aiyer, Sriram S.; Green, Patrick L.; Wu, Li; Roth, Monica J.; Bushman, Frederic D.; Kvaratskhelia, Mamuka

    2013-01-01

    The selection of chromosomal targets for retroviral integration varies markedly, tracking with the genus of the retrovirus, suggestive of targeting by binding to cellular factors. γ-Retroviral murine leukemia virus (MLV) DNA integration into the host genome is favored at transcription start sites, but the underlying mechanism for this preference is unknown. Here, we have identified bromodomain and extraterminal domain (BET) proteins (Brd2, -3, -4) as cellular-binding partners of MLV integrase. We show that purified recombinant Brd4(1-720) binds with high affinity to MLV integrase and stimulates correct concerted integration in vitro. JQ-1, a small molecule that selectively inhibits interactions of BET proteins with modified histone sites impaired MLV but not HIV-1 integration in infected cells. Comparison of the distribution of BET protein-binding sites analyzed using ChIP-Seq data and MLV-integration sites revealed significant positive correlations. Antagonism of BET proteins, via JQ-1 treatment or RNA interference, reduced MLV-integration frequencies at transcription start sites. These findings elucidate the importance of BET proteins for MLV integration efficiency and targeting and provide a route to developing safer MLV-based vectors for human gene therapy. PMID:23818621

  6. Genomic characterization of viral integration sites in HPV-related cancers.

    PubMed

    Bodelon, Clara; Untereiner, Michael E; Machiela, Mitchell J; Vinokurova, Svetlana; Wentzensen, Nicolas

    2016-11-01

    Persistent infection with carcinogenic human papillomaviruses (HPV) causes the majority of anogenital cancers and a subset of head and neck cancers. The HPV genome is frequently found integrated into the host genome of invasive cancers. The mechanisms of how it may promote disease progression are not well understood. Thoroughly characterizing integration events can provide insights into HPV carcinogenesis. Individual studies have reported limited number of integration sites in cell lines and human samples. We performed a systematic review of published integration sites in HPV-related cancers and conducted a pooled analysis to formally test for integration hotspots and genomic features enriched in integration events using data from the Encyclopedia of DNA Elements (ENCODE). Over 1,500 integration sites were reported in the literature, of which 90.8% (N = 1,407) were in human tissues. We found 10 cytobands enriched for integration events, three previously reported ones (3q28, 8q24.21 and 13q22.1) and seven additional ones (2q22.3, 3p14.2, 8q24.22, 14q24.1, 17p11.1, 17q23.1 and 17q23.2). Cervical infections with HPV18 were more likely to have breakpoints in 8q24.21 (p = 7.68 × 10(-4) ) than those with HPV16. Overall, integration sites were more likely to be in gene regions than expected by chance (p = 6.93 × 10(-9) ). They were also significantly closer to CpG regions, fragile sites, transcriptionally active regions and enhancers. Few integration events occurred within 50 Kb of known cervical cancer driver genes. This suggests that HPV integrates in accessible regions of the genome, preferentially genes and enhancers, which may affect the expression of target genes. PMID:27343048

  7. CRISPR Outsourcing: Commissioning IHF for Site-Specific Integration of Foreign DNA at the CRISPR Array.

    PubMed

    Wei, Yunzhou; Terns, Michael P

    2016-06-16

    In this issue of Molecular Cell, Nuñez et al. (2016) report that site-specific integration of foreign DNA into CRISPR loci by the Cas1-Cas2 integrase complex is promoted by a host factor, IHF (integration host factor), that binds and bends CRISPR leader DNA. PMID:27315553

  8. Multiplex Identification of Human Papillomavirus 16 DNA Integration Sites in Cervical Carcinomas

    PubMed Central

    Xu, Bo; Chotewutmontri, Sasithorn; Wolf, Stephan; Klos, Ursula; Schmitz, Martina; Dürst, Matthias; Schwarz, Elisabeth

    2013-01-01

    Cervical cancer is caused by high-risk human papillomaviruses (HPV), in more than half of the worldwide cases by HPV16. Viral DNA integration into the host genome is a frequent mutation in cervical carcinogenesis. Because integration occurs into different genomic locations, it creates unique viral-cellular DNA junctions in every single case. This singularity complicates the precise identification of HPV integration sites enormously. We report here the development of a novel multiplex strategy for sequence determination of HPV16 DNA integration sites. It includes DNA fragmentation and adapter tagging, PCR enrichment of the HPV16 early region, Illumina next-generation sequencing, data processing, and validation of candidate integration sites by junction-PCR. This strategy was performed with 51 cervical cancer samples (47 primary tumors and 4 cell lines). Altogether 75 HPV16 integration sites (3′-junctions) were identified and assigned to the individual samples. By comparing the DNA junctions with the presence of viral oncogene fusion transcripts, 44 tumors could be classified into four groups: Tumors with one transcriptionally active HPV16 integrate (n = 12), tumors with transcribed and silent DNA junctions (n = 8), tumors carrying episomal HPV16 DNA (n = 10), and tumors with one to six DNA junctions, but without fusion transcripts (n = 14). The 3′-breakpoints of integrated HPV16 DNA show a statistically significant (p<0.05) preferential distribution within the early region segment upstream of the major splice acceptor underscoring the importance of deregulated viral oncogene expression for carcinogenesis. Half of the mapped HPV16 integration sites target cellular genes pointing to a direct influence of HPV integration on host genes (insertional mutagenesis). In summary, the multiplex strategy for HPV16 integration site determination worked very efficiently. It will open new avenues for comprehensive mapping of HPV integration sites and for the

  9. TG1 integrase-based system for site-specific gene integration into bacterial genomes.

    PubMed

    Muroi, Tetsurou; Kokuzawa, Takaaki; Kihara, Yoshihiko; Kobayashi, Ryuichi; Hirano, Nobutaka; Takahashi, Hideo; Haruki, Mitsuru

    2013-05-01

    Serine-type phage integrases catalyze unidirectional site-specific recombination between the attachment sites, attP and attB, in the phage and host bacterial genomes, respectively; these integrases and DNA target sites function efficiently when transferred into heterologous cells. We previously developed an in vivo site-specific genomic integration system based on actinophage TG1 integrase that introduces ∼2-kbp DNA into an att site inserted into a heterologous Escherichia coli genome. Here, we analyzed the TG1 integrase-mediated integrations of att site-containing ∼10-kbp DNA into the corresponding att site pre-inserted into various genomic locations; moreover, we developed a system that introduces ∼10-kbp DNA into the genome with an efficiency of ∼10(4) transformants/μg DNA. Integrations of attB-containing DNA into an attP-containing genome were more efficient than integrations of attP-containing DNA into an attB-containing genome, and integrations targeting attP inserted near the replication origin, oriC, and the E. coli "centromere" analogue, migS, were more efficient than those targeting attP within other regions of the genome. Because the genomic region proximal to the oriC and migS sites is located at the extreme poles of the cell during chromosomal segregation, the oriC-migS region may be more exposed to the cytosol than are other regions of the E. coli chromosome. Thus, accessibility of pre-inserted attP to attB-containing incoming DNA may be crucial for the integration efficiency by serine-type integrases in heterologous cells. These results may be beneficial to the development of serine-type integrases-based genomic integration systems for various bacterial species.

  10. Evaluation of an integrated treatment system for MGP site groundwaters

    SciTech Connect

    Scheible, O.K.; Grey, G.M.; Maiello, J.A.

    1995-12-31

    Initially studied at bench scale, process sequences comprising dissolved air flotation (DAF), aerobic biological oxidation, air stripping, filtration, and carbon adsorption were demonstrated at pilot scale at a manufactured gas plant (MGP) site in New Jersey. Benzene, toluene, ethylbenzene, and xylenes (BTEX), and polycyclic aromatic hydrocarbons (PAHs) were the primary organics in the groundwater, ranging from levels of 2 to 8 mg/L and 0.3 to 27 mg/L, respectively; chemical oxygen demand (COD) levels were from 60 to 4,500 mg/L. Significant levels of dense, emulsified, and nonaqueous tars and oils were present in the more highly contaminated waters and were effectively removed by DAF. Carbon-based fluidized-bed biological treatment of the DAF subnatant at COD loadings between 2 and 4 g/L-d yielded effluent-soluble COD levels between 40 and 60 mg/L, with both residual BTEX and PAH concentrations ranging from nondetect levels to 0.1 mg/L. Subsequent polishing by filtration and carbon adsorption resulted in additional COD removal and nondetect levels of volatiles and semivolatiles. Air stripping was effective in lieu of the biological process for both volatile organic compound (VOC) and PAH removal.

  11. Lentiviral-mediated phenotypic correction of cystic fibrosis pigs

    PubMed Central

    Cooney, Ashley L.; Abou Alaiwa, Mahmoud H.; Shah, Viral S.; Bouzek, Drake C.; Stroik, Mallory R.; Powers, Linda S.; Gansemer, Nick D.; Meyerholz, David K.; Welsh, Michael J.; Stoltz, David A.; Sinn, Patrick L.; McCray, Paul B.

    2016-01-01

    Cystic Fibrosis (CF) is an autosomal recessive disease caused by mutations in CF transmembrane conductance regulator (CFTR), resulting in defective anion transport. Regardless of the disease-causing mutation, gene therapy is a strategy to restore anion transport to airway epithelia. Indeed, viral vector–delivered CFTR can complement the anion channel defect. In this proof-of-principle study, functional in vivo CFTR channel activity was restored in the airways of CF pigs using a feline immunodeficiency virus–based (FIV-based) lentiviral vector pseudotyped with the GP64 envelope. Three newborn CF pigs received aerosolized FIV-CFTR to the nose and lung. Two weeks after viral vector delivery, epithelial tissues were analyzed for functional correction. In freshly excised tracheal and bronchus tissues and cultured ethmoid sinus cells, we observed a significant increase in transepithelial cAMP-stimulated current, evidence of functional CFTR. In addition, we observed increases in tracheal airway surface liquid pH and bacterial killing in CFTR vector–treated animals. Together, these data provide the first evidence to our knowledge that lentiviral delivery of CFTR can partially correct the anion channel defect in a large-animal CF model and validate a translational strategy to treat or prevent CF lung disease.

  12. Lentiviral vectors for cancer immunotherapy and clinical applications.

    PubMed

    Liechtenstein, Therese; Perez-Janices, Noemi; Escors, David

    2013-09-01

    The success of immunotherapy against infectious diseases has shown us the powerful potential that such a treatment offers, and substantial work has been done to apply this strategy in the fight against cancer. Cancer is however a fiercer opponent than pathogen-caused diseases due to natural tolerance towards tumour associated antigens and tumour-induced immunosuppression. Recent gene therapy clinical trials with viral vectors have shown clinical efficacy in the correction of genetic diseases, HIV and cancer. The first successful gene therapy clinical trials were carried out with onco(γ-)retroviral vectors but oncogenesis by insertional mutagenesis appeared as a serious complication. Lentiviral vectors have emerged as a potentially safer strategy, and recently the first clinical trial of patients with advanced leukemia using lentiviral vectors has proven successful. Additionally, therapeutic lentivectors have shown clinical efficacy for the treatment of HIV, X-linked adrenoleukodystrophy, and β-thalassaemia. This review aims at describing lentivectors and how they can be utilized to boost anti-tumour immune responses by manipulating the effector immune cells. PMID:24078865

  13. Lentiviral-mediated phenotypic correction of cystic fibrosis pigs

    PubMed Central

    Cooney, Ashley L.; Abou Alaiwa, Mahmoud H.; Shah, Viral S.; Bouzek, Drake C.; Stroik, Mallory R.; Powers, Linda S.; Gansemer, Nick D.; Meyerholz, David K.; Welsh, Michael J.; Stoltz, David A.; Sinn, Patrick L.; McCray, Paul B.

    2016-01-01

    Cystic Fibrosis (CF) is an autosomal recessive disease caused by mutations in CF transmembrane conductance regulator (CFTR), resulting in defective anion transport. Regardless of the disease-causing mutation, gene therapy is a strategy to restore anion transport to airway epithelia. Indeed, viral vector–delivered CFTR can complement the anion channel defect. In this proof-of-principle study, functional in vivo CFTR channel activity was restored in the airways of CF pigs using a feline immunodeficiency virus–based (FIV-based) lentiviral vector pseudotyped with the GP64 envelope. Three newborn CF pigs received aerosolized FIV-CFTR to the nose and lung. Two weeks after viral vector delivery, epithelial tissues were analyzed for functional correction. In freshly excised tracheal and bronchus tissues and cultured ethmoid sinus cells, we observed a significant increase in transepithelial cAMP-stimulated current, evidence of functional CFTR. In addition, we observed increases in tracheal airway surface liquid pH and bacterial killing in CFTR vector–treated animals. Together, these data provide the first evidence to our knowledge that lentiviral delivery of CFTR can partially correct the anion channel defect in a large-animal CF model and validate a translational strategy to treat or prevent CF lung disease. PMID:27656681

  14. Visualization of targeted transduction by engineered lentiviral vectors.

    PubMed

    Joo, K-I; Wang, P

    2008-10-01

    We have reported a method to target lentiviral vectors to specific cell types. This method requires the incorporation of two distinct molecules on the viral vector surface: one is an antibody that renders the targeting specificity for the engineered vector, and the other is a fusogenic protein that allows the engineered vector to enter the target cell. However, the molecular mechanism that controls the targeted infection needs to be defined. In this report, we tracked the individual lentiviral particles by labeling the virus with the GFP-Vpr fusion protein. We were able to visualize the surface-displayed proteins on a single virion as well as antibody-directed targeting to a desired cell type. We also demonstrated the dynamics of virus fusion with endosomes and monitored endosome-associated transport of viruses in target cells. Our results suggest that the fusion between the engineered lentivirus and endosomes takes place at the early endosome level, and that the release of the viral core into the cytosol at the completion of the virus-endosome fusion is correlated with the endosome maturation process. This imaging study sheds some light on the infection mechanism of the engineered lentivirus and can be beneficial to the design of more efficient gene delivery vectors.

  15. DNFSB Recommendation 94-1 Hanford site integrated stabilization management plan, volumes 1 and 2

    SciTech Connect

    Gerber, E.W.

    1996-03-15

    This document comprises the Hanford Site Integrated Stabilization Management Plan (SISMP). This document describes the DOE`s plans at the Hanford Site to address concerns identified in Defense Nuclear Facilites Safety Board (DNFSB) Recommendation 94-1. This document also identifies plans for other spent nuclear fuel (SNF) inventories at the Hanford Site which are not within the scope of DNFSB Recommendation 94-1 for reference purposes because of their interrelationship with plans for SNF within the scope of DNFSB Recommendation 94-1. The SISMP was also developed to assist DOE in initial formulation of the Research and Development Plan and the Integrated Facilities Plan.

  16. [Progress of φC31 integrase system in site-specific integration].

    PubMed

    Ma, Qing-Wen

    2011-06-01

    Integrase of phage fC31 catalyses the homologous recombination between Streptomyces attachment site attB and the phage attachment site attP. Meanwhile, this integrase can mediate integration of attB-containing donor plasmids into the pseudo attP sites in eukaryotic genomes by a site-specific manner and resulting long-term and robust expression of integrated genes. Nowadays, fC31 integrase system is becoming a potential tool for genome modification, gene therapy and transgenic research. Recent progress of fC31 integrase system in integration mode in mammalian genomes, efficiency improvement and researches concerned on transgenic safety were summarized in this review.

  17. Optimization of the transductional efficiency of lentiviral vectors: effect of sera and polycations.

    PubMed

    Denning, Warren; Das, Suvendu; Guo, Siqi; Xu, Jun; Kappes, John C; Hel, Zdenek

    2013-03-01

    Lentiviral vectors are widely used as effective gene-delivery vehicles. Optimization of the conditions for efficient lentiviral transduction is of a high importance for a variety of research applications. Presence of positively charged polycations reduces the electrostatic repulsion forces between a negatively charged cell and an approaching enveloped lentiviral particle resulting in an increase in the transduction efficiency. Although a variety of polycations are commonly used to enhance the transduction with retroviruses, the relative effect of various types of polycations on the efficiency of transduction and on the potential bias in the determination of titer of lentiviral vectors is not fully understood. Here, we present data suggesting that DEAE-dextran provides superior results in enhancing lentiviral transduction of most tested cell lines and primary cell cultures. Specific type and source of serum affects the efficiency of transduction of target cell populations. Non-specific binding of enhanced green fluorescent protein (EGFP)-containing membrane aggregates in the presence of DEAE-dextran does not significantly affect the determination of the titer of EGFP-expressing lentiviral vectors. In conclusion, various polycations and types of sera should be tested when optimizing lentiviral transduction of target cell populations.

  18. HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency

    PubMed Central

    Skupsky, Ron; Burnett, John C.; Foley, Jonathan E.; Schaffer, David V.; Arkin, Adam P.

    2010-01-01

    Mammalian gene expression patterns, and their variability across populations of cells, are regulated by factors specific to each gene in concert with its surrounding cellular and genomic environment. Lentiviruses such as HIV integrate their genomes into semi-random genomic locations in the cells they infect, and the resulting viral gene expression provides a natural system to dissect the contributions of genomic environment to transcriptional regulation. Previously, we showed that expression heterogeneity and its modulation by specific host factors at HIV integration sites are key determinants of infected-cell fate and a possible source of latent infections. Here, we assess the integration context dependence of expression heterogeneity from diverse single integrations of a HIV-promoter/GFP-reporter cassette in Jurkat T-cells. Systematically fitting a stochastic model of gene expression to our data reveals an underlying transcriptional dynamic, by which multiple transcripts are produced during short, infrequent bursts, that quantitatively accounts for the wide, highly skewed protein expression distributions observed in each of our clonal cell populations. Interestingly, we find that the size of transcriptional bursts is the primary systematic covariate over integration sites, varying from a few to tens of transcripts across integration sites, and correlating well with mean expression. In contrast, burst frequencies are scattered about a typical value of several per cell-division time and demonstrate little correlation with the clonal means. This pattern of modulation generates consistently noisy distributions over the sampled integration positions, with large expression variability relative to the mean maintained even for the most productive integrations, and could contribute to specifying heterogeneous, integration-site-dependent viral production patterns in HIV-infected cells. Genomic environment thus emerges as a significant control parameter for gene expression

  19. DNFSB recommendation 94-1 Hanford site integrated stabilization management plan - VOLUMES 1-3

    SciTech Connect

    Gerber, E.W.

    1996-09-23

    The US Department of Energy (DOE) has developed an Integrated Program Plan (IPP) to address concerns identified in Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 94-1. The IPP describes the actions that DOE plans to implement at its various sites to convert excess fissile materials to forms or conditions suitable for safe interim storage. The baseline IPP was issued as DOE's DNFSB Recommendation 94-1 Implementation Plan (IP), which was transmitted to the DNFSB on February 28, 1995. The IPP was subsequently supplemented with an Integrated Facilities Plan and a Research and Development Plan, which further develop complex-wide research and development and long-range facility requirements and plans. These additions to the baseline IPP were developed based on a systems engineering approach that integrated facilities and capabilities at the various DOE sites and focused on attaining safe interim storage with minimum safety risks and environmental impacts. Each affected DOE site has developed a Site Integrated Stabilization Management Plan (SISMP) to identify individual site plans to implement the DNFSB Recommendation 94-1 IPP. The SISMPs were developed based on the objectives, requirements, and commitments identified in the DNFSB Recommendation 94-1 IP. The SISMPs supported formulation of the initial versions of the Integrated Facilities Plan and the Research and Development Plan. The SISMPs are periodically updated to reflect improved integration between DOE sites as identified during the IPP systems engineering evaluations. This document constitutes the Hanford SISMP. This document includes the planned work scope, costs and schedules for activities at the Hanford site to implement the DNFSB Recommendation 94-1 IPP.

  20. DNFSB Recommendation 94-1 Hanford Site Integrated Stabilization Management Plan. Volume 1

    SciTech Connect

    Gerber, E.W.

    1995-10-01

    The US Department of Energy (DOE) has developed an Integrated Program Plan (IPP) to address concerns identified in Defense Nuclear Facilities Safety Board Recommendation 94-1. The IPP describes the actions that DOE plans to implement at its various sites to convert excess fissile materials to forms or conditions suitable for safe interim storage. The baseline IPP was issued as DOE`s Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 94-1 Implementation Plan (IP), which was transmitted to the DNFSB on February 28, 1995. The IPP is being further developed to include complex-wide requirements for research and development and a long-range facility requirements section. The planned additions to the baseline IPP are being developed based on a systems engineering approach that integrates facilities and capabilities at the various DOE sites and focuses on attaining safe interim storage with minimum safety risks and environmental impacts. Each affected DOE site has developed a Site Integrated Stabilization Management Plan (SISMP) to identify individual site plans to implement the DNFSB Recommendation 94-1 and to provide a basis for formulating planned additions to the IPP. The SISMPs were developed based on the objectives, requirements, and commitments identified in the baseline DNFSB Recommendation 94-1 IPP. The SISMPs will be periodically updated to reflect improved integration between DOE sites as identified during the IPP systems engineering evaluations.

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

    PubMed

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

    1998-12-01

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

  2. Common Viral Integration Sites Identified in Avian Leukosis Virus-Induced B-Cell Lymphomas

    PubMed Central

    Justice, James F.; Morgan, Robin W.

    2015-01-01

    ABSTRACT Avian leukosis virus (ALV) induces B-cell lymphoma and other neoplasms in chickens by integrating within or near cancer genes and perturbing their expression. Four genes—MYC, MYB, Mir-155, and TERT—have previously been identified as common integration sites in these virus-induced lymphomas and are thought to play a causal role in tumorigenesis. In this study, we employ high-throughput sequencing to identify additional genes driving tumorigenesis in ALV-induced B-cell lymphomas. In addition to the four genes implicated previously, we identify other genes as common integration sites, including TNFRSF1A, MEF2C, CTDSPL, TAB2, RUNX1, MLL5, CXorf57, and BACH2. We also analyze the genome-wide ALV integration landscape in vivo and find increased frequency of ALV integration near transcriptional start sites and within transcripts. Previous work has shown ALV prefers a weak consensus sequence for integration in cultured human cells. We confirm this consensus sequence for ALV integration in vivo in the chicken genome. PMID:26670384

  3. The Nef-Infectivity Enigma: Mechanisms of Enhanced Lentiviral Infection

    PubMed Central

    Vermeire, Jolien; Vanbillemont, Griet; Witkowski, Wojciech; Verhasselt, Bruno

    2011-01-01

    The Nef protein is an essential factor for lentiviral pathogenesis in humans and other simians. Despite a multitude of functions attributed to this protein, the exact role of Nef in disease progression remains unclear. One of its most intriguing functions is the ability of Nef to enhance the infectivity of viral particles. In this review we will discuss current insights in the mechanism of this well-known, yet poorly understood Nef effect. We will elaborate on effects of Nef, on both virion biogenesis and the early stage of the cellular infection, that might be involved in infectivity enhancement. In addition, we provide an overview of different HIV-1 Nef domains important for optimal infectivity and briefly discuss some possible sources of the frequent discrepancies in the field. Hereby we aim to contribute to a better understanding of this highly conserved and therapeutically attractive Nef function. PMID:22103831

  4. AGU Launches Web Site for New Scientific Integrity and Professional Ethics Policy

    NASA Astrophysics Data System (ADS)

    Townsend, Randy

    2013-03-01

    AGU's Scientific Integrity and Professional Ethics policy, approved by the AGU Board of Directors and Council in December 2012, is now available online on a new Web site, http://ethics.agu.org. As the Web site states, the policy embodies a "set of guidelines for scientific integrity and professional ethics for the actions of the members and the governance of the Union in its internal activities; in its public persona; and most importantly, in the research and peer review processes of its scientific publications, its communications and outreach, and its scientific meetings."

  5. Demonstration of innovative monitoring technologies at the Savannah River Integrated Demonstration Site

    SciTech Connect

    Rossabi, J.; Jenkins, R.A.; Wise, M.B.

    1993-12-31

    The Department of Energy`s Office of Technology Development initiated an Integrated Demonstration Program at the Savannah River Site in 1989. The objective of this program is to develop, demonstrate, and evaluate innovative technologies that can improve present-day environmental restoration methods. The Integrated Demonstration Program at SRS is entitled ``Cleanup of Organics in Soils and Groundwater at Non-Arid Sites.`` New technologies in the areas of drilling, characterization, monitoring, and remediation are being demonstrated and evaluated for their technical performance and cost effectiveness in comparison with baseline technologies. Present site characterization and monitoring methods are costly, time-consuming, overly invasive, and often imprecise. Better technologies are required to accurately describe the subsurface geophysical and geochemical features of a site and the nature and extent of contamination. More efficient, nonintrusive characterization and monitoring techniques are necessary for understanding and predicting subsurface transport. More reliable procedures are also needed for interpreting monitoring and characterization data. Site characterization and monitoring are key elements in preventing, identifying, and restoring contaminated sites. The remediation of a site cannot be determined without characterization data, and monitoring may be required for 30 years after site closure.

  6. Archaeological site protection: An integral component of the Exxon Valdez shoreline cleanup

    SciTech Connect

    Wooley, C.B.; Haggarty, J.C.

    1995-12-31

    A major cultural site identification and protection program in Prince William Sound and the Gulf of Alaska was conducted as part of the Exxon Valdez spill response. In cooperation with state and federal agencies and Native corporations with historic preservation mandates, the four-year program was designed to identify archaeological sites in the area of the spill, determine the effect of planned cleanup on them, and mitigate impacts to sites during cleanup. Archaeological site protection constraints, augmented by an extensive cultural resource training program, were an integral part of each shoreline-specific cleanup plan. As a result, impacts attributable to the cleanup were limited to minor disturbances and two vandalism incidents. Impacts from oiling were minimal largely because most intertidal cultural sites had lost their fragile constituents and contextual integrity as a result of prespill erosion. State and federal studies confirmed the efficacy of the site identification and protection program, finding negligible impacts attributable to either direct oiling or the cleanup at intact sites. The Cultural Resource Program also developed innovative management strategies with implications for future emergency responses involving complex land management and site protection issues. The program greatly enhanced the knowledge of the area`s history by collecting and synthesizing considerable new archaeological information. 27 refs., 5 figs., 1 tab.

  7. The Advanced Integration Matrix Project and Analog Sites: Difference or Duplication?

    NASA Technical Reports Server (NTRS)

    Wells, Kevin M.

    2004-01-01

    Several project teams have conducted Mars and Lunar mission simulations at analog sites and facilities over the past decade. These projects have a range of scope, participants, and objectives. NASA has provided many of these projects with funding, equipment, and personnel. Despite their variety, a consistent aim of these sites is advancing our capability to return to the Moon or to go to Mars. The Advanced Integration Matrix (AIM) Project was begun in 2002 with a corollary aim: that of advancing the technology needed for long duration human exploration of space. As a new project, it is prudent to ask and answer the question: "What does AIM offer to NASA that is distinct from what current and past analog sites offer?" The price tag for human spaceflight is high enough without needless duplication of efforts. The AIM Project concept is distinct from currently operating terrestrial analogs in three important ways. First, AIM is not strictly an analog site or facility; second, AIM is primarily focused on systems and integration issues; and finally, AIM is organizationally related to NASA s advanced development groups and subject to the rigors of the JSC Engineering Directorate s development process. The successful development of destination-independent, cost-effective, safe, and reliable long duration human exploration systems requires that NASA use both the analog sites and ground-based systems integration efforts. The Advanced Integration Matrix Project will not simply duplicate the former, but will give the agency the capability for the latter.

  8. Factors influencing the titer and infectivity of lentiviral vectors.

    PubMed

    Logan, Aaron C; Nightingale, Sarah J; Haas, Dennis L; Cho, Gerald J; Pepper, Karen A; Kohn, Donald B

    2004-10-01

    Lentiviral vectors have undergone several generations of design improvement to enhance their biosafety and expression characteristics, and have been approved for use in human clinical studies. Most preclinical studies with these vectors have employed easily assayed marker genes for the purpose of determining vector titers and transduction efficiencies. Naturally, the adaptation of these vector systems to clinical use will increasingly involve the transfer of genes whose products may not be easily measured, meaning that the determination of vector titer will be more complicated. One method for determining vector titer that can be universally employed on all human immunodeficiency virus type 1-based lentiviral vector supernatants involves the measurement of Gag (p24) protein concentration in vector supernatants by immunoassay. We have studied the effects that manipulation of several variables involved in vector design and production by transient transfection have on vector titer and infectivity. We have determined that manipulation of the amount of transfer vector, packaging, and envelope plasmids used to transfect the packaging cells does not alter vector infectivity, but does influence vector titer. We also found that modifications to the transfer vector construct, such as replacing the internal promoter or transgene, do not generally alter vector infectivity, whereas inclusion of the central polypurine tract in the transfer vector increases vector infectivity on HEK293 cells and human umbilical cord blood CD34+ hematopoietic progenitor cells (HPCs). The infectivities of vector supernatants can also be increased by harvesting at early time points after the initiation of vector production, collection in serum-free medium, and concentration by ultracentrifugation. For the transduction of CD34+ HPCs, we found that the simplest method of increasing vector infectivity is to pseudotype vector particles with the RD114 envelope instead of vesicular stomatitis virus G

  9. Co-transduction of lentiviral and adenoviral vectors for co-delivery of growth factor and shRNA genes in mesenchymal stem cells-based chondrogenic system.

    PubMed

    Zhang, Feng; Yao, Yongchang; Su, Kai; Fang, Yu; Citra, Fudiman; Wang, Dong-An

    2015-09-01

    Gene delivery takes advantage of cellular mechanisms to express gene products and is an efficient way to deliver them into cells, influencing cellular behaviours and expression patterns. Among the delivery methods, viral vectors are applied due to their high efficiency. Two typical viral vectors for gene delivery include lentiviral vector for integrative transduction and adenoviral vector for transient episomal transduction, respectively. The selection and formulation of proper viral vectors applied to cells can modulate gene expression profiles and further impact the downstream pathways. In this study, recombinant lentiviral and adenoviral vectors were co-transduced in a synovial mesenchymal stem cells (SMSCs)-based articular chondrogenic system by which two transgenes were co-delivered - the gene for transforming growth factor (TGF)β3, to facilitate SMSC chondrogenesis, and the gene for small hairpin RNA (shRNA), targeting the mRNA of type I collagen (Col I) α1 chain to silence Col I expression and minimize fibrocartilage formation. Delivery of either gene could be achieved with either lentiviral or adenoviral vectors. Therefore, co-delivery of the two transgenes via the two types of vectors was performed to determine which combination was optimal for three-dimensional (3D) articular chondrogenesis to construct articular hyaline cartilage tissue. Suppression of Col I and expression of cartilage markers, including type II collagen, aggrecan and cartilage oligomeric matrix protein (COMP), were assessed at both the transcriptome and protein phenotypic levels. It was concluded that the combination of lentiviral-mediated TGFβ3 release and adenoviral-mediated shRNA expression (LV-T + Ad-sh) generally demonstrated optimal efficacy in engineered articular cartilage with SMSCs.

  10. Using the Choquet integral for screening geological CO2 storage sites

    SciTech Connect

    Zhang, Y.

    2011-03-01

    For geological CO{sub 2} storage site selection, it is desirable to reduce the number of candidate sites through a screening process before detailed site characterization is performed. Screening generally involves defining a number of criteria which then need to be evaluated for each site. The importance of each criterion to the final evaluation will generally be different. Weights reflecting the relative importance of these criteria can be provided by experts. To evaluate a site, each criterion must be evaluated and scored, and then aggregated, taking into account the importance of the criteria. We propose the use of the Choquet integral for aggregating the scores. The Choquet integral considers the interactions among criteria, i.e. whether they are independent, complementary to each other, or partially repetitive. We also evaluate the Shapley index, which demonstrates how the importance of a given piece of information may change if it is considered by itself or together with other available information. An illustrative example demonstrates how the Choquet integral properly accounts for the presence of redundancy in two site-evaluation criteria, making the screening process more defensible than the standard weighted-average approach.

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

    PubMed

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

    2014-10-29

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

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

    PubMed

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

    2014-10-29

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

  13. Integrating Risk Analyses and Tools at the U.S. Department of Energy Hanford Site

    SciTech Connect

    Lober, R. W.; Yasek, R. M.; Morse, J. G.; Buck, J. W.; Henderson, C. C.; Sams, T. L.; Bunn, A. L.; Vaughn, P.

    2002-02-26

    Risk assessment and environmental impact analysis at the U.S. Department of Energy (DOE) Hanford Site in Washington State has made significant progress in refining the strategy for using risk analysis to support closing of several hundred waste sites plus 149 single-shell tanks at the Hanford Site. A Single-Shell Tank System Closure Work Plan outlines the current basis for closing the single-shell tank systems. An analogous site approach has been developed to address closure of aggregated groups of similar waste sites. Because of the complexity, decision time frames, proximity of non-tank farm waste sites to tank farms, scale, and regulatory considerations, various projects are providing integrated assessments to support risk analyses and decision-making. This paper will describe the approach for using risk assessment to support waste site and tank closure decisions, the tools being developed, and how integration of these risk assessments and analyses are being performed to ad dress near-term and longterm decisions.

  14. Escherichia coli Flagellar Genes as Target Sites for Integration and Expression of Genetic Circuits

    PubMed Central

    Juhas, Mario; Evans, Lewis D. B.; Frost, Joe; Davenport, Peter W.; Yarkoni, Orr; Fraser, Gillian M.; Ajioka, James W.

    2014-01-01

    E. coli is a model platform for engineering microbes, so genetic circuit design and analysis will be greatly facilitated by simple and effective approaches to introduce genetic constructs into the E. coli chromosome at well-characterised loci. We combined the Red recombinase system of bacteriophage λ and Isothermal Gibson Assembly for rapid integration of novel DNA constructs into the E. coli chromosome. We identified the flagellar region as a promising region for integration and expression of genetic circuits. We characterised integration and expression at four candidate loci, fliD, fliS, fliT, and fliY, of the E. coli flagellar region 3a. The integration efficiency and expression from the four integrations varied considerably. Integration into fliD and fliS significantly decreased motility, while integration into fliT and fliY had only a minor effect on the motility. None of the integrations had negative effects on the growth of the bacteria. Overall, we found that fliT was the most suitable integration site. PMID:25350000

  15. Integrated decision support, sensor networks and adaptive control for wireless site-specific sprinkler irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of site-specific sprinkler irrigation water management systems will be a major factor in future efforts to improve the various efficiencies of water-use and to support a sustainable irrigated environment. The challenge is to develop fully integrated management systems with supporting...

  16. Integrated Decision Support, Sensor Networks and Adaptive Control for Wireless Site-specific Sprinkler Irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of site-specific sprinkler irrigation water management systems will be a major factor in future efforts to improve the various efficiencies of water-use and to support a sustainable irrigated environment. The challenge is to develop fully integrated management systems with supporting...

  17. Multiethnic Neighbourhoods as Sites of Social Capital Formation: Examining Social to Political "Integration" in Schools

    ERIC Educational Resources Information Center

    Basu, Ranu

    2006-01-01

    In an "ideal" democratic society, publicly funded schools serve many purposes. Aside from its educational mandate, schools are places for neighbourhood integration, social capital formation and the fostering of civil society. For newly arrived immigrants, especially those with young children, schools are important sites of settlement experiences.…

  18. Technology development for phosphoric acid fuel cell powerplant (phase 2). [on site integrated energy systems

    NASA Technical Reports Server (NTRS)

    Christner, L.

    1980-01-01

    Progress is reported in the development of material, cell components, and reformers for on site integrated energy systems. Internal resistance and contact resistance were improved. Dissolved gases (O2, N2, and CO2) were found to have no effect on the electrochemical corrosion of phenolic composites. Stack performance was increased by 100 mV over the average 1979 level.

  19. TECHNOLOGY INTEGRATION FOR CONTAMINATED SITE REMEDIATION: CLEANUP GOALS AND PERFORMANCE CRITERIA

    EPA Science Inventory

    There is a need to develop and field-test integrated remediation technologies that operate in a synergistic manner for cost-effective treatment of contaminated sites to achieve risk-based and rational endpoints. Aggressive technologies designed for rapid source-zone remediation m...

  20. Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology

    PubMed Central

    Xu, Ruiping; Ke, Yang

    2016-01-01

    Integration of human papillomavirus (HPV) DNA into the host genome can be a driver mutation in cervical carcinoma. Identification of HPV integration at base resolution has been a longstanding technical challenge, largely due to sensitivity masking by HPV in episomes or concatenated forms. The aim was to enhance the understanding of the precise localization of HPV integration sites using an innovative strategy. Using HPV capture technology combined with next generation sequencing, HPV prevalence and the exact integration sites of the HPV DNA in 47 primary cervical cancer samples and 2 cell lines were investigated. A total of 117 unique HPV integration sites were identified, including HPV16 (n = 101), HPV18 (n = 7), and HPV58 (n = 9). We observed that the HPV16 integration sites were broadly located across the whole viral genome. In addition, either single or multiple integration events could occur frequently for HPV16, ranging from 1 to 19 per sample. The viral integration sites were distributed across almost all the chromosomes, except chromosome 22. All the cervical cancer cases harboring more than four HPV16 integration sites showed clinical diagnosis of stage III carcinoma. A significant enrichment of overlapping nucleotides shared between the human genome and HPV genome at integration breakpoints was observed, indicating that it may play an important role in the HPV integration process. The results expand on knowledge from previous findings on HPV16 and HPV18 integration sites and allow a better understanding of the molecular basis of the pathogenesis of cervical carcinoma. PMID:26735580

  1. Efficient site-specific integration in Plasmodium falciparum chromosomes mediated by mycobacteriophage Bxb1 integrase

    PubMed Central

    Nkrumah, Louis J; Muhle, Rebecca A; Moura, Pedro A; Ghosh, Pallavi; Hatfull, Graham F; Jacobs, William R; Fidock, David A

    2010-01-01

    Here we report an efficient, site-specific system of genetic integration into Plasmodium falciparum malaria parasite chromosomes. This is mediated by mycobacteriophage Bxb1 integrase, which catalyzes recombination between an incoming attP and a chromosomal attB site. We developed P. falciparum lines with the attB site integrated into the glutaredoxin-like cg6 gene. Transfection of these attB+ lines with a dual-plasmid system, expressing a transgene on an attP-containing plasmid together with a drug resistance gene and the integrase on a separate plasmid, produced recombinant parasites within 2 to 4 weeks that were genetically uniform for single-copy plasmid integration. Integrase-mediated recombination resulted in proper targeting of parasite proteins to intra-erythrocytic compartments, including the apicoplast, a plastid-like organelle. Recombinant attB × attP parasites were genetically stable in the absence of drug and were phenotypically homogeneous. This system can be exploited for rapid genetic integration and complementation analyses at any stage of the P. falciparum life cycle, and it illustrates the utility of Bxb1-based integrative recombination for genetic studies of intracellular eukaryotic organisms. PMID:16862136

  2. DNFSB Recommendation 94-1 Hanford Site Integrated Stabilization Management Plan. Volume 2

    SciTech Connect

    Gerber, E.W.

    1995-10-01

    The Hanford Site Integrated Stabilization Management Plan (SISMP) was developed in support of the US Department of Energy`s (DOE) Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 94-1 Integrated Program Plan (IPP). Volume 1 of the SISMP identifies the technical scope and costs associated with Hanford Site plans to resolve concerns identified in DNFSB Recommendation 94-1. Volume 2 of the SISMP provides the Resource Loaded Integrated Schedules for Spent Nuclear Fuel Project and Plutonium Finishing Plant activities identified in Volume 1 of the SISMP. Appendix A provides the schedules and progress curves related to spent nuclear fuel management. Appendix B provides the schedules and progress curves related to plutonium-bearing material management. Appendix C provides programmatic logic diagrams that were referenced in Volume 1 of the SISMP.

  3. DNFSB Recommendation 94-1 Hanford Site Integrated Stabilization Management Plan. Volume 2

    SciTech Connect

    McCormack, R.L.

    1995-08-01

    The Hanford Site Integrated Stabilization Management Plan (SISMP) is being developed in support of the US Department of Energy`s (DOE) Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 94-1 Integrated Program Plan (IPP). Volume 1 of the SISMP identifies the technical scope and costs associated with Hanford Site plans to resolve concerns identified in DNFSB Recommendation 94-1. Volume 2 of the SISMP provides the Resource Loaded Integrated Schedules for Spent Nuclear Fuel Project and Plutonium Finishing Plant activities identified in Volume 1 of the SISMP. Appendix A provides the schedules and progress curves related to spent nuclear fuel management. Appendix B provides the schedules and progress curves related to plutoniumbearing material management. Appendix C provides programmatic logic diagrams that were referenced in Volume 1 of the SISMP.

  4. Retrotransposons. An RNA polymerase III subunit determines sites of retrotransposon integration.

    PubMed

    Bridier-Nahmias, Antoine; Tchalikian-Cosson, Aurélie; Baller, Joshua A; Menouni, Rachid; Fayol, Hélène; Flores, Amando; Saïb, Ali; Werner, Michel; Voytas, Daniel F; Lesage, Pascale

    2015-05-01

    Mobile genetic elements are ubiquitous. Their integration site influences genome stability and gene expression. The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae integrates upstream of RNA polymerase III (Pol III)-transcribed genes, yet the primary determinant of target specificity has remained elusive. Here we describe an interaction between Ty1 integrase and the AC40 subunit of Pol III and demonstrate that AC40 is the predominant determinant targeting Ty1 integration upstream of Pol III-transcribed genes. Lack of an integrase-AC40 interaction dramatically alters target site choice, leading to a redistribution of Ty1 insertions in the genome, mainly to chromosome ends. The mechanism of target specificity allows Ty1 to proliferate and yet minimizes genetic damage to its host. PMID:25931562

  5. Heat recovery subsystem and overall system integration of fuel cell on-site integrated energy systems

    NASA Technical Reports Server (NTRS)

    Mougin, L. J.

    1983-01-01

    The best HVAC (heating, ventilating and air conditioning) subsystem to interface with the Engelhard fuel cell system for application in commercial buildings was determined. To accomplish this objective, the effects of several system and site specific parameters on the economic feasibility of fuel cell/HVAC systems were investigated. An energy flow diagram of a fuel cell/HVAC system is shown. The fuel cell system provides electricity for an electric water chiller and for domestic electric needs. Supplemental electricity is purchased from the utility if needed. An excess of electricity generated by the fuel cell system can be sold to the utility. The fuel cell system also provides thermal energy which can be used for absorption cooling, space heating and domestic hot water. Thermal storage can be incorporated into the system. Thermal energy is also provided by an auxiliary boiler if needed to supplement the fuel cell system output. Fuel cell/HVAC systems were analyzed with the TRACE computer program.

  6. Integrated test plan for crosswell compressional and shear wave seismic tomography for site characterization at the VOC Arid Site

    SciTech Connect

    Elbring, G.J.; Narbutovskih, S.M.

    1994-02-01

    This integrated test plan describes the demonstration of the crosswell acoustic tomography technique as part of the Volatile Organic Compounds-Arid Integrated Demonstration (VOC-Arid ID). The purpose of this demonstration is to image the subsurface seismic velocity structure and to relate the resulting velocity model to lithology and saturation. In fiscal year (FY) 1994 an initial fielding will test three different downhole sources at two different sites at the Hanford US Department of Energy facility to identify which sources will provide the energy required to propagate between existing steel-cased wells at these two sites. Once this has been established, a second fielding will perform a full compressional and shear wave tomographic survey at the most favorable site. Data reduction, analysis, and interpretation of this full data set will be completed by the end of this fiscal year. Data collection for a second survey will be completed by the end of the fiscal year, and data reduction for this data set will be completed in FY 1995. The specific need is detailed subsurface characterization with minimum intrusion. This technique also has applications for long term vadose zone monitoring for both Resource Conservation and Recovery Act (RCRA) waste storage facilities and for remediation monitoring. Images produced are continuous between boreholes. This is a significant improvement over the single point data derived solely from core information. Saturation changes, either naturally occurring (e.g., perched water tables) or remediation induced (e.g., water table mounding from injection wells or during inwell air sparging) could be imaged. These crosswell data allow optimal borehole placement for groundwater remediation, associated monitoring wells and possibly evaluation of the effective influence of a particular remediation technique.

  7. Actinophage R4 integrase-based site-specific chromosomal integration of non-replicative closed circular DNA.

    PubMed

    Miura, Takamasa; Nishizawa, Akito; Nishizawa, Tomoyasu; Asayama, Munehiko; Shirai, Makoto

    2016-06-01

    The actinophage R4 integrase (Sre)-based molecular genetic engineering system was developed for the chromosomal integration of multiple genes in Escherichia coli. A cloned DNA fragment containing two attP sites, green fluorescent protein (gfp) as a first transgene, and an antibiotic resistance gene as a selection marker was self-ligated to generate non-replicative closed circular DNA (nrccDNA) for integration. nrccDNA was introduced into attB-inserted E. coli cells harboring the plasmid expressing Sre by electroporation. The expressed Sre catalyzed site-specific integration between one of the two attP sites on nrccDNA and the attB site on the E. coli chromosome. The integration frequency was affected by the chromosomal location of the target site. A second nrccDNA containing two attB sites, lacZα encoding the alpha fragment of β-galactosidase as a transgene, and another antibiotic resistance gene was integrated into the residual attP site on the gfp-integrated E. coli chromosome via one of the two attB sites according to reiterating site-specific recombination. The integrants clearly exhibited β-galactosidase activity and green fluorescence, suggesting the simultaneous expression of multiple recombinant proteins in E. coli. The results of the present study showed that a step-by-step integration procedure using nrccDNA achieved the chromosomal integration of multiple genes. PMID:26870903

  8. Improved lentiviral transduction of ALS motoneurons in vivo via dual targeting.

    PubMed

    O'Leary, Valerie B; Ovsepian, Saak V; Bodeker, Macdara; Dolly, J Oliver

    2013-11-01

    Treatment of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease, is hampered by its complex etiology and lack of efficient means for targeted transfer of therapeutics into motoneurons. The objective of this research was engineering of a versatile motoneuron targeting adapter--a full-length atoxic tetanus toxin fused to core-streptavidin (CS-TeTIM)--for retro-axonal transduction of viral vectors; validation of the targeting efficiency of CS-TeTIM in vivo, by expression of green fluorescence protein (GFP) reporter in motoneurons of presymptomatic and symptomatic ALS-like SOD1(G93A) mice, and comparison with age-matched controls; and appraisal of lentiviral transduction with CS-TeTIM relative to (1) a HC binding fragment of tetanus toxin CS-TeTx(HC), (2) rabies glycoprotein (RG), and (3) a CS-TeTIM-RG dual targeting approach. CS-TeTIM and CS-TeTx(HC) were engineered using recombinant technology and site-directed mutagenesis. Biotinylated vectors, pseudotyped with vesicular stomatitis virus glycoprotein (VSV-G) or RG, were linked to these adaptors and injected intraperitoneally (ip) into presymptomatic (12 weeks old), symptomatic SOD1(G93A) (22 weeks old) or wild type control mice, followed by monitoring of GFP expression in the spinal cord and supraspinal motor structures with quantitative PCR and immuno-histochemistry. Transcripts were detected in the spinal cord and supraspinal motor structures of all mice 2 weeks after receiving a single ip injection, although in symptomatic SOD1(G93A) animals reporter RNA levels were lower compared to presymptomatic and wild-type controls irrespective of the targeting approach. GFP transduction with CS-TeTIM proved more efficient than CS-TeTx(HC) across all groups while CS-TeTIM-RG dual-targeted vectors yielded the highest transcript numbers. Importantly, in both wild-type and presymptomatic SOD1(G93A) mice strong colabeling of choline-acetyltransferase (ChAT) and GFP was visualized in neurons of the

  9. Improved lentiviral transduction of ALS motoneurons in vivo via dual targeting.

    PubMed

    O'Leary, Valerie B; Ovsepian, Saak V; Bodeker, Macdara; Dolly, J Oliver

    2013-11-01

    Treatment of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease, is hampered by its complex etiology and lack of efficient means for targeted transfer of therapeutics into motoneurons. The objective of this research was engineering of a versatile motoneuron targeting adapter--a full-length atoxic tetanus toxin fused to core-streptavidin (CS-TeTIM)--for retro-axonal transduction of viral vectors; validation of the targeting efficiency of CS-TeTIM in vivo, by expression of green fluorescence protein (GFP) reporter in motoneurons of presymptomatic and symptomatic ALS-like SOD1(G93A) mice, and comparison with age-matched controls; and appraisal of lentiviral transduction with CS-TeTIM relative to (1) a HC binding fragment of tetanus toxin CS-TeTx(HC), (2) rabies glycoprotein (RG), and (3) a CS-TeTIM-RG dual targeting approach. CS-TeTIM and CS-TeTx(HC) were engineered using recombinant technology and site-directed mutagenesis. Biotinylated vectors, pseudotyped with vesicular stomatitis virus glycoprotein (VSV-G) or RG, were linked to these adaptors and injected intraperitoneally (ip) into presymptomatic (12 weeks old), symptomatic SOD1(G93A) (22 weeks old) or wild type control mice, followed by monitoring of GFP expression in the spinal cord and supraspinal motor structures with quantitative PCR and immuno-histochemistry. Transcripts were detected in the spinal cord and supraspinal motor structures of all mice 2 weeks after receiving a single ip injection, although in symptomatic SOD1(G93A) animals reporter RNA levels were lower compared to presymptomatic and wild-type controls irrespective of the targeting approach. GFP transduction with CS-TeTIM proved more efficient than CS-TeTx(HC) across all groups while CS-TeTIM-RG dual-targeted vectors yielded the highest transcript numbers. Importantly, in both wild-type and presymptomatic SOD1(G93A) mice strong colabeling of choline-acetyltransferase (ChAT) and GFP was visualized in neurons of the

  10. Arid site characterization and technology assessment: Volatile Organic Compounds-Arid Integrated Demonstration

    SciTech Connect

    Riley, R.G.

    1993-06-01

    The US Department of Energy`s (DOE`s) Volatile Organic Compounds-Arid Integrated Demonstration (VOC-Arid ID) program was initiated in March 1991 to evaluate technologies for all phases of remediation of VOCs in soils and groundwater at DOE arid/semiarid sites. The primary site for field demonstrations under the VOC-Arid ID program is the Hanford Site. The purpose of this report is to describe (1) the bases for technologies currently under evaluation in the VOC-Arid ID program; (2) the types of subsurface contamination at DOE arid/semiarid sites; and (3) the areas of potential common technology interests based on perceived technology needs at other DOE sites. This report was compiled by Pacific Northwest Laboratory in response to DOE`s Office of Technology Development`s mission to carry out an aggressive program to accelerate the development and implementation of new and existing technologies to meet a 30-year goal set by DOE in June 1989 to clean up all of its sites and to bring all sites into compliance with current and future environmental regulations. A key component of this program is the development of technologies that are better, faster, safer, and cheaper than those technologies currently available. Included in this report are an evaluation of technologies currently (fiscal year 1993) being pursued at the Hanford Site under the auspices of the VOC-Arid ID program, an assessment of subsurface contaminants at arid/semiarid sites, a summarization of technologies under consideration at other DOE sites, a discussion of areas of potential common technology interests, and the conclusions. Also included are a summary of the extent of contamination at the DOE arid/semiarid sites under consideration and a bibliography of source documents from which this report was prepared.

  11. Lentiviral vector-mediated genetic modification of human neural progenitor cells for ex vivo gene therapy.

    PubMed

    Capowski, Elizabeth E; Schneider, Bernard L; Ebert, Allison D; Seehus, Corey R; Szulc, Jolanta; Zufferey, Romain; Aebischer, Patrick; Svendsen, Clive N

    2007-07-30

    Human neural progenitor cells (hNPC) hold great potential as an ex vivo system for delivery of therapeutic proteins to the central nervous system. When cultured as aggregates, termed neurospheres, hNPC are capable of significant in vitro expansion. In the current study, we present a robust method for lentiviral vector-mediated gene delivery into hNPC that maintains the differentiation and proliferative properties of neurosphere cultures while minimizing the amount of viral vector used and controlling the number of insertion sites per population. This method results in long-term, stable expression even after differentiation of the hNPC to neurons and astrocytes and allows for generation of equivalent transgenic populations of hNPC. In addition, the in vitro analysis presented predicts the behavior of transgenic lines in vivo when transplanted into a rodent model of Parkinson's disease. The methods presented provide a powerful tool for assessing the impact of factors such as promoter systems or different transgenes on the therapeutic utility of these cells.

  12. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome.

    PubMed

    Cui, Pin; Löber, Ulrike; Alquezar-Planas, David E; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N; Lenz, Dorina; Helgen, Kristofer M; Roca, Alfred L; Hartman, Stefanie; Greenwood, Alex D

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

  13. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

    PubMed Central

    Alquezar-Planas, David E.; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N.; Lenz, Dorina; Helgen, Kristofer M.; Roca, Alfred L.; Hartman, Stefanie

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. PMID:27069793

  14. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome.

    PubMed

    Cui, Pin; Löber, Ulrike; Alquezar-Planas, David E; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N; Lenz, Dorina; Helgen, Kristofer M; Roca, Alfred L; Hartman, Stefanie; Greenwood, Alex D

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. PMID:27069793

  15. An integrated subsurface modeling and risk assessment approach for managing the petroleum-contaminated sites.

    PubMed

    Liu, L; Huang, G H; Hao, R X; Cheng, S Y

    2004-01-01

    Soil and groundwater contamination can lead to a variety of impacts and risks to the communities. Identifications of management schemes with sound environmental and socio-economic efficiencies is desired. In fact, before any decisions regarding site remediation actions can be made, three major questions may have to be answered. They include "What happened underground, and what will happen in the future under the given remediation scenarios?," "Are there specific risks on the surrounding community?" and "What remediation alternatives are suitable for the site?" In this study, an integrated subsurface modeling and risk assessment method for petroleum-contaminated site management is proposed. It incorporates multi-phase flow multi-component transport modeling and ELCR-based human health risk assessment into a general framework. The proposed method is applied to a case study within a western Canada context for identifying effective management schemes with improved environmental and socio-economic efficiencies. Given conditions at the study site, six remediation alternatives based on combinations of several technologies are recommended, with the provision of analyses for equipment/manpower requirements, system designs, operations, efficiencies, and costs. These alternatives can be categorized into two groups: hybrid ex situ and in situ remediation approaches, and integrated in situ remediation approaches. This study is a new attempt that integrates issues of subsurface-contamination simulation, risk assessment, and site remediation for a real-world problem within a general research framework. The research outputs are directly useful for the industry to gain insight of the site and to make decisions of the relevant remediation actions.

  16. Oak Ridge National Laboratory Management & Integration Perspective Subcontractors as Partners in Site Restoration

    SciTech Connect

    Brill, A.; Eidam, G.

    2002-02-26

    In 1997, the U. S. Department of Energy (DOE) Oak Ridge Operations (ORO) Office awarded the Management and Integration (M&I) contract for all five of their Oak Ridge Operations facilities to Bechtel Jacobs Company, LLC (BJC). This paper will focus on the success and challenges of several of the M&I projects at the Oak Ridge National Laboratory (ORNL). The initial goals for BJC were to transition up to 93% of their staff to the subcontract community as they moved away from operations to ''integration.'' The perspectives of BJC and one of their Remedial Action/Decontamination & Decommissioning (RADD) subcontractors will be combined in this paper to share with others how ''partnering'' together was essential for success. Projects completed by Safety and Ecology Corporation (SEC) under their RADD subcontract will be used to illustrate the process and the challenges/successes to completion. These projects will include pond remediation, tank remediation, and building cleanup for reuse. All these projects were ''fixed price'' with defined milestones keyed into award fee for BJC and regulatory milestones for DOE. By working together to form integrated teams focused on site remediation without sacrificing safety, all milestones were met. This paper will discuss the following items associated with the M&I environmental restoration projects at ORNL: overview of the M&I Contract; challenges in transitioning from ''operations'' to ''integration''; subcontracting strategies; subcontractor pre-qualification process; overview of ORNL Projects; and integrated team effort required to achieve site restoration goals.

  17. Integration of HIV in the Human Genome: Which Sites Are Preferential? A Genetic and Statistical Assessment

    PubMed Central

    Gonçalves, Juliana; Moreira, Elsa; Sequeira, Inês J.; Rodrigues, António S.; Rueff, José; Brás, Aldina

    2016-01-01

    Chromosomal fragile sites (FSs) are loci where gaps and breaks may occur and are preferential integration targets for some viruses, for example, Hepatitis B, Epstein-Barr virus, HPV16, HPV18, and MLV vectors. However, the integration of the human immunodeficiency virus (HIV) in Giemsa bands and in FSs is not yet completely clear. This study aimed to assess the integration preferences of HIV in FSs and in Giemsa bands using an in silico study. HIV integration positions from Jurkat cells were used and two nonparametric tests were applied to compare HIV integration in dark versus light bands and in FS versus non-FS (NFSs). The results show that light bands are preferential targets for integration of HIV-1 in Jurkat cells and also that it integrates with equal intensity in FSs and in NFSs. The data indicates that HIV displays different preferences for FSs compared to other viruses. The aim was to develop and apply an approach to predict the conditions and constraints of HIV insertion in the human genome which seems to adequately complement empirical data. PMID:27294106

  18. Erace--an integrated system for treating organic-contaminated sites

    SciTech Connect

    Caley, S.M.; Heath, W.O.; Bergsman, T.M.; Gauglitz, P.A.; Pillay, C.; Moss, R.W.; Shah, R.R.; Goheen, S.C.; Camiaoni, D.M.

    1994-11-01

    The U.S. Department of Energy`s (DOE) Pacific Northwest Laboratory (PNL) is developing a suite of electrical technologies for treating sites contaminated with hazardous organic compounds. These include: (1) Six-Phase Soil Heating (SPSH) to remove volatile and semi-volatile organic compounds from soils; (2) In Situ Corona (ISC) to decompose nonvolatile and bound organic contaminants in soils; (3) High-Energy Corona (HEC) to treat contaminated off-gases; and (4) Liquid Corona (LC) to treat contaminated liquids. These four technologies comprise ERACE (Electrical Remediation at Contaminated Environments), an integrated system for accomplishing site remediation with little or no secondary wastes produced that would require off-site treatment or disposal. Each ERACE technology can be employed individually as a stand-alone treatment process, or combined as a system for total site remediation. For example, an ERACE system for treating sites contaminated with volatile organics would integrate SPSH to remove the contaminants from the soil, LC to continuously treat an aqueous stream condensed out of the soil off-gas, and HEC to treat non-condensibles remaining in the off-gas, before atmospheric release.

  19. Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene

    PubMed Central

    Luo, Yumei; Zhang, Zhizhuo; Chen, Yaoyong; Sun, Xiaofang

    2015-01-01

    Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has emerged as a powerful customizable artificial nuclease to facilitate precise genetic correction for tissue regeneration and isogenic disease modeling. However, previous studies reported substantial off-target activities of CRISPR system in human cells, and the enormous putative off-target sites are labor-intensive to be validated experimentally, thus motivating bioinformatics methods for rational design of CRISPR system and prediction of its potential off-target effects. Here, we describe an integrative analytical process to identify specific CRISPR target sites in the human β-globin gene (HBB) and predict their off-target effects. Our method includes off-target analysis in both coding and noncoding regions, which was neglected by previous studies. It was found that the CRISPR target sites in the introns have fewer off-target sites in the coding regions than those in the exons. Remarkably, target sites containing certain transcriptional factor motif have enriched binding sites of relevant transcriptional factor in their off-target sets. We also found that the intron sites have fewer SNPs, which leads to less variation of CRISPR efficiency in different individuals during clinical applications. Our studies provide a standard analytical procedure to select specific CRISPR targets for genetic correction. PMID:25918715

  20. Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene.

    PubMed

    Luo, Yumei; Zhu, Detu; Zhang, Zhizhuo; Chen, Yaoyong; Sun, Xiaofang

    2015-01-01

    Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has emerged as a powerful customizable artificial nuclease to facilitate precise genetic correction for tissue regeneration and isogenic disease modeling. However, previous studies reported substantial off-target activities of CRISPR system in human cells, and the enormous putative off-target sites are labor-intensive to be validated experimentally, thus motivating bioinformatics methods for rational design of CRISPR system and prediction of its potential off-target effects. Here, we describe an integrative analytical process to identify specific CRISPR target sites in the human β-globin gene (HBB) and predict their off-target effects. Our method includes off-target analysis in both coding and noncoding regions, which was neglected by previous studies. It was found that the CRISPR target sites in the introns have fewer off-target sites in the coding regions than those in the exons. Remarkably, target sites containing certain transcriptional factor motif have enriched binding sites of relevant transcriptional factor in their off-target sets. We also found that the intron sites have fewer SNPs, which leads to less variation of CRISPR efficiency in different individuals during clinical applications. Our studies provide a standard analytical procedure to select specific CRISPR targets for genetic correction.

  1. Background Information for the Nevada National Security Site Integrated Sampling Plan, Revision 0

    SciTech Connect

    Farnham, Irene; Marutzky, Sam

    2014-12-01

    This document describes the process followed to develop the Nevada National Security Site (NNSS) Integrated Sampling Plan (referred to herein as the Plan). It provides the Plan’s purpose and objectives, and briefly describes the Underground Test Area (UGTA) Activity, including the conceptual model and regulatory requirements as they pertain to groundwater sampling. Background information on other NNSS groundwater monitoring programs—the Routine Radiological Environmental Monitoring Plan (RREMP) and Community Environmental Monitoring Program (CEMP)—and their integration with the Plan are presented. Descriptions of the evaluations, comments, and responses of two Sampling Plan topical committees are also included.

  2. Study of component technologies for fuel cell on-site integrated energy system. Volume 2: Appendices

    NASA Technical Reports Server (NTRS)

    Lee, W. D.; Mathias, S.

    1980-01-01

    This data base catalogue was compiled in order to facilitate the analysis of various on site integrated energy system with fuel cell power plants. The catalogue is divided into two sections. The first characterizes individual components in terms of their performance profiles as a function of design parameters. The second characterizes total heating and cooling systems in terms of energy output as a function of input and control variables. The integrated fuel cell systems diagrams and the computer analysis of systems are included as well as the cash flows series for baseline systems.

  3. Integrated system for gathering, processing, and reporting data relating to site contamination

    DOEpatents

    Long, D.D.; Goldberg, M.S.; Baker, L.A.

    1997-11-11

    An integrated screening system comprises an intrusive sampling subsystem, a field mobile laboratory subsystem, a computer assisted design/geographical information subsystem, and a telecommunication linkup subsystem, all integrated to provide synergistically improved data relating to the extent of site soil/groundwater contamination. According to the present invention, data samples related to the soil, groundwater or other contamination of the subsurface material are gathered and analyzed to measure contaminants. Based on the location of origin of the samples in three-dimensional space, the analyzed data are transmitted to a location display. The data from analyzing samples and the data from the locating the origin are managed to project the next probable sample location. The next probable sample location is then forwarded for use as a guide in the placement of ensuing sample location, whereby the number of samples needed to accurately characterize the site is minimized. 10 figs.

  4. Integrated system for gathering, processing, and reporting data relating to site contamination

    DOEpatents

    Long, Delmar D.; Goldberg, Mitchell S.; Baker, Lorie A.

    1997-01-01

    An integrated screening system comprises an intrusive sampling subsystem, a field mobile laboratory subsystem, a computer assisted design/geographical information subsystem, and a telecommunication linkup subsystem, all integrated to provide synergistically improved data relating to the extent of site soil/groundwater contamination. According to the present invention, data samples related to the soil, groundwater or other contamination of the subsurface material are gathered and analyzed to measure contaminants. Based on the location of origin of the samples in three-dimensional space, the analyzed data are transmitted to a location display. The data from analyzing samples and the data from the locating the origin are managed to project the next probable sample location. The next probable sample location is then forwarded for use as a guide in the placement of ensuing sample location, whereby the number of samples needed to accurately characterize the site is minimized.

  5. DNFSB recommendation 94-1 Hanford site integrated stabilization management plan

    SciTech Connect

    McCormack, R.L.

    1997-05-07

    In May 1994, the Defense Nuclear Facilities Safety Board (DNFSB) issued DNFSB Recommendation 94-1 (Conway 1994), which identified concerns related to US Department of Energy (DOE) management of legacy fissile materials remaining from past defense production activities. The DNFSB expressed concern about the existing storage conditions for these materials and the slow pace at which the conditions were being remediated. The DNFSB also expressed its belief that additional delays in stabilizing these fissile materials would be accompanied by further deterioration of safety and unnecessary increased risks to workers and the public. In February 1995, DOE issued the DNFSB Recommendation 94-1 Implementation Plan (O`Leary 1995) to address the concerns identified in DNFSB Recommendation 94-1. The Implementation Plan (IP) identifies several DOE commitments to achieve safe interim storage for the legacy fissile materials, and constitutes DOE`s baseline DNFSB Recommendation 94-1 Integrated Program Plan (IPP). The IPP describes the actions DOE plans to implement within the DOE complex to convert its excess fissile materials to forms or conditions suitable for safe interim storage. The IPP was subsequently supplemented with an Integrated Facilities Plan and a Research and Development Plan, which further develop complex-wide research and development and long-range facility requirements and plans. The additions to the baseline IPP were developed based on a systems engineering approach that integrated facilities and capabilities at the various DOE sites and focused on attaining safe interim storage with minimum safety risks and environmental impacts. Each affected DOE site has developed a Site Integrated Stabilization Management Plan (SISMP) to identify individual site plans to implement the DNFSB Recommendation 94-1 IPP. The SISMPs were developed based on the objectives, requirements, and commitments identified in the DNFSB Recommendation 94-1 IP. The SISMPs also supported

  6. Develop and test fuel cell powered on-site integrated total energy system

    NASA Technical Reports Server (NTRS)

    1983-01-01

    Test results are given for a 5 kW stack and initial results for an integrated, grid connected system operating from methanol fuel. Site selection criteria are presented for future demonstration of a 50 or 100 kW OS/IES. Preliminary results are also given with approximate internal rates of return to the building owner. Progress in development and construction of a 50 kW modular methanol/steam reformer is reported.

  7. Develop and test fuel cell powered on-site integrated total energy system

    NASA Technical Reports Server (NTRS)

    Kaufman, A.; Feigenbaum, H.; Wang, C. L.; Werth, J.; Whelan, J. A.

    1983-01-01

    Test results are presented for a 24 cell, two sq ft (4kW) stack. This stack is a precursor to a 25kW stack that is a key milestone. Results are discussed in terms of cell performance, electrolyte management, thermal management, and reactant gas manifolding. The results obtained in preliminary testing of a 50kW methanol processing subsystem are discussed. Subcontracting activities involving application analysis for fuel cell on site integrated energy systems are updated.

  8. Integration site and clonal expansion in human chronic retroviral infection and gene therapy.

    PubMed

    Niederer, Heather A; Bangham, Charles R M

    2014-10-31

    Retroviral vectors have been successfully used therapeutically to restore expression of genes in a range of single-gene diseases, including several primary immunodeficiency disorders. Although clinical trials have shown remarkable results, there have also been a number of severe adverse events involving malignant outgrowth of a transformed clonal population. This clonal expansion is influenced by the integration site profile of the viral integrase, the transgene expressed, and the effect of the viral promoters on the neighbouring host genome. Infection with the pathogenic human retrovirus HTLV-1 also causes clonal expansion of cells containing an integrated HTLV-1 provirus. Although the majority of HTLV-1-infected people remain asymptomatic, up to 5% develop an aggressive T cell malignancy. In this review we discuss recent findings on the role of the genomic integration site in determining the clonality and the potential for malignant transformation of cells carrying integrated HTLV-1 or gene therapy vectors, and how these results have contributed to the understanding of HTLV-1 pathogenesis and to improvements in gene therapy vector safety.

  9. Polybrene: Observations on cochlear hair cell necrosis and minimal lentiviral transduction of cochlear hair cells.

    PubMed

    Han, Miaomiao; Yu, Dongzhen; Song, Qiang; Wang, Jiping; Dong, Pin; He, Jingchun

    2015-07-23

    Polybrene is widely used to enhance viral transduction; however, little is known about the utility thereof, in enhancing lentiviral transduction of cochlear cells. In the present study, we examined the cytotoxic effects of polybrene, and the further effects thereof, on lentiviral transduction of cochlear cells, especially sensory hair cells. Cochlear basilar membranes of newborn rats were cultured and treated with 0.1-10 μg/mL polybrene for 24h to explore the potential development of ototoxicity. PI staining and TUNEL detection were used to evaluate necrosis or apoptosis of hair cell. Various doses of lentivirus-GFP were added to cochlear organotypic cultures with safe concentrations of polybrene, incubated for 24h, and cultured (in the absence of the virus and polybrene) for a further 48 h. Transduction efficiencies were evaluated. The results showed that polybrene at 0.1 μg/mL was safe to cochlear cells, and 0.5-10 μg/mL concentration induced hair cell necrosis in a dose-dependent manner. However, supporting cells were not damaged. Lentiviral vectors transduced into cochlear cells and 0.1 μg/mL polybrene enhanced transduction efficiency. However, hair cells were hardly transduced with lentiviral vectors either alone or in the presence of 0.1 μg/mL polybrene. The use of polybrene to aid lentiviral transduction of cochlear hair cells requires further attention.

  10. Polybrene: Observations on cochlear hair cell necrosis and minimal lentiviral transduction of cochlear hair cells.

    PubMed

    Han, Miaomiao; Yu, Dongzhen; Song, Qiang; Wang, Jiping; Dong, Pin; He, Jingchun

    2015-07-23

    Polybrene is widely used to enhance viral transduction; however, little is known about the utility thereof, in enhancing lentiviral transduction of cochlear cells. In the present study, we examined the cytotoxic effects of polybrene, and the further effects thereof, on lentiviral transduction of cochlear cells, especially sensory hair cells. Cochlear basilar membranes of newborn rats were cultured and treated with 0.1-10 μg/mL polybrene for 24h to explore the potential development of ototoxicity. PI staining and TUNEL detection were used to evaluate necrosis or apoptosis of hair cell. Various doses of lentivirus-GFP were added to cochlear organotypic cultures with safe concentrations of polybrene, incubated for 24h, and cultured (in the absence of the virus and polybrene) for a further 48 h. Transduction efficiencies were evaluated. The results showed that polybrene at 0.1 μg/mL was safe to cochlear cells, and 0.5-10 μg/mL concentration induced hair cell necrosis in a dose-dependent manner. However, supporting cells were not damaged. Lentiviral vectors transduced into cochlear cells and 0.1 μg/mL polybrene enhanced transduction efficiency. However, hair cells were hardly transduced with lentiviral vectors either alone or in the presence of 0.1 μg/mL polybrene. The use of polybrene to aid lentiviral transduction of cochlear hair cells requires further attention. PMID:26071903

  11. Development of a doxycycline-inducible lentiviral plasmid with an instant regulatory feature.

    PubMed

    Yang, Tian; Burrows, Christopher; Park, Jeong Hyeon

    2014-03-01

    Lentiviruses provide highly efficient gene delivery vehicles in both dividing and non-dividing cells. Inducible gene expression systems often employ a specific cell line that constitutively expresses a regulatory protein for transgene expression. As one of such inducible expression systems the Tet-On system uses a cell line expressing reverse tetracycline-responsive transcriptional activator (rtTA). The rtTA protein binds to the tetracycline-responsive element (TRE) in the promoter and activates transcription of a transgene in a doxycycline-dependent manner. To establish a universal and instant regulatory system without generating Tet-On cell lines, the cDNAs of rtTA and a testing target gene (PPM1B) were cloned in the bi-directional TRE-containing promoters. Here, we examined whether a basal leaky expression of rtTA allows instantly inducible expression of both rtTA itself and the target gene, PPM1B in a single plasmid using the two mini-CMV promoters. Transient transfection of the lentiviral plasmids into human embryonic kidney HEK293T cells showed a significant induction of PPM1B expression in response to doxycycline, suggesting that these lentiviral plasmids can be used as an instantly inducible mammalian expression vector. However, the expression of rtTA by lentiviral transduction shows a minimal expression without a consistent response to doxycycline, suggesting that the utility of these lentiviral vectors is limited. A potential solution to overcome lentiviral transgene inactivation is proposed. PMID:24727543

  12. Technology needs for remediation: Hanford and other DOE sites. Buried Waste Integrated Demonstration Program

    SciTech Connect

    Stapp, D.C.

    1993-01-01

    Technologies are being developed under the Buried Waste Integrated Demonstration (BWID) program to facilitate remediation of the US Department of Energy`s (DOE) buried and stored low-level radioactive, transuranic (TRU), and mixed radioactive and hazardous buried wastes. The BWID program is being coordinated by the Idaho National Engineering Laboratory (INEL) in southeastern Idaho, a DOE site that has large volumes of buried radioactive wastes. The program is currently focusing its efforts on the problems at INEL`s Subsurface Disposal Area (SDA) of the Radioactive Waste Management Complex (RWMC). As specific technologies are successfully demonstrated, they will be available for transfer to applications at other DOE buried waste sites. The purpose of this study is to present buried waste technology needs that have been identified for DOE sites other than INEL.

  13. Integrated Weed Control for Land Stewardship at Legacy Management's Rocky Flats Site in Colorado - 13086

    SciTech Connect

    Nelson, Jody K.

    2013-07-01

    Land stewardship is one of nine sustainability programs in the U.S. Department of Energy's Environmental Management System. Land stewardship includes maintaining and improving ecosystem health. At the Rocky Flats Site near Westminster, Colorado, land stewardship is an integral component of the Office of Legacy Management's post-closure monitoring and management at the site. Nearly 263 hectares (650 acres) were disturbed and re-vegetated during site cleanup and closure operations. Proactive management of revegetation areas is critical to the successful reestablishment of native grasslands, wetlands, and riparian communities. The undisturbed native plant communities that occur at the site also require active management to maintain the high-quality wetlands and other habitats that are home to numerous species of birds and other wildlife such as elk and deer, rare plant communities, and the federally listed threatened Preble's meadow jumping mouse. Over the past several decades, an increase of Noxious weeds has impacted much of Colorado's Front Range. As a result, weed control is a key component of the land stewardship program at Rocky Flats. Thirty-three species of state-listed Noxious weeds are known to occur in the Central and Peripheral Operable Units at Rocky Flats, along with another five species that are considered invasive at the site. Early detection and rapid response to control new invasive species is crucial to the program. An integrated weed control/vegetation management approach is key to maintaining healthy, sustainable plant communities that are able to resist Noxious weed invasions. Weed mapping, field surveys, and field-staff training sessions (to learn how to identify new potential problem species) are conducted to help detect and prevent new weed problems. The integrated approach at Rocky Flats includes administrative and cultural techniques (prevention), mechanical controls, biological controls, and chemical controls. Several species of biocontrol

  14. Testing an Integrated Ground-Water Monitoring Strategy for Nuclear Waste and Decommissioning Sites

    NASA Astrophysics Data System (ADS)

    Price, V.; Dai, Z.; Heffner, D.; Temples, T. J.; Nicholson, T. J.

    2005-05-01

    This talk discusses a Nuclear Regulatory Commission-sponsored research project designed to develop an integrated and systematic strategy for monitoring ground-water flow and transport through the unsaturated zone to the underlying water-table aquifer at waste disposal sites. The goal is to provide scientifically-based guidance for monitoring across a wide range of geologic settings, waste compositions, and site designs. The monitoring will specifically support performance assessment studies and modeling. The research objectives include: (1) the strategy will couple performance confirmation monitoring to site characterization and performance assessment, and will consist of an ordered and logical sequence of procedures; (2) the research will develop the technical bases as citable references, identified guidance and analytical tools, and test case applications of the developed integrated ground-water monitoring strategy for confirming performance of nuclear waste and decommissioning sites; (3) this strategy will focus on identifying and monitoring critical performance indicators (e.g., water contents over time in the unsaturated zone, and ground-water potentials in the saturated zone) of the hydrologic system; and (4) the strategy will demonstrate the connection between performance indicators and site performance. The monitoring strategy has been developed in draft form, and the testing phase of this work is beginning. The test plan includes: 1. develop testing objectives; 2. develop success criteria based on objectives; 3. select test datasets from field sites; 4. apply the draft strategy to field data; 5. feed-back for strategy improvement. Testing objectives will include: 1. develop rules for selection of performance indicators; 2. evaluate efficient methods to develop conceptual site models; 3. develop rules for selection of monitoring points (in the spatial and temporal domain) and rules for identification of monitoring approaches (e.g., geophysical methods) and

  15. Different integrated geophysical approaches to investigate archaeological sites in urban and suburban area.

    NASA Astrophysics Data System (ADS)

    Piro, Salvatore; Papale, Enrico; Zamuner, Daniela

    2016-04-01

    Geophysical methods are frequently used in archaeological prospection in order to provide detailed information about the presence of structures in the subsurface as well as their position and their geometrical reconstruction, by measuring variations of some physical properties. Often, due to the limited size and depth of an archaeological structure, it may be rather difficult to single out its position and extent because of the generally low signal-to-noise ratio. This problem can be overcome by improving data acquisition, processing techniques and by integrating different geophysical methods. In this work, two sites of archaeological interest, were investigated employing several methods (Ground Penetrating Radar (GPR), Electrical Resistivity Tomography (ERT), Fluxgate Differential Magnetic) to obtain precise and detailed maps of subsurface bodies. The first site, situated in a suburban area between Itri and Fondi, in the Aurunci Natural Regional Park (Central Italy), is characterized by the presence of remains of past human activity dating from the third century B.C. The second site, is instead situated in an urban area in the city of Rome (Basilica di Santa Balbina), where historical evidence is also present. The methods employed, allowed to determine the position and the geometry of some structures in the subsurface related to this past human activity. To have a better understanding of the subsurface, we then performed a qualitative and quantitative integration of this data, which consists in fusing the data from all the methods used, to have a complete visualization of the investigated area. Qualitative integration consists in graphically overlaying the maps obtained by the single methods; this method yields only images, not new data that may be subsequently analyzed. Quantitative integration is instead performed by mathematical and statistical solutions, which allows to have a more accurate reconstruction of the subsurface and generates new data with high

  16. Optimization of lentiviral vector production using polyethylenimine-mediated transfection.

    PubMed

    Tang, Yong; Garson, Kenneth; Li, Li; Vanderhyden, Barbara C

    2015-01-01

    The aim of the present study was to optimize the polyethylenimine (PEI)-mediated transfection method in order to simplify the efficient production of lentiviral vectors (LvVs), and to compare the CaPO4- and PEI-mediated transfection methods for producing LvVs. Different titration methods of LvV stocks, as well as different culture media, culture durations, cell densities and DNA quantities were compared to obtain an optimized procedure for the production of LvVs. Optimization of the production method for LvVs was achieved using PEI-mediated transient transfections. Serum-free Opti-MEM(®) was used to directly produce LvVs that could be harvested 48 h after transfection. Furthermore, a cell density of 15×10(6) cells/10-cm plate and a DNA concentration of 1X were selected for the optimum production of LvVs. The optimized LvV titration method was simple and direct; it involved LvVs carrying fluorescent reporters, which proved to be faster than the standard methods but equally as sensitive. In conclusion, a scalable process for production of LvVs by PEI-mediated transfection was established and optimized. The optimized PEI-mediated transfection method was easy to use, as well as providing greater reliability with a higher degree of reproducibility and consistency. Despite using less DNA, the PEI-mediated transfection method resulted in viral titers that were the same as those achieved using the CaPO4-mediated method.

  17. Packaging of HCV-RNA into lentiviral vector

    SciTech Connect

    Caval, Vincent; Piver, Eric; Ivanyi-Nagy, Roland; Darlix, Jean-Luc; Pages, Jean-Christophe

    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 and 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.

  18. Integrated Site Characterization for the Proposed Deep Underground Science and Engineering Laboratory (DUSEL) at Kimballton, Virginia

    NASA Astrophysics Data System (ADS)

    Shumaker, A. N.; Henika, W. S.; Hole, J. A.; Imhof, M. G.; Burbey, T. J.; Bodnar, R. J.

    2004-12-01

    The National Science Foundation has announced a plan to establish a Deep Underground Science and Engineering Laboratory (DUSEL) for interdisciplinary research in physics, geosciences, biosciences and engineering. The proposed laboratory will extend to a depth of about 2000 meters and will consist of a series of research facilities for long term study. To date, 8 sites in North America have been proposed to host DUSEL. One of these sites, known as Kimballton, is located near Butt Mountain in Giles County in southwestern Virginia. The Kimballton site is in the Valley and Ridge Province of the southern Appalachians and consists of repeated sequences folded and thrusted Paleozoic dolomite, limestone and clastic rocks. The site is located near the active Kimballton mine, which extends to 700 meters depth in the Butt Mountain Synclinorium and produces chemical-grade lime from the Five Oaks Formation. Surface and mine geology at Kimballton have been projected to the DUSEL horizon, and indicate that the facility would be hosted in Ordovician limestone of the Saint Clair thrust sheet that lies beneath the Narrows thrust fault. Two 3 km seismic reflection lines were acquired along the top of Butt Mountain to characterize the subsurface geology in the vicinity of the DUSEL site. Preliminary interpretations of the seismic data are consistent with the structural model derived from surface geology. A 2.2 km borehole from the top of Butt Mountain to the DUSEL horizon will be drilled to further constrain the geology and to construct an integrated 3D subsurface model.

  19. Lentiviral gene transfer into human and murine hematopoietic stem cells: size matters.

    PubMed

    Canté-Barrett, Kirsten; Mendes, Rui D; Smits, Willem K; van Helsdingen-van Wijk, Yvette M; Pieters, Rob; Meijerink, Jules P P

    2016-01-01

    Contemporary biomedical research increasingly depends on techniques to induce or to inhibit expression of genes in hematopoietic stem cells (HSCs) or other primary cells to assess their roles on cellular processes including differentiation, apoptosis and migration. Surprisingly little information is available to optimize lentiviral transduction of HSCs. We have therefore carefully optimized transduction of murine and human HSCs by optimizing vector design, serum-free virus production and virus quantitation. We conclude that the viral RNA length, even in relatively small vectors, is an important factor affecting the lentiviral gene transfer on the level of both the virus production and the cellular transduction efficiency. Efficient transfer of large gene sequences into difficult-to-transduce primary cells will benefit from reducing the lentiviral construct size. PMID:27306375

  20. Lentiviral Transduction of Neurons in Adult Brain: Evaluation of Inflammatory Response and Cognitive Effects in Mice.

    PubMed

    Kunitsyna, T A; Ivashkina, O I; Roshchina, M A; Toropova, K A; Anokhin, K V

    2016-06-01

    We evaluated the effect of hippocampal injection of lentiviral particles p156-CMV-EGFP on behavior, learning, and microglial Iba1(+) cells activation in mice. Testing in the open field and elevated plus-maze revealed higher anxiety levels in lentiviral-injected mice in comparison with animals injected with vehicle. At the same time, lentivirus injection did not change learning and memory of mice in the hippocampal-dependent fear conditioning task. Microglia density in lentivirus-injected mice was significantly higher than in vehicle-injected mice. Thus, hippocampal injection of lentiviral particles with minimum content of transgenes produced evident inflammation process, changed anxiety level of experimental animals, but had no effect on hippocampal-dependent learning and memory. PMID:27383167

  1. Integration of various subsurface exploration techniques to solve problems at sites contaminated with petroleum hydrocarbons

    SciTech Connect

    Hickey, J.C.; Hatheway, M.H.

    1996-12-31

    As a result of both regulatory and property transfer driven investigations of petroleum distribution and storage sites, countless contamination issues have been identified. Thoughtful selection and use of different geochemical, geologic, and geophysical subsurface exploration techniques can significantly increase the cost effectiveness of investigation, remedial design/implementation, and post-closure monitoring programs. Three case histories highlighting the approach are presented. In each case, careful consideration of data needs, methods capabilities and limitations resulted in the sequenced integration of specific investigatory tools to generate the required information. These are: (1) First discussed will be the use of ground penetrating radar, seismic refraction, active and passive soil vapor surveys, installation of monitoring wells, and use of lineament/fracture trace analysis to guide the remedial investigation and system design meant to evaluate and correct gasoline and diesel releases at a major highway truck stop. (2) The use of a passive soil vapor survey, grab soil and groundwater sampling, and traditional monitoring well program at a former retail gasoline distribution site in Colorado will be presented next. Data generated by this integrated investigation were used in support of a risk assessment and remediation system design. (3) Lastly, the use of an active soil vapor survey, grab sampling and field analyses and integration with results from previous remedial investigations and emergency response measures at a commercial truck leasing facility will be overviewed. The results identified areas of residual soil contamination not addressed during the emergency response measures.

  2. Integration of various subsurface exploration techniques to solve problems at sites contaminated with petroleum hydrocarbons

    SciTech Connect

    Hickey, J.C.; Hatheway, M.H. ); Tingley, A.C. )

    1996-01-01

    As a result of both regulatory and property transfer driven investigations of petroleum distribution and storage sites, countless contamination issues have been identified. Thoughtful selection and use of different geochemical, geologic, and geophysical subsurface exploration techniques can significantly increase the cost effectiveness of investigation, remedial design/implementation, and post-closure monitoring programs. Three case histories highlighting the approach are presented. In each case, careful consideration of data needs, methods capabilities and limitations resulted in the sequenced integration of specific investigatory tools to generate the required information. These are: (1) First discussed will be the use of ground penetrating radar, seismic refraction, active and passive soil vapor surveys, installation of monitoring wells, and use of lineament/fracture trace analysis to guide the remedial investigation and system design meant to evaluate and correct gasoline and diesel releases at a major highway truck stop. (2) The use of a passive soil vapor survey, grab soil and groundwater sampling, and traditional monitoring well program at a former retail gasoline distribution site in Colorado will be presented next. Data generated by this integrated investigation were used in support of a risk assessment and remediation system design. (3) Lastly, the use of an active soil vapor survey, grab sampling and field analyses and integration with results from previous remedial investigations and emergency response measures at a commercial truck leasing facility will be overviewed. The results identified areas of residual soil contamination not addressed during the emergency response measures.

  3. Hanford Integrated Planning Process: 1993 Hanford Site-specific science and technology plan

    SciTech Connect

    Not Available

    1993-12-01

    This document is the FY 1993 report on Hanford Site-specific science and technology (S&T) needs for cleanup of the Site as developed via the Hanford Integrated Planning Process (HIPP). It identifies cleanup problems that lack demonstrated technology solutions and technologies that require additional development. Recommendations are provided regarding allocation of funding to address Hanford`s highest-priority technology improvement needs, technology development needs, and scientific research needs, all compiled from a Sitewide perspective. In the past, the S&T agenda for Hanford Site cleanup was sometimes driven by scientists and technologists, with minimal input from the ``problem owners`` (i.e., Westinghouse Hanford Company [WHC] staff who are responsible for cleanup activities). At other times, the problem-owners made decisions to proceed with cleanup without adequate scientific and technological inputs. Under both of these scenarios, there was no significant stakeholder involvement in the decision-making process. One of the key objectives of HIPP is to develop an understanding of the integrated S&T requirements to support the cleanup mission, (a) as defined by the needs of the problem owners, the values of the stakeholders, and the technology development expertise that exists at Hanford and elsewhere. This requires a periodic, systematic assessment of these needs and values to appropriately define a comprehensive technology development program and a complementary scientific research program. Basic to our success is a methodology that is defensible from a technical perspective and acceptable to the stakeholders.

  4. Icebreaker-3 Drill Integration and Testing at Two Mars-Analog Sites

    NASA Technical Reports Server (NTRS)

    Glass, B.; Bergman, D.; Yaggi, B.; Dave, A.; Zacny, K.

    2016-01-01

    A decade of evolutionary development of integrated automated drilling and sample handling at analog sites and in test chambers has made it possible to go 1 meter through hard rocks and ice layers on Mars. The latest Icebreaker-3 drill has been field tested in 2014 at the Haughton Crater Marsanalog site in the Arctic and in 2015 with a Mars lander mockup in Rio Tinto, Spain, (with sample transfer arm and with a prototype life-detection instrument). Tests in Rio Tinto in 2015 successfully demonstrated that the drill sample (cuttings) was handed-off from the drill to the sample transfer arm and thence to the on-deck instrument inlet where it was taken in and analyzed ("dirt-to-data").

  5. Analysis of a fuel cell on-site integrated energy system for a residential complex

    NASA Technical Reports Server (NTRS)

    Simons, S. N.; Maag, W. L.

    1979-01-01

    Declining supplies of domestic oil and gas and the increased cost of energy resulted in a renewed emphasis in utilizing available resources in the most efficient manner possible. This, in turn, brought about a reassessment of a number of methods for converting fossil fuels to end uses at the highest practical efficiency. One of these is the on-site integrated energy system (OS/IES). This system provides electric power from an on-site power plant and recovers heat from the power plant that would normally be rejected to the environment. An OS/IES is potentially useful in any application that requires both electricity and heat. Several OS/IES are analyzed for a residential complex. The paper is divided into two sections; the first compares three energy supply systems, the second compares various designs for fuel cell OS/IES.

  6. MAC Europe 1991 campaign: AIRSAR/AVIRIS data integration for agricultural test site classification

    NASA Technical Reports Server (NTRS)

    Sangiovanni, S.; Buongiorno, M. F.; Ferrarini, M.; Fiumara, A.

    1993-01-01

    During summer 1991, multi-sensor data were acquired over the Italian test site 'Otrepo Pavese', an agricultural flat area in Northern Italy. This area has been the Telespazio pilot test site for experimental activities related to agriculture applications. The aim of the investigation described in the following paper is to assess the amount of information contained in the AIRSAR (Airborne Synthetic Aperture Radar) and AVIRIS (Airborne Visible/Infrared Imaging Spectrometer) data, and to evaluate classification results obtained from each sensor data separately and from the combined dataset. All classifications are examined by means of the resulting confusion matrices and Khat coefficients. Improvements of the classification results obtained by using the integrated dataset are finally evaluated.

  7. D Integrated Methodologies for the Documentation and the Virtual Reconstruction of AN Archaeological Site

    NASA Astrophysics Data System (ADS)

    Balletti, C.; Guerra, F.; Scocca, V.; Gottardi, C.

    2015-02-01

    Highly accurate documentation and 3D reconstructions are fundamental for analyses and further interpretations in archaeology. In the last years the integrated digital survey (ground-based survey methods and UAV photogrammetry) has confirmed its main role in the documentation and comprehension of excavation contexts, thanks to instrumental and methodological development concerning the on site data acquisition. The specific aim of the project, reported in this paper and realized by the Laboratory of Photogrammetry of the IUAV University of Venice, is to check different acquisition systems and their effectiveness test, considering each methodology individually or integrated. This research focuses on the awareness that the integration of different survey's methodologies can as a matter of fact increase the representative efficacy of the final representations; these are based on a wider and verified set of georeferenced metric data. Particularly the methods' integration allows reducing or neutralizing issues related to composite and complex objects' survey, since the most appropriate tools and techniques can be chosen considering the characteristics of each part of an archaeological site (i.e. urban structures, architectural monuments, small findings). This paper describes the experience in several sites of the municipality of Sepino (Molise, Italy), where the 3d digital acquisition of cities and structure of monuments, sometimes hard to reach, was realized using active and passive techniques (rage-based and image based methods). This acquisition was planned in order to obtain not only the basic support for interpretation analysis, but also to achieve models of the actual state of conservation of the site on which some reconstructive hypotheses can be based on. Laser scanning data were merged with Structure from Motion techniques' clouds into the same reference system, given by a topographical and GPS survey. These 3d models are not only the final results of the metric

  8. INTEGRATED PROCESS GAS MODELING FOR TRITIUM SYSTEMS AT THE SAVANNAH RIVER SITE

    SciTech Connect

    Hang, T; Anita Poore, A

    2007-08-30

    Significant savings are being realized from the consolidated tritium gas-processing operations at the Savannah River Site. However, the trade-off is some reduction of operational flexibility due to decreased storage capacity for process and waste gases. Savannah River National Laboratory researchers are developing an integrated process gas model for tritium processing using Aspen Custom Modeler{trademark} (ACM) software. The modeling involves fully characterizing process flow streams (gas composition, quantity), frequency of batch transfers, and availability of equipment in the flow stream. The model provides a valuable engineering tool to identify flow bottlenecks, thereby enabling adjustments to be made to improve process operations.

  9. Fuel cell on-site integrated energy system parametric analysis of a residential complex

    NASA Technical Reports Server (NTRS)

    Simons, S. N.

    1977-01-01

    A parametric energy-use analysis was performed for a large apartment complex served by a fuel cell on-site integrated energy system (OS/IES). The variables parameterized include operating characteristics for four phosphoric acid fuel cells, eight OS/IES energy recovery systems, and four climatic locations. The annual fuel consumption for selected parametric combinations are presented and a breakeven economic analysis is presented for one parametric combination. The results show fuel cell electrical efficiency and system component choice have the greatest effect on annual fuel consumption; fuel cell thermal efficiency and geographic location have less of an effect.

  10. Site-controlled Ag nanocrystals grown by molecular beam epitaxy-Towards plasmonic integration technology

    SciTech Connect

    Urbanczyk, Adam; Noetzel, Richard

    2012-12-15

    We demonstrate site-controlled growth of epitaxial Ag nanocrystals on patterned GaAs substrates by molecular beam epitaxy with high degree of long-range uniformity. The alignment is based on lithographically defined holes in which position controlled InAs quantum dots are grown. The Ag nanocrystals self-align preferentially on top of the InAs quantum dots. No such ordering is observed in the absence of InAs quantum dots, proving that the ordering is strain-driven. The presented technique facilitates the placement of active plasmonic nanostructures at arbitrarily defined positions enabling their integration into complex devices and plasmonic circuits.

  11. Radionuclide disequilibria studies for investigating the integrity of potential nuclear waste disposal sites: subseabed studies.

    SciTech Connect

    Laul, J.C.; Thomas, C.W.; Petersen, M.R.; Perkins, R.W.

    1981-09-01

    This study of subseabed sediments indicates that natural radionuclides can be employed to define past long-term migration rates and thereby evaluate the integrity of potential disposal sites in ocean sediments. The study revealed the following conclusions: (1) the sedimentation rate of both the long and short cores collected in the North Pacific is 2.5 mm/1000 yr or 2.5 m/m.yr in the upper 3 meters; (2) the sedimentation rate has been rather constant over the last one million years; and (3) slow diffusive processes dominate within the sediment. Reworking of the sediment by physical processes or organisms is not observed.

  12. MicroRNA Target Site Identification by Integrating Sequence and Binding Information

    PubMed Central

    Majoros, William H.; Lekprasert, Parawee; Mukherjee, Neelanjan; Skalsky, Rebecca L.; Corcoran, David L.; Cullen, Bryan R.; Ohler, Uwe

    2013-01-01

    High-throughput sequencing has opened numerous possibilities for the identification of regulatory RNA-binding events. Cross-linking and immunoprecipitation of Argonaute protein members can pinpoint microRNA target sites within tens of bases, but leaves the identity of the microRNA unresolved. A flexible computational framework that integrates sequence with cross-linking features reliably identifies the microRNA family involved in each binding event, considerably outperforms sequence-only approaches, and quantifies the prevalence of noncanonical binding modes. PMID:23708386

  13. Establishment of a rapid and scalable gene expression system in livestock by site-specific integration.

    PubMed

    Yu, Huiqing; Wang, Xuebin; Zhu, Li; He, Zhuzi; Liu, Guohui; Xu, Xujun; Chen, Jianquan; Cheng, Guoxiang

    2013-02-25

    Somatic cell-mediated transgenesis is routinely used to transfer exogenous genes to livestock genomes. However, transgene insertion events are essentially random which may lead to transgene silencing or alter animal phenotype because of insertional mutagenesis. To overcome these problems, we established a gene manipulation system in goat somatic cells based on homologous recombination and flp recombinase-mediated site-specific integration. First, we performed gene targeting to introduce an frt-docking site into the α1 (I) procollagen (ColA1) locus in goat somatic cells. Second, the targeted cell clones were rejuvenated by embryo cloning, and the vigorous cells with targeted frt were reestablished. Third, a gene-replacement system was used to introduce an EGFP reporter gene into the targeted ColA1 locus via flp mediated recombination. As a result, the transgenic somatic cell exhibited faithful expression of EGFP gene under control of the CMV promoter. Similarly, other expression vectors can be introduced into the defined site to evaluate gene functions or express valuable proteins. The gene manipulation system described here will be applicable in other livestock somatic cells, and would allow for the rapid generation of livestock with transgene targeted to the defined site.

  14. 2001 Columbia River Recreation Survey -- Implications for Hanford Site Integrated Assessment

    SciTech Connect

    Anderson, Dave M.; Scott, Michael J.; Bunn, Amoret L.; Fowler, Richard A.; Prendergast, Ellen L.; Miley, Terri B.; Eschbach, Tara O.; Jaksch, John A.

    2002-05-16

    This report presents the results from the Columbia River Recreation Survey conducted in the summer of 2001. The survey combined on-site personal interviews with parties engaged in river recreation with on-site field observations to develop a picture of summer river recreation on the Columbia. The study area stretched from just below Priest Rapids Dam in the north to McNary Dam in the south, and was divided into four "Areas" that correspond to the river areas used by the Groundwater/Vadose Zone Integration Project. This study is part of the Groundwater/Vadose Zone Integration Project and was commissioned specifically to document the current recreation use levels in these areas of the river, and to elicit recreation-related expenditure information from visitors. This information informs economic and environmental models used to measure the economic risk posed by possible, but unlikely, releases of contaminants from the Hanford site into the Columbia River. During the study period, researchers collected 256 survey responses and 396 field observations from recreation sites up and down both shores of the river in the study area. Results presented include analysis of trip duration by river activity, trip frequency, and visitor place of origin. Economics-related results include trip expenditure profiles by activity and place of origin. Data also were collected on fishing effort. Visitors also were asked to indicate what activity or destination substitution they would choose in the hypothetical example that the river could not be accessed. The report also highlights some limitations in the approach. Principally, by doing this research in the summer, the recreational use of the river in the other seasons was not documented. The report provides data that suggest the significance of the other seasons - particularly spring and fall - for salmon and steelhead fishing. This stretch of the Columbia is also well known for waterfowl hunting.

  15. The EuroSITES network: Integrating and enhancing fixed-point open ocean observatories around Europe

    NASA Astrophysics Data System (ADS)

    Lampitt, Richard S.; Larkin, Kate E.; EuroSITES Consortium

    2010-05-01

    EuroSITES is a 3 year (2008-2011) EU collaborative project (3.5MEuro) with the objective to integrate and enhance the nine existing open ocean fixed point observatories around Europe (www.eurosites.info). These observatories are primarily composed of full depth moorings and make multidisciplinary in situ observations within the water column as the European contribution to the global array OceanSITES (www.oceansites.org). In the first 18 months, all 9 observatories have been active and integration has been significant through the maintenance and enhancement of observatory hardware. Highlights include the enhancement of observatories with sensors to measure O2, pCO2, chlorophyll, and nitrate in near real-time from the upper 1000 m. In addition, some seafloor missions are also actively supported. These include seafloor platforms currently deployed in the Mediterranean, one for tsunami detection and one to monitor fluid flow related to seismic activity and slope stability. Upcoming seafloor science missions in 2010 include monitoring benthic biological communities and associated biogeochemistry as indicators of climate change in both the Northeast Atlantic and Mediterranean. EuroSITES also promotes the development of innovative sensors and samplers in order to progress capability to measure climate-relevant properties of the ocean. These include further developing current technologies for autonomous long-term monitoring of oxygen consumption in the mesopelagic, pH and mesozooplankton abundance. Many of these science missions are directly related to complementary activities in other European projects such as EPOCA, HYPOX and ESONET. In 2010 a direct collaboration including in situ field work will take place between ESONET and EuroSITES. The demonstration mission MODOO (funded by ESONET) will be implemented in 2010 at the EuroSITES PAP observatory. Field work will include deployment of a seafloor lander system with various sensors which will send data to shore in real

  16. Lentiviral vectors with CMV or MHCII promoters administered in vivo: immune reactivity versus persistence of expression.

    PubMed

    Kimura, Takahiro; Koya, Richard C; Anselmi, Laura; Sternini, Catia; Wang, He-Jing; Comin-Anduix, Begonya; Prins, Robert M; Faure-Kumar, Emmanuelle; Rozengurt, Nora; Cui, Yan; Kasahara, Noriyuki; Stripecke, Renata

    2007-07-01

    Lentiviral vectors (LVs) are potential tools for genetic vaccination. To improve the safety of LV vaccines, we evaluated the selectivity, bio-distribution, persistence of expression, and immune potency of vesicular stomatitis virus G (VSV-G)-pseudotyped vectors transcriptionally targeted to antigen presenting cells (APCs) through a major histocompatibility complex class II (MHCII) promoter. Control vectors contained the ubiquitous cytomegalovirus (CMV) promoter. Bio-distribution studies after intravenous injections of LVs expressing green fluorescent protein (GFP) or luciferase were conducted by a combination of flow cytometry, immunofluorescence, real-time quantitative polymerase chain reaction (RT-Q-PCR) and whole-body bioluminescence analyses. GFP-expressing vectors showed selective expression in MHCII(+) cells of spleen and LV-CMV-GFP administration produced noticeable spleen inflammation, whereas LV-MHCII-GFP did not. Long-term optical imaging analyses of C57BL/6 mice injected with LV-CMV-LUC showed diminishing luciferase expression in the liver and spleen over time. Vaccination/boost with LV-CMV expressing the melanoma antigen tyrosinase-related protein 2 (TRP2) yielded dose-dependent antigen-specific CD8(+) T-cell reactivity and high protection against B16 melanoma challenge. Unexpectedly, administration of LVs containing the MHCII promoter resulted in persistence of luciferase expression and viral integration in MHCII(+) splenocytes and virtually no CD8(+) T-cell responses against TRP2. These studies reveal that APC transduction by LVs could lead to immune reactivity (LV-CMV) or persistence of transgene expression (LV-MHCII), providing a relevant paradigm for vaccination and gene replacement approaches. PMID:17505480

  17. Lentiviral Vector-Mediated Correction of a Mouse Model of Leukocyte Adhesion Deficiency Type I

    PubMed Central

    Leon-Rico, Diego; Aldea, Montserrat; Sanchez-Baltasar, Raquel; Mesa-Nuñez, Cristina; Record, Julien; Burns, Siobhan O.; Santilli, Giorgia; Thrasher, Adrian J.; Bueren, Juan A.; Almarza, Elena

    2016-01-01

    Leukocyte adhesion deficiency type I (LAD-I) is a primary immunodeficiency caused by mutations in the ITGB2 gene and is characterized by recurrent and life-threatening bacterial infections. These mutations lead to defective or absent expression of β2 integrins on the leukocyte surface, compromising adhesion and extravasation at sites of infection. Three different lentiviral vectors (LVs) conferring ubiquitous or preferential expression of CD18 in myeloid cells were constructed and tested in human and mouse LAD-I cells. All three hCD18-LVs restored CD18 and CD11a membrane expression in LAD-I patient-derived lymphoblastoid cells. Corrected cells recovered the ability to aggregate and bind to sICAM-1 after stimulation. All vectors induced stable hCD18 expression in hematopoietic cells from mice with a hypomorphic Itgb2 mutation (CD18HYP), both in vitro and in vivo after transplantation of corrected cells into primary and secondary CD18HYP recipients. hCD18+ hematopoietic cells from transplanted CD18HYP mice also showed restoration of mCD11a surface co-expression. The analysis of in vivo neutrophil migration in CD18HYP mice subjected to two different inflammation models demonstrated that the LV-mediated gene therapy completely restored neutrophil extravasation in response to inflammatory stimuli. Finally, these vectors were able to correct the phenotype of human myeloid cells derived from CD34+ progenitors defective in ITGB2 expression. These results support for the first time the use of hCD18-LVs for the treatment of LAD-I patients in clinical trials. PMID:27056660

  18. HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay

    PubMed Central

    Sunshine, Sara; Kirchner, Rory; Amr, Sami S.; Mansur, Leandra; Shakhbatyan, Rimma; Kim, Michelle; Bosque, Alberto; Siliciano, Robert F.; Planelles, Vicente; Hofmann, Oliver; Ho Sui, Shannan

    2016-01-01

    ABSTRACT Antiretroviral therapy (ART) is successful in the suppression of HIV but cannot target and eradicate the latent proviral reservoir. The location of retroviral integration into the human genome is thought to play a role in the clonal expansion of infected cells and HIV persistence. We developed a high-throughput targeted sequence capture assay that uses a pool of HIV-specific probes to enrich Illumina libraries prior to deep sequencing. Using an expanded clonal population of ACH-2 cells, we demonstrate that this sequence capture assay has an extremely low false-positive rate. This assay assessed four cellular models commonly used to study HIV latency and latency-reversing agents: ACH-2 cells, J-Lat cells, the Bcl-2-transduced primary CD4+ model, and the cultured TCM (central memory) CD4+ model. HIV integration site characteristics and genes were compared between these cellular models and to previously reported patient data sets. Across these cellular models, there were significant differences in integration site characteristics, including orientation relative to that of the host gene, the proportion of clonally expanded sites, and the proportion located within genic regions and exons. Despite a greater diversity of minority integration sites than expected in ACH-2 cells, their integration site characteristics consistently differed from those of the other models and from the patient samples. Gene ontology analysis of highly represented genes from the patient samples found little overlap with HIV-containing genes from the cell lines. These findings show that integration site differences exist among the commonly used cellular models of HIV latency and in comparison to integration sites found in patient samples. IMPORTANCE Despite the success of ART, currently there is no successful therapy to eradicate integrated proviruses. Cellular models of HIV latency are used to test the efficacy of latency-reversing agents, but it is unclear how well these models reflect

  19. Integrated Geophysycal Prospecting in Late Antiquity and Early Medieval Sites in Italy

    NASA Astrophysics Data System (ADS)

    Giannotta, Maria Teresa; Leucci, Giovanni; De Giorgi, Lara; Matera, Loredana; Persico, Raffaele; Muci, Giuseppe

    2016-04-01

    In this contribution, the results of some integrated geophysical prospecting (magnetometric and GPR) are exposed. This work has been performed in collaboration between archaeologists and geophysicists within the research project "History and Global Archaeology of the Rural Landascapes in Italy, between Late Antiquity and Medieval period. Integrated systems of sources, methodologies, and technologies for a sustainable development", financed by the Italian Ministry for Instruction, University and Research MIUR. In particular, the archaeological sites of Badia and San Giovanni in Malcantone, both in the Apulia Region (eastern-southern Italy) have been prospect. The sites have been identified on the basis of available documents, archaeological surveys and testimonies. In particular, we know that in Badia [1] it was probable the presence of an ancient roman villa of the late ancient period (strongly damaged by the subsequent ploughing activities). Whereas in San Giovanni there is still, today, a small chapel (deconsecrated) that was likely to be part of a previous larger church (probably a basilica of the early Christian period) restricted in the subsequent centuries (probably in more phases). The Saracen raids of the XVI centuries made the site ruined and abandoned. In both sites integrated prospecting have been performed [2-6] with a the integration of archaeological, magnetometer and a GPR data have provided some interesting results, allowing to overcome the difficulties relative to an extensive GPR prospecting, that could not be performed because of the intrinsic superficial roughness and/or the intensive ploughing activities. The prospecting activities, in particular, have added elements that seem to confirm the main archaeological hypothesis that motivate their performing, as it will be show at the conference. References [1] M. T, Giannotta, G. Leucci, R. Persico, M. Leo Imperiale, The archaeological site of Badia in terra d'Otranto: contribution of the

  20. Large-scale production of lentiviral vector in a closed system hollow fiber bioreactor

    PubMed Central

    Sheu, Jonathan; Beltzer, Jim; Fury, Brian; Wilczek, Katarzyna; Tobin, Steve; Falconer, Danny; Nolta, Jan; Bauer, Gerhard

    2015-01-01

    Lentiviral vectors are widely used in the field of gene therapy as an effective method for permanent gene delivery. While current methods of producing small scale vector batches for research purposes depend largely on culture flasks, the emergence and popularity of lentiviral vectors in translational, preclinical and clinical research has demanded their production on a much larger scale, a task that can be difficult to manage with the numbers of producer cell culture flasks required for large volumes of vector. To generate a large scale, partially closed system method for the manufacturing of clinical grade lentiviral vector suitable for the generation of induced pluripotent stem cells (iPSCs), we developed a method employing a hollow fiber bioreactor traditionally used for cell expansion. We have demonstrated the growth, transfection, and vector-producing capability of 293T producer cells in this system. Vector particle RNA titers after subsequent vector concentration yielded values comparable to lentiviral iPSC induction vector batches produced using traditional culture methods in 225 cm2 flasks (T225s) and in 10-layer cell factories (CF10s), while yielding a volume nearly 145 times larger than the yield from a T225 flask and nearly three times larger than the yield from a CF10. Employing a closed system hollow fiber bioreactor for vector production offers the possibility of manufacturing large quantities of gene therapy vector while minimizing reagent usage, equipment footprint, and open system manipulation. PMID:26151065

  1. Construction of stable packaging cell lines for clinical lentiviral vector production

    PubMed Central

    Sanber, Khaled S.; Knight, Sean B.; Stephen, Sam L.; Bailey, Ranbir; Escors, David; Minshull, Jeremy; Santilli, Giorgia; Thrasher, Adrian J.; Collins, Mary K.; Takeuchi, Yasuhiro

    2015-01-01

    Lentiviral vectors are useful experimental tools for stable gene delivery and have been used to treat human inherited genetic disorders and hematologic malignancies with promising results. Because some of the lentiviral vector components are cytotoxic, transient plasmid transfection has been used to produce the large batches needed for clinical trials. However, this method is costly, poorly reproducible and hard to scale up. Here we describe a general method for construction of stable packaging cell lines that continuously produce lentiviral vectors. This uses Cre recombinase-mediated cassette exchange to insert a codon-optimised HIV-1 Gag-Pol expression construct in a continuously expressed locus in 293FT cells. Subsequently Rev, envelope and vector genome expression cassettes are serially transfected. Vector titers in excess of 106 transducing units/ml can be harvested from the final producer clones, which can be increased to 108 TU/ml by concentration. This method will be of use to all basic and clinical investigators who wish to produce large batches of lentiviral vectors. PMID:25762005

  2. Transfer and Expression of Small Interfering RNAs in Mammalian Cells Using Lentiviral Vectors.

    PubMed

    Lebedev, T D; Spirin, P V; Prassolov, V S

    2013-04-01

    RNA interference is a convenient tool for modulating gene expression. The widespread application of RNA interference is made difficult because of the imperfections of the methods used for efficient target cell delivery of whatever genes are under study. One of the most convenient and efficient gene transfer and expression systems is based on the use of lentiviral vectors, which direct the synthesis of small hairpin RNAs (shRNAs), the precursors of siRNAs. The application of these systems enables one to achieve sustainable and long-term shRNA expression in cells. This review considers the adaptation of the processing of artificial shRNA to the mechanisms used by cellular microRNAs and simultaneous expression of several shRNAs as potential approaches for producing lentiviral vectors that direct shRNA synthesis. Approaches to using RNA interference for the treatment of cancer, as well as hereditary and viral diseases, are under active development today. The improvement made to the methods for constructing lentiviral vectors and the investigation into the mechanisms of processing of small interfering RNA allow one to now consider lentiviral vectors that direct shRNA synthesis as one of the most promising tools for delivering small interfering RNAs.

  3. Transfer and Expression of Small Interfering RNAs in Mammalian Cells Using Lentiviral Vectors

    PubMed Central

    Lebedev, T. D.; Spirin, P. V.; Prassolov, V. S.

    2013-01-01

    RNA interference is a convenient tool for modulating gene expression. The widespread application of RNA interference is made difficult because of the imperfections of the methods used for efficient target cell delivery of whatever genes are under study. One of the most convenient and efficient gene transfer and expression systems is based on the use of lentiviral vectors, which direct the synthesis of small hairpin RNAs (shRNAs), the precursors of siRNAs. The application of these systems enables one to achieve sustainable and long-term shRNA expression in cells. This review considers the adaptation of the processing of artificial shRNA to the mechanisms used by cellular microRNAs and simultaneous expression of several shRNAs as potential approaches for producing lentiviral vectors that direct shRNA synthesis. Approaches to using RNA interference for the treatment of cancer, as well as hereditary and viral diseases, are under active development today. The improvement made to the methods for constructing lentiviral vectors and the investigation into the mechanisms of processing of small interfering RNA allow one to now consider lentiviral vectors that direct shRNA synthesis as one of the most promising tools for delivering small interfering RNAs. PMID:23819033

  4. Polyploidization without mitosis improves in vivo liver transduction with lentiviral vectors.

    PubMed

    Pichard, Virginie; Couton, Dominique; Desdouets, Chantal; Ferry, Nicolas

    2013-02-01

    Lentiviral vectors are efficient gene delivery vehicles for therapeutic and research applications. In contrast to oncoretroviral vectors, they are able to infect most nonproliferating cells. In the liver, induction of cell proliferation dramatically improved hepatocyte transduction using all types of retroviral vectors. However, the precise relationship between hepatocyte division and transduction efficiency has not been determined yet. Here we compared gene transfer efficiency in the liver after in vivo injection of recombinant lentiviral or Moloney murine leukemia viral (MoMuLV) vectors in hepatectomized rats treated or not with retrorsine, an alkaloid that blocks hepatocyte division and induces megalocytosis. Partial hepatectomy alone resulted in a similar increase in hepatocyte transduction using either vector. In retrorsine-treated and partially hepatectomized rats, transduction with MoMuLV vectors dropped dramatically. In contrast, we observed that retrorsine treatment combined with partial hepatectomy increased lentiviral transduction to higher levels than hepatectomy alone. Analysis of nuclear ploidy in single cells showed that a high level of transduction was associated with polyploidization. In conclusion, endoreplication could be exploited to improve the efficiency of liver-directed lentiviral gene therapy.

  5. HIV latency and integration site placement in five cell-based models

    PubMed Central

    2013-01-01

    Background HIV infection can be treated effectively with antiretroviral agents, but the persistence of a latent reservoir of integrated proviruses prevents eradication of HIV from infected individuals. The chromosomal environment of integrated proviruses has been proposed to influence HIV latency, but the determinants of transcriptional repression have not been fully clarified, and it is unclear whether the same molecular mechanisms drive latency in different cell culture models. Results Here we compare data from five different in vitro models of latency based on primary human T cells or a T cell line. Cells were infected in vitro and separated into fractions containing proviruses that were either expressed or silent/inducible, and integration site populations sequenced from each. We compared the locations of 6,252 expressed proviruses to those of 6,184 silent/inducible proviruses with respect to 140 forms of genomic annotation, many analyzed over chromosomal intervals of multiple lengths. A regularized logistic regression model linking proviral expression status to genomic features revealed no predictors of latency that performed better than chance, though several genomic features were significantly associated with proviral expression in individual models. Proviruses in the same chromosomal region did tend to share the same expressed or silent/inducible status if they were from the same cell culture model, but not if they were from different models. Conclusions The silent/inducible phenotype appears to be associated with chromosomal position, but the molecular basis is not fully clarified and may differ among in vitro models of latency. PMID:23953889

  6. Site-specific integration and tailoring of cassette design for sustainable gene transfer.

    PubMed

    Lombardo, Angelo; Cesana, Daniela; Genovese, Pietro; Di Stefano, Bruno; Provasi, Elena; Colombo, Daniele F; Neri, Margherita; Magnani, Zulma; Cantore, Alessio; Lo Riso, Pietro; Damo, Martina; Pello, Oscar M; Holmes, Michael C; Gregory, Philip D; Gritti, Angela; Broccoli, Vania; Bonini, Chiara; Naldini, Luigi

    2011-08-21

    Integrative gene transfer methods are limited by variable transgene expression and by the consequences of random insertional mutagenesis that confound interpretation in gene-function studies and may cause adverse events in gene therapy. Site-specific integration may overcome these hurdles. Toward this goal, we studied the transcriptional and epigenetic impact of different transgene expression cassettes, targeted by engineered zinc-finger nucleases to the CCR5 and AAVS1 genomic loci of human cells. Analyses performed before and after integration defined features of the locus and cassette design that together allow robust transgene expression without detectable transcriptional perturbation of the targeted locus and its flanking genes in many cell types, including primary human lymphocytes. We thus provide a framework for sustainable gene transfer in AAVS1 that can be used for dependable genetic manipulation, neutral marking of the cell and improved safety of therapeutic applications, and demonstrate its feasibility by rapidly generating human lymphocytes and stem cells carrying targeted and benign transgene insertions.

  7. Develop and test fuel cell powered on-site integrated total energy systems

    NASA Astrophysics Data System (ADS)

    Kaufman, A.; Werth, J.

    1984-10-01

    Work has been performed leading toward the development of a 50kW on-site integrated energy system. A sub-scale 5kW system was constructed and tested in the steady-load (with shutdowns) and transient modes. A parallel effort has been conducted to develop the full-size sub-systems for the on-site system; these include the fuel cell stack, a methanol processor, and a d.c.-a.c. power conditioner. Stack technology development activities have been carried out to improve the performance, cost and reliability of stack components and hardware. In the fuel processing area, screening tests have been conducted for various methanol steam-reforming catalysts, and the preferred catalysts have been subjected to extended testing. Application-related work has been pursued largely under subcontracts. A study has been completed in which the applicability of on-site fuel cell cogeneration systems to various building types was analyzed and the potential economic attractiveness ascertained. The overall system was analyzed in terms of its operating characteristics at part load and its response to transients. Preferred heating, ventilating, and air conditioning approaches for various building types using fuel cell cogeneration units are determined.

  8. LASAGNA-Search: an integrated web tool for transcription factor binding site search and visualization.

    PubMed

    Lee, Chic; Huang, Chun-Hsi

    2013-03-01

    The release of ChIP-seq data from the ENCyclopedia Of DNA Elements (ENCODE) and Model Organism ENCyclopedia Of DNA Elements (modENCODE) projects has significantly increased the amount of transcription factor (TF) binding affinity information available to researchers. However, scientists still routinely use TF binding site (TFBS) search tools to scan unannotated sequences for TFBSs, particularly when searching for lesser-known TFs or TFs in organisms for which ChIP-seq data are unavailable. The sequence analysis often involves multiple steps such as TF model collection, promoter sequence retrieval, and visualization; thus, several different tools are required. We have developed a novel integrated web tool named LASAGNA-Search that allows users to perform TFBS searches without leaving the web site. LASAGNA-Search uses the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm for TFBS alignment. Important features of LASAGNA-Search include (i) acceptance of unaligned variable-length TFBSs, (ii) a collection of 1726 TF models, (iii) automatic promoter sequence retrieval, (iv) visualization in the UCSC Genome Browser, and (v) gene regulatory network inference and visualization based on binding specificities. LASAGNA-Search is freely available at http://biogrid.engr.uconn.edu/lasagna_search/.

  9. An Integrated Approach to Quantify Groundwater - Surface Water Interactions: the Norman Research Site, Oklahoma

    NASA Astrophysics Data System (ADS)

    Mendoza-Sanchez, I.; Phanikumar, M. S.; Masoner, J.; Cozzarelli, I.; McGuire, J. T.

    2009-12-01

    An intensive investigation of hydrogeologic and biogeochemical processes controlling contaminant migration and attenuation is in progress at the Norman Landfill Research Site in Oklahoma. The site involves a wetland that overlies a landfill leachate plume. The wetland-aquifer system actively exchanges contaminants and nutrients. These chemicals move from the wetland to the aquifer and vice versa depending on the groundwater-surface water (GW-SW) exchange rate and flow direction. The GW-SW flux has to be quantified to better understand the fate and transport of contaminants and nutrients. Different types of data have been collected at the site over a period of ten years including meteorological data, isotopic composition of water samples, water levels, pan evaporation rates, and seepage fluxes. This paper reports the development and application of a process-based water balance model based on long-term climate, soil, vegetation and hydrological dynamics of the system to determine the GW-SW flow rates. Our integrated approach involved model evaluation by means of the following independent measurements: (a) groundwater inflow calculation using stable isotopes of oxygen and hydrogen ( ) (b) seepage flux measurements in the wetland hyporheic sediment and c) pan evaporation measurements on land and in the wetland. The approach was found to be useful for identifying the dominant hydrological processes at the site, including recharge and subsurface flows. Recharge results from the model compared well with estimates obtained using isotope methods from previous studies and allowed us to identify specific annual signatures of this important process during the period of study. Results indicate that subsurface flow components in the system are seasonal and readily respond to rainfall events. The wetland water balance is dominated by local groundwater inputs and regional groundwater flow contributes little to the overall water balance.

  10. Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics.

    PubMed

    Doolittle-Hall, Janet M; Cunningham Glasspoole, Danielle L; Seaman, William T; Webster-Cyriaque, Jennifer

    2015-01-01

    Oncoviruses cause tremendous global cancer burden. For several DNA tumor viruses, human genome integration is consistently associated with cancer development. However, genomic features associated with tumor viral integration are poorly understood. We sought to define genomic determinants for 1897 loci prone to hosting human papillomavirus (HPV), hepatitis B virus (HBV) or Merkel cell polyomavirus (MCPyV). These were compared to HIV, whose enzyme-mediated integration is well understood. A comprehensive catalog of integration sites was constructed from the literature and experimentally-determined HPV integration sites. Features were scored in eight categories (genes, expression, open chromatin, histone modifications, methylation, protein binding, chromatin segmentation and repeats) and compared to random loci. Random forest models determined loci classification and feature selection. HPV and HBV integrants were not fragile site associated. MCPyV preferred integration near sensory perception genes. Unique signatures of integration-associated predictive genomic features were detected. Importantly, repeats, actively-transcribed regions and histone modifications were common tumor viral integration signatures.

  11. Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics

    PubMed Central

    Doolittle-Hall, Janet M.; Cunningham Glasspoole, Danielle L.; Seaman, William T.; Webster-Cyriaque, Jennifer

    2015-01-01

    Oncoviruses cause tremendous global cancer burden. For several DNA tumor viruses, human genome integration is consistently associated with cancer development. However, genomic features associated with tumor viral integration are poorly understood. We sought to define genomic determinants for 1897 loci prone to hosting human papillomavirus (HPV), hepatitis B virus (HBV) or Merkel cell polyomavirus (MCPyV). These were compared to HIV, whose enzyme-mediated integration is well understood. A comprehensive catalog of integration sites was constructed from the literature and experimentally-determined HPV integration sites. Features were scored in eight categories (genes, expression, open chromatin, histone modifications, methylation, protein binding, chromatin segmentation and repeats) and compared to random loci. Random forest models determined loci classification and feature selection. HPV and HBV integrants were not fragile site associated. MCPyV preferred integration near sensory perception genes. Unique signatures of integration-associated predictive genomic features were detected. Importantly, repeats, actively-transcribed regions and histone modifications were common tumor viral integration signatures. PMID:26569308

  12. Integration Preferences of Wildtype AAV-2 for Consensus Rep-Binding Sites at Numerous Loci in the Human Genome

    PubMed Central

    Hüser, Daniela; Gogol-Döring, Andreas; Lutter, Timo; Weger, Stefan; Winter, Kerstin; Hammer, Eva-Maria; Cathomen, Toni; Reinert, Knut; Heilbronn, Regine

    2010-01-01

    Adeno-associated virus type 2 (AAV) is known to establish latency by preferential integration in human chromosome 19q13.42. The AAV non-structural protein Rep appears to target a site called AAVS1 by simultaneously binding to Rep-binding sites (RBS) present on the AAV genome and within AAVS1. In the absence of Rep, as is the case with AAV vectors, chromosomal integration is rare and random. For a genome-wide survey of wildtype AAV integration a linker-selection-mediated (LSM)-PCR strategy was designed to retrieve AAV-chromosomal junctions. DNA sequence determination revealed wildtype AAV integration sites scattered over the entire human genome. The bioinformatic analysis of these integration sites compared to those of rep-deficient AAV vectors revealed a highly significant overrepresentation of integration events near to consensus RBS. Integration hotspots included AAVS1 with 10% of total events. Novel hotspots near consensus RBS were identified on chromosome 5p13.3 denoted AAVS2 and on chromsome 3p24.3 denoted AAVS3. AAVS2 displayed seven independent junctions clustered within only 14 bp of a consensus RBS which proved to bind Rep in vitro similar to the RBS in AAVS3. Expression of Rep in the presence of rep-deficient AAV vectors shifted targeting preferences from random integration back to the neighbourhood of consensus RBS at hotspots and numerous additional sites in the human genome. In summary, targeted AAV integration is not as specific for AAVS1 as previously assumed. Rather, Rep targets AAV to integrate into open chromatin regions in the reach of various, consensus RBS homologues in the human genome. PMID:20628575

  13. Characterization of Equine Infectious Anemia Virus Integration in the Horse Genome

    PubMed Central

    Liu, Qiang; Wang, Xue-Feng; Ma, Jian; He, Xi-Jun; Wang, Xiao-Jun; Zhou, Jian-Hua

    2015-01-01

    Human immunodeficiency virus (HIV)-1 has a unique integration profile in the human genome relative to murine and avian retroviruses. Equine infectious anemia virus (EIAV) is another well-studied lentivirus that can also be used as a promising retro-transfection vector, but its integration into its native host has not been characterized. In this study, we mapped 477 integration sites of the EIAV strain EIAVFDDV13 in fetal equine dermal (FED) cells during in vitro infection. Published integration sites of EIAV and HIV-1 in the human genome were also analyzed as references. Our results demonstrated that EIAVFDDV13 tended to integrate into genes and AT-rich regions, and it avoided integrating into transcription start sites (TSS), which is consistent with EIAV and HIV-1 integration in the human genome. Notably, the integration of EIAVFDDV13 favored long interspersed elements (LINEs) and DNA transposons in the horse genome, whereas the integration of HIV-1 favored short interspersed elements (SINEs) in the human genome. The chromosomal environment near LINEs or DNA transposons potentially influences viral transcription and may be related to the unique EIAV latency states in equids. The data on EIAV integration in its natural host will facilitate studies on lentiviral infection and lentivirus-based therapeutic vectors. PMID:26102582

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

    PubMed

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

    2014-01-01

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

  15. Interim Status of the Accelerated Site Technology Deployment Integrated Decontamination and Decommissioning Project

    SciTech Connect

    A. M Smith; G. E. Matthern; R. H. Meservey

    1998-11-01

    The Idaho National Engineering and Environmental Laboratory (INEEL), Fernald Environmental Management Project (FEMP), and Argonne National Laboratory - East (ANL-E) teamed to establish the Accelerated Site Technology Deployment (ASTD) Integrated Decontamination and Decommissioning (ID&D) project to increase the use of improved technologies in D&D operations. The project is making the technologies more readily available, providing training, putting the technologies to use, and spreading information about improved performance. The improved technologies are expected to reduce cost, schedule, radiation exposure, or waste volume over currently used baseline methods. They include some of the most successful technologies proven in the large-scale demonstrations and in private industry. The selected technologies are the Pipe Explorer, the GammaCam, the Decontamination Decommissioning and Remediation Optimal Planning System (DDROPS), the BROKK Demolition Robot, the Personal Ice Cooling System (PICS), the Oxy-Gasoline Torch, the Track-Mounted Shear, and the Hand-Held Shear.

  16. Added value for on-site fuel cells through equipment and application integration

    SciTech Connect

    Whitaker, R.

    1996-12-31

    On-site fuel cell power plants are not an exciting new electricity generating technology. They are an economic and beneficial addition to the operating systems of commercial buildings and industrial facilities. ONSI Corporation is part of International Fuel Cells Corporation and is jointly owned by United Technologies Corporation, Toshiba, and Ansaldo. ONSI has proven in the last three years that initial demand for packaged fuel cell power plants, like our 200 kW PC25{trademark} fuel cell shown in Figure 1, comes from the commercial building sector. However, this sector and the companies which service it are only tangentially interested in fuel cells as an emerging electricity generating technology. What they are most interested in is how the PC25 can integrate into their building`s system; how it can deliver energy efficient dollars to the bottom line, and how it can deliver operating benefits to their business.

  17. Interstitial telomeric sequences in human chromosomes cluster with common fragile sites, mutagen sensitive sites, viral integration sites, cancer breakpoints, proto-oncogenes and breakpoints involved in primate evolution

    SciTech Connect

    Adekunle, S.S.A.; Wyandt, H.; Mark, H.F.L.

    1994-09-01

    Recently we mapped the telomeric repeat sequences to 111 interstitial sites in the human genome and to sites of gaps and breaks induced by aphidicolin and sister chromatid exchange sites detected by BrdU. Many of these sites correspond to conserved fragile sites in man, gorilla and chimpazee, to sites of conserved sister chromatid exchange in the mammalian X chromosome, to mutagenic sensitive sites, mapped locations of proto-oncogenes, breakpoints implicated in primate evolution and to breakpoints indicated as the sole anomaly in neoplasia. This observation prompted us to investigate if the interstitial telomeric sites cluster with these sites. An extensive literature search was carried out to find all the available published sites mentioned above. For comparison, we also carried out a statistical analysis of the clustering of the sites of the telomeric repeats with the gene locations where only nucleotide mutations have been observed as the only chromosomal abnormality. Our results indicate that the telomeric repeats cluster most with fragile sites, mutagenic sensitive sites and breakpoints implicated in primate evolution and least with cancer breakpoints, mapped locations of proto-oncogenes and other genes with nucleotide mutations.

  18. Efficient Expression of Igf-1 from Lentiviral Vectors Protects In Vitro but Does Not Mediate Behavioral Recovery of a Parkinsonian Lesion in Rats.

    PubMed

    Lu-Nguyen, Ngoc B; Broadstock, Martin; Yáñez-Muñoz, Rafael J

    2015-11-01

    Gene therapy approaches delivering neurotrophic factors have offered promising results in both preclinical and clinical trials of Parkinson's disease (PD). However, failure of glial cell line-derived neurotrophic factor in phase 2 clinical trials has sparked a search for other trophic factors that may retain efficacy in the clinic. Direct protein injections of one such factor, insulin-like growth factor (IGF)-1, in a rodent model of PD has demonstrated impressive protection of dopaminergic neurons against 6-hydroxydopamine (6-OHDA) toxicity. However, protein infusion is associated with surgical risks, pump failure, and significant costs. We therefore used lentiviral vectors to deliver Igf-1, with a particular focus on the novel integration-deficient lentiviral vectors (IDLVs). A neuron-specific promoter, from the human synapsin 1 gene, excellent for gene expression from IDLVs, was additionally used to enhance Igf-1 expression. An investigation of neurotrophic effects on primary rat neuronal cultures demonstrated that neurons transduced with IDLV-Igf-1 vectors had complete protection on withdrawal of exogenous trophic support. Striatal transduction of such vectors into 6-OHDA-lesioned rats, however, provided neither protection of dopaminergic substantia nigra neurons nor improvement of animal behavior.

  19. A Two-site Randomized Clinical Trial of Integrated Psychosocial Treatment for ADHD-Inattentive Type

    PubMed Central

    Pfiffner, Linda J.; Hinshaw, Stephen P.; Owens, Elizabeth; Zalecki, Christine; Kaiser, Nina M.; Villodas, Miguel; McBurnett, Keith

    2014-01-01

    Objective This study evaluated the efficacy of the Child Life and Attention Skills (CLAS) program, a behavioral psychosocial treatment integrated across home and school, for youth with Attention Deficit Hyperactivity Disorder-Inattentive Type (ADHD-I). Method In a two-site randomized controlled trial, 199 children (ages 7-11) were randomized to CLAS (N=74), parent-focused treatment (PFT, N=74), or treatment as usual (TAU, N=51). We compared groups on parent and teacher ratings of inattention symptoms, organizational skills, social skills, and global improvement at post-treatment, and also at follow-up during the subsequent school year. Results CLAS resulted in greater improvements in teacher-reported inattention, organizational skills, social skills, and global functioning relative to both PFT and TAU at post-treatment. Parents of children in CLAS reported greater improvement in organizational skills than PFT and greater improvements on all outcomes relative to TAU at post-treatment. Differences between CLAS and TAU were maintained at follow-up for most parent-reported measures but were not significant for teacher-reported outcomes. Conclusions These findings extend support for CLAS across two study sites, revealing that integrating parent, teacher, and child treatment components, specifically adapted for ADHD-I, is superior to parent training alone and to usual care. Direct involvement of teachers and children in CLAS appears to amplify effects at school and home and underscores the importance of coordinating parent, teacher, and child treatment components for cross-setting effects on symptoms and impairment associated with ADHD-I. PMID:24865871

  20. Combination of grafted Schwann cells and lentiviral-mediated prevention of glial scar formation improve recovery of spinal cord injured rats.

    PubMed

    Do-Thi, Anh; Perrin, Florence E; Desclaux, Mathieu; Saillour, Paulette; Amar, Lahouari; Privat, Alain; Mallet, Jacques

    2016-10-01

    The present study was intended to combine three therapeutic approaches in a well-defined rat model of spinal cord injury, a lateral hemisection at thoracic level. A guidance channel was implanted at the lesion site. This channel was seeded with native Schwann cells or Schwann cells that had been previously transduced with a lentiviral vector carrying the GDNF gene. Thereafter, these experiences were reproduced in animals injected with lentiviral vectors carrying a shRNA for GFAP (Lv-shGFAP), which has recently been shown to block glial scar formation. Functional evaluations showed that Lv-shGFAP induced a significant improvement in recovery in animals grafted with Schwann cells. Histological studies demonstrated the outgrowth of axons in the guidance channel containing Schwann cells transduced or not with GDNF. This axonal growth was enhanced in rats receiving Lv-shGFAP vector. Also, a significant increase of serotonergic innervation of the injured hemicord, distal to the lesion, was found only in animals treated with Lv-shGFAP vectors. Importantly, this study confirms that glial scar formation is a major impediment for axonal sprouting after spinal cord injury, and emphasizes the importance of serotonergic innervation for locomotor function. Moreover we show a significant additive effect of a combinatorial approach to axonal regeneration in the injured spinal cord.

  1. Integrated Closure and Monitoring Plan for the Area 3 and Area 5 Radioactive Waste Management Sites at the Nevada Test Site

    SciTech Connect

    S. E. Rawlinson

    2001-09-01

    Bechtel Nevada (BN) manages two low-level Radioactive Waste Management Sites (RWMSs) (one site is in Area 3 and the other is in Area 5) at the Nevada Test Site (NTS) for the U.S. Department of Energy's (DOE's) National Nuclear Security Administration Nevada Operations Office (NNSA/NV). The current DOE Order governing management of radioactive waste is 435.1. Associated with DOE Order 435.1 is a Manual (DOE M 435.1-1) and Guidance (DOE G 435.1-1). The Manual and Guidance specify that preliminary closure and monitoring plans for a low-level waste (LLW) management facility be developed and initially submitted with the Performance Assessment (PA) and Composite Analysis (CA) for that facility. The Manual and Guidance, and the Disposal Authorization Statement (DAS) issued for the Area 3 RWMS further specify that the preliminary closure and monitoring plans be updated within one year following issuance of a DAS. This Integrated Closure and Monitoring Plan (ICMP) fulfills both requirements. Additional updates will be conducted every third year hereafter. This document is an integrated plan for closing and monitoring both RWMSs, and is based on guidance issued in 1999 by the DOE for developing closure plans. The plan does not follow the format suggested by the DOE guidance in order to better accommodate differences between the two RWMSs, especially in terms of operations and site characteristics. The modification reduces redundancy and provides a smoother progression of the discussion. The closure and monitoring plans were integrated because much of the information that would be included in individual plans is the same, and integration provides efficient presentation and program management. The ICMP identifies the regulatory requirements, describes the disposal sites and the physical environment where they are located, and defines the approach and schedule for both closing and monitoring the sites.

  2. HIV Provirus Stably Reproduces Parental Latent and Induced Transcription Phenotypes Regardless of the Chromosomal Integration Site

    PubMed Central

    Hashemi, Farhad B.; Barreto, Kris; Bernhard, Wendy; Hashemi, Pargol; Lomness, Adam

    2016-01-01

    ABSTRACT Understanding the mechanisms of HIV proviral latency is essential for development of a means to eradicate infection and achieve a cure. We have previously described an in vitro latency model that reliably identifies HIV expression phenotypes of infected cells using a dual-fluorescence reporter virus. Our results have demonstrated that ∼50% of infected cells establish latency immediately upon integration of provirus, a phenomenon termed early latency, which appears to occur by mechanisms that are distinct from epigenetic silencing observed with HIV provirus that establishes productive infections. In this study, we have used a mini-dual HIV reporter virus (mdHIV) to compare the long-term stability of provirus produced as early latent or productive infections using Jurkat-Tat T cell clones. Cloned lines bearing mdHIV provirus integrated at different chromosomal locations display unique differences in responsiveness to signaling agonists and chromatin-modifying compounds, and they also produce characteristic expression patterns from the 5′ long terminal repeat (LTR) dsRed and internal EIF1α-enhanced green fluorescent protein (EIF1α-eGFP) reporters. Furthermore, reporter expression profiles of single cell sorted subcultures faithfully reproduce expression profiles identical to that of their original parental population, following prolonged growth in culture, without shifting toward expression patterns resembling that of cell subclones at the time of sorting. Comparison of population dispersion coefficient (CV) and mean fluorescence intensity (MFI) of the subcloned lines showed that both untreated and phorbol myristate acetate (PMA)-ionomycin-stimulated cultures produce expression patterns identical to those of their parental lines. These results indicate that HIV provirus expression characteristics are strongly influenced by the epigenetic landscape at the site of chromosomal integration. IMPORTANCE There is currently considerable interest in development

  3. Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

    PubMed Central

    Levy, Asaf; Schwartz, Schraga; Ast, Gil

    2010-01-01

    Throughout evolution, eukaryotic genomes have been invaded by transposable elements (TEs). Little is known about the factors leading to genomic proliferation of TEs, their preferred integration sites and the molecular mechanisms underlying their insertion. We analyzed hundreds of thousands nested TEs in the human genome, i.e. insertions of TEs into existing ones. We first discovered that most TEs insert within specific ‘hotspots’ along the targeted TE. In particular, retrotransposed Alu elements contain a non-canonical single nucleotide hotspot for insertion of other Alu sequences. We next devised a method for identification of integration sequence motifs of inserted TEs that are conserved within the targeted TEs. This method revealed novel sequences motifs characterizing insertions of various important TE families: Alu, hAT, ERV1 and MaLR. Finally, we performed a global assessment to determine the extent to which young TEs tend to nest within older transposed elements and identified a 4-fold higher tendency of TEs to insert into existing TEs than to insert within non-TE intergenic regions. Our analysis demonstrates that TEs are highly biased to insert within certain TEs, in specific orientations and within specific targeted TE positions. TE nesting events also reveal new characteristics of the molecular mechanisms underlying transposition. PMID:20008508

  4. Space Borne and Ground Based InSAR Data Integration: The Åknes Test Site

    NASA Astrophysics Data System (ADS)

    Bardi, Federica; Raspini, Federico; Ciampalini, Andrea; Kristensen, Lene; Rouyet, Line; Rune Lauknes, Tom; Frauenfelder, Regula; Casagli, Nicola

    2016-04-01

    This work concerns a proposal of integration between InSAR (Interferometric Synthetic Aperture Radar) data acquired by ground based (GB) and satellite platforms. The selected test site is the Åknes rockslide, which affects the western Norwegian coast; the availability of GB-InSAR and satellite InSAR data, and the accessibility of a wide literature make the landslide suitable for testing the proposed procedure. The first step consists in the organization of a geodatabase, performed in GIS environment, containing all the available data. The second step concerns the analysis of satellite and GB-InSAR data, separately. Two datasets, acquired by RADARSAT-2 (related to a period between October 2008 and August 2013) and by a combination of TerraSAR-X and TanDEM-X (acquired between July 2010 and October 2012), both of them in ascending orbit, processed applying SBAS (Small BAseline Subset), are available. GB-InSAR data related to 5 different campaigns of measurements, referred to the summer seasons of 2006, 2008, 2009, 2010 and 2012 are available too. The third step relies on data integration, performed firstly on a qualitative point of view and lately on a semi-quantitative point of view. The results of the proposed procedure have been validated by comparing them with GPS (Global Positioning System) data.

  5. Study of component technologies for fuel cell on-site integrated energy systems

    NASA Technical Reports Server (NTRS)

    Lee, W. D.; Mathias, S.

    1980-01-01

    Heating, ventilation and air conditioning equipment are integrated with three types of fuel cells. System design and computer simulations are developed to utilize the thermal energy discharge of the fuel in the most cost effective manner. The fuel provides all of the electric needs and a loss of load probability analysis is used to ensure adequate power plant reliability. Equipment cost is estimated for each of the systems analyzed. A levelized annual cost reflecting owning and operating costs including the cost of money was used to select the most promising integrated system configurations. Cash flows are presented for the most promising 16 systems. Several systems for the 96 unit apartment complex (a retail store was also studied) were cost competitive with both gas and electric based conventional systems. Thermal storage is shown to be beneficial and the optimum absorption chiller sizing (waste heat recovery) in connection with electric chillers are developed. Battery storage was analyzed since the system is not electric grid connected. Advanced absorption chillers were analyzed as well. Recommendations covering financing, technical development, and policy issues are given to accelerate the commercialization of the fuel cell for on-site power generation in buildings.

  6. OC ToGo: bed site image integration into OpenClinica with mobile devices

    NASA Astrophysics Data System (ADS)

    Haak, Daniel; Gehlen, Johan; Jonas, Stephan; Deserno, Thomas M.

    2014-03-01

    Imaging and image-based measurements nowadays play an essential role in controlled clinical trials, but electronic data capture (EDC) systems insufficiently support integration of captured images by mobile devices (e.g. smartphones and tablets). The web application OpenClinica has established as one of the world's leading EDC systems and is used to collect, manage and store data of clinical trials in electronic case report forms (eCRFs). In this paper, we present a mobile application for instantaneous integration of images into OpenClinica directly during examination on patient's bed site. The communication between the Android application and OpenClinica is based on the simple object access protocol (SOAP) and representational state transfer (REST) web services for metadata, and secure file transfer protocol (SFTP) for image transfer, respectively. OpenClinica's web services are used to query context information (e.g. existing studies, events and subjects) and to import data into the eCRF, as well as export of eCRF metadata and structural information. A stable image transfer is ensured and progress information (e.g. remaining time) visualized to the user. The workflow is demonstrated for a European multi-center registry, where patients with calciphylaxis disease are included. Our approach improves the EDC workflow, saves time, and reduces costs. Furthermore, data privacy is enhanced, since storage of private health data on the imaging devices becomes obsolete.

  7. The explosion sites of nearby supernovae seen with integral field spectroscopy

    NASA Astrophysics Data System (ADS)

    Kuncarayakti, Hanindyo

    2015-08-01

    The progenitor stars of supernovae are still not very well constrained, despite numerous efforts in studying these objects directly or indirectly. There have been detections of the progenitor candidates in pre-explosion Hubble Space Telescope images, but these are rare and it is difficult to increase the statistics due to the limited availability of usable pre-explosion images. Alternatively, one may perform statistical studies on the supernova environments to derive useful constraints on the SN progenitor star. Integral field spectroscopy of nearby supernova sites within ~30 Mpc have been obtained using multiple IFU spectrographs in Hawaii and Chile. This technique enables both spatial and spectral information of the explosion sites to be acquired simultaneously, thus providing the identification of the parent stellar population of the supernova progenitor and the estimates for its physical parameters including age and metallicity. While this work has mainly been done in the optical wavelengths using instruments such as VIMOS, GMOS, and MUSE, a near-infrared approach has also been carried out using the AO-assisted SINFONI. By studying the supernova parent stellar population, we aim to characterize the mass and metallicity of the progenitors of different types of supernovae.

  8. Analysis of a fuel cell on-site integrated energy system for a residential complex

    NASA Technical Reports Server (NTRS)

    Simons, S. N.; Maag, W. L.

    1979-01-01

    The energy use and costs of the on-site integrated energy system (OS/IES) which provides electric power from an on-site power plant and recovers heat that would normally be rejected to the environment is compared to a conventional system purchasing electricity from a utility and a phosphoric acid fuel cell powered system. The analysis showed that for a 500-unit apartment complex a fuel OS/IES would be about 10% more energy conservative in terms of total coal consumption than a diesel OS/IES system or a conventional system. The fuel cell OS/IES capital costs could be 30 to 55% greater than the diesel OS/IES capital costs for the same life cycle costs. The life cycle cost of a fuel cell OS/IES would be lower than that for a conventional system as long as the cost of electricity is greater than $0.05 to $0.065/kWh. An analysis of several parametric combinations of fuel cell power plant and state-of-art energy recovery systems and annual fuel requirement calculations for four locations were made. It was shown that OS/IES component choices are a major factor in fuel consumption, with the least efficient system using 25% more fuel than the most efficient. Central air conditioning and heat pumps result in minimum fuel consumption while individual air conditioning units increase it, and in general the fuel cell of highest electrical efficiency has the lowest fuel consumption.

  9. Analysis of the site-specific integration system of the Streptomyces aureofaciens phage μ1/6.

    PubMed

    Farkašovská, Jarmila; Godány, Andrej

    2012-03-01

    The bacteriophage μ1/6 integrates its DNA into the chromosome of tetracycline producing strains of Streptomyces aureofaciens by a site-specific recombination process. A bioinformatic analysis of the μ1/6 genome revealed that orf5 encodes a putative integrase, a basic protein of 416 amino acids. The μ1/6 integrase was found to belong to the integrase family of site-specific tyrosine recombinases. The phage attachment site (attP) was localized downstream of the int gene. The attachment junctions (attL and attR) were determined, allowing identification of the bacterial attachment site (attB). All attachment sites shared a 46-bp common core sequence within which a site-specific recombination occurs. This core sequence comprises the 3' end of a putative tRNA(Thr) gene (anticodon TGT) which is completely restored in attL after integration of the phage into the host genome. An integration vector containing μ1/6 int-attP region was inserted stably into the S. aureofaciens B96, S. lividans TK24, and S. coelicolor A3. The μ1/6 integrase was shown to be functional in vivo in heterologous Escherichia coli without any other factors encoded by Streptomyces. In vitro recombination assay using purified μ1/6 integrase demonstrated its ability to catalyze integrative recombination in the presence of a crude extract of E. coli cells.

  10. Integrating intrusive and nonintrusive characterization methods to achieve a conceptual site model for the SLDA FUSRAP site - 8265.

    SciTech Connect

    Durham, L. A.; Peterson, J. M.; Frothingham, D. G.; Frederick, W. T.; Lenart, W.; Environmental Science Division; U. S. Army Corps of Engineers, Pittsburg District; U. S. Army Corps of Engineers, Buffalo District

    2008-01-01

    The US Army Corps of Engineers (USACE) is addressing radiological contamination following Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) requirements at the Shallow Land Disposal Area (SLDA) site, which is a radiologically contaminated property that is part of the Formerly utilized Sites Remedial Action Program (FUSRAP). The SLDA is an 18-hectare (44-acre) site in Parks township, Armstrong County, Pennsylvania, about 37 kilometers (23 miles) east-northeast of Pittsburgh. According to historical record, radioactive wastes were disposed of at the SLDA in a series of trenches by the Nuclear Materials and Equipment Company (NUMEC) in the 1960s. The wastes originated from the nearby Apollo nuclear fuel fabrication facility, which began operations under NUMEC in the late 1950s and fabricated enriched uranium into naval reactor fuel elements. It is believed that the waste materials were buried in a series of pits constructed adjacent to one another in accordance with an Atomic Energy Commission (AEC) regulation that has since been rescinded. A CERCLA remedial investigation/feasibility study (RI/FS) process was completed for the SLDA site, and the results of the human health risk assessment indicated that the radiologically contaminated wastes could pose a risk to human health in the future. There are no historical records that provide the exact location of these pits. However, based on geophysical survey results conducted in the 1980s, these pits were defined by geophysical anomalies and were depicted on historical site drawings as trenches. At the SLDA site, a combination of investigative methods and tools was used in the RI/FS and site characterization activities. The SLDA site provides an excellent example of how historical documents and data, historical aerial photo analysis, physical sampling, and nonintrusive geophysical and gamma walkover surveys were used in combination to reduce the uncertainty in the location of the trenches. The

  11. An integrated study of spatial multicriteria analysis and mathematical modelling for managed aquifer recharge site suitability mapping and site ranking at Northern Gaza coastal aquifer.

    PubMed

    Rahman, Mohammad Azizur; Rusteberg, Bernd; Uddin, Mohammad Salah; Lutz, Annegret; Saada, Muath Abu; Sauter, Martin

    2013-07-30

    This paper describes an integrated approach of site suitability mapping and ranking of the most suitable sites, for the implementation of Managed Aquifer Recharge (MAR) projects, using spatial multicriteria decision analysis (SMCDA) techniques and mathematical modelling. The SMCDA procedure contains constraint mapping, site suitability analysis with criteria standardization and weighting, criteria overlay by analytical hierarchy process (AHP) combined with weighted linear combination (WLC) and ordered weighted averaging (OWA), and sensitivity analysis. The hydrogeological impacts of the selected most suitable sites were quantified by using groundwater flow and transport modelling techniques. Finally, ranking of the selected sites was done with the WLC method. The integrated approach is demonstrated by a case study in the coastal aquifer of North Gaza. Constraint mapping shows that 50% of the total study area is suitable for MAR implementation. About 25% of the total area is "very good" and 25% percent is "good" for MAR, according to the site suitability analysis. Six locations were selected and ranked against six representative decision criteria. Long term (year 2003 to year 2040) groundwater flow and transport simulations were performed to quantify the selected criteria under MAR project operation conditions at the selected sites. Finally, the suitability mapping and hydrogeological investigation recommends that the location of the existing infiltration ponds, constructed near the planned North Gaza Wastewater Treatment Plant (NGWWTP) is most suitable for MAR project implementation. This paper concludes that mathematical modelling should be combined with the SMCDA technique in order to select the best location for MAR project implementation. Besides MAR project implementation, the generalised approach can be applicable for any other water resources development project that deals with site selection and implementation. PMID:23603773

  12. Fitness Cost Implications of PhiC31-Mediated Site-Specific Integrations in Target-Site Strains of the Mexican Fruit Fly, Anastrepha ludens (Diptera: Tephritidae)

    PubMed Central

    Meza, José S.; Díaz-Fleischer, Francisco; Sánchez-Velásquez, Lázaro R.; Zepeda-Cisneros, Cristina Silvia; Handler, Alfred M.; Schetelig, Marc F.

    2014-01-01

    Site-specific recombination technologies are powerful new tools for the manipulation of genomic DNA in insects that can improve transgenesis strategies such as targeting transgene insertions, allowing transgene cassette exchange and DNA mobilization for transgene stabilization. However, understanding the fitness cost implications of these manipulations for transgenic strain applications is critical. In this study independent piggyBac-mediated attP target-sites marked with DsRed were created in several genomic positions in the Mexican fruit fly, Anastrepha ludens. Two of these strains, one having an autosomal (attP_F7) and the other a Y-linked (attP_2-M6y) integration, exhibited fitness parameters (dynamic demography and sexual competitiveness) similar to wild type flies. These strains were thus selected for targeted insertion using, for the first time in mexfly, the phiC31-integrase recombination system to insert an additional EGFP-marked transgene to determine its effect on host strain fitness. Fitness tests showed that the integration event in the int_2-M6y recombinant strain had no significant effect, while the int_F7 recombinant strain exhibited significantly lower fitness relative to the original attP_F7 target-site host strain. These results indicate that while targeted transgene integrations can be achieved without an additional fitness cost, at some genomic positions insertion of additional DNA into a previously integrated transgene can have a significant negative effect. Thus, for targeted transgene insertions fitness costs must be evaluated both previous to and subsequent to new site-specific insertions in the target-site strain. PMID:25303238

  13. The Skogaryd Research Site - Integration of terrestrial and freshwater greenhouse gas sources and sinks

    NASA Astrophysics Data System (ADS)

    Klemedtsson, L.

    2012-04-01

    atmosphere. The budgets have ignored dissolved carbon (C) and nitrogen (N) transport in water to streams and lakes and the subsequent exchange between the atmosphere and surface waters. Aquatic habitats can be significant net sources of CO2 and methane (CH4) and potential hot spots for N2O release, all important for natural greenhouse gas (GHG) emissions. Inland waters need to be included in the C and GHG balances for terrestrial landscapes. This project aims to quantify GHG balances at the landscape scale in forested regions that include land-atmosphere, land-water, and water-atmosphere exchange of CO2, CH4 and N2O. Different terrestrial and aquatic ecosystems will be linked holistically, using site specific techniques at different scales, from aircraft (km2) to chambers (m2) to develop integrated models that can be used to quantify net GHG flux for management strategies. The LAGGE project involves six Swedish universities and site is open for more cooperations.

  14. Integrated bio-magnetostratigraphy of ODP Site 709 (equatorial Indian Ocean).

    NASA Astrophysics Data System (ADS)

    Villa, Giuliana; Fioroni, Chiara; Florindo, Fabio

    2015-04-01

    Over the last decade, calcareous nannofossil biostratigraphy of the lower Eocene-Oligocene sediments has shown great potential, through identification of several new nannofossil species and bioevents (e.g. Fornaciari et al., 2010; Bown and Dunkley Jones, 2012; Toffanin et al., 2013). These studies formed the basis for higher biostratigraphic resolution leading to definition of a new nannofossil biozonation (Agnini et al., 2014). In this study, we investigate the middle Eocene-lower Oligocene sediments from ODP Hole 709C (ODP Leg 115) by means of calcareous nannofossils and magnetostratigraphy. Ocean Drilling Program (ODP) Site 709 was located in the equatorial Indian Ocean and biostratigraphy has been investigated in the nineties (Okada, 1990; Fornaciari et al., 1990) while paleomagnetic data from the Initial Report provided only a poorly constrained magnetostratigraphic interpretation, thus the cored succession was dated only by means of biostratigraphy. Our goal is to test the reliability in the Indian Ocean of the biohorizons recently identified at Site 711 (Fioroni et al., in press), by means of high resolution sampling, new taxonomic updates, quantitative analyses on calcareous nannofossils allowed to increase the number of useful bioevents and to compare their reliability and synchroneity. The new magnetostratigraphic analyses and integrated stratigraphy allow also to achieve an accurate biochronology of the time interval spanning Chrons C20 (middle Eocene) and C12 (early Oligocene). In addition, this equatorial site represents an opportunity to study the carbonate accumulation history and the large fluctuations of the carbonate compensation depth (CCD) during the Eocene (e.g. Pälike et al., 2012). The investigated interval encompasses the Middle Eocene Climatic Optimum (MECO), and the long cooling trend that leads to the Oligocene glacial state. By means of our new bio-magnetostratigraphic data and paleoecological results we provide further insights on

  15. A legal and ecological perspective of 'site integrity' to inform policy development and management of Special Areas of Conservation in Europe.

    PubMed

    Rees, Siân E; Sheehan, Emma V; Jackson, Emma L; Gall, Sarah C; Cousens, Sophie L; Solandt, Jean-Luc; Boyer, Matthew; Attrill, Martin J

    2013-07-15

    The European Union Habitats Directive (92/43/EEC) provides for the designation and management of Special Areas of Conservation (SACs) and requires that impacting activities are subject to 'an appropriate assessment' of their implications for the 'integrity' of the site. We define the term 'site integrity' from a legal and an ecological perspective. We demonstrate that 'site integrity' is the maintenance of ecological processes and functions that support the wider delivery of ecosystem services. 'Site integrity' can be influenced by SAC management. Management that seeks to support 'site integrity' may include the use of buffer zones or connecting areas that extend beyond the SAC site's designated features. We conclude that 'site integrity' and 'favourable conservation status' are powerful legal terms that if fully transposed into the law and policy of Member States can enable the achievement of broader European and International goals for marine conservation.

  16. Lentiviral vectors express chondroitinase ABC in cortical projections and promote sprouting of injured corticospinal axons.

    PubMed

    Zhao, Rong-Rong; Muir, Elizabeth M; Alves, João Nuno; Rickman, Hannah; Allan, Anna Y; Kwok, Jessica C; Roet, Kasper C D; Verhaagen, Joost; Schneider, Bernard L; Bensadoun, Jean-Charles; Ahmed, Sherif G; Yáñez-Muñoz, Rafael J; Keynes, Roger J; Fawcett, James W; Rogers, John H

    2011-09-30

    Several diseases and injuries of the central nervous system could potentially be treated by delivery of an enzyme, which might most effectively be achieved by gene therapy. In particular, the bacterial enzyme chondroitinase ABC is beneficial in animal models of spinal cord injury. We have adapted the chondroitinase gene so that it can direct secretion of active chondroitinase from mammalian cells, and inserted it into lentiviral vectors. When injected into adult rat brain, these vectors lead to extensive secretion of chondroitinase, both locally and from long-distance axon projections, with activity persisting for more than 4 weeks. In animals which received a simultaneous lesion of the corticospinal tract, the vector reduced axonal die-back and promoted sprouting and short-range regeneration of corticospinal axons. The same beneficial effects on damaged corticospinal axons were observed in animals which received the chondroitinase lentiviral vector directly into the vicinity of a spinal cord lesion.

  17. Transgenic chimera quail production by microinjecting lentiviral vector into the blood vessel of the early embryo.

    PubMed

    Sun, Peng; Zhang, Zifu; Wu, Guojin; Yan, Li; Yuan, Fang; Zhang, Wenxin; Gao, Junshuang; Jin, Wenjing; Li, Zandong

    2012-04-01

    In the past, several strategies have been used to generate transgenic birds. The most successful method has proven to be injection of lentiviral vector into the subgerminal cavity of the newly laid egg. In this study, we directly injected lentiviral vector into the blood vessel of HH13-15 quail embryos to produce transgenic chimeras. In the manipulated, hatched birds, the green fluorescent protein (GFP) gene driven by a cytomegalovirus (CMV) promoter was extensively expressed. All tissues analyzed were GFP-positive, and gonad cells from some of the manipulated embryos expressed GFP. The semen genome of 21.4% of mature male birds was determined to be GFP-positive by PCR, indicating these male birds were transgenic chimeras.

  18. A rapid and efficient branched DNA hybridization assay to titer lentiviral vectors.

    PubMed

    Nair, Ayyappan; Xie, Jinger; Joshi, Sarasijam; Harden, Paul; Davies, Joan; Hermiston, Terry

    2008-11-01

    A robust assay to titer lentiviral vectors is imperative to qualifying their use in drug discovery, target validation and clinical applications. In this study, a novel branched DNA based hybridization assay was developed to titer lentiviral vectors by quantifying viral RNA genome copy numbers from viral lysates without having to purify viral RNA, and this approach was compared with other non-functional (p24 protein ELISA and viral RT-qPCR) and a functional method (reporter gene expression) used commonly. The RT-qPCR method requires purification of viral RNA and the accuracy of titration therefore depends on the efficiency of purification; this requirement is ameliorated in the hybridization assay as RNA is measured directly in viral lysates. The present study indicates that the hybridization based titration assay performed on viral lysates was more accurate and has additional advantages of being rapid, robust and not dependent on transduction efficiency in different cell types.

  19. Lentiviral vector transduction of spermatozoa as a tool for the study of early development.

    PubMed

    Chandrashekran, Anil; Isa, Ihsan; Dudhia, Jayesh; Thrasher, Adrian J; Dibb, Nicholas; Casimir, Colin; Readhead, Carol; Winston, Robert

    2014-01-01

    Spermatozoa and lentiviruses are two of nature's most efficient gene delivery vehicles. Both can be genetically modified and used independently for the generation of transgenic animals or gene transfer/therapy of inherited disorders. Here we show that mature spermatozoa can be directly transduced with various pseudotyped lentiviral vectors and used in in vitro fertilisation studies. Lentiviral vectors encoding Green Fluorescent Protein (GFP) were shown to be efficiently processed and expressed in sperm. When these transduced sperm were used in in vitro fertilisation studies, GFP expression was observed in arising blastocysts. This simple technique of directly transducing spermatozoa has potential to be a powerful tool for the study of early and pre-implantation development and could be used as a technique in transgenic development and vertical viral transmission studies. PMID:24918038

  20. Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4(+) T cells.

    PubMed

    Kok, Yik Lim; Vongrad, Valentina; Shilaih, Mohaned; Di Giallonardo, Francesca; Kuster, Herbert; Kouyos, Roger; Günthard, Huldrych F; Metzner, Karin J

    2016-01-01

    The host genetic landscape surrounding integrated HIV-1 has an impact on the fate of the provirus. Studies analysing HIV-1 integration sites in macrophages are scarce. We studied HIV-1 integration site patterns in monocyte-derived macrophages (MDMs) and activated CD4(+) T cells derived from seven antiretroviral therapy (ART)-treated HIV-1-infected individuals whose cells were infected ex vivo with autologous HIV-1 isolated during the acute phase of infection. A total of 1,484 unique HIV-1 integration sites were analysed. Their distribution in the human genome and genetic features, and the effects of HIV-1 integrase polymorphisms on the nucleotide selection specificity at these sites were indistinguishable between the two cell types, and among HIV-1 isolates. However, the repertoires of HIV-1-hosting gene clusters overlapped to a higher extent in MDMs than in CD4(+) T cells. The frequencies of HIV-1 integration events in genes encoding HIV-1-interacting proteins were also different between the two cell types. Lastly, HIV-1-hosting genes linked to clonal expansion of latently HIV-1-infected CD4(+) T cells were over-represented in gene hotspots identified in CD4(+) T cells but not in those identified in MDMs. Taken together, the repertoire of genes targeted by HIV-1 in MDMs is distinct from and more restricted than that of CD4(+) T cells.

  1. Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4+ T cells

    PubMed Central

    Kok, Yik Lim; Vongrad, Valentina; Shilaih, Mohaned; Di Giallonardo, Francesca; Kuster, Herbert; Kouyos, Roger; Günthard, Huldrych F.; Metzner, Karin J.

    2016-01-01

    The host genetic landscape surrounding integrated HIV-1 has an impact on the fate of the provirus. Studies analysing HIV-1 integration sites in macrophages are scarce. We studied HIV-1 integration site patterns in monocyte-derived macrophages (MDMs) and activated CD4+ T cells derived from seven antiretroviral therapy (ART)-treated HIV-1-infected individuals whose cells were infected ex vivo with autologous HIV-1 isolated during the acute phase of infection. A total of 1,484 unique HIV-1 integration sites were analysed. Their distribution in the human genome and genetic features, and the effects of HIV-1 integrase polymorphisms on the nucleotide selection specificity at these sites were indistinguishable between the two cell types, and among HIV-1 isolates. However, the repertoires of HIV-1-hosting gene clusters overlapped to a higher extent in MDMs than in CD4+ T cells. The frequencies of HIV-1 integration events in genes encoding HIV-1-interacting proteins were also different between the two cell types. Lastly, HIV-1-hosting genes linked to clonal expansion of latently HIV-1-infected CD4+ T cells were over-represented in gene hotspots identified in CD4+ T cells but not in those identified in MDMs. Taken together, the repertoire of genes targeted by HIV-1 in MDMs is distinct from and more restricted than that of CD4+ T cells. PMID:27067385

  2. Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo.

    PubMed

    Tal, Asaf; Arbel-Goren, Rinat; Costantino, Nina; Court, Donald L; Stavans, Joel

    2014-05-20

    The search for specific sequences on long genomes is a key process in many biological contexts. How can specific target sequences be located with high efficiency, within physiologically relevant times? We addressed this question for viral integration, a fundamental mechanism of horizontal gene transfer driving prokaryotic evolution, using the infection of Escherichia coli bacteria with bacteriophage λ and following the establishment of a lysogenic state. Following the targeting process in individual live E. coli cells in real time revealed that λ DNA remains confined near the entry point of a cell following infection. The encounter between the 15-bp-long target sequence on the chromosome and the recombination site on the viral genome is facilitated by the directed motion of bacterial DNA generated during chromosome replication, in conjunction with constrained diffusion of phage DNA. Moving the native bacterial integration site to different locations on the genome and measuring the integration frequency in these strains reveals that the frequencies of the native site and a site symmetric to it relative to the origin are similar, whereas both are significantly higher than when the integration site is moved near the terminus, consistent with the replication-driven mechanism we propose. This novel search mechanism is yet another example of the exquisite coevolution of λ with its host. PMID:24799672

  3. Integrated Geophysical and Archaeological investigations to study the site of Aquinum (Frosinone, Italy)

    NASA Astrophysics Data System (ADS)

    Piro, Salvatore; Ceraudo, Giuseppe; Zamuner, Daniela

    2010-05-01

    To enhance the knowledge finalised to the location and conservation of the unknown buried structures below the actual studied levels, in the territory of the Ancient Aquinum (Frosinone, Italy) a scientific collaboration, inside the "Ager Aquinas Project" between the University of Salento (Department of Cultural Heritage - Laboratory of Ancient Topography and Photogrammetry) and the Institute of Technologies Applied to Cultural Heritage (ITABC-C.N.R.) has been developed, during 2008-2009 and it is still in progress. The site which is the subject of this paper had been identified in the past through air photo interpretation of vertical historical coverage and field - walking surveys. Ancient Aquinum is characterised by two main aspects: the first depends by the presence of a very big defence-system with mighty walls and large ditch; the second characteristic is the presence or regular but not orthogonal road - system of the town, bordered by an unusual parallelogram shape of the blocks. With the results obtained after the elaborations of the first aerial data sets and field surveys, has been possible to map the main town - planning, drawing the main road system inside and outside the town. Although the analysis of the air photo evidence allowed the global interpretation of the site, it was not possible to reconstruct the archaeological evidences in the central portion of the town. Therefore the Project, during 2008, started with new acquisition and elaboration of aerial photos, field-walking surveys and GPR surveys with the aim to better define the urban plan of the central portion of the ancient town. The location, depth, and size of the buried buildings were effectively estimated from non-destructive remote sensing with a gradiometric and ground-penetrating radar systems. Recent archaeological excavations made (by Prof. Giuseppe Ceraudo - University of Salento, Lecce) during the summer 2009, have confirmed the structures individuated with the geophysical methods

  4. Elements of lentiviral vector design toward gene therapy for treating mucopolysaccharidosis I.

    PubMed

    Ou, Li; Przybilla, Michael J; Koniar, Brenda L; Whitley, Chester B

    2016-09-01

    Mucopolysaccharidosis type I (MPS I) is a lysosomal disease caused by α-l-iduronidase (IDUA) deficiency and accumulation of glycosaminoglycans (GAG). Lentiviral vector encoding correct IDUA cDNA could be used for treating MPS I. To optimize the lentiviral vector design, 9 constructs were designed by combinations of various promoters, enhancers, and codon optimization. After in vitro transfection into 293FT cells, 5 constructs achieved the highest IDUA activities (5613 to 7358 nmol/h/mg protein). These 5 candidate vectors were then tested by injection (1 × 10(7) TU/g) into neonatal MPS I mice. After 30 days, one vector, CCEoIDW, achieved the highest IDUA levels: 2.6% of wildtype levels in the brain, 9.9% in the heart, 200% in the liver and 257% in the spleen. CCEoIDW achieved the most significant GAG reduction: down 49% in the brain, 98% in the heart, 100% in the liver and 95% in the spleen. Further, CCEoIDW had the lowest transgene frequency, especially in the gonads (0.03 ± 0.01 copies/100 cells), reducing the risk of insertional mutagenesis and germ-line transmission. Therefore, CCEoIDW is selected as the optimal lentiviral vector for treating MPS I disease and will be applied in large animal preclinical studies. Further, taken both in vitro and in vivo comparisons together, codon optimization, use of EF-1α promoter and woodchuck hepatitis virus posttranscriptional response element (WPRE) could enhance transgene expression. These results provided a better understanding of factors contributing efficient transgene expression in lentiviral gene therapies. PMID:27556013

  5. Embryo development, fetal growth and postnatal phenotype of eGFP lambs generated by lentiviral transgenesis.

    PubMed

    Crispo, M; Vilariño, M; dos Santos-Neto, P C; Núñez-Olivera, R; Cuadro, F; Barrera, N; Mulet, A P; Nguyen, T H; Anegón, I; Menchaca, A

    2015-02-01

    Lentiviral technology has been recently proposed to generate transgenic farm animals more efficiently and easier than traditional techniques. The objective was to evaluate several parameters of lambs obtained by lentiviral transgenesis in comparison with non-transgenic counterparts. In vitro produced embryos were microinjected (TG group) at two-cell stage with a lentiviral construct containing enhanced green fluorescent protein (eGFP) gene, while embryos produced by in vitro fertilization (IVF group) or intrauterine insemination (IUI group) were not microinjected. Microinjection technique efficiently generated eight-cell transgenic embryos (97.4%; 114/117). Development rate on day 5 after fertilization was similar for TG (39.3%, 46/117) and IVF embryos (39.6%, 44/111). Pregnancy rate was detected in 50.0% (6/12) of recipient ewes with TG embryos, in 46.7% (7/15) with IVF embryos, and in 65.0% (13/20) of IUI ewes (P = NS). Nine lambs were born in TG group, six lambs in IVF group, and 16 lambs in IUI group. All TG lambs (9/9) were GFP positive to real-time PCR and eight (88.9%) showed a strong and evident GFP expression in mucosae, eyes and keratin tissues. Fetal growth monitored every 15 day by ultrasonography did not show significant differences. Transgenic lambs neither differ in morphometric variables in comparison with non transgenic IVF lambs within 3 months after birth. Transmission of the transgene to the progeny was observed in green fluorescent embryos produced by IVF using semen from the TG founder lambs. In conclusion, this study demonstrates the high efficiency of lentiviral technology to produce transgenic sheep, with no clinic differences in comparison with non transgenic lambs.

  6. Generating Transgenic Mice by Lentiviral Transduction of Spermatozoa Followed by In Vitro Fertilization and Embryo Transfer.

    PubMed

    Chandrashekran, Anil; Casimir, Colin; Dibb, Nick; Readhead, Carol; Winston, Robert

    2016-01-01

    Most transgenic technologies rely on the oocyte as a substrate for genetic modification. Transgenics animals are usually generated by the injection of the gene constructs (including lentiviruses encoding gene constructs or modified embryonic stem cells) into the pronucleus of a fertilized egg followed by the transfer of the injected embryos into the uterus of a foster mother. Male germ cells also have potential as templates for transgenic development. We have previously shown that mature sperm can be utilized as template for lentiviral transduction and as such used to generate transgenic mice efficiently with germ line capabilities. We provide here a detailed protocol that is relatively simple, to establish transgenic mice using lentivirally transduced spermatozoa. This protocol employs a well-established lentiviral gene delivery system (usual for somatic cells) delivering a variety of transgenes to be directly used with sperm, and the subsequent use of these modified sperm in in vitro fertilization studies and embryo transfer into foster female mice, for the establishment of transgenic mice. PMID:27317176

  7. Lentiviral hematopoietic stem cell gene therapy for X-linked severe combined immunodeficiency.

    PubMed

    De Ravin, Suk See; Wu, Xiaolin; Moir, Susan; Anaya-O'Brien, Sandra; Kwatemaa, Nana; Littel, Patricia; Theobald, Narda; Choi, Uimook; Su, Ling; Marquesen, Martha; Hilligoss, Dianne; Lee, Janet; Buckner, Clarissa M; Zarember, Kol A; O'Connor, Geraldine; McVicar, Daniel; Kuhns, Douglas; Throm, Robert E; Zhou, Sheng; Notarangelo, Luigi D; Hanson, I Celine; Cowan, Mort J; Kang, Elizabeth; Hadigan, Coleen; Meagher, Michael; Gray, John T; Sorrentino, Brian P; Malech, Harry L

    2016-04-20

    X-linked severe combined immunodeficiency (SCID-X1) is a profound deficiency of T, B, and natural killer (NK) cell immunity caused by mutations inIL2RGencoding the common chain (γc) of several interleukin receptors. Gamma-retroviral (γRV) gene therapy of SCID-X1 infants without conditioning restores T cell immunity without B or NK cell correction, but similar treatment fails in older SCID-X1 children. We used a lentiviral gene therapy approach to treat five SCID-X1 patients with persistent immune dysfunction despite haploidentical hematopoietic stem cell (HSC) transplant in infancy. Follow-up data from two older patients demonstrate that lentiviral vector γc transduced autologous HSC gene therapy after nonmyeloablative busulfan conditioning achieves selective expansion of gene-marked T, NK, and B cells, which is associated with sustained restoration of humoral responses to immunization and clinical improvement at 2 to 3 years after treatment. Similar gene marking levels have been achieved in three younger patients, albeit with only 6 to 9 months of follow-up. Lentiviral gene therapy with reduced-intensity conditioning appears safe and can restore humoral immune function to posthaploidentical transplant older patients with SCID-X1. PMID:27099176

  8. Efficient transduction of liver and muscle after in utero injection of lentiviral vectors with different pseudotypes.

    PubMed

    MacKenzie, Tippi C; Kobinger, Gary P; Kootstra, Neeltje A; Radu, Antoneta; Sena-Esteves, Miguel; Bouchard, Sarah; Wilson, James M; Verma, Inder M; Flake, Alan W

    2002-09-01

    In this study we investigate the efficacy of lentiviral vectors of different pseudotypes for gene transfer to tissues of the preimmune fetus. BALB/c fetuses at 14-15 days' gestation received lentiviral vectors carrying the transgene lacZ under the control of the human cytomegalovirus (CMV) promoter by intramuscular (i.m.) or intrahepatic (i.h.) injection. We pseudotyped the lentiviral vectors with vesicular stomatitis virus (VSV-G), with Mokola virus, or with Ebola virus envelope glycoproteins. We harvested the pups at time points between 5 days and 9 months following injection and performed a detailed histologic assessment. The efficiency and distribution of transduction after in utero administration was highly dependent upon the route of administration and the pseudotype of vector used. Biodistribution studies showed widespread distribution of vector sequences in multiple tissues, albeit at very low levels, and transduced cells were found in significant numbers only in liver, heart, and muscle. Overall, VSV-G was the most efficient in transducing hepatocytes, whereas Mokola and Ebola were more efficient in transducing myocytes. Transduction of cardiomyocytes was observed after both i.m. and i.h. injection of all three vectors. Our findings of long-term transduction of skeletal myocytes and cardiomyocytes after in utero administration suggest a novel strategy for the treatment of congenital muscular dystrophies. PMID:12231171

  9. Biosafety in Ex Vivo Gene Therapy and Conditional Ablation of Lentivirally Transduced Hepatocytes in Nonhuman Primates

    PubMed Central

    Menzel, Olivier; Birraux, Jacques; Wildhaber, Barbara E; Jond, Caty; Lasne, Françoise; Habre, Walid; Trono, Didier; Nguyen, Tuan H; Chardot, Christophe

    2009-01-01

    Ex vivo gene therapy is an interesting alternative to orthotopic liver transplantation (OLT) for treating metabolic liver diseases. In this study, we investigated its efficacy and biosafety in nonhuman primates. Hepatocytes isolated from liver lobectomy were transduced in suspension with a bicistronic liver-specific lentiviral vector and immediately autotransplanted (SLIT) into three cynomolgus monkeys. The vector encoded cynomolgus erythropoietin (EPO) and the conditional suicide gene herpes simplex virus-thymidine kinase (HSV-TK). Survival of transduced hepatocytes and vector dissemination were evaluated by detecting transgene expression and vector DNA. SLIT was safely performed within a day in all three subjects. Serum EPO and hematocrit rapidly increased post-SLIT and their values returned to baseline within about 1 month. Isoforms of EPO detected in monkeys' sera differed from the physiological renal EPO. In liver biopsies at months 8 and 15, we detected EPO protein, vector mRNA and DNA, demonstrating long-term survival and functionality of transplanted lentivirally transduced hepatocytes. Valganciclovir administration resulted in complete ablation of the transduced hepatocytes. We demonstrated the feasibility and biosafety of SLIT, and the long term (>1 year) functionality of lentivirally transduced hepatocytes in nonhuman primates. The HSV-TK/valganciclovir suicide strategy can increase the biosafety of liver gene therapy protocols by safely and completely ablating transduced hepatocytes on demand. PMID:19568222

  10. Lentiviral Vectors for the Engineering of Implantable Cells Secreting Recombinant Antibodies.

    PubMed

    Lathuilière, Aurélien; Schneider, Bernard L

    2016-01-01

    The implantation of genetically modified cells is considered for the chronic delivery of therapeutic recombinant proteins in vivo. In the context of gene therapy, the genetic engineering of cells faces two main challenges. First, it is critical to generate expandable cell sources, which can maintain stable high productivity of the recombinant protein of interest over time, both in culture and after transplantation. In addition, gene transfer techniques need to be developed to engineer cells synthetizing complex polypeptides, such as recombinant monoclonal antibodies, to broaden the range of potential therapeutic applications. Here, we provide a workflow for the use of lentiviral vectors as a flexible tool to generate antibody-producing cells. In particular, lentiviral vectors can be used to genetically engineer the cell types compatible with encapsulation devices protecting the implanted cells from the host immune system. Detailed methods are provided for the design and production of lentiviral vectors, optimization of cell transduction, as well as for the quantification and quality control of the produced recombinant antibody. PMID:27317179

  11. Development of Endothelial-Specific Single Inducible Lentiviral Vectors for Genetic Engineering of Endothelial Progenitor Cells.

    PubMed

    Yang, Guanghua; Kramer, M Gabriela; Fernandez-Ruiz, Veronica; Kawa, Milosz P; Huang, Xin; Liu, Zhongmin; Prieto, Jesus; Qian, Cheng

    2015-11-27

    Endothelial progenitor cells (EPC) are able to migrate to tumor vasculature. These cells, if genetically modified, can be used as vehicles to deliver toxic material to, or express anticancer proteins in tumor. To test this hypothesis, we developed several single, endothelial-specific, and doxycycline-inducible self-inactivating (SIN) lentiviral vectors. Two distinct expression cassettes were inserted into a SIN-vector: one controlled by an endothelial lineage-specific, murine vascular endothelial cadherin (mVEcad) promoter for the expression of a transactivator, rtTA2S-M2; and the other driven by an inducible promoter, TREalb, for a firefly luciferase reporter gene. We compared the expression levels of luciferase in different vector constructs, containing either the same or opposite orientation with respect to the vector sequence. The results showed that the vector with these two expression cassettes placed in opposite directions was optimal, characterized by a robust induction of the transgene expression (17.7- to 73-fold) in the presence of doxycycline in several endothelial cell lines, but without leakiness when uninduced. In conclusion, an endothelial lineage-specific single inducible SIN lentiviral vector has been developed. Such a lentiviral vector can be used to endow endothelial progenitor cells with anti-tumor properties.

  12. Priming of hepatocytes enhances in vivo liver transduction with lentiviral vectors in adult mice.

    PubMed

    Pichard, Virginie; Boni, Sébastien; Baron, William; Nguyen, Tuan Huy; Ferry, Nicolas

    2012-02-01

    Lentiviral vectors are promising tools for liver disease gene therapy, because they can achieve protracted expression of transgenes in hepatocytes. However, the question as to whether cell division is required for optimal hepatocyte transduction has still not been completely answered. Liver gene-transfer efficiency after in vivo administration of recombinant lentiviral vectors carrying a green fluorescent protein reporter gene under the control of a liver-specific promoter in mice that were either hepatectomized or treated with cholic acid or phenobarbital was compared. Phenobarbital is known as a weak inducer of hepatocyte proliferation, whereas cholic acid has no direct effect on the cell cycle. This study shows that cholic acid is able to prime hepatocytes without mitosis induction. Both phenobarbital and cholic acid significantly increased hepatocyte transduction six- to ninefold, although cholic acid did not modify the mitotic index or cell-cycle entry. However, the effect of either compound was weaker than that observed after partial hepatectomy. In no cases was there a correlation between the expression of cell-cycle marker and transduction efficiency. We conclude that priming of hepatocytes should be considered a clinically applicable strategy to enhance in vivo liver gene therapy with lentiviral vectors.

  13. Cytotoxicity associated with artemis overexpression after lentiviral vector-mediated gene transfer.

    PubMed

    Multhaup, Megan; Karlen, Andrea D; Swanson, Debra L; Wilber, Andrew; Somia, Nikunj V; Cowan, Morton J; McIvor, R Scott

    2010-07-01

    Artemis is a hairpin-opening endonuclease involved in nonhomologous end-joining and V(D)J recombination. Deficiency of Artemis results in radiation-sensitive severe combined immunodeficiency (SCID) characterized by complete absence of T and B cells due to an arrest at the receptor recombination stage. We have generated several lentiviral vectors for transduction of the Artemis sequence, intending to complement the deficient phenotype. We found that transduction by a lentiviral vector in which Artemis is regulated by a strong EF-1alpha promoter resulted in a dose-dependent loss of cell viability due to perturbed cell cycle distribution, increased DNA damage, and increased apoptotic cell frequency. This toxic response was not observed in cultures exposed to identical amounts of control vector. Loss of cell viability was also observed in cells transfected with an Artemis expression construct, indicating that toxicity is independent of lentiviral transduction. Reduced toxicity was observed when cells were transduced with a moderate-strength phosphoglycerate kinase promoter to regulate Artemis expression. These results present a novel challenge in the establishment of conditions that support Artemis expression at levels that are nontoxic yet sufficient to correct the T(-)B(-) phenotype, crucial for preclinical studies and clinical application of Artemis gene transfer in the treatment of human SCID-A. PMID:20163250

  14. Endeavour Segment, Juan de Fuca Ridge, Integrated Studies Site (ISS) Update and Opportunities

    NASA Astrophysics Data System (ADS)

    Butterfield, D.; Ridge Community

    2003-12-01

    The Ridge 2000 (R2K) Integrated Studies bull's eye on the Juan de Fuca Ridge is focused on the Main Endeavour hydrothermal field, located on the central portion of the Endeavour Segment. This vent field is one of the most vigorously venting systems along the global mid-ocean ridge spreading network, hosting at least 18 large sulfide structures that contains more than100 smokers. Prior to a magmatic event in 2000 some of the edifices had been venting 380C, volatile-rich fluids with extremely low chlorinities for a decade. In addition to the Main Endeavour Field there are four other known high temperature vent fields spaced approximately 2 kilometers apart along the segment (with hints of more) and abundant areas of diffuse flow, both nearby and distal to the high temperature venting. Diffuse flow from the structures and from a variety of basaltic-hosted sites provides rich habitats abundant with microbial and macrofaunal communities. There are well-developed gradients in volatile concentrations along axis that may reflect influence from a sedimentary source to the north, and high chlorinity fluids vent from the most southern (Mothra) and northern fields (Sasquatch). Twenty years of research have laid a firm base for the 5-year plans of R2K at this site, which include examining the response of this segment to perturbations induced by tectonic and magmatic events, identification of the reservoirs, fluxes, and feedbacks of mass and energy at this site, and predictive modeling coupled with field observations. Since designation as an IS site, high-resolution bathymetric mapping (EM300) and an extensive multi-channel seismic survey have been conducted along the entire segment. Smaller focused areas have also been mapped at meter resolution by SM2000 sonar. Intense field programs in 2003 established the first in-situ seismic array along a mid-ocean ridge, which includes installation of a buried broadband seismometer and 7 short-period seismometers emplaced within basaltic

  15. Monitoring groundwater contamination and delineating source zones at industrial sites: uncertainty analyses using integral pumping tests.

    PubMed

    Jarsjö, Jerker; Bayer-Raich, Martí; Ptak, Thomas

    2005-10-01

    Field-scale characterisations of contaminant plumes in groundwater, as well as source zone delineations, are associated with uncertainties that can be considerable. A major source of uncertainty in environmental datasets is due to variability of sampling results, as a direct consequence of the heterogeneity of environmental matrices. We develop a methodology for quantifying uncertainties in field-scale mass flow and average concentration estimations, using integral pumping tests (IPTs), where the contaminant concentration is measured as a function of time in a pumping well. This procedure increases the sampling volume and reduces the effect of small-scale variability that may bias point-scale measurements. In particular, using IPTs, the interpolation uncertainty of conventional point-scale measurements is transformed to a quantifiable uncertainty related to the (unknown) plume position relative to the pumping well. We show that this plume position uncertainty generally influenced the predicted mass flows and average concentrations (of acenapthene, benzene and CHCs) to a greater extent than a boundary condition uncertainty related to the local water balance, considering 19 control planes at a highly heterogeneous industrial site in southwest Germany. Furthermore, large (order of magnitude) uncertainties only occurred if the conditions were strongly heterogeneous in the nearest vicinity of the well. We also develop a consistent methodology for an assessment of the combined effect of uncertainty in hydraulic conditions and uncertainty in reactive transport parameters for delimiting of both contaminant source zones and zones absent of source, based on (downgradient) IPTs.

  16. Multicopy integration of mini-Tn7 transposons into selected chromosomal sites of a Salmonella vaccine strain

    PubMed Central

    Roos, Karen; Werner, Esther; Loessner, Holger

    2015-01-01

    Chromosomal integration of expression modules for transgenes is an important aspect for the development of novel Salmonella vectors. Mini-Tn7 transposons have been used for the insertion of one such module into the chromosomal site attTn7, present only once in most Gram-negative bacteria. However, integration of multiple mini-Tn7 copies might be suitable for expression of appropriate amounts of antigen or combination of different modules. Here we demonstrate that integration of a 9.6 kb mini-Tn7 harbouring the luciferase luxCDABE (lux) occurs at the natural attTn7 site and simultaneously other locations of the Salmonella chromosome, which were engineered using λ-Red recombinase to contain one or two additional artificial attTn7 sites (a-attTn7). Multicopy integration even at closely spaced attTn7 sites was unexpected in light of the previously reported distance-dependent Tn7 target immunity. Integration of multiple copies of a mini-Tn7 containing a gfp cassette resulted in increasing green fluorescence of bacteria. Stable consecutive integration of two mini-Tn7 encoding lacZ and lux was achieved by initial transposition of lacZ-mini-Tn7, subsequent chromosomal insertion of a-attTn7 and a second round of transposition with lux-mini-Tn7. Mini-Tn7 thus constitutes a versatile method for multicopy integration of expression cassettes into the chromosome of Salmonella and possibly other bacteria. PMID:25488129

  17. Clonetegration Using OSIP Plasmids: One-Step DNA Assembly and Site-Specific Genomic Integration in Bacteria.

    PubMed

    Cui, Lun; Shearwin, Keith E

    2017-01-01

    Clonetegration is a method for site-specific insertion of DNA into prokaryotic chromosomes, based on bacteriophage integrases. The method combines DNA cloning/assembly and chromosomal integration into a single step, providing a simple and rapid strategy for inserting DNA sequences into bacterial chromosomes. PMID:27671938

  18. Low-Impact Development Design—Integrating Suitability Analysis and Site Planning For Reduction Of Post-Development Stormwater Quantity

    EPA Science Inventory

    A land-suitability analysis (LSA) was integrated with open-space conservation principles, based on watershed physiographic and soil characteristics, to derive a low-impact development (LID) residential plan for a three hectare site in Coshocton OH, USA. The curve number method wa...

  19. Low Impact Development Design—Integrating Suitability Analysis and Site Planning for Reduction of Post-Development Stormwater Quantity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A land-suitability analysis (LSA) was integrated with open-space conservation principles, based on watershed physiographic and soil characteristics, to derive a low-impact development (LID) residential plan for a three hectare site in Coshocton OH, USA. The curve number method was used to estimate t...

  20. Using remote sensing data for exploitation of integrated renewable energy at coastal site in South Italy

    NASA Astrophysics Data System (ADS)

    Calaudi, Rosamaria; Lo Feudo, Teresa; Calidonna, Claudia Roberta; Sempreviva, Anna Maria

    2016-04-01

    Renewable energy sources are major components of the strategy to reduce harmful emissions and to replace depleting fossil energy resources. Data from Remote Sensing can provide detailed information for analysis for sources of renewable energy and to determine the potential energy and socially acceptability of suggested location. Coastal sites of Southern Italy have the advantage of favorable climatic conditions to use renewable energy, such us cloud free days and local breeze phenomena. Many ports are located where they have opportunities for exploitation of renewable energy, by using existing port area and by taking advantage of their coastal locations. Policies of European-Committee and Global-Navigation-PIANC for a better use of energy and an efficient supply from renewable sources are also focused on the construction of port facilities in zero emissions. Using data from Remote Sensing, can reduce the financial resources currently required for finding and assessing suitable areas, we defined an integrated methodology for potential wind and solar energy in harbor areas. In this study we compared the hourly solar power energy using MSG-SEVIRI (Meteosat Second Generation Spinning Enhanced Visible and Infrared) data products DSSF (Down-welling Surface Short-wave-Flux), and PV-Plant measurements with Nominal Power Peak of 19,85 kWp. The PV Plant is situated at a coastal site in Calabrian region, located near Vibo Valentia harbor area. We estimate potential energy by using input solar radiation of Satellite data, with same characteristics of the PV-plant. The RMSE and BIAS for hourly averaged solar electrical reproducibility are estimated including clear and sky conditions. Comparison between energy reproducibility by using DSSF product and PV-plant measurements, made over the period October 2013-June 2014, showed a good agreement in our costal site and generally overestimate (RMSE(35W/m2) and BIAS(4W/m2)) electrical reproducibility from a PV-plant. For wind resource

  1. Improved production of genetically modified fetuses with homogeneous transgene expression after transgene integration site analysis and recloning in cattle.

    PubMed

    Bressan, Fabiana Fernandes; Dos Santos Miranda, Moyses; Perecin, Felipe; De Bem, Tiago Henrique; Pereira, Flavia Thomaz Verechia; Russo-Carbolante, Elisa Maria; Alves, Daiani; Strauss, Bryan; Bajgelman, Marcio; Krieger, José Eduardo; Binelli, Mario; Meirelles, Flavio Vieira

    2011-02-01

    Animal cloning by nuclear transfer (NT) has made the production of transgenic animals using genetically modified donor cells possible and ensures the presence of the gene construct in the offspring. The identification of transgene insertion sites in donor cells before cloning may avoid the production of animals that carry undesirable characteristics due to positional effects. This article compares blastocyst development and competence to establish pregnancies of bovine cloned embryos reconstructed with lentivirus-mediated transgenic fibroblasts containing either random integration of a transgene (random integration group) or nuclear transfer derived transgenic fibroblasts with known transgene insertion sites submitted to recloning (recloned group). In the random integration group, eGFP-expressing bovine fetal fibroblasts were selected by fluorescence activated cell sorting (FACS) and used as nuclei donor cells for NT. In the recloned group, a fibroblast cell line derived from a transgenic cloned fetus was characterized regarding transgene insertion and submitted to recloning. The recloned group had higher blastocyst production (25.38 vs. 14.42%) and higher percentage of 30-day pregnancies (14.29 vs. 2.56%) when compared to the random integration group. Relative eGFP expression analysis in fibroblasts derived from each cloned embryo revealed more homogeneous expression in the recloned group. In conclusion, the use of cell lines recovered from transgenic fetuses after identification of the transgene integration site allowed for the production of cells and fetuses with stable transgene expression, and recloning may improve transgenic animal yields.

  2. Verification of geomechanical integrity and prediction of long-term mineral trapping for the Ketzin CO2 storage pilot site

    NASA Astrophysics Data System (ADS)

    Kempka, Thomas; De Lucia, Marco; Kühn, Michael

    2014-05-01

    Static and dynamic numerical modelling generally accompany the entire CO2 storage site life cycle. Thereto, it is required to match the employed models with field observations on a regular basis in order to predict future site behaviour. We investigated the coupled processes at the Ketzin CO2 storage pilot site [1] using a model coupling concept focusing on the temporal relevance of processes involved (hydraulic, chemical and mechanical) at given time-scales (site operation, abandonment and long-term stabilization). For that purpose, long-term dynamic multi-phase flow simulations [2], [3] established the basis for all simulations discussed in the following. Hereby, pressure changes resulting in geomechanical effects are largest during site operation, whereas geochemical reactions are governed by slow kinetics resulting in a long-term stabilization. To account for mechanical integrity, which may be mainly affected during site operation, we incorporated a regional-scale coupled hydro-mechanical model. Our simulation results show maximum ground surface displacements of about 4 mm, whereas shear and tensile failure are not observed. Consequently, the CO2 storage operation at the Ketzin pilot site does not compromise reservoir, caprock and fault integrity. Chemical processes responsible for mineral trapping are expected to mainly occur during long-term stabilization at the Ketzin pilot site [4]. Hence, our previous assessment [3] was extended by integrating two long-term mineral trapping scenarios. Thereby, mineral trapping contributes to the trapping mechanisms with 11.7 % after 16,000 years of simulation in our conservative and with 30.9 % in our maximum reactivity scenarios. Dynamic flow simulations indicate that only 0.2 % of the CO2 injected (about 67,270 t CO2 in total) is in gaseous state, but structurally trapped after 16,000 years. Depending on the studied long-term scenario, CO2 dissolution is the dominating trapping mechanism with 68.9 % and 88

  3. A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells.

    PubMed Central

    Dietz, A; Kay, V; Schlake, T; Landsmann, J; Bode, J

    1994-01-01

    Integration of foreign genes into plant genomes by the Agrobacterium T-DNA transfer system has been considered to occur at random. It has been speculated that the chromosomal structure of the integration site might affect the expression pattern of the introduced genes. To gain insight into the molecular structure of T-DNA integration sites and its possible impact on gene expression, we have examined plant DNA sequences in the vicinity of T-DNA borders. Analysis of a transgenic petunia plant containing a chloramphenicol acetyltransferase (CAT) gene regulated by the hemoglobin promoter (PAR) from Parasponia andersonii revealed a scaffold attachment region (SAR) close to one T-DNA end. In addition to having strong binding affinities for both animal and plant nuclear scaffolds this petunia SAR element is as active in mammalian cells as the authentic elements from mammalian sources. Images PMID:8052530

  4. Combining microseismic and geomechanical observations to interpret storage integrity at the In Salah CCS site

    NASA Astrophysics Data System (ADS)

    Goertz-Allmann, Bettina P.; Kühn, Daniela; Oye, Volker; Bohloli, Bahman; Aker, Eyvind

    2014-07-01

    We present results from microseismic monitoring and geomechanical analysis obtained at the industrial-scale CO2 sequestration site at the In Salah gas development project in Algeria. More than 5000 microseismic events have been detected at a pilot monitoring well using a master event cross-correlation method. The microseismic activity occurs in four distinct clusters and thereof three clearly correlate with injection rates and wellhead pressures. These event clusters are consistent with a location within the reservoir interval. However, due to insufficient network geometry there are large uncertainties on event location. We estimate a fracture pressure of 155 bar (at the wellhead) from the comparison of injection pressure and injection rate and conclude that reservoir fracture pressure of the injection horizon has most likely been exceeded occasionally, accompanied by increased microseismic activity. Our analysis of 3-D ray tracing for direct and converted phases suggests that one of the event clusters is located at a shallower depth than the reservoir injection interval. However, this event cluster is most likely unrelated to changes in the injection activity at a single well, as the event times do not correlate with the wellhead pressures. Furthermore, this event cluster shows b-values close to one, indicating re-activated natural or tectonic seismicity on pre-existing weakness zones rather than injection induced seismicity. Analysis of event azimuths and significant shear wave splitting of up to 5 per cent provide further valuable insight into fluid migration and fracture orientation at the reservoir level. Although only one geophone was available during the critical injection period, the microseismic monitoring of CO2 injection at In Salah is capable of addressing some of the most relevant questions about fluid migration and reservoir integrity. An improved monitoring array with larger aperture and higher sensitivity is highly recommended, as it could greatly

  5. Use of an integrated flow model to estimate ecologically relevant hydrologic characteristics at stream biomonitoring sites

    USGS Publications Warehouse

    Kennen, J.G.; Kauffman, L.J.; Ayers, M.A.; Wolock, D.M.; Colarullo, S.J.

    2008-01-01

    We developed an integrated hydroecological model to provide a comprehensive set of hydrologic variables representing five major components of the flow regime at 856 aquatic-invertebrate monitoring sites in New Jersey. The hydroecological model simulates streamflow by routing water that moves overland and through the subsurface from atmospheric delivery to the watershed outlet. Snow accumulation and melt, evapotranspiration, precipitation, withdrawals, discharges, pervious- and impervious-area runoff, and lake storage were accounted for in the water balance. We generated more than 78 flow variables, which describe the frequency, magnitude, duration, rate of change, and timing of flow events. Highly correlated variables were filtered by principal component analysis to obtain a non-redundant subset of variables that explain the majority of the variation in the complete set. This subset of variables was used to evaluate the effect of changes in the flow regime on aquatic-invertebrate assemblage structure at 856 biomonitoring sites. We used non-metric multidimensional scaling (NMS) to evaluate variation in aquatic-invertebrate assemblage structure across a disturbance gradient. We employed multiple linear regression (MLR) analysis to build a series of MLR models that identify the most important environmental and hydrologic variables driving the differences in the aquatic-invertebrate assemblages across the disturbance gradient. The first axis of NMS ordination was significantly related to many hydrologic, habitat, and land-use/land-cover variables, including the average number of annual storms producing runoff, ratio of 25-75% exceedance flow (flashiness), diversity of natural stream substrate, and the percentage of forested land near the stream channel (forest buffer). Modifications in the hydrologic regime as the result of changes in watershed land use appear to promote the retention of highly tolerant aquatic species; in contrast, species that are sensitive to

  6. Integrated Site Investigation Methods and Modeling: Recent Developments at the BHRS (Invited)

    NASA Astrophysics Data System (ADS)

    Barrash, W.; Bradford, J. H.; Cardiff, M. A.; Dafflon, B.; Johnson, B. A.; Malama, B.; Thoma, M. J.

    2010-12-01

    The Boise Hydrogeophysical Research Site (BHRS) is a field-scale test facility in an unconfined aquifer with the goals of: developing cost-effective, non-invasive methods for quantitative characterization of heterogeneous aquifers using hydrologic and geophysical techniques; understanding fundamental relations and processes at multiple scales; and testing theories and models for groundwater flow and solute transport. The design of the BHRS supports a wide range of single-well, cross-hole, multiwell and multilevel hydrologic, geophysical, and combined hydrogeophysical experiments. New installations support direct and geophysical monitoring of hydrologic fluxes and states from the aquifer through the vadose zone to the atmosphere, including ET and river boundary behavior. Efforts to date have largely focused on establishing the 1D, 2D, and 3D distributions of geologic, hydrologic, and geophysical parameters which can then be used as the basis for testing methods to integrate direct and indirect data and invert for “known” parameter distributions, material boundaries, and tracer test or other system state behavior. Aquifer structure at the BHRS is hierarchical and includes layers and lenses that are recognized with geologic, hydrologic, radar, electrical, and seismic methods. Recent advances extend findings and method developments, but also highlight the need to examine assumptions and understand secular influences when designing and modeling field tests. Examples of advances and caveats include: New high-resolution 1D K profiles obtained from multi-level slug tests (inversion improves with priors for aquifer K, wellbore skin, and local presence of roots) show variable correlation with porosity and bring into question a Kozeny-Carman-type relation for much of the system. Modeling of 2D conservative tracer transport through a synthetic BHRS-like heterogeneous system shows the importance of including porosity heterogeneity (rather than assuming constant porosity for

  7. Response of a simian immunodeficiency virus (SIVmac251) to raltegravir: a basis for a new treatment for simian AIDS and an animal model for studying lentiviral persistence during antiretroviral therapy

    PubMed Central

    2010-01-01

    Background In this study we successfully created a new approach to ART in SIVmac251 infected nonhuman primates. This drug regimen is entirely based on drugs affecting the pre-integration stages of replication and consists of only two nucleotidic/nucleosidic reverse transcriptase inhibitors (Nt/NRTIs) and raltegravir, a promising new drug belonging to the integrase strand transfer inhibitor (INSTI) class. Results In acutely infected human lymphoid CD4+ T-cell lines MT-4 and CEMx174, SIVmac251 replication was efficiently inhibited by raltegravir, which showed an EC90 in the low nanomolar range. This result was confirmed in primary macaque PBMCs and enriched CD4+ T cell fractions. In vivo monotherapy with raltegravir for only ten days resulted in reproducible decreases in viral load in two different groups of animals. When emtricitabine (FTC) and tenofovir (PMPA) were added to treatment, undetectable viral load was reached in two weeks, and a parallel increase in CD4 counts was observed. In contrast, the levels of proviral DNA did not change significantly during the treatment period, thus showing persistence of this lentiviral reservoir during therapy. Conclusions In line with the high conservation of the three main amino acids Y143, Q148 and N155 (responsible for raltegravir binding) and molecular docking simulations showing similar binding modes of raltegravir at the SIVmac251 and HIV-1 IN active sites, raltegravir is capable of inhibiting SIVmac251 replication both in tissue culture and in vivo. This finding may help to develop effective ART regimens for the simian AIDS model entirely based on drugs adopted for treatment in humans. This ART-treated AIDS nonhuman primate model could be employed to find possible strategies for virus eradication from the body. PMID:20233398

  8. Petrophysical properties of saprolites from the Oak Ridge Integrated Field Research Challenge site, Tennessee

    SciTech Connect

    Revil, André; Skold, Magnus; Hubbard, Susan S.; Wu, Yuxin; Watson, David B.; Karaoulis, Marios

    2013-01-01

    At the Oak Ridge Integrated Field Research Challenge site, near Oak Ridge, Tennessee, the shallow saprolitic aquifer is contaminated by nitric acid, uranium, and metals originating from the former S3 settling ponds. To interpret low-frequency geophysical methods used to image contaminant plumes, we have characterized the petrophysical properties of three representative saprolite core samples. Their hydraulic conductivity ranges from to in agreement with field data. Complex conductivity measurements, in the frequency range of 1 mHz to 45 kHz, were performed with NaCl solutions with electrical conductivities in the range to , a range representative of field conditions. The electrical conductivity data were well reproduced with a simple linear conductivity model between the saprolite conductivity and the pore water conductivity. The conductivity plots were used to estimate the formation factor (the cementation exponent was about ) and the surface conductivity ( ). The magnitude of the surface conductivity depended on the degree of weathering and therefore on the amount of smectite and mixed layer (illite-smectite) clays present in the saprolite. The chargeability of the core samples was in the range of and is strongly dependent on the salinity. We also performed streaming potential measurements with the same pore fluid composition as that used for the complex conductivity measurements. We found an excess of movable electrical charges on the order of 100 to in agreement with previous investigations connecting the movable excess charge density to permeability. The zeta potential was in the range of to independent on the salinity. The electrical measurements were consistent with an average cation exchange capacity in the range of 1.4 to and a specific surface area on the order of 4000 to about 30,000 . Read More: http://library.seg.org/doi/abs/10.1190/geo2012-0176.1

  9. The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites.

    PubMed

    Li, Meng Amy; Pettitt, Stephen J; Eckert, Sabine; Ning, Zemin; Rice, Stephen; Cadiñanos, Juan; Yusa, Kosuke; Conte, Nathalie; Bradley, Allan

    2013-04-01

    The DNA transposon piggyBac is widely used as a tool in mammalian experimental systems for transgenesis, mutagenesis, and genome engineering. We have characterized genome-wide insertion site preferences of piggyBac by sequencing a large set of integration sites arising from transposition from two separate genomic loci and a plasmid donor in mouse embryonic stem cells. We found that piggyBac preferentially integrates locally to the excision site when mobilized from a chromosomal location and identified other nonlocal regions of the genome with elevated insertion frequencies. piggyBac insertions were associated with expressed genes and markers of open chromatin structure and were excluded from heterochromatin. At the nucleotide level, piggyBac prefers to insert into TA-rich regions within a broader GC-rich context. We also found that piggyBac can insert into sites other than its known TTAA insertion site at a low frequency (2%). Such insertions introduce mismatches that are repaired with signatures of host cell repair pathways. Transposons could be mobilized from plasmids with the observed noncanonical flanking regions, indicating that piggyBac could generate point mutations in the genome. PMID:23358416

  10. Integral equations in the study of polar and ionic interaction site fluids

    PubMed Central

    Howard, Jesse J.

    2011-01-01

    In this review article we consider some of the current integral equation approaches and application to model polar liquid mixtures. We consider the use of multidimensional integral equations and in particular progress on the theory and applications of three dimensional integral equations. The IEs we consider may be derived from equilibrium statistical mechanical expressions incorporating a classical Hamiltonian description of the system. We give example including salt solutions, inhomogeneous solutions and systems including proteins and nucleic acids. PMID:22383857

  11. Using integrated geospatial mapping and conceptual site models to guide risk-based environmental clean-up decisions.

    PubMed

    Mayer, Henry J; Greenberg, Michael R; Burger, Joanna; Gochfield, Michael; Powers, Charles; Kosson, David; Keren, Roger; Danis, Christine; Vyas, Vikram

    2005-04-01

    Government and private sector organizations are increasingly turning to the use of maps and other visual models to provide a depiction of environmental hazards and the potential risks they represent to humans and ecosystems. Frequently, the graphic presentation is tailored to address a specific contaminant, its location and possible exposure pathways, and potential receptors. Its format is usually driven by the data available, choice of graphics technology, and the audience being served. A format that is effective for displaying one contaminant at one scale at one site, however, may be ineffective in accurately portraying the circumstances surrounding a different contaminant at the same site, or the same contaminant at a different site, because of limitations in available data or the graphics technology being used. This is the daunting challenge facing the U.S. Department of Energy (DOE), which is responsible for the nation's legacy wastes from nuclear weapons research, testing, and production at over 100 sites in the United States. In this article, we discuss the development and use of integrated geospatial mapping and conceptual site models to identify hazards and evaluate alternative long-term environmental clean-up strategies at DOE sites located across the United States. While the DOE probably has the greatest need for such information, the Department of Defense and other public and private responsible parties for many large and controversial National Priority List or Superfund sites would benefit from a similar approach.

  12. A multi-site intercomparison of integrated water vapour observations for climate change analysis

    NASA Astrophysics Data System (ADS)

    Van Malderen, R.; Brenot, H.; Pottiaux, E.; Beirle, S.; Hermans, C.; De Mazière, M.; Wagner, T.; De Backer, H.; Bruyninx, C.

    2014-08-01

    Water vapour plays a dominant role in the climate change debate. However, observing water vapour over a climatological time period in a consistent and homogeneous manner is challenging. On one hand, networks of ground-based instruments able to retrieve homogeneous integrated water vapour (IWV) data sets are being set up. Typical examples are Global Navigation Satellite System (GNSS) observation networks such as the International GNSS Service (IGS), with continuous GPS (Global Positioning System) observations spanning over the last 15+ years, and the AErosol RObotic NETwork (AERONET), providing long-term observations performed with standardized and well-calibrated sun photometers. On the other hand, satellite-based measurements of IWV already have a time span of over 10 years (e.g. AIRS) or are being merged to create long-term time series (e.g. GOME, SCIAMACHY, and GOME-2). This study performs an intercomparison of IWV measurements from satellite devices (in the visible, GOME/SCIAMACHY/GOME-2, and in the thermal infrared, AIRS), in situ measurements (radiosondes) and ground-based instruments (GPS, sun photometer), to assess their use in water vapour trends analysis. To this end, we selected 28 sites world-wide for which GPS observations can directly be compared with coincident satellite IWV observations, together with sun photometer and/or radiosonde measurements. The mean biases of the different techniques compared to the GPS estimates vary only between -0.3 to 0.5 mm of IWV. Nevertheless these small biases are accompanied by large standard deviations (SD), especially for the satellite instruments. In particular, we analysed the impact of clouds on the IWV agreement. The influence of specific issues for each instrument on the intercomparison is also investigated (e.g. the distance between the satellite ground pixel centre and the co-located ground-based station, the satellite scan angle, daytime/nighttime differences). Furthermore, we checked if the properties of

  13. Lentiviral Vectors Mediate Long-Term and High Efficiency Transgene Expression in HEK 293T cells

    PubMed Central

    Mao, Yingying; Yan, Renhe; Li, Andrew; Zhang, Yanling; Li, Jinlong; Du, Hongyan; Chen, Baihong; Wei, Wenjin; Zhang, Yi; Sumners, Colin; Zheng, Haifa; Li, Hongwei

    2015-01-01

    Objectives:Lentiviral vectors have been used successfully to rapidly produce decigram quantities of active recombinant proteins in mammalian cell lines. To optimize the protein production platform, the roles of Ubiquitous Chromatin Opening Element (UCOE), an insulator, and selected promoters were evaluated based on efficiency and stability of foreign gene expression mediated by lentiviral vectors. Methods: Five lentiviral vectors, pFIN-EF1α-GFP-2A-mCherH-WPRE containing EF1α promoter and HS4 insulator, p'HR.cppt.3'1.2kb-UCOE-SFFV-eGFP containing SFFV promoter and UCOE, pTYF-CMV(β-globin intron)-eGFP containing CMV promoter and β-globin intron, pTYF-CMV-eGFP containing CMV promoter, and pTYF-EF1α-eGFP with EF1α promoter were packaged, titered, and then transduced into 293T cells (1000 viral genomes per cell). The transduced cells were passaged once every three days at a ratio of 1:10. Expression level and stability of the foreign gene, green fluorescence protein (GFP), was evaluated using fluorescent microscopy and flow cytometry. Furthermore, we constructed a hepatitis C virus (HCV) E1 recombinant lentiviral vector, pLV-CMV-E1, driven by the CMV promoter. This vector was packaged and transduced into 293T cells, and the recombinant cell lines with stable expression of E1 protein were established by limiting dilution. Results:GFP expression in 293T cells transduced with the five lentiviral vectors peaked between passages 3 and 5 and persisted for more than 5 weeks. The expression was prolonged in the cells transduced with TYF-CMV (β-globin intron)-eGFP or TYF-CMV-eGFP, demonstrating less than a 50% decrease even at 9 weeks post transduction (p>0.05). The TYF-CMV-eGFP-transduced cells began with a higher level of GFP expression than other vectors did. The percentage of GFP positive cells for any of the five lentiviral vectors sustained over time. Moreover, the survival rates of all transfected cells exceeded 80% at both 5 and 9 weeks post transduction

  14. A Lentiviral Vector Expressing Desired Gene Only in Transduced Cells: An Approach for Suicide Gene Therapy.

    PubMed

    Mohammadi, Zahra; Shariati, Laleh; Khanahmad, Hossein; Kolahdouz, Mahsa; Kianpoor, Fariborz; Ghanbari, Jahan Afrooz; Hejazi, Zahra; Salehi, Mansoor; Nikpour, Parvaneh; Tabatabaiefar, Mohammad Amin

    2015-09-01

    Suicide gene therapy is a therapeutic strategy, in which cell suicide inducing transgenes are introduced into target cells. Inserting a toxin-encoding gene into a lentiviral vector leads to decreased efficiency of virus production due to lethal effect of toxin on packaging cells. In this study, we designed and constructed a transfer vector to express the toxin in transduced cells but not in packaging cells. Plasmid pLenti-F/GFP was constructed by cutting out R 5'LTR-R 3'LTR fragment with the AflII restriction endonuclease from a plasmid pLenti4-GW/H1/TO-laminshRNA, followed by ligating R 5'LTR-R 3'LTR fragment, constructed by three PCR stages. The promoter and GFP CDS were inserted in opposite strand. For lentiviral production, the HEK293T cell line was co-transfected with the PMD2G, psPAX2, and pLenti-F/GFP plasmids (envelope, packaging, and transfer plasmids).Viral vector titers were assayed. The HEK293T cell line was transduced with this virus. PCR was performed to confirm the presence of the promoter fragment between the R and U5 in 3'LTR. The lentivirus titers were approximately 2 × 10(5). The GFP expression was seen in 51 % of the HEK293T cells transduced with lentivirus. The PCR product size was 1440 bp confirming the promoter fragment position between the R and U5 in 3'LTR. The strategy enables us to use a broad spectrum of toxin genes in gene therapy and helps avoid the death of the packaging cells with lentiviral vectors carrying a toxin-encoding gene, thereby increasing the efficiency of viral production in packaging cells.

  15. An integrated multi criteria approach for landfill siting in a conflicting environmental, economical and socio-cultural area.

    PubMed

    Eskandari, Mahnaz; Homaee, Mehdi; Mahmodi, Shahla

    2012-08-01

    Landfill site selection is a complicated multi criteria land use planning that should convince all related stakeholders with different insights. This paper addresses an integrating approach for landfill siting based on conflicting opinions among environmental, economical and socio-cultural expertise. In order to gain optimized siting decision, the issue was investigated in different viewpoints. At first step based on opinion sampling and questionnaire results of 35 experts familiar with local situations, the national environmental legislations and international practices, 13 constraints and 15 factors were built in hierarchical structure. Factors divided into three environmental, economical and socio-cultural groups. In the next step, the GIS-database was developed based on the designated criteria. In the third stage, the criteria standardization and criteria weighting were accomplished. The relative importance weights of criteria and subcriteria were estimated, respectively, using analytical hierarchy process and rank ordering methods based on different experts opinions. Thereafter, by using simple additive weighting method, the suitability maps for landfill siting in Marvdasht, Iran, was evaluated in environmental, economical and socio-cultural visions. The importance of each group of criteria in its own vision was assigned to be higher than two other groups. In the fourth stage, the final suitability map was obtained after crossing three resulted maps in different visions and reported in five suitability classes for landfill construction. This map indicated that almost 1224 ha of the study area can be considered as best suitable class for landfill siting considering all visions. In the last stage, a comprehensive field visit was performed to verify the selected site obtained from the proposed model. This field inspection has confirmed the proposed integrating approach for the landfill siting.

  16. Lentiviral-based approach for the validation of cancer therapeutic targets in vivo.

    PubMed

    Ambrogio, Chiara; Stern, Patrick; Scuoppo, Claudio; Kranz, Harald; Barbacid, Mariano; Santamaría, David

    2014-10-01

    Despite the pressing need for novel cancer treatments, our improved understanding of tumor biology is not being successfully translated into better therapies. Here we present a lentiviral vector that enables in vivo validation of cancer therapeutic targets when combined with existing cancer animal models that faithfully reproduce the natural history of human disease. Unlike the conventional genetic approaches with targeted alleles, the outlined experimental strategy could be used to assess the preclinical efficacy of a growing number of putative therapeutic hits in a rapid and cost-effective manner. PMID:25312087

  17. Resting lymphocyte transduction with measles virus glycoprotein pseudotyped lentiviral vectors relies on CD46 and SLAM

    SciTech Connect

    Zhou Qi; Schneider, Irene C.; Gallet, Manuela; Kneissl, Sabrina; Buchholz, Christian J.

    2011-05-10

    The measles virus (MV) glycoproteins hemagglutinin (H) and fusion (F) were recently shown to mediate transduction of resting lymphocytes by lentiviral vectors. MV vaccine strains use CD46 or signaling lymphocyte activation molecule (SLAM) as receptor for cell entry. A panel of H protein mutants derived from vaccine strain or wild-type MVs that lost or gained CD46 or SLAM receptor usage were investigated for their ability to mediate gene transfer into unstimulated T lymphocytes. The results demonstrate that CD46 is sufficient for efficient vector particle association with unstimulated lymphocytes. For stable gene transfer into these cells, however, both MV receptors were found to be essential.

  18. Model coupling methodology for thermo-hydro-mechanical-chemical numerical simulations in integrated assessment of long-term site behaviour

    NASA Astrophysics Data System (ADS)

    Kempka, Thomas; De Lucia, Marco; Kühn, Michael

    2015-04-01

    The integrated assessment of long-term site behaviour taking into account a high spatial resolution at reservoir scale requires a sophisticated methodology to represent coupled thermal, hydraulic, mechanical and chemical processes of relevance. Our coupling methodology considers the time-dependent occurrence and significance of multi-phase flow processes, mechanical effects and geochemical reactions (Kempka et al., 2014). Hereby, a simplified hydro-chemical coupling procedure was developed (Klein et al., 2013) and validated against fully coupled hydro-chemical simulations (De Lucia et al., 2015). The numerical simulation results elaborated for the pilot site Ketzin demonstrate that mechanical reservoir, caprock and fault integrity are maintained during the time of operation and that after 10,000 years CO2 dissolution is the dominating trapping mechanism and mineralization occurs on the order of 10 % to 25 % with negligible changes to porosity and permeability. De Lucia, M., Kempka, T., Kühn, M. A coupling alternative to reactive transport simulations for long-term prediction of chemical reactions in heterogeneous CO2 storage systems (2014) Geosci Model Dev Discuss 7:6217-6261. doi:10.5194/gmdd-7-6217-2014. Kempka, T., De Lucia, M., Kühn, M. Geomechanical integrity verification and mineral trapping quantification for the Ketzin CO2 storage pilot site by coupled numerical simulations (2014) Energy Procedia 63:3330-3338, doi:10.1016/j.egypro.2014.11.361. Klein E, De Lucia M, Kempka T, Kühn M. Evaluation of longterm mineral trapping at the Ketzin pilot site for CO2 storage: an integrative approach using geo-chemical modelling and reservoir simulation. Int J Greenh Gas Con 2013; 19:720-730. doi:10.1016/j.ijggc.2013.05.014.

  19. Role of SV40 Integration Site at Chromosomal Interval 1q21.1 in Immortalized CRL2504 Cells

    PubMed Central

    Liu, Jinglan; Kaur, Gurpreet; Zhawar, Vikramjit K.; Zimonjic, Drazen B.; Popescu, Nicholas C.; Kandpal, Raj P.; Athwal, Raghbir S.

    2009-01-01

    We have applied a functional gene transfer strategy to demonstrate the importance of viral integration site in cellular immortalization. The large tumor antigen of SV40 is capable of extending the cellular life span by sequestering tumor suppressor proteins pRB and p53 in virus-transformed human cells. Although SV40-LT is essential, it is not sufficient for cellular immortalization, suggesting that additional alterations in cellular genes are required to attain infinite proliferation. We demonstrate here that the disruption of human chromosomal interval at 1q21.1, by SV40 integration, can be an essential step for cellular immortalization. The transfer of a 150Kb bacterial artificial chromosome (BAC) clone, RP364B14, corresponding to viral integration site in CRL2504 cells, reverted their immortal phenotype. Interestingly, the BAC transfer clones of CRL-2504 cells displayed characteristics of either senescence as shown by β-galactosidase activity or apoptosis as revealed by positive staining with M30 cytoDeath antibody. The SV40 integration at 1q21.1, in the vicinity of epidermal differentiation complex genes, resulted in the down-regulation of the filaggrin (FLG) gene that is part of the epidermal differentiation complex. FLG gene expression was restored to its normal levels in BAC transfer senescent and apoptotic clones. Our results suggest that the disruption of native genomic sequence by SV40 may alter expression of genes involved in senescence and apoptosis by modulating chromatin structure. These studies imply that identification of genes located in the vicinity of viral integration sites in human cancers may be helpful in developing new diagnostic and therapeutic strategies. PMID:19789346

  20. Digital Reconstruction of AN Archaeological Site Based on the Integration of 3d Data and Historical Sources

    NASA Astrophysics Data System (ADS)

    Guidi, G.; Russo, M.; Angheleddu, D.

    2013-02-01

    The methodology proposed in this paper in based on an integrated approach for creating a 3D digital reconstruction of an archaeological site, using extensively the 3D documentation of the site in its current state, followed by an iterative interaction between archaeologists and digital modelers, leading to a progressive refinement of the reconstructive hypotheses. The starting point of the method is the reality-based model, which, together with ancient drawings and documents, is used for generating the first reconstructive step. Such rough approximation of a possible architectural structure can be annotated through archaeological considerations that has to be confronted with geometrical constraints, producing a reduction of the reconstructive hypotheses to a limited set, each one to be archaeologically evaluated. This refinement loop on the reconstructive choices is iterated until the result become convincing by both points of view, integrating in the best way all the available sources. The proposed method has been verified on the ruins of five temples in the My Son site, a wide archaeological area located in central Vietnam. The integration of 3D surveyed data and historical documentation has allowed to support a digital reconstruction of not existing architectures, developing their three-dimensional digital models step by step, from rough shapes to highly sophisticate virtual prototypes.

  1. TTP AL921102: An integrated geophysics program for non-intrusive characterization of mixed-Waste landfill sites. Final report

    SciTech Connect

    Hasbrouck, J.C.

    1993-09-01

    This Technical Task conducted for the US Department of Energy Office of Technology Development demonstrates the effectiveness of integrating several surface geophysical techniques to nonintrusively characterize mixed-waste landfill sites. An integrated approach enables an area to be characterized faster and cheaper because repeated access is not necessary and offers data and interpretations not attainable by a single technique. Field demonstrations using the complex galvanic resistivity, spontaneous potential (SP), ground-penetrating radar (GPR), time-domain electromagnetic (TDEM), shear-wave (S-wave) seismic and compressional-wave (P-wave) seismic geophysical techniques were conducted at the Mixed-Waste Landfill Integrated Demonstration (MWLID) test site at the Sandia National Laboratories/New Mexico in Albuquerque. Data were acquired in two areas that have both known and unknown attributes. Although data from numerous profiles were analyzed, three lines were chosen as representative of the landfill site: Line 20E that crosses both the known Chromic Acid and Organics Pits, Line 60E that transectes an essentially barren area, and Line 125E located in an area with unknown subsurface conditions.

  2. Hybrid Lentivirus-phiC31-int-NLS Vector Allows Site-Specific Recombination in Murine and Human Cells but Induces DNA Damage

    PubMed Central

    Grandchamp, Nicolas; Altémir, Dorothée; Philippe, Stéphanie; Ursulet, Suzanna; Pilet, Héloïse; Serre, Marie-Claude; Lenain, Aude; Serguera, Che; Mallet, Jacques; Sarkis, Chamsy

    2014-01-01

    Gene transfer allows transient or permanent genetic modifications of cells for experimental or therapeutic purposes. Gene delivery by HIV-derived lentiviral vector (LV) is highly effective but the risk of insertional mutagenesis is important and the random/uncontrollable integration of the DNA vector can deregulate the cell transcriptional activity. Non Integrative Lentiviral Vectors (NILVs) solve this issue in non-dividing cells, but they do not allow long term expression in dividing cells. In this context, obtaining stable expression while avoiding the problems inherent to unpredictable DNA vector integration requires the ability to control the integration site. One possibility is to use the integrase of phage phiC31 (phiC31-int) which catalyzes efficient site-specific recombination between the attP site in the phage genome and the chromosomal attB site of its Streptomyces host. Previous studies showed that phiC31-int is active in many eukaryotic cells, such as murine or human cells, and directs the integration of a DNA substrate into pseudo attP sites (pattP) which are homologous to the native attP site. In this study, we combined the efficiency of NILV for gene delivery and the specificity of phiC31-int for DNA substrate integration to engineer a hybrid tool for gene transfer with the aim of allowing long term expression in dividing and non-dividing cells preventing genotoxicity. We demonstrated the feasibility to target NILV integration in human and murine pattP sites with a dual NILV vectors system: one which delivers phiC31-int, the other which constitute the substrate containing an attB site in its DNA sequence. These promising results are however alleviated by the occurrence of significant DNA damages. Further improvements are thus required to prevent chromosomal rearrangements for a therapeutic use of the system. However, its use as a tool for experimental applications such as transgenesis is already applicable. PMID:24956106

  3. Hybrid lentivirus-phiC31-int-NLS vector allows site-specific recombination in murine and human cells but induces DNA damage.

    PubMed

    Grandchamp, Nicolas; Altémir, Dorothée; Philippe, Stéphanie; Ursulet, Suzanna; Pilet, Héloïse; Serre, Marie-Claude; Lenain, Aude; Serguera, Che; Mallet, Jacques; Sarkis, Chamsy

    2014-01-01

    Gene transfer allows transient or permanent genetic modifications of cells for experimental or therapeutic purposes. Gene delivery by HIV-derived lentiviral vector (LV) is highly effective but the risk of insertional mutagenesis is important and the random/uncontrollable integration of the DNA vector can deregulate the cell transcriptional activity. Non Integrative Lentiviral Vectors (NILVs) solve this issue in non-dividing cells, but they do not allow long term expression in dividing cells. In this context, obtaining stable expression while avoiding the problems inherent to unpredictable DNA vector integration requires the ability to control the integration site. One possibility is to use the integrase of phage phiC31 (phiC31-int) which catalyzes efficient site-specific recombination between the attP site in the phage genome and the chromosomal attB site of its Streptomyces host. Previous studies showed that phiC31-int is active in many eukaryotic cells, such as murine or human cells, and directs the integration of a DNA substrate into pseudo attP sites (pattP) which are homologous to the native attP site. In this study, we combined the efficiency of NILV for gene delivery and the specificity of phiC31-int for DNA substrate integration to engineer a hybrid tool for gene transfer with the aim of allowing long term expression in dividing and non-dividing cells preventing genotoxicity. We demonstrated the feasibility to target NILV integration in human and murine pattP sites with a dual NILV vectors system: one which delivers phiC31-int, the other which constitute the substrate containing an attB site in its DNA sequence. These promising results are however alleviated by the occurrence of significant DNA damages. Further improvements are thus required to prevent chromosomal rearrangements for a therapeutic use of the system. However, its use as a tool for experimental applications such as transgenesis is already applicable. PMID:24956106

  4. Distribution and integrated assessment of lead in an abandoned lead-acid battery site in Southwest China before redevelopment.

    PubMed

    Wang, Mei; Zhang, Chao; Zhang, Zhuo; Li, Fasheng; Guo, Guanlin

    2016-06-01

    Lead-acid battery sites have contributed enormous amounts of lead to the environment, significantly affecting its global biogeochemical cycle and leaving the potential risks to human health. An abandoned lead-acid battery site prepared for redevelopment was selected in order to study the distribution of lead in soils, plants, rhizosphere soils and soil solutions. In total, 197 samples from 77 boreholes were collected and analyzed. Single extractions by acetic acid (HOAc) were conducted to assess the bioavailability and speciation of lead in soils for comparison with the parts of the plants that are aboveground. Health risks for future residential development were evaluated by the integrated exposure uptake biokinetic (IEUBK) model. The results indicated that lead concentrations in 83% of the soil samples exceeded the Chinese Environmental Quality Standard for soil (350 mg/kg for Pb) and mainly occurred at depths between 0 and 1.5 m while accumulating at the surface of demolished construction waste and miscellaneous fill. Lead concentrations in soil solutions and HOAc extraction leachates were linked closely to the contents of aboveground Broussonetia papyrifera and Artemisia annua, two main types of local plants that were found at the site. The probability density of lead in blood (PbB) in excess of 10 µg/dL could overtake the 99% mark in the residential scenario. The findings provided a relatively integrated method to illustrate the onsite investigations and assessment for similar sites before remediation and future development from more comprehensive aspects.

  5. Development of an Integrated Natural Barrier Database System for Site Evaluation of a Deep Geologic Repository in Korea - 13527

    SciTech Connect

    Jung, Haeryong; Lee, Eunyong; Jeong, YiYeong; Lee, Jeong-Hwan

    2013-07-01

    Korea Radioactive-waste Management Corporation (KRMC) established in 2009 has started a new project to collect information on long-term stability of deep geological environments on the Korean Peninsula. The information has been built up in the integrated natural barrier database system available on web (www.deepgeodisposal.kr). The database system also includes socially and economically important information, such as land use, mining area, natural conservation area, population density, and industrial complex, because some of this information is used as exclusionary criteria during the site selection process for a deep geological repository for safe and secure containment and isolation of spent nuclear fuel and other long-lived radioactive waste in Korea. Although the official site selection process has not been started yet in Korea, current integrated natural barrier database system and socio-economic database is believed that the database system will be effectively utilized to narrow down the number of sites where future investigation is most promising in the site selection process for a deep geological repository and to enhance public acceptance by providing readily-available relevant scientific information on deep geological environments in Korea. (authors)

  6. Distribution and integrated assessment of lead in an abandoned lead-acid battery site in Southwest China before redevelopment.

    PubMed

    Wang, Mei; Zhang, Chao; Zhang, Zhuo; Li, Fasheng; Guo, Guanlin

    2016-06-01

    Lead-acid battery sites have contributed enormous amounts of lead to the environment, significantly affecting its global biogeochemical cycle and leaving the potential risks to human health. An abandoned lead-acid battery site prepared for redevelopment was selected in order to study the distribution of lead in soils, plants, rhizosphere soils and soil solutions. In total, 197 samples from 77 boreholes were collected and analyzed. Single extractions by acetic acid (HOAc) were conducted to assess the bioavailability and speciation of lead in soils for comparison with the parts of the plants that are aboveground. Health risks for future residential development were evaluated by the integrated exposure uptake biokinetic (IEUBK) model. The results indicated that lead concentrations in 83% of the soil samples exceeded the Chinese Environmental Quality Standard for soil (350 mg/kg for Pb) and mainly occurred at depths between 0 and 1.5 m while accumulating at the surface of demolished construction waste and miscellaneous fill. Lead concentrations in soil solutions and HOAc extraction leachates were linked closely to the contents of aboveground Broussonetia papyrifera and Artemisia annua, two main types of local plants that were found at the site. The probability density of lead in blood (PbB) in excess of 10 µg/dL could overtake the 99% mark in the residential scenario. The findings provided a relatively integrated method to illustrate the onsite investigations and assessment for similar sites before remediation and future development from more comprehensive aspects. PMID:26921546

  7. Development of Site-Specific Soil Design Basis Earthquake (DBE) Parameters for the Integrated Waste Treatment Unit (IWTU)

    SciTech Connect

    Payne, Suzette

    2008-08-01

    Horizontal and vertical PC 3 (2,500 yr) Soil Design Basis Earthquake (DBE) 5% damped spectra, corresponding time histories, and strain-compatible soil properties were developed for the Integrated Waste Treatment Unit (IWTU). The IWTU is located at the Idaho Nuclear Technology and Engineering Center (INTEC) at the Idaho National Laboratory (INL). Mean and 84th percentile horizontal DBE spectra derived from site-specific site response analyses were evaluated for the IWTU. The horizontal and vertical PC 3 (2,500 yr) Soil DBE 5% damped spectra at the 84th percentile were selected for Soil Structure Interaction (SSI) analyses at IWTU. The site response analyses were performed consistent with applicable Department of Energy (DOE) Standards, recommended guidance of the Nuclear Regulatory Commission (NRC), American Society of Civil Engineers (ASCE) Standards, and recommendations of the Blue Ribbon Panel (BRP) and Defense Nuclear Facilities Safety Board (DNFSB).

  8. The gravity of pollination: integrating at-site features into spatial analysis of contemporary pollen movement.

    PubMed

    DiLeo, Michelle F; Siu, Jenna C; Rhodes, Matthew K; López-Villalobos, Adriana; Redwine, Angela; Ksiazek, Kelly; Dyer, Rodney J

    2014-08-01

    Pollen-mediated gene flow is a major driver of spatial genetic structure in plant populations. Both individual plant characteristics and site-specific features of the landscape can modify the perceived attractiveness of plants to their pollinators and thus play an important role in shaping spatial genetic variation. Most studies of landscape-level genetic connectivity in plants have focused on the effects of interindividual distance using spatial and increasingly ecological separation, yet have not incorporated individual plant characteristics or other at-site ecological variables. Using spatially explicit simulations, we first tested the extent to which the inclusion of at-site variables influencing local pollination success improved the statistical characterization of genetic connectivity based upon examination of pollen pool genetic structure. The addition of at-site characteristics provided better models than those that only considered interindividual spatial distance (e.g. IBD). Models parameterized using conditional genetic covariance (e.g. population graphs) also outperformed those assuming panmixia. In a natural population of Cornus florida L. (Cornaceae), we showed that the addition of at-site characteristics (clumping of primary canopy opening above each maternal tree and maternal tree floral output) provided significantly better models describing gene flow than models including only between-site spatial (IBD) and ecological (isolation by resistance) variables. Overall, our results show that including interindividual and local ecological variation greatly aids in characterizing landscape-level measures of contemporary gene flow.

  9. Design and in vitro characterization of a single regulatory module for efficient control of gene expression in both plasmid DNA and a self-inactivating lentiviral vector.

    PubMed Central

    Ogueta, S. B.; Yao, F.; Marasco, W. A.

    2001-01-01

    BACKGROUND: Regulation of transgene expression in target cells represents a critical and challenging aspect of gene therapy. Recently, a two-plasmid tetracycline-inducible system was developed in which the tetracycline repressor (tetR) alone, rather than the tetR-VP16 fusion derivative, was shown to function as a potent trans-modulator of a second plasmid that contains two tandem repeats of the tetracycline operator (tetO) inserted between the TATA box and the transcription start site of the hCMV major immediate-early promoter. A technological advance in this area would be the development of a single autoregulatory cassette that incorporates both of these components into nonviral and viral gene transfer vectors. For the latter, an inducible lentiviral vector that is capable of temporal and quantitative control of gene expression in either dividing or nondividing cells is highly desirable. MATERIALS AND METHODS: A one-piece inducible (1Pi) autoregulatory cassette was constructed to provide IRES-mediated translation of the tetR as well as tight control over the tetO unit preventing transcription initiation of the first cistron in the absence of the tetracycline. To increase efficiency of tetR-mediated repression, a nuclear localization signal was incorporated at the 3' end of the tetR gene. Regulation of gene expression at the transcriptional and protein level was analyzed in transient transfection experiments using plasmid DNA. Construction of a self-inactivating lentiviral vector containing this 1Pi cassette allowed the study of its long-term effectiveness in primary human cells. RESULTS: The 1Pi autoregulatory cassette when incorporated into plasmid DNA allows efficient control of the secretable hEGF as well as eGFP expression in a variety of cell types. Transient transfection studies demonstrated that the time course of repression is different for the 1Pi and two-plasmid system (2Pi). In the 2Pi system, greater repression is seen with the first 24-48 hr; however

  10. Optimization of lentiviral vectors generation for biomedical and clinical research purposes: contemporary trends in technology development and applications.

    PubMed

    Kumar, Pankaj; Woon-Khiong, Chan

    2011-04-01

    Classical non-viral methods of gene transfer, such as chemical transfection, have met with limited success of instillation of genetic material into non-proliferating cells in vitro. Among the different kinds of viral vectors, Lentiviral vectors (LVs) have emerged as robust and versatile tool for ex vivo and in vivo gene delivery into multiple cell types including non-dividing cells such as neurons. The capacity of LVs to maintain stable, long-term transgene expression and the substantial flexibility in the design of the expression cassettes account for their increasing use in various pre-clinical and clinical applications. Additionally, LVs have been hugely successful in reprogramming induced pluripotent stem cells (iPSCs). Recent development using LVs in conjunction with a Cre-Lox based reversible system has opened up many new possibilities towards therapeutic application of iPSC technology in various clinical settings. Moreover, improvements in term of biosafety and efficacy, achieved either by modifying the vector design or by involving integration-deficient LVs (IDLVs), have important implications for adoption of LV as the vector of choice for clinical trials. Several human gene therapy clinical trials evaluating the use of LVs for treatment: of human diseases such as Parkinson's disease, β-thalassemia, X-linked adrenoleukodystrophy (ALD), and AIDS are currently ongoing. This review will describe the state of the art achieved by LV technology, its impact on biomedical research, and implications to human clinical trials as therapeutic gene delivery vehicle for a wide range of infectious and genetic diseases.

  11. Decitabine suspends human CD34+ cell differentiation and proliferation during lentiviral transduction.

    PubMed

    Uchida, Naoya; Hsieh, Matthew M; Platner, Charlotte; Saunthararajah, Yogen; Tisdale, John F

    2014-01-01

    Efficient ex vivo transduction of hematopoietic stem cells (HSCs) is encumbered by differentiation which reduces engraftment. We hypothesized that inhibiting DNA methyltransferase with decitabine would block differentiation of transduced CD34+ cells under cytokine stimulation and thus improve transduction efficiency for engrafting HSCs. Human CD34+ cells in cytokine-containing media were treated with or without decitabine for 24 or 48 hours, and then these cells were transduced with a GFP-expressing lentiviral vector. Utilizing decitabine pre-treatment for 48 hours, we observed an equivalent percentage of successfully transduced cells (GFP-positivity) and a higher percentage of cells that retained CD34 positivity, compared to no decitabine exposure. Cell proliferation was inhibited after decitabine exposure. Similar results were observed among CD34+ cells from six different donors. Repopulating activity was evaluated by transplantation into NOD/SCID/IL2Rγnull mice and demonstrated an equivalent percentage of GFP-positivity in human cells from decitabine-treated samples and a trend for higher human cell engraftment (measured 20-24 weeks after transplantation), compared to no decitabine exposure. In conclusion, ex vivo decitabine exposure inhibits both differentiation and proliferation in transduced human CD34+ cells and modestly increases the engraftment ability in xenograft mice, while the transduction efficiency is equivalent in decitabine exposure, suggesting improvement of lentiviral transduction for HSCs.

  12. Comparative analysis of lentiviral vectors and modular protein nanovectors for traumatic brain injury gene therapy

    PubMed Central

    Negro-Demontel, María Luciana; Saccardo, Paolo; Giacomini, Cecilia; Yáñez-Muñoz, Rafael Joaquín; Ferrer-Miralles, Neus; Vazquez, Esther; Villaverde, Antonio; Peluffo, Hugo

    2014-01-01

    Traumatic brain injury (TBI) remains as one of the leading causes of mortality and morbidity worldwide and there are no effective treatments currently available. Gene therapy applications have emerged as important alternatives for the treatment of diverse nervous system injuries. New strategies are evolving with the notion that each particular pathological condition may require a specific vector. Moreover, the lack of detailed comparative studies between different vectors under similar conditions hampers the selection of an ideal vector for a given pathological condition. The potential use of lentiviral vectors versus several modular protein-based nanovectors was compared using a controlled cortical impact model of TBI under the same gene therapy conditions. We show that variables such as protein/DNA ratio, incubation volume, and presence of serum or chloroquine in the transfection medium impact on both nanovector formation and transfection efficiency in vitro. While lentiviral vectors showed GFP protein 1 day after TBI and increased expression at 14 days, nanovectors showed stable and lower GFP transgene expression from 1 to 14 days. No toxicity after TBI by any of the vectors was observed as determined by resulting levels of IL-1β or using neurological sticky tape test. In fact, both vector types induced functional improvement per se. PMID:26015985

  13. Lentiviral transgenesis in mice via a simple method of viral concentration.

    PubMed

    Cheng, Pei-Hsun; Chang, Yu-Fan; Mao, Su-Han; Lin, Hsiu-Lien; Chen, Chuan-Mu; Yang, Shang-Hsun

    2016-10-01

    Transgenic animals are important in vivo models for biological research. However, low transgenic rates are commonly reported in the literature. Lentiviral transgenesis is a promising method that has greater efficiency with regard to generating transgenic animals, although the transgenic rate of this approach is highly dependent on different transgenes and concentrated lentiviruses. In this study, we modified a method to concentrate lentiviruses using a table centrifuge, commonly available in most laboratories, and carried out analysis of the transgenic efficiency in mice. Based on 26 individual constructs and 627 live pups, we found that the overall transgenic rate was more than 30%, which is higher than obtained with pronuclear microinjection. In addition, we did not find any significant differences in transgenic efficiency when the size of inserts was less than 5000 bp. These results not only show that our modified method can successfully generate transgenic mice but also suggest that this approach could be generally applied to different constructs when the size of inserts is less than 5000 bp. It is anticipated that the results of this study can help encourage the wider laboratory use of lentiviral transgenesis in mice. PMID:27264740

  14. Expression Profiles of Vpx/Vpr Proteins Are Co-related with the Primate Lentiviral Lineage

    PubMed Central

    Sakai, Yosuke; Miyake, Ariko; Doi, Naoya; Sasada, Hikari; Miyazaki, Yasuyuki; Adachi, Akio; Nomaguchi, Masako

    2016-01-01

    Viruses of human immunodeficiency virus type 2 (HIV-2) and some simian immunodeficiency virus (SIV) lineages carry a unique accessory protein called Vpx. Vpx is essential or critical for viral replication in natural target cells such as macrophages and T lymphocytes. We have previously shown that a poly-proline motif (PPM) located at the C-terminal region of Vpx is required for its efficient expression in two strains of HIV-2 and SIVmac, and that the Vpx expression levels of the two clones are significantly different. Notably, the PPM sequence is conserved and confined to Vpx and Vpr proteins derived from certain lineages of HIV-2/SIVs. In this study, Vpx/Vpr proteins from diverse primate lentiviral lineages were experimentally and phylogenetically analyzed to obtain the general expression picture in cells. While both the level and PPM-dependency of Vpx/Vpr expression in transfected cells varied among viral strains, each viral group, based on Vpx/Vpr amino acid sequences, was found to exhibit a characteristic expression profile. Moreover, phylogenetic tree analyses on Gag and Vpx/Vpr proteins gave essentially the same results. Taken together, our study described here suggests that each primate lentiviral lineage may have developed a unique expression pattern of Vpx/Vpr proteins for adaptation to its hostile cellular and species environments in the process of viral evolution. PMID:27536295

  15. Tumor Therapy Mediated by Lentiviral Expression of shBcl-2 and S-TRAIL1

    PubMed Central

    Kock, Norman; Kasmieh, Randa; Weissleder, Ralph; Shah, Khalid

    2007-01-01

    Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) can selectively kill tumor cells and, in combination with other agents, could enhance tumor therapy. We explored the combined therapeutic effects of a secretable form of (S) TRAIL-induced apoptosis and the downregulation of Bcl-2 in human gliomas. We constructed a lentiviral delivery system: 1) for the expression of short hairpin (sh) RNA to downregulate Bcl-2 and for the expression of S-TRAIL to induce apoptosis in glioma cells; and 2) to follow delivery in vitro and the fate of tumors in real time in vivo. We demonstrate that lentiviral-mediated simultaneous downregulation of Bcl-2 and S-TRAIL-induced apoptosis leads to an increased expression of activated caspase-3 and caspase-7, thus resulting in accelerated S-TRAIL-mediated apoptosis in glioma cells in vitro. Using a highly malignant human glioma model expressing EGFRvIII and firefly luciferase, we show that the combined effect of Bcl-2 downregulation and S-TRAIL-induced apoptosis results in complete eradication of gliomas compared to S-TRAIL monotherapy. These results show that simultaneous triggering of TRAIL-mediated death receptor pathway and downregulation of Bcl-2 by shRNA leads to enhanced eradication of gliomas and serves as a template in developing and monitoring combination therapies for the treatment of drug-resistant cancers. PMID:17534449

  16. RNAi technology and lentiviral delivery as a powerful tool to suppress Tpr-Met-mediated tumorigenesis.

    PubMed

    Taulli, Riccardo; Accornero, Paolo; Follenzi, Antonia; Mangano, Tony; Morotti, Alessandro; Scuoppo, Claudio; Forni, Paolo E; Bersani, Francesca; Crepaldi, Tiziana; Chiarle, Roberto; Naldini, Luigi; Ponzetto, Carola

    2005-05-01

    Tpr-Met, the oncogenic counterpart of the Met receptor, has been detected in gastric cancers, as well as in precursor lesions and in the adjacent normal gastric mucosa. This has prompted the suggestion that Tpr-Met may predispose to the development of gastric tumors. Given the sequence specificity of RNA interference, oncogenes activated by point mutation or rearrangements can be targeted while spearing the product of the wild-type allele. In this work, we report specific suppression of Tpr-Met expression and inhibition of Tpr-Met-mediated transformation and tumorigenesis by means of a short interfering RNA (siRNA) directed toward the Tpr-Met junction (anti-TM2). When delivered by a lentiviral vector, anti-TM2 siRNA was effective also in mouse embryonal fibroblasts or epithelial cells expressing high levels of Tpr-Met. Our results suggest that lentiviral-mediated delivery of anti-TM2 siRNA may be developed into a powerful tool to treat Tpr-Met-positive cancers.

  17. Genetic engineering of cell lines using lentiviral vectors to achieve antibody secretion following encapsulated implantation.

    PubMed

    Lathuilière, Aurélien; Bohrmann, Bernd; Kopetzki, Erhard; Schweitzer, Christoph; Jacobsen, Helmut; Moniatte, Marc; Aebischer, Patrick; Schneider, Bernard L

    2014-01-01

    The controlled delivery of antibodies by immunoisolated bioimplants containing genetically engineered cells is an attractive and safe approach for chronic treatments. To reach therapeutic antibody levels there is a need to generate renewable cell lines, which can long-term survive in macroencapsulation devices while maintaining high antibody specific productivity. Here we have developed a dual lentiviral vector strategy for the genetic engineering of cell lines compatible with macroencapsulation, using separate vectors encoding IgG light and heavy chains. We show that IgG expression level can be maximized as a function of vector dose and transgene ratio. This approach allows for the generation of stable populations of IgG-expressing C2C12 mouse myoblasts, and for the subsequent isolation of clones stably secreting high IgG levels. Moreover, we demonstrate that cell transduction using this lentiviral system leads to the production of a functional glycosylated antibody by myogenic cells. Subsequent implantation of antibody-secreting cells in a high-capacity macroencapsulation device enables continuous delivery of recombinant antibodies in the mouse subcutaneous tissue, leading to substantial levels of therapeutic IgG detectable in the plasma.

  18. Highly Efficient Large-Scale Lentiviral Vector Concentration by Tandem Tangential Flow Filtration

    PubMed Central

    Cooper, Aaron R.; Patel, Sanjeet; Senadheera, Shantha; Plath, Kathrin; Kohn, Donald B.; Hollis, Roger P.

    2014-01-01

    Large-scale lentiviral vector (LV) concentration can be inefficient and time consuming, often involving multiple rounds of filtration and centrifugation. This report describes a simpler method using two tangential flow filtration (TFF) steps to concentrate liter-scale volumes of LV supernatant, achieving in excess of 2000-fold concentration in less than 3 hours with very high recovery (>97%). Large volumes of LV supernatant can be produced easily through the use of multi-layer flasks, each having 1720 cm2 surface area and producing ~560 mL of supernatant per flask. Combining the use of such flasks and TFF greatly simplifies large-scale production of LV. As a demonstration, the method is used to produce a very high titer LV (>1010 TU/mL) and transduce primary human CD34+ hematopoietic stem/progenitor cells at high final vector concentrations with no overt toxicity. A complex LV (STEMCCA) for induced pluripotent stem cell generation is also concentrated from low initial titer and used to transduce and reprogram primary human fibroblasts with no overt toxicity. Additionally, a generalized and simple multiplexed real- time PCR assay is described for lentiviral vector titer and copy number determination. PMID:21784103

  19. Lentiviral-mediated Genetic Correction of Hematopoietic and Mesenchymal Progenitor Cells From Fanconi Anemia Patients

    PubMed Central

    Jacome, Ariana; Navarro, Susana; Río, Paula; Yañez, Rosa M; González-Murillo, Africa; Luz Lozano, M; Lamana, Maria Luisa; Sevilla, Julian; Olive, Teresa; Diaz-Heredia, Cristina; Badell, Isabel; Estella, Jesus; Madero, Luis; Guenechea, Guillermo; Casado, José; Segovia, Jose C; Bueren, Juan A

    2009-01-01

    Previous clinical trials based on the genetic correction of purified CD34+ cells with γ-retroviral vectors have demonstrated clinical efficacy in different monogenic diseases, including X-linked severe combined immunodeficiency, adenosine deaminase deficient severe combined immunodeficiency and chronic granulomatous disease. Similar protocols, however, failed to engraft Fanconi anemia (FA) patients with genetically corrected cells. In this study, we first aimed to correlate the hematological status of 27 FA patients with CD34+ cell values determined in their bone marrow (BM). Strikingly, no correlation between these parameters was observed, although good correlations were obtained when numbers of colony-forming cells (CFCs) were considered. Based on these results, and because purified FA CD34+ cells might have suboptimal repopulating properties, we investigated the possibility of genetically correcting unselected BM samples from FA patients. Our data show that the lentiviral transduction of unselected FA BM cells mediates an efficient phenotypic correction of hematopoietic progenitor cells and also of CD34− mesenchymal stromal cells (MSCs), with a reported role in hematopoietic engraftment. Our results suggest that gene therapy protocols appropriate for the treatment of different monogenic diseases may not be adequate for stem cell diseases like FA. We propose a new approach for the gene therapy of FA based on the rapid transduction of unselected hematopoietic grafts with lentiviral vectors (LVs). PMID:19277017

  20. A minimally invasive, lentiviral based method for the rapid and sustained genetic manipulation of renal tubules.

    PubMed

    Espana-Agusti, Judit; Tuveson, David A; Adams, David J; Matakidou, Athena

    2015-01-01

    The accelerated discovery of disease-related genes emerging from genomic studies has strained the capacity of traditional genetically engineered mouse models (GEMMs) to provide in-vivo validation. Direct, somatic, genetic engineering approaches allow for accelerated and flexible genetic manipulation and represent an attractive alternative to GEMMs. In this study we investigated the feasibility, safety and efficiency of a minimally invasive, lentiviral based approach for the sustained in-vivo modification of renal tubular epithelial cells. Using ultrasound guidance, reporter vectors were directly injected into the mouse renal parenchyma. We observed transgene expression confined to the renal cortex (specifically proximal and distal tubules) and sustained beyond 2 months post injection. Furthermore, we demonstrate the ability of this methodology to induce long-term, in-vivo knockdown of candidate genes either through somatic recombination of floxed alleles or by direct delivery of specific shRNA sequences. This study demonstrates that ultrasound-guided injection of lentiviral vectors provides a safe and efficient method for the genetic manipulation of renal tubules, representing a quick and versatile alternative to GEMMs for the functional characterisation of disease-related genes. PMID:26046460

  1. Engineering Cellular Resistance to HIV-1 Infection In Vivo Using a Dual Therapeutic Lentiviral Vector.

    PubMed

    Burke, Bryan P; Levin, Bernard R; Zhang, Jane; Sahakyan, Anna; Boyer, Joshua; Carroll, Maria V; Colón, Joanna Camba; Keech, Naomi; Rezek, Valerie; Bristol, Gregory; Eggers, Erica; Cortado, Ruth; Boyd, Maureen P; Impey, Helen; Shimizu, Saki; Lowe, Emily L; Ringpis, Gene-Errol E; Kim, Sohn G; Vatakis, Dimitrios N; Breton, Louis R; Bartlett, Jeffrey S; Chen, Irvin S Y; Kitchen, Scott G; An, Dong Sung; Symonds, Geoff P

    2015-01-01

    We described earlier a dual-combination anti-HIV type 1 (HIV-1) lentiviral vector (LVsh5/C46) that downregulates CCR5 expression of transduced cells via RNAi and inhibits HIV-1 fusion via cell surface expression of cell membrane-anchored C46 antiviral peptide. This combinatorial approach has two points of inhibition for R5-tropic HIV-1 and is also active against X4-tropic HIV-1. Here, we utilize the humanized bone marrow, liver, thymus (BLT) mouse model to characterize the in vivo efficacy of LVsh5/C46 (Cal-1) vector to engineer cellular resistance to HIV-1 pathogenesis. Human CD34+ hematopoietic stem/progenitor cells (HSPC) either nonmodified or transduced with LVsh5/C46 vector were transplanted to generate control and treatment groups, respectively. Control and experimental groups displayed similar engraftment and multilineage hematopoietic differentiation that included robust CD4+ T-cell development. Splenocytes isolated from the treatment group were resistant to both R5- and X4-tropic HIV-1 during ex vivo challenge experiments. Treatment group animals challenged with R5-tropic HIV-1 displayed significant protection of CD4+ T-cells and reduced viral load within peripheral blood and lymphoid tissues up to 14 weeks postinfection. Gene-marking and transgene expression were confirmed stable at 26 weeks post-transplantation. These data strongly support the use of LVsh5/C46 lentiviral vector in gene and cell therapeutic applications for inhibition of HIV-1 infection. PMID:25872029

  2. DNA transposition by protein transduction of the piggyBac transposase from lentiviral Gag precursors

    PubMed Central

    Cai, Yujia; Bak, Rasmus O.; Krogh, Louise Bechmann; Staunstrup, Nicklas H.; Moldt, Brian; Corydon, Thomas J.; Schrøder, Lisbeth Dahl; Mikkelsen, Jacob Giehm

    2014-01-01

    DNA transposon-based vectors have emerged as gene vehicles with a wide biomedical and therapeutic potential. So far, genomic insertion of such vectors has relied on the co-delivery of genetic material encoding the gene-inserting transposase protein, raising concerns related to persistent expression, insertional mutagenesis and cytotoxicity. This report describes potent DNA transposition achieved by direct delivery of transposase protein. By adapting integrase-deficient lentiviral particles (LPs) as carriers of the hyperactive piggyBac transposase protein (hyPBase), we demonstrate rates of DNA transposition that are comparable with the efficiency of a conventional plasmid-based strategy. Embedded in the Gag polypeptide, hyPBase is robustly incorporated into LPs and liberated from the viral proteins by the viral protease during particle maturation. We demonstrate lentiviral co-delivery of the transposase protein and vector RNA carrying the transposon sequence, allowing robust DNA transposition in a variety of cell types. Importantly, this novel delivery method facilitates a balanced cellular uptake of hyPBase, as shown by confocal microscopy, and allows high-efficiency production of clones harboring a single transposon insertion. Our findings establish engineered LPs as a new tool for transposase delivery. We believe that protein transduction methods will increase applicability and safety of DNA transposon-based vector technologies. PMID:24270790

  3. Lentiviral gene therapy using cellular promoters cures type 1 Gaucher disease in mice.

    PubMed

    Dahl, Maria; Doyle, Alexander; Olsson, Karin; Månsson, Jan-Eric; Marques, André R A; Mirzaian, Mina; Aerts, Johannes M; Ehinger, Mats; Rothe, Michael; Modlich, Ute; Schambach, Axel; Karlsson, Stefan

    2015-05-01

    Gaucher disease is caused by an inherited deficiency of the enzyme glucosylceramidase. Due to the lack of a fully functional enzyme, there is progressive build-up of the lipid component glucosylceramide. Insufficient glucosylceramidase activity results in hepatosplenomegaly, cytopenias, and bone disease in patients. Gene therapy represents a future therapeutic option for patients unresponsive to enzyme replacement therapy and lacking a suitable bone marrow donor. By proof-of-principle experiments, we have previously demonstrated a reversal of symptoms in a murine disease model of type 1 Gaucher disease, using gammaretroviral vectors harboring strong viral promoters to drive glucosidase β-acid (GBA) gene expression. To investigate whether safer vectors can correct the enzyme deficiency, we utilized self-inactivating lentiviral vectors (SIN LVs) with the GBA gene under the control of human phosphoglycerate kinase (PGK) and CD68 promoter, respectively. Here, we report prevention of, as well as reversal of, manifest disease symptoms after lentiviral gene transfer. Glucosylceramidase activity above levels required for clearance of glucosylceramide from tissues resulted in reversal of splenomegaly, reduced Gaucher cell infiltration and a restoration of hematological parameters. These findings support the use of SIN-LVs with cellular promoters in future clinical gene therapy protocols for type 1 Gaucher disease.

  4. Development of a Multipurpose GATEWAY-Based Lentiviral Tetracycline-Regulated Conditional RNAi System (GLTR)

    PubMed Central

    Shivalingaiah, Giridhar; Kofler, Reinhard; Geley, Stephan

    2014-01-01

    RNA interference (RNAi) has become an essential technology for functional gene analysis. Its success, however, depends on the effective expression of RNAi-inducing small double-stranded interfering RNA molecules (siRNAs) in target cells. In many cell types, RNAi can be achieved by transfection of chemically synthesised siRNAs, which results in transient knockdown of protein expression. Expression of double-stranded short hairpin RNA (shRNA) provides another means to induce RNAi in cells that are hard to transfect. To facilitate the generation of stable, conditional RNAi cell lines, we have developed novel one- and two-component vector GATEWAY-compatible lentiviral tetracycline-regulated RNAi (GLTR) systems. The combination of a modified RNA-polymerase-III-dependent H1 RNA promoter (designated ‘THT’) for conditional shRNA expression with different lentiviral delivery vectors allows (1) the use of fluorescent proteins for colour-coded combinatorial RNAi or for monitoring RNAi induction (pGLTR-FP), (2) selection of transduced cells (pGLTR-S), and (3) the generation of conditional cell lines using a one vector system (pGLTR-X). All three systems were found to be suitable for the analysis of essential genes, such as CDC27, a component of the mitotic ubiquitin ligase APC/C, in cell lines and primary human cells. PMID:24841113

  5. Lentiviral gene therapy using cellular promoters cures type 1 Gaucher disease in mice.

    PubMed

    Dahl, Maria; Doyle, Alexander; Olsson, Karin; Månsson, Jan-Eric; Marques, André R A; Mirzaian, Mina; Aerts, Johannes M; Ehinger, Mats; Rothe, Michael; Modlich, Ute; Schambach, Axel; Karlsson, Stefan

    2015-05-01

    Gaucher disease is caused by an inherited deficiency of the enzyme glucosylceramidase. Due to the lack of a fully functional enzyme, there is progressive build-up of the lipid component glucosylceramide. Insufficient glucosylceramidase activity results in hepatosplenomegaly, cytopenias, and bone disease in patients. Gene therapy represents a future therapeutic option for patients unresponsive to enzyme replacement therapy and lacking a suitable bone marrow donor. By proof-of-principle experiments, we have previously demonstrated a reversal of symptoms in a murine disease model of type 1 Gaucher disease, using gammaretroviral vectors harboring strong viral promoters to drive glucosidase β-acid (GBA) gene expression. To investigate whether safer vectors can correct the enzyme deficiency, we utilized self-inactivating lentiviral vectors (SIN LVs) with the GBA gene under the control of human phosphoglycerate kinase (PGK) and CD68 promoter, respectively. Here, we report prevention of, as well as reversal of, manifest disease symptoms after lentiviral gene transfer. Glucosylceramidase activity above levels required for clearance of glucosylceramide from tissues resulted in reversal of splenomegaly, reduced Gaucher cell infiltration and a restoration of hematological parameters. These findings support the use of SIN-LVs with cellular promoters in future clinical gene therapy protocols for type 1 Gaucher disease. PMID:25655314

  6. Characterization and biodistribution of human mesenchymal stem cells transduced with lentiviral-mediated BMP2.

    PubMed

    Choi, Kyoung Suk; Ahn, Soon Young; Kim, Tek Seung; Kim, Jiseon; Kim, Byoung-Guk; Han, Kyung Ho; Ban, Sang Ja; Kim, Hyung Soo; Choi, Youngju; Lim, Chul-Joo

    2011-04-01

    Recently, the genetic modification of mesenchymal stem cells (MSCs) has led to increased differentiation potential. For the therapeutic application of genetically modified MSCs, it is crucial to evaluate their characteristics and safety. In this study, we investigated the effects of bone morphogenetic protein 2 (BMP2) gene transfer on the characteristics and biodistribution of human MSCs. Lentiviral-mediated BMP2 transduction to MSCs enhanced osteocyte differentiation and decreased adipocyte differentiation. Although there is no significant difference in cell proliferation capacity, MSCs transduced BMP2 proliferate somewhat higher than nontransduced or GFP transduced MSCs. No significant changes were observed in surface antigen expression in genetically modified MSCs. In vivo transplantation of lentiviral-mediated BMP2 gene transferred MSCs to nude mice did not result in tumor formation. To evaluate the biodistribution of genetically modified cells, MSCs carrying BMP2 were injected into the tail vein of femur fractured mice. The introduced MSCs were detected in the spleen, testis and fractured femur 28 days post-implantation. These findings suggest that diverse safety tests for genetically modified MSCs should be considered, particularly when a lentivirus mediated gene transfer method is used.

  7. Restoring ciliary function to differentiated Primary Ciliary Dyskinesia cells with a lentiviral vector

    PubMed Central

    Ostrowski, Lawrence E; Yin, Weining; Patel, Manij; Sechelski, John; Rogers, Troy; Burns, Kimberlie; Grubb, Barbara R; Olsen, John C

    2014-01-01

    Primary ciliary dyskinesia is a genetically heterogeneous autosomal recessive disease in which mutations disrupt ciliary function, leading to impaired mucociliary clearance and life-long lung disease. Mouse tracheal cells with a targeted deletion in the axonemal dynein intermediated chain gene Dnaic1 differentiate normally in culture but lack ciliary activity. Gene transfer to undifferentiated cultures of mouse Dnaic1−/− cells with a lentiviral vector pseudotyped with avian influenza hemagglutinin restored Dnaic1 expression and ciliary activity. Importantly, apical treatment of well-differentiated cultures of mouse Dnaic1−/− with lentiviral vector also restored ciliary activity, demonstrating successful gene transfer from the apical surface. Treatment of Dnaic1flox/flox mice expressing an estrogen responsive Cre recombinase with different doses of tamoxifen indicated that restoration of ~20% of ciliary activity may be sufficient to prevent the development of rhinosinusitis. However, while administration of a β-galactosidase expressing vector to control mice demonstrated efficient gene transfer to the nasal epithelium, treatment of Dnaic1−/− mice resulted in a low level of gene transfer, demonstrating that the severe rhinitis present in these animals impedes gene transfer. The results demonstrate that gene replacement therapy may be a viable treatment option for primary ciliary dyskinesia, but further improvements in the efficiency of gene transfer are necessary. PMID:24451115

  8. Digital signature embedding (DSE) for medical image integrity in a data grid off-site backup archive

    NASA Astrophysics Data System (ADS)

    Zhou, Zheng; Huang, H. K.; Liu, Brent J.

    2005-04-01

    One of the new trends to protect the PACS image data against disaster situations is to store clinical images at an off-site backup archive. In order to support the mission-critical clinical PACS, the backup archive must be 24/7 continuously available (CA). We have developed a novel Data Grid for this purpose using the grid computing technology. With the federation of several PAC systems in a grid, the Data Grid can provide the true CA (99.999%) backup for the PAC systems. However, image integrity becomes a new critical issue to the Data Grid where the image data are not under the protection of local PACS anymore. In this paper, we presented a digital signature embedding (DSE) method, which can assure image integrity in image transmission or archive. The DSE method permanently embeds the digital signature (DS) of the image in the image pixels using lossless data embedding approaches, which can completely recover the original image whenever desired. The permanently embedded DS in the image would provide the integrity assurance for medical image during its lifetime. The embedding process can be utilized by the local PACS archive server to embed the DS in every image before it is sent to the Data Grid. The embedded DS can then be extracted for verification to ensure image integrity when images arrived in the Data Grid or when images were retrieved back. Therefore, with the DSE method, we have extended our protection of image integrity from local PACS to the backup Data Grid.

  9. Adeno-associated virus (AAV) Rep proteins mediate complex formation between AAV DNA and its integration site in human DNA.

    PubMed Central

    Weitzman, M D; Kyöstiö, S R; Kotin, R M; Owens, R A

    1994-01-01

    AAV is unique among eukaryotic viruses in the ability of its DNA to integrate preferentially into a specific region of the human genome. Understanding AAV integration may aid in developing gene therapy systems with predictable integration sites. Using a gel mobility-shift assay, we have identified a DNA sequence within the AAV integration locus on human chromosome 19 which is specifically bound by the AAV Rep78 and Rep68 proteins. This Rep recognition sequence is a GCTC repeating motif very similar to sequences within the inverted terminal repeats of the AAV genome which are also bound by Rep78 and Rep68. Cloned oligonucleotides containing the recognition sequence can direct specific binding by Rep proteins. Binding assays with mutant Rep proteins show that the amino-terminal portion of Rep78 and Rep68 can direct binding to either the AAV terminal repeat hairpin DNA or chromosome 19. This human genomic DNA can be complexed with AAV DNA by Rep proteins as demonstrated by a dual-label (32P/biotin) assay. These results suggest a role for Rep in targeting viral integration. Images PMID:8016070

  10. Identifying 2'-O-methylationation sites by integrating nucleotide chemical properties and nucleotide compositions.

    PubMed

    Chen, Wei; Feng, Pengmian; Tang, Hua; Ding, Hui; Lin, Hao

    2016-06-01

    2'-O-methylationation is an important post-transcriptional modification and plays important roles in many biological processes. Although experimental technologies have been proposed to detect 2'-O-methylationation sites, they are cost-ineffective. As complements to experimental techniques, computational methods will facilitate the identification of 2'-O-methylationation sites. In the present study, we proposed a support vector machine-based method to identify 2'-O-methylationation sites. In this method, RNA sequences were formulated by nucleotide chemical properties and nucleotide compositions. In the jackknife cross-validation test, the proposed method obtained an accuracy of 95.58% for identifying 2'-O-methylationation sites in the human genome. Moreover, the model was also validated by identifying 2'-O-methylation sites in the Mus musculus and Saccharomyces cerevisiae genomes, and the obtained accuracies are also satisfactory. These results indicate that the proposed method will become a useful tool for the research on 2'-O-methylation.

  11. Identifying 2'-O-methylationation sites by integrating nucleotide chemical properties and nucleotide compositions.

    PubMed

    Chen, Wei; Feng, Pengmian; Tang, Hua; Ding, Hui; Lin, Hao

    2016-06-01

    2'-O-methylationation is an important post-transcriptional modification and plays important roles in many biological processes. Although experimental technologies have been proposed to detect 2'-O-methylationation sites, they are cost-ineffective. As complements to experimental techniques, computational methods will facilitate the identification of 2'-O-methylationation sites. In the present study, we proposed a support vector machine-based method to identify 2'-O-methylationation sites. In this method, RNA sequences were formulated by nucleotide chemical properties and nucleotide compositions. In the jackknife cross-validation test, the proposed method obtained an accuracy of 95.58% for identifying 2'-O-methylationation sites in the human genome. Moreover, the model was also validated by identifying 2'-O-methylation sites in the Mus musculus and Saccharomyces cerevisiae genomes, and the obtained accuracies are also satisfactory. These results indicate that the proposed method will become a useful tool for the research on 2'-O-methylation. PMID:27191866

  12. An integration of aeromagnetic and electrical resistivity methods in dam site investigation

    SciTech Connect

    Aina, A.; Olorunfemi, M.O.; Ojo, J.S.

    1996-03-01

    Aeromagnetic map and electrical resistivity sounding data obtained along eight traverses were examined at two sites across the Katsina-Ala River. The principal goals of this exercise were to define depths to the bedrock, bedrock relief, geologic structures, define the nature of the superficial deposit, and select probable minor and major axes for hydroelectric power dams. The aeromagnetic map shows that the basement rocks trend roughly northeast-southwest, which correlates with the strike of foliation measurements made on rock outcrops along the river channel. A network of cross cutting lineaments, suspected to be faults/fractures that trend approximately northeast/southwest and northwest/southeast, was also delineated from the magnetic map. The depths to the bedrock estimated from resistivity depth sounding data at site 1 generally vary from 1--53.1 m. Depths to the bedrock estimated at site 2 range from 1.9--19.5 m. The superficial deposit varies from clay to sandy clay, to clayey sand (with boulders in places), and to sand and laterite. The bedrock relief is relatively flat and gently undulates along most of the traverses, with an overall dip towards the river channel. Traverses E-F or I-J at site 1 and K-L at site 2 are probable dame axes. These traverses are characterized by relatively thin overburden thicknesses and rock heads dipping toward the river channel, thereby reducing the likelihood of water seepages from the flanks of the proposed dam axes.

  13. Replication forks of Escherichia coli are not the preferred sites for lysogenic integration of bacteriophage Mu.

    PubMed Central

    Sivan, S; Zaritsky, A; Kagan-Zur, V

    1988-01-01

    The question of whether bacteriophage Mu prefers replication forks for lysogenic integration into Escherichia coli chromosomes was tested by using two different systems. In the first, inactivation of genes was scored in synchronized cultures infected by Mu at various times. No increase in the mutation frequency of a gene was found after infection at the time of its replication. In the second, the composition of colonies formed by bacteria lysogenized by Mu was determined; the newly formed lysogens should give rise to mixed colonies (containing lysogenized as well as nonlysogenized bacteria), uniform colonies, or both, depending on the mode of integration. Both types of colonies were found, and the fraction of uniform colonies was proportional to the relative length of the unreplicated segment of an average chromosome in the culture. The results in both systems clearly preclude the possibility that a lysogenizing Mu integrates with high preference at the chromosome replication forks. PMID:2968339

  14. Integration of site-specific health information: Agency for Toxic Substances and Disease Registry health assessments

    SciTech Connect

    Lesperance, A.M.; Siegel, M.R.

    1990-12-01

    The Agency for Toxic Substances and Disease Registry is required to conduct a health assessment of any site that is listed on or proposed for the US Environmental Protection Agency's National Priorities List. Sixteen US Department of Energy (DOE) sites currently fall into this category. Health assessments contain a qualitative description of impacts to public health and the environment from hazardous waste sites, as well as recommendations for actions to mitigate or eliminate risk. Because these recommendations may have major impacts on compliance activities at DOE facilities, the health assessments are an important source of information for the monitoring activities of DOE's Office of Environmental Compliance (OEC). This report provides an overview of the activities involved in preparing the health assessment, its role in environmental management, and its key elements.

  15. NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome

    PubMed Central

    Chandrani, P; Kulkarni, V; Iyer, P; Upadhyay, P; Chaubal, R; Das, P; Mulherkar, R; Singh, R; Dutt, A

    2015-01-01

    Background: Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool ‘HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets. Methods: We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a ‘quick mode' to identify presence of HPV types and an ‘integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html. Results: On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene E7, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71. Conclusions: HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge. PMID:25973533

  16. Scientific Opportunities for Monitoring at Environmental Remediation Sites (SOMERS): Integrated Systems-Based Approaches to Monitoring

    SciTech Connect

    Bunn, Amoret L.; Wellman, Dawn M.; Deeb, Rula A.; Hawley, Elizabeth L.; Truex, Michael J.; Peterson, Mark; Freshley, Mark D.; Pierce, Eric M.; McCord, John; Young, Michael H.; Gilmore, Tyler J.; Miller, Rick; Miracle, Ann L.; Kaback, Dawn; Eddy-Dilek, Carol; Rossabi, Joe; Lee, Michelle H.; Bush, Richard P.; Beam , Paul; Chamberlain, G. M.; Marble, Justin; Whitehurst, Latrincy; Gerdes, Kurt D.; Collazo, Yvette

    2012-05-15

    Through an inter-disciplinary effort, DOE is addressing a need to advance monitoring approaches from sole reliance on cost- and labor-intensive point-source monitoring to integrated systems-based approaches such as flux-based approaches and the use of early indicator parameters. Key objectives include identifying current scientific, technical and implementation opportunities and challenges, prioritizing science and technology strategies to meet current needs within the DOE complex for the most challenging environments, and developing an integrated and risk-informed monitoring framework.

  17. A slingram survey on the Nevada Test Site: part of an integrated geologic geophysical study of site evaluation for nuclear waste disposal

    USGS Publications Warehouse

    Flanigan, Vincent J.

    1979-01-01

    A slingram geophysical survey was made in early 1978 as part of the integrated geologlcal-geophysical study aimed at evaluating the Eleana Formation as a possible repository for nuclear waste. The slingram data were taken over an alluvial fan and pediments along the eastern flank of Syncline Ridge about 45 km north of Mercury, Nevada, on the Nevada Test Site. The data show that the more conductive argillaceous Eleana Formation varies in depth from 40 to 85 m from west to east along traverse lines. Northeast-trending linear anomalies suggest rather abrupt changes in subsurface geology that may be associated with faults and fractures. The results of the slingram survey will, when interpreted in the light of other geologic and geophysical evidence, assist in understanding the shallow parts of the geologic setting of the Eleana Formation.

  18. Integration of Rooftop Photovoltaic Systems in St. Paul Ford Site's Redevelopment Plans

    SciTech Connect

    Olis, D.; Mosey, G.

    2015-03-01

    The purpose of this analysis is to estimate how much electricity the redeveloped Ford Motor Company assembly plant site in St. Paul, Minnesota, might consume under different development scenarios and how much rooftop photovoltaic (PV) generation might be possible at the site. Because the current development scenarios are high-level, preliminary sketches that describe mixes of residential, retail, commercial, and industrial spaces, electricity consumption and available rooftop area for PV under each scenario can only be grossly estimated. These results are only indicative and should be used for estimating purposes only and to help inform development goals and requirements moving forward.

  19. Chicken β-globin insulators fail to shield the nkx2.5 promoter from integration site effects in zebrafish.

    PubMed

    Grajevskaja, Viktorija; Balciuniene, Jorune; Balciunas, Darius

    2013-12-01

    Genetic lineage tracing and conditional mutagenesis are developmental genetics techniques reliant on precise tissue-specific expression of transgenes. In the mouse, high specificity is usually achieved by inserting the transgene into the locus of interest through homologous recombination in embryonic stem cells. In the zebrafish, DNA containing the transgenic construct is randomly integrated into the genome, usually through transposon-mediated transgenesis. Expression of such transgenes is affected by regulatory features surrounding the integration site from general accessibility of chromatin to tissue-specific enhancers. We tested if the 1.2 kb cHS4 insulators derived from the chicken β-globin locus can shield a transgene from chromosomal position effects in the zebrafish genome. As our test promoters, we used two different-length versions of the zebrafish nkx2.5. We found that flanking a transgenic construct by cHS4 insulation sequences leads to overall increase in the expression of nkx2.5:mRFP. However, we also observed a very high degree of variability of mRFP expression, indicating that cHS4 insulators fail to protect nkx2.5:mRFP from falling under the control of enhancers in the vicinity of integration site.

  20. SITE EMERGING TECHNOLOGY SUMMARY: INTEGRATION OF PHOTOCATALYTIC OXIDATION WITH AIR STRIPPING OF CONTAMINATED AQUIFERS

    EPA Science Inventory

    In a recently completed test program, bench-scale laboratory studies at Arizona State University (ASU) in Tempe, AZ, and pilot-scale studies in a simulated field test situation at Zentox Corp in Ocala, FL, were performed to evaluate the integration of gas-solid ultraviolet (UV) p...

  1. Integrating Vocational & Academic Education. A Handbook Featuring Four Demonstration Sites Including Students from Special Populations.

    ERIC Educational Resources Information Center

    Tindall, Lloyd W.; And Others

    This handbook describes the processes and techniques used to develop, implement, and evaluate four integrated vocational and academic learning programs in Wisconsin that included students from special populations. The handbook contains seven chapters. Chapter 1 presents an overview of the project, including the request for proposal process and…

  2. Implementation of an Integrated, Portable Transformer Condition Monitoring Instrument in the Classroom and On-Site

    ERIC Educational Resources Information Center

    Chatterjee, B.; Dey, D.; Chakravorti, S.

    2010-01-01

    The development of integrated, portable, transformer condition monitoring (TCM) equipment for classroom demonstrations as well as for student exercises conducted in the field is discussed. Demonstrations include experimentation with real-world transformers to illustrate concepts such as polarization and depolarization current through oil-paper…

  3. Reference site selection for wetland condition assessments: Integrating best professional judgement and objective selection criteria

    EPA Science Inventory

    The National Wetlands Condition Assessment (NWCA), one of a series of water assessments being conducted by states, tribes, the U.S. Environmental Protection Agency (EPA), and other partners, surveyed over 900 wetland sites across the lower 48 states during Summer 2011. The NWCA ...

  4. UAS Integration in the NAS Project Test Site Kick-off Meeting

    NASA Technical Reports Server (NTRS)

    Kopardekar, Parimal; Witzberger, Kevin; Hackenberg, Davis L.; Murphy, Jim

    2015-01-01

    This briefing was presented during the Test Site Kick Off Meeting to discuss the contract awards for Task 1 and Task 2. This briefing covered a high level overview for contract deliverables, Task 1 - UAS Traffic Management and Task 2, Live Virtual Constructive Distributed Environment.

  5. Ambulatory Care in Medical Residency: Integration of Private Practitioner's Office with Traditional Sites.

    ERIC Educational Resources Information Center

    Bane, Susan; Criscione, Teri

    1983-01-01

    An Albany Medical College program utilizes private internists' offices as sites for resident ambulatory education. The private practitioner is perceived as an excellent teacher and role model who provides a positive effect on the long-term career goals of residents. (MLW)

  6. Alignment of Surface-Atmosphere Exchange Sensors at Sloped Sites: An Integrated Strategy

    NASA Astrophysics Data System (ADS)

    Metzger, S.; Ayres, E.; Clement, R.; Durden, D.; Foken, T.; Kowalski, A. S.; Luo, H.; McCaughey, J. H.; Durden, N. P.; Serrano-Ortiz, P.; Sun, J.

    2015-12-01

    Closure of the energy balance on the earth's surface is regarded as an indicator that the measurements of radiative, turbulent, diffusive and storage fluxes fulfill fundamental methodological assumptions. However, for sloped measurement sites the different terms contributing to the energy balance are not aligned along the axes of a single reference coordinate system. Consequently, a measurement and data processing strategy is needed that enables consistently quantifying each contributing term. The National Ecological Observatory Network (NEON) is currently deploying surface-atmosphere exchange sensors at several dozen measurement sites, 50% of which are located on slopes up to 20 degrees. To enable unbiased observations across sites, the incident angle between a flux and its measurement should be minimized, and instrument limitations and spatial representativeness need to be considered. Here, we present a strategy that combines site-adaptive instrument alignment with real-time attitude tracking and a set of trigonometric, radiative and source area conversions. This allows obeying the physical limitations underlying radiation, turbulence, profile and soil heat flux sensors, while providing observations in a consistent frame of reference. The strategy is evaluated against initial findings from the first months of surface-atmosphere exchange sensor deployments at NEON.

  7. An Integrated Decision Model for Evaluating Educational Web Sites from the Fuzzy Subjective and Objective Perspectives

    ERIC Educational Resources Information Center

    Huang, Tony Cheng-Kui; Huang, Chih-Hong

    2010-01-01

    With advances in information and network technologies, lots of data have been digitized to reveal information for users by the construction of Web sites. Unfortunately, they are both overloading and overlapping in Internet so that users cannot distinguish their quality. To address this issue in education, Hwang, Huang, and Tseng proposed a group…

  8. Long-term integrating samplers for indoor air and sub slab soil gas at VI sites

    EPA Science Inventory

    Vapor intrusion (VI) site assessments are plagued by substantial spatial and temporal variability that makes exposure and risk assessment difficult. Most risk-based decision making for volatile organic compound (VOC) exposure in the indoor environment is based on health benchmark...

  9. Role of the mammalian target of rapamycin pathway and rapamycin in lentiviral vector gene transduction of hematopoietic stem cells

    PubMed Central

    Wang, Cathy X.; Torbett, Bruce E.

    2015-01-01

    Purpose of review A major goal in repopulating hematopoietic stem cell (HSC) gene therapies is achieving high-efficacy gene transfer, while maintaining robust HSC engraftment and differentiation in vivo. Recent studies have documented that rapamycin treatment of HSC during lentiviral vector transduction enhances gene transfer to human and mouse HSCs and maintains engraftment capacity. In this review, we place into context the role of mammalian target of rapamycin (mTOR) pathways in HSC quiescence and function, endocytic regulation, and lentiviral gene delivery. Recent findings Lentiviral vector transduction of human and mouse HSCs is considerably enhanced by rapamycin treatment. Furthermore, rapamycin preserves long-term engraftment of human and mouse HSCs. Investigations of cellular mechanisms that contribute to increased transduction in HSCs uncovered a role for mTOR inhibition-dependent activation of endocytosis. Summary Rapamycin enhances lentiviral vector transduction of HSCs through regulation of endocytic activity via mTOR inhibition. An important attribute of rapamycin treatment during transduction is the preservation of HSC function, allowing reconstitution of long-term hematopoiesis in vivo in murine models. PMID:26049750

  10. A quasi-lentiviral green fluorescent protein reporter exhibits nuclear export features of late human immunodeficiency virus type 1 transcripts

    SciTech Connect

    Graf, Marcus; Ludwig, Christine; Kehlenbeck, Sylvia; Jungert, Kerstin; Wagner, Ralf . E-mail: ralf.wagner@klinik.uni-regensburg.de

    2006-09-01

    We have previously shown that Rev-dependent expression of HIV-1 Gag from CMV immediate early promoter critically depends on the AU-rich codon bias of the gag gene. Here, we demonstrate that adaptation of the green fluorescent protein (GFP) reporter gene to HIV codon bias is sufficient to turn this hivGFP RNA into a quasi-lentiviral message following the rules of late lentiviral gene expression. Accordingly, GFP expression was significantly decreased in transfected cells strictly correlating with reduced RNA levels. In the presence of the HIV 5' major splice donor, the hivGFP RNAs were stabilized in the nucleus and efficiently exported to the cytoplasm following fusion of the 3' Rev-responsive element (RRE) and coexpression of HIV-1 Rev. This Rev-dependent translocation was specifically inhibited by leptomycin B suggesting export via the CRM1-dependent pathway used by late lentiviral transcripts. In conclusion, this quasi-lentiviral reporter system may provide a new platform for developing sensitive Rev screening assays.

  11. Lentiviral vector-mediated genetic modification of cell substrates for the manufacture of proteins and other biologics.

    PubMed

    Baranyi, Lajos; Roy, Andre; Embree, Heather D; Dropulic, Boro

    2010-01-01

    Transduction with Lentiviral vectors has been shown to be the most efficient method for the stable delivery of nucleic acid sequences into mammalian cells. Lentiviral vectors have been widely used in research and have recently shown success in clinical trials for human gene therapy. In this paper, we describe the use of lentiviral vectors to generate genetically modified cell substrates for the manufacture of proteins and other complex biologics. The use of lentiviral vectors for the generation of genetically modified cell substrates for the production of biologic material has several advantages over other systems: (1) highly productive mammalian cell lines can be rapidly generated without selection or gene amplification; (2) the high number of vector copies are distributed throughout the open chromatin of the genome, resulting in cell lines that are extremely stable for high levels of gene expression and, consequently, protein production; and (3) high levels of protein glycosylation are maintained despite very high levels of protein production. These advantages offer the potential to significantly improve the quality, time-to-market, and manufacturing cost of biologics for human use.

  12. Multigenic lentiviral vectors for combined and tissue-specific expression of miRNA- and protein-based antiangiogenic factors

    PubMed Central

    Askou, Anne Louise; Aagaard, Lars; Kostic, Corinne; Arsenijevic, Yvan; Hollensen, Anne Kruse; Bek, Toke; Jensen, Thomas Gryesten; Mikkelsen, Jacob Giehm; Corydon, Thomas Juhl

    2015-01-01

    Lentivirus-based gene delivery vectors carrying multiple gene cassettes are powerful tools in gene transfer studies and gene therapy, allowing coexpression of multiple therapeutic factors and, if desired, fluorescent reporters. Current strategies to express transgenes and microRNA (miRNA) clusters from a single vector have certain limitations that affect transgene expression levels and/or vector titers. In this study, we describe a novel vector design that facilitates combined expression of therapeutic RNA- and protein-based antiangiogenic factors as well as a fluorescent reporter from back-to-back RNApolII-driven expression cassettes. This configuration allows effective production of intron-embedded miRNAs that are released upon transduction of target cells. Exploiting such multigenic lentiviral vectors, we demonstrate robust miRNA-directed downregulation of vascular endothelial growth factor (VEGF) expression, leading to reduced angiogenesis, and parallel impairment of angiogenic pathways by codelivering the gene encoding pigment epithelium-derived factor (PEDF). Notably, subretinal injections of lentiviral vectors reveal efficient retinal pigment epithelium-specific gene expression driven by the VMD2 promoter, verifying that multigenic lentiviral vectors can be produced with high titers sufficient for in vivo applications. Altogether, our results suggest the potential applicability of combined miRNA- and protein-encoding lentiviral vectors in antiangiogenic gene therapy, including new combination therapies for amelioration of age-related macular degeneration. PMID:26052532

  13. Integrated wastewater management planning for DOE`s Rocky Flats Environmental Technology Site

    SciTech Connect

    Hopkins, J.; Barthel, J.; Wheeler, M.; Conroy, K.

    1996-02-01

    Rocky Mountain Remediation Services, L.L.C. (RMRS), jointly formed by Morrison Knudsen Corporation and BNFL Inc., provides international experience in the nuclear, environmental, waste management, decontamination and decommissioning (D&D) , and project management industry. The company is currently the environmental restoration, waste management, and D&D subcontractor for Kaiser-Hill Company at the Rocky Flats Environmental Technology Site (RFETS). RMRS offers unique solutions and state-of-the-art technology to assist in resolving the issues that face industries today. RMRS has been working on methods to improve cost savings recognized at RFETS, through application of unique technologies and process engineering. RMRS prepared and is implementing a strategy that focused on identifying an approach to improve cost savings in current wastewater treatment systems and to define a low-cost, safe and versatile wastewater treatment system for the future. Development of this strategy, was targeted by Department of Energy (DOE) Headquarters, DOE Rocky Flats Field Office and Kaiser-Hill as a ``Project Breakthrough`` where old concepts were thrown out the door and the project goals and objectives were developed from the groundup. The objectives of the strategy developed in a project break through session with DOE included lower lifecycle costs, shutdown of one of two buildings at RFETS, Building 374 or Building 774, reduced government capital investment, and support of site closure program goals, identified as the site`s Accelerated Site Action Plan (ASAP). The recommended option allows for removal of water treatment functions from Building 374, the existing process wastewater treatment facility. This option affords the lowest capital cost, lowest unit operating cost, lowest technical management risk, greatest support of ASAP phasing and provides the greatest flexibility for design with unforeseen future needs.

  14. Integrated Cropland and Grassland Flux Tower Observation Sites over Grazinglands for Quantifying Surface-Atmosphere Exchange

    NASA Astrophysics Data System (ADS)

    Mahan, H. R.; Wagle, P.; Bajgain, R.; Zhou, Y.; Basara, J. B.; Xiao, X.; Duckles, J. M.; Steiner, J. L.; Starks, P. J.; Northup, B. K.

    2014-12-01

    Quantifying methane (CH4), carbon dioxide (CO2), and water vapor fluxes between land surface and boundary layer using the eddy covariance method have many applicable uses across several disciplines. Three eddy flux towers have been established over no-till winter wheat (Triticum aestivum L.), and native and improved pastures at the USDA ARS Grazinglands Research Laboratory, El Reno, OK. An additional tower will be established in fall 2014 over till winter wheat. Each flux site is equipped with an eddy covariance system, PhenoCam, COSMOS, and in-situ observations of soil and atmospheric state variables. The objective of this research is to measure, compare, and model the land-atmosphere exchange of CO2, water vapor, and CH4 in different land cover types and management practices (till vs no-till, grazing vs no-grazing, native vs improved pasture). Models that focus on net ecosystem CO2 exchange (NEE), gross primary production (GPP), evapotranspiration (ET), and CH4 fluxes can be improved by the cross verification of these measurements. Another application will be to link the in-situ measurements with satellite remote sensing in order to scale-up flux measurements from small spatial scales to local and regional scales. Preliminary data analysis from the native grassland site revealed that CH4 concentration was negligible (~ 0), and it increased significantly when cattle were introduced into the site. In summer 2014, daily ET magnitude was about 4-5 mm day-1 and the NEE magnitude was 4-5 g C day-1 at the native grassland site. Further analysis of data for all the sites for longer temporal periods will enhance understanding of biotic and abiotic factors that govern carbon, water, and energy exchanges between the land surface and atmosphere under different land cover and management systems. The research findings will help predict the responses of these ecosystems to management practices and global environmental change in the future.

  15. HIV Integration at Certain Sites in Host DNA Is Linked to the Expansion and Persistence of Infected Cells | Poster

    Cancer.gov

    Editor’s note: This article was originally published on the Center for Cancer Research website. When the Human Immunodeficiency Virus (HIV) infects a cell, the virus inserts a copy of its genetic material into the host cell’s DNA. The inserted genetic material, which is also called a provirus, is used to produce new viruses. Because the viral DNA can be inserted at many sites in the host cell DNA, the site of integration marks each infected cell. Patients infected with HIV are currently treated with combined antiretroviral therapy (cART), which prevents viral replication in the majority of treated patients. When cART is initiated, most HIV-infected cells die in one or two days, and more of the infected cells die over a period of weeks to months. However there are some long-lived infected cells that do not die, which prevents patients from being cured.

  16. The implications of integrated assessment and modelling studies for the future remediation of chromite ore processing residue disposal sites.

    PubMed

    Farmer, J G; Paterson, E; Bewley, R J F; Geelhoed, J S; Hillier, S; Meeussen, J C L; Lumsdon, D G; Thomas, R P; Graham, M C

    2006-05-01

    Chromite ore processing residue (COPR) waste from a former chromium chemical works (1830-1968) is still contaminating groundwater in Glasgow, Scotland, with carcinogenic hexavalent chromium, Cr(VI). An integrated analytical, experimental and modelling approach has identified and accounted for mineral phases and processes responsible for the retention and release of Cr(VI) under prevailing field conditions. Both the nature of mineral phase retention and the buffered high pH of the sites, however, militate against direct remediative treatment of the source material, for example by the application of generic methods (e.g. FeSO4) that have been successfully employed elsewhere for the reduction of Cr(VI) to Cr(III) in other matrices. The interception and treatment of groundwater to remove Cr(VI) and the capping of sites to reduce human exposure to airborne Cr(VI)-contaminated dust may well be more realistic and effective, at least in the short to medium term.

  17. Integration site of polyoma virus DNA in the inducible LPT line of polyoma-transformed rat cells.

    PubMed Central

    Mendelsohn, E; Baran, N; Neer, A; Manor, H

    1982-01-01

    The structure of the polyoma virus (Py) integration site in the inducible LPT line of Py-transformed rat cells was determined by biochemical methods of gene mapping. LPT cell DNA was digested with various restriction enzymes. The digestion products were electrophoresed in agarose gels and transferred onto nitrocellulose sheets by Southern blotting. Fragments containing viral or cell DNA sequences, or both, were identified by hybridization with Py DNA or with a cloned flanking cell DNA probe. Cleavage of LPT DNA with enzymes that restrict the Py genome once generated linear Py DNA molecules and two fragments containing both cell and viral DNA sequences. Cleavage of LPT DNA with enzymes which do not restrict Py DNA generated series of fragments whose lengths were found to differ by increments of a whole Py genome; the smallest fragment in each series was found to be longer than the viral genome. These data indicate that LPT cultures contain Py insertions of various lengths integrated into the same chromosomal site in all the cells. The length heterogeneity of the viral insertions is due to the presence of 0, 1, 2, 3. . . Py genomes arranged in a direct tandem repeat within invariable sequences of viral DNA. Double-digestion experiments were also carried out with the above enzymes and with enzymes that cleave the Py genome at multiple sites. The data obtained in these experiments were used to construct a physical map of the integration site. This map showed that the early region of the virus remained intact even in the smallest insertion (which contains no whole duplicated genomes), whereas the late region was partially duplicated and split during integration. The smallest insertion is colinear with the Py physical map over a region including the entire Py genome and at least a part of the duplicated segment. This structure could give rise to nondefective circular viral DNA molecules by single homologous recombination events. Similar recombination events may occur at

  18. Integrated chemical management system: A tool for managing chemical information at the Rocky Flats Environmental Technology Site

    SciTech Connect

    Costain, D.

    1995-07-01

    The Integrated Chemical Management System is a computer-based chemical information at the Rocky Flats Environmental Technology Site. Chemical containers are identified by bar code labels and information on the type, quantity and location of chemicals are tracked on individual data bases in separate buildings. Chemical inventories from multiple buildings are uploaded to a central sitewide chemical data base where reports are available from Product, Waste, and Chemical Use modules. Hazardous chemical information is provided by a separate Material Safety Data Sheet module and excess chemicals are traded between chemical owners and users with the aid of the Chemical Exchange Module.

  19. Preoperational test report, cross-site transfer system integrated test (POTR-007)

    SciTech Connect

    Pacquet, E.A.

    1998-04-02

    This report documents the results obtained during the performance of Preoperational Test POTP-007, from December 12, 1997 to March 27, 1998. The main objectives were to demonstrate the operation of the following Cross-Site Transfer System components: Booster pumps P-3125A and P-3125B interlocks and controls, both local and remote; Booster pump P-3125A and P-3125B and associated variable speed drives VSD-1 and VSD-2 performance in both manual and automatic modes; and Water filling, circulation, venting and draining of the transfer headers (supernate and slurry line). As described in reference 1, the following components of the Cross-Site Transfer System that would normally be used during an actual waste transfer, are not used in this specific test: Water Flush System; Valving and instrumentation associated with the 241-SY-A valve pit jumpers; and Valving and instrumentation associated with the 244-A lift station.

  20. The role of short-range Cys171-Cys178 disulfide bond in maintaining cutinase active site integrity: A molecular dynamics simulation

    SciTech Connect

    Matak, Mehdi Youssefi; Moghaddam, Majid Erfani

    2009-12-11

    Understanding structural determinants in enzyme active site integrity can provide a good knowledge to design efficient novel catalytic machineries. Fusarium solani pisi cutinase with classic triad Ser-His-Asp is a promising enzyme to scrutinize these structural determinants. We performed two MD simulations: one, with the native structure, and the other with the broken Cys171-Cys178 disulfide bond. This disulfide bond stabilizes a turn in active site on which catalytic Asp175 is located. Functionally important H-bonds and atomic fluctuations in catalytic pocket have been changed. We proposed that this disulfide bond within active site can be considered as an important determinant of cutinase active site structural integrity.

  1. Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes.

    PubMed

    Tomar, Navneet; Mishra, Akhilesh; Mrinal, Nirotpal; Jayaram, B

    2016-01-01

    Transcription factors (TFs) bind at multiple sites in the genome and regulate expression of many genes. Regulating TF binding in a gene specific manner remains a formidable challenge in drug discovery because the same binding motif may be present at multiple locations in the genome. Here, we present Onco-Regulon (http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm), an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP) a software suite that identifies unique sequences for each of these regulatory DNA motifs at the specified position in the genome. USP works by extending a given DNA motif, in 5'→3', 3' →5' or both directions by adding one nucleotide at each step, and calculates the frequency of each extended motif in the genome by Frequency Counter programme. This step is iterated till the frequency of the extended motif becomes unity in the genome. Thus, for each given motif, we get three possible unique sequences. Closest Sequence Finder program predicts off-target drug binding in the genome. Inclusion of DNA-Protein structural information further makes Onco-Regulon a highly informative repository for gene specific drug development. We believe that Onco-Regulon will help researchers to design drugs which will bind to an exclusive site in the genome with no off-target effects, theoretically.Database URL: http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm.

  2. Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes

    PubMed Central

    Tomar, Navneet; Mishra, Akhilesh; Mrinal, Nirotpal; Jayaram, B.

    2016-01-01

    Transcription factors (TFs) bind at multiple sites in the genome and regulate expression of many genes. Regulating TF binding in a gene specific manner remains a formidable challenge in drug discovery because the same binding motif may be present at multiple locations in the genome. Here, we present Onco-Regulon (http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm), an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP) a software suite that identifies unique sequences for each of these regulatory DNA motifs at the specified position in the genome. USP works by extending a given DNA motif, in 5′→3′, 3′ →5′ or both directions by adding one nucleotide at each step, and calculates the frequency of each extended motif in the genome by Frequency Counter programme. This step is iterated till the frequency of the extended motif becomes unity in the genome. Thus, for each given motif, we get three possible unique sequences. Closest Sequence Finder program predicts off-target drug binding in the genome. Inclusion of DNA-Protein structural information further makes Onco-Regulon a highly informative repository for gene specific drug development. We believe that Onco-Regulon will help researchers to design drugs which will bind to an exclusive site in the genome with no off-target effects, theoretically. Database URL: http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm PMID:27515825

  3. Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes.

    PubMed

    Tomar, Navneet; Mishra, Akhilesh; Mrinal, Nirotpal; Jayaram, B

    2016-01-01

    Transcription factors (TFs) bind at multiple sites in the genome and regulate expression of many genes. Regulating TF binding in a gene specific manner remains a formidable challenge in drug discovery because the same binding motif may be present at multiple locations in the genome. Here, we present Onco-Regulon (http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm), an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP) a software suite that identifies unique sequences for each of these regulatory DNA motifs at the specified position in the genome. USP works by extending a given DNA motif, in 5'→3', 3' →5' or both directions by adding one nucleotide at each step, and calculates the frequency of each extended motif in the genome by Frequency Counter programme. This step is iterated till the frequency of the extended motif becomes unity in the genome. Thus, for each given motif, we get three possible unique sequences. Closest Sequence Finder program predicts off-target drug binding in the genome. Inclusion of DNA-Protein structural information further makes Onco-Regulon a highly informative repository for gene specific drug development. We believe that Onco-Regulon will help researchers to design drugs which will bind to an exclusive site in the genome with no off-target effects, theoretically.Database URL: http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm. PMID:27515825

  4. Development of an integrated strategy for the disposal of solid low level waste at BNFL`s Drigg site

    SciTech Connect

    Higson, S.G.

    1989-11-01

    During the past 12 months, the first phase of a major upgrading of disposal operations at Drigg has been completed. This has involved the introduction of waste containerization and orderly emplacement in open concrete vaults. A further phase over the next few years will involve the introduction of compaction of all suitable waste. While the current upgrade has clearly resulted in a major improvement in the visual impact and management control of the site, the desire to implement such an improvement on a timescale consistent with the short term need for new facilities at Drigg has not allowed sufficient time for a detailed assessment of the full implications of the proposed system. This paper describes the development of the strategy for upgrading the Drigg site, highlights improvements that have been implemented as the project has progressed and outlines major outstanding concerns, particularly in relation to long term site management, that may eventually lead to a requirement for further optimization of the overall strategy. Progress under the Drigg Technical Development Programme is reviewed with specific emphasis on the preliminary results of engineering studies aimed at defining an integrated strategy that will meet the requirements of both acceptable visual impact and long term site stability and safety.

  5. Complete Genome Sequence of Streptomyces parvulus 2297, Integrating Site-Specifically with Actinophage R4.

    PubMed

    Nishizawa, Tomoyasu; Miura, Takamasa; Harada, Chizuko; Guo, Yong; Narisawa, Kazuhiko; Ohta, Hiroyuki; Takahashi, Hideo; Shirai, Makoto

    2016-01-01

    Streptomyces parvulus 2297, which is a host for site-specific recombination according to actinophage R4, is derived from the type strain ATCC 12434. Species of S. parvulus are known as producers of polypeptide antibiotic actinomycins and have been considered for industrial applications. We herein report for the first time the complete genome sequence of S. parvulus 2297. PMID:27563047

  6. Complete Genome Sequence of Streptomyces parvulus 2297, Integrating Site-Specifically with Actinophage R4

    PubMed Central

    Miura, Takamasa; Harada, Chizuko; Guo, Yong; Narisawa, Kazuhiko; Ohta, Hiroyuki; Takahashi, Hideo; Shirai, Makoto

    2016-01-01

    Streptomyces parvulus 2297, which is a host for site-specific recombination according to actinophage R4, is derived from the type strain ATCC 12434. Species of S. parvulus are known as producers of polypeptide antibiotic actinomycins and have been considered for industrial applications. We herein report for the first time the complete genome sequence of S. parvulus 2297. PMID:27563047

  7. Integrated risk and recovery monitoring of ecosystem restorations on contaminated sites

    USGS Publications Warehouse

    Hooper, Michael J.; Glomb, Stephen J.; Harper, David; Hoelzle, Timothy B.; McIntosh, Lisa M.; Mulligan, David R.

    2016-01-01

    Ecological restorations of contaminated sites balance the human and ecological risks of residual contamination with the benefits of ecological recovery and the return of lost ecological function and ecosystem services. Risk and recovery are interrelated dynamic conditions, changing as remediation and restoration activities progress through implementation into long-term management and ecosystem maturation. Monitoring restoration progress provides data critical to minimizing residual contaminant risk and uncertainty, while measuring ecological advancement toward recovery goals. Effective monitoring plans are designed concurrently with restoration plan development and implementation and are focused on assessing the effectiveness of activities performed in support of restoration goals for the site. Physical, chemical, and biotic measures characterize progress toward desired structural and functional ecosystem components of the goals. Structural metrics, linked to ecosystem functions and services, inform restoration practitioners of work plan modifications or more substantial adaptive management actions necessary to maintain desired recovery. Monitoring frequency, duration, and scale depend on specific attributes and goals of the restoration project. Often tied to restoration milestones, critical assessment of monitoring metrics ensures attainment of risk minimization and ecosystem recovery. Finally, interpretation and communication of monitoring findings inform and engage regulators, other stakeholders, the scientific community, and the public. Because restoration activities will likely cease before full ecosystem recovery, monitoring endpoints should demonstrate risk reduction and a successional trajectory toward the condition established in the restoration goals. A detailed assessment of the completed project's achievements, as well as unrealized objectives, attained through project monitoring, will determine if contaminant risk has been minimized, if injured

  8. Integrated risk and recovery monitoring of ecosystem restorations on contaminated sites.

    PubMed

    Hooper, Michael J; Glomb, Stephen J; Harper, David D; Hoelzle, Timothy B; McIntosh, Lisa M; Mulligan, David R

    2016-04-01

    Ecological restorations of contaminated sites balance the human and ecological risks of residual contamination with the benefits of ecological recovery and the return of lost ecological function and ecosystem services. Risk and recovery are interrelated dynamic conditions, changing as remediation and restoration activities progress through implementation into long-term management and ecosystem maturation. Monitoring restoration progress provides data critical to minimizing residual contaminant risk and uncertainty, while measuring ecological advancement toward recovery goals. Effective monitoring plans are designed concurrently with restoration plan development and implementation and are focused on assessing the effectiveness of activities performed in support of restoration goals for the site. Physical, chemical, and biotic measures characterize progress toward desired structural and functional ecosystem components of the goals. Structural metrics, linked to ecosystem functions and services, inform restoration practitioners of work plan modifications or more substantial adaptive management actions necessary to maintain desired recovery. Monitoring frequency, duration, and scale depend on specific attributes and goals of the restoration project. Often tied to restoration milestones, critical assessment of monitoring metrics ensures attainment of risk minimization and ecosystem recovery. Finally, interpretation and communication of monitoring findings inform and engage regulators, other stakeholders, the scientific community, and the public. Because restoration activities will likely cease before full ecosystem recovery, monitoring endpoints should demonstrate risk reduction and a successional trajectory toward the condition established in the restoration goals. A detailed assessment of the completed project's achievements, as well as unrealized objectives, attained through project monitoring, will determine if contaminant risk has been minimized, if injured

  9. Apodized structures for the integration of defect sites into photonic lattices

    SciTech Connect

    Boguslawski, Martin Kelberer, Andreas; Rose, Patrick; Denz, Cornelia

    2014-09-15

    We introduce a versatile concept to optically induce photonic structures of local refractive index modulations as well as photonic lattices holding single defect sites. For a given structure, we develop a set of nondiffracting beams obtained by fractionalizing the corresponding spatial spectrum. By combining this set in a multiplexing procedure, we achieve an incoherent combination of all individual structures of the set resulting in a locally addressable refractive index manipulation. We exemplarily present experimental results for apodized, meaning locally confined index changes in a photorefractive crystal resembling a sixfold and a circular symmetric structure. By an additional multiplexing step, we furthermore create periodic photonic lattices featuring embedded defects.

  10. Integration of geological, geochemical, and geophysical spatial data of the Cement oil field, Oklahoma, test site

    USGS Publications Warehouse

    Termain, Patricia A.; Donovan, Terrence J.; Chavez, Pat S.

    1980-01-01

    Measurement pertaining to geology, geochemistry, and geophysics of the Cement oil field, Oklahoma, test site were collected employing both airborne sensors and ground-based data collection. The measurements include: (1) airborne gamma-ray spectrometry (supplying bismuth 214, thalium 208, and potassium 40 gamma-ray intensities); (2) aeromagnetic survey data; (3) multi-frequency airborne resistivity survey data (supplying apparent electrical resistivity of near surface materials); (4) gravity data; (5) geological and topographic maps; and (6) image data from Landsat MSS and U-2 photography.

  11. DNFSB Recommendation 94-1 Hanford Site Integrated Stabilization Management Plan. Volume 1

    SciTech Connect

    McCormack, R.L.

    1995-08-01

    This document describes the plans of the Hanford Site for the safe interim storage of fissile materials. Currently, spent nuclear fuels reside in storage basins that have leaked in the past and are projected to leak in the future. Other problems in the basins include; sludge from decomposition, degraded cladding of fuel elements, and construction defects which make the basins seismically unsafe. This management plan describes the time and cost that it will take to implement a safe interim storage plan for the fissile materials.

  12. Differential methylation of E2 binding sites in episomal and integrated HPV 16 genomes in preinvasive and invasive cervical lesions.

    PubMed

    Chaiwongkot, Arkom; Vinokurova, Svetlana; Pientong, Chamsai; Ekalaksananan, Tipaya; Kongyingyoes, Bunkerd; Kleebkaow, Pilaiwan; Chumworathayi, Bandit; Patarapadungkit, Natcha; Reuschenbach, Miriam; von Knebel Doeberitz, Magnus

    2013-05-01

    Enhanced expression of the HPV 16 E6-E7 oncogenes may trigger neoplastic transformation of the squamous epithelial cells at the uterine cervix. The HPV E2 protein is a key transcriptional regulator of the E6-E7 genes. It binds to four E2 binding sites (E2BSs 1-4) in the viral upstream regulatory region (URR). Modification of E2 functions, for example, by methylation of E2BSs is hypothesized to trigger enhanced expression of the viral E6-E7 oncogenes. In the majority of HPV-transformed premalignant lesions and about half of cervical carcinomas HPV genomes persist in an extra-chromosomal, episomal state, whereas they are integrated into host cells chromosomes in the remaining lesions. Here we compared the methylation profile of E2BSs 1-4 of the HPV 16 URR in a series of 18 HPV16-positive premalignant lesions and 33 invasive cervical cancers. CpGs within the E2BSs 1, 3, and 4 were higher methylated in all lesions with only episomal HPV16 genomes compared with lesions displaying single integrated copies. Samples with multiple HPV16 integrated copies displayed high methylation levels for all CpGs suggesting that the majority of multiple copies were silenced by extensive methylation. These data support the hypothesis that differential methylation of the E2BSs 1, 3 and 4 is related to the activation of viral oncogene expression in cervical lesions as long as the viral genome remains in the episomal state. Once the virus becomes integrated into host cell chromosomes these methylation patterns may be substantially altered due to complex epigenetic changes of integrated HPV genomes.

  13. Meiotic chromosome segregation mutants identified by insertional mutagenesis of fission yeast Schizosaccharomyces pombe; tandem-repeat, single-site integrations

    PubMed Central

    Davidson, Mari K.; Young, Nathan P.; Glick, Gloria G.; Wahls, Wayne P.

    2004-01-01

    Identification of genes required for segregation of chromosomes in meiosis (scm) is difficult because in most organisms high-fidelity chromosome segregation is essential to produce viable meiotic products. The biology of fission yeast Schizosaccharomyces pombe facilitates identification of such genes. Insertional mutagenesis was achieved by electroporation of linear ura4+ DNA into cells harboring a ura4 deletion. Approximately 1000 stable transformants were screened individually for the production of elevated frequencies of aneuploid spore colonies. Twenty-two candidates were subjected to a secondary screen for cytological defects. Five mutants exhibited significant levels of aberrant meiotic chromosome segregation, but were proficient for mating and completion of meiosis. Each mutant's phenotype cosegregated with its respective ura4+ transgene. The mutations were recessive and defined five complementation groups, revealing five distinct genes (scm1, scm2, scm3, scm4 and scm5). Southern blotting revealed single-site integration in each transformant, indicating that insertional mutagenesis is useful for generating single-locus scm mutations linked to a selectable marker. The transgene insertion points were refractory to analysis by inverse-PCR. Molecular and real-time PCR analyses revealed the presence of multiple, truncated copies of ura4+ at each integration site. Thus, electroporation-mediated insertional mutagenesis in S.pombe is preceded by exonucleolytic processing and concatomerization of the transforming DNA. PMID:15316103

  14. Meiotic chromosome segregation mutants identified by insertional mutagenesis of fission yeast Schizosaccharomyces pombe; tandem-repeat, single-site integrations.

    PubMed

    Davidson, Mari K; Young, Nathan P; Glick, Gloria G; Wahls, Wayne P

    2004-01-01

    Identification of genes required for segregation of chromosomes in meiosis (scm) is difficult because in most organisms high-fidelity chromosome segregation is essential to produce viable meiotic products. The biology of fission yeast Schizosaccharomyces pombe facilitates identification of such genes. Insertional mutagenesis was achieved by electroporation of linear ura4+ DNA into cells harboring a ura4 deletion. Approximately 1000 stable transformants were screened individually for the production of elevated frequencies of aneuploid spore colonies. Twenty-two candidates were subjected to a secondary screen for cytological defects. Five mutants exhibited significant levels of aberrant meiotic chromosome segregation, but were proficient for mating and completion of meiosis. Each mutant's phenotype cosegregated with its respective ura4+ transgene. The mutations were recessive and defined five complementation groups, revealing five distinct genes (scm1, scm2, scm3, scm4 and scm5). Southern blotting revealed single-site integration in each transformant, indicating that insertional mutagenesis is useful for generating single-locus scm mutations linked to a selectable marker. The transgene insertion points were refractory to analysis by inverse-PCR. Molecular and real-time PCR analyses revealed the presence of multiple, truncated copies of ura4+ at each integration site. Thus, electroporation-mediated insertional mutagenesis in S.pombe is preceded by exonucleolytic processing and concatomerization of the transforming DNA. PMID:15316103

  15. Integrated ecological hazard assessment of waste site soil extracts using FETAX and short-term fathead minnow teratogenesis assay

    SciTech Connect

    Fort, D.J.; Stover, E.L.; Bantle, J.A.

    1996-12-31

    Frog Embryo Teratogenesis Assay-Xenopus (FETAX) is a 96-h whole embryo-larval assay designed to detect environmental developmental toxicants for use in ecological hazard assessment. FETAX offers several advantages in integrated biological hazard assessment including, time- and cost-effectiveness, technical ease, and versatility. FETAX has undergone extensive intra- and more recently interlaboratory validation with known mammalian teratogens and non-teratogens. Ecological hazard evaluations of contaminated sediments, waste site soils, and complex surface and groundwaters have also been performed. An integrated hazard assessment study using FETAX, the conventional, Pimephales promelas 7-d teratogenecity test, and an abbreviated P. promelas teratogenecity test utilizing the general FETAX protocol was conducted with specific reference toxicants and aqueous extracts of contaminated hazardous waste site soils. Results from the studies indicated that FETAX can be used as a component of a battery of bioassays designed to assess potential ecological hazard. Furthermore, the generalized FETAX protocol may be useful with other species in evaluating developmental toxicity hazard.

  16. Immune modulation by genetic modification of dendritic cells with lentiviral vectors.

    PubMed

    Liechtenstein, Therese; Perez-Janices, Noemi; Bricogne, Christopher; Lanna, Alessio; Dufait, Inès; Goyvaerts, Cleo; Laranga, Roberta; Padella, Antonella; Arce, Frederick; Baratchian, Mehdi; Ramirez, Natalia; Lopez, Natalia; Kochan, Grazyna; Blanco-Luquin, Idoia; Guerrero-Setas, David; Breckpot, Karine; Escors, David

    2013-09-01

    Our work over the past eight years has focused on the use of HIV-1 lentiviral vectors (lentivectors) for the genetic modification of dendritic cells (DCs) to control their functions in immune modulation. DCs are key professional antigen presenting cells which regulate the activity of most effector immune cells, including T, B and NK cells. Their genetic modification provides the means for the development of targeted therapies towards cancer and autoimmune disease. We have been modulating with lentivectors the activity of intracellular signalling pathways and co-stimulation during antigen presentation to T cells, to fine-tune the type and strength of the immune response. In the course of our research, we have found unexpected results such as the surprising immunosuppressive role of anti-viral signalling pathways, and the close link between negative co-stimulation in the immunological synapse and T cell receptor trafficking. Here we review our major findings and put them into context with other published work.

  17. Integrated characterization of the geologic framework of a contaminated site in West Trenton, New Jersey

    USGS Publications Warehouse

    Ellefsen, Karl J.; Burton, William C.; Lacombe, Pierre J.

    2012-01-01

    Fractured sedimentary bedrock and groundwater at the former Naval Air Warfare Center in West Trenton, New Jersey (United States of America) are contaminated with chlorinated solvents. Predicting contaminant migration or removing the contaminants requires an understanding of the geology. Consequently, the geologic framework near the site was characterized with four different methods having different spatial scales: geologic field mapping, analyses of bedrock drill core, analyses of soil and regolith, and S-wave refraction surveys. A fault zone is in the southeast corner of the site and separates two distinct sedimentary formations; the fault zone dips (steeply) southeasterly, strikes northeasterly, and extends at least 550 m along its strike direction. Drill core from the fault zone is extensively brecciated and includes evidence of tectonic contraction. Approximately 300 m east of this fault zone is another fault zone, which offsets the contact between the two sedimentary formations. The S-wave refraction surveys identified both fault zones beneath soil and regolith and thereby provided constraints on their lateral extent and location.

  18. Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo

    PubMed Central

    Rudicell, Rebecca S.; Kwon, Young Do; Ko, Sung-Youl; Pegu, Amarendra; Louder, Mark K.; Georgiev, Ivelin S.; Wu, Xueling; Zhu, Jiang; Boyington, Jeffrey C.; Chen, Xuejun; Shi, Wei; Yang, Zhi-yong; Doria-Rose, Nicole A.; McKee, Krisha; O'Dell, Sijy; Schmidt, Stephen D.; Chuang, Gwo-Yu; Druz, Aliaksandr; Soto, Cinque; Yang, Yongping; Zhang, Baoshan; Zhou, Tongqing; Todd, John-Paul; Lloyd, Krissey E.; Eudailey, Joshua; Roberts, Kyle E.; Donald, Bruce R.; Bailer, Robert T.; Ledgerwood, Julie; Mullikin, James C.; Shapiro, Lawrence; Koup, Richard A.; Graham, Barney S.; Nason, Martha C.; Connors, Mark; Haynes, Barton F.; Rao, Srinivas S.; Roederer, Mario; Kwong, Peter D.

    2014-01-01

    ABSTRACT Over the past 5 years, a new generation of highly potent and broadly neutralizing HIV-1 antibodies has been identified. These antibodies can protect against lentiviral infection in nonhuman primates (NHPs), suggesting that passive antibody transfer would prevent HIV-1 transmission in humans. To increase the protective efficacy of such monoclonal antibodies, we employed next-generation sequencing, computational bioinformatics, and structure-guided design to enhance the neutralization potency and breadth of VRC01, an antibody that targets the CD4 binding site of the HIV-1 envelope. One variant, VRC07-523, was 5- to 8-fold more potent than VRC01, neutralized 96% of viruses tested, and displayed minimal autoreactivity. To compare its protective efficacy to that of VRC01 in vivo, we performed a series of simian-human immunodeficiency virus (SHIV) challenge experiments in nonhuman primates and calculated the doses of VRC07-523 and VRC01 that provide 50% protection (EC50). VRC07-523 prevented infection in NHPs at a 5-fold lower concentration than VRC01. These results suggest that increased neutralization potency in vitro correlates with improved protection against infection in vivo, documenting the improved functional efficacy of VRC07-523 and its potential clinical relevance for protecting against HIV-1 infection in humans. IMPORTANCE In the absence of an effective HIV-1 vaccine, alternative strategies are needed to block HIV-1 transmission. Direct administration of HIV-1-neutralizing antibodies may be able to prevent HIV-1 infections in humans. This approach could be especially useful in individuals at high risk for contracting HIV-1 and could be used together with antiretroviral drugs to prevent infection. To optimize the chance of success, such antibodies can be modified to improve their potency, breadth, and in vivo half-life. Here, knowledge of the structure of a potent neutralizing antibody, VRC01, that targets the CD4-binding site of the HIV-1 envelope

  19. Site-specific landslide assessment in Alpine area using a reliable integrated monitoring system

    NASA Astrophysics Data System (ADS)

    Romeo, Saverio; Di Matteo, Lucio; Kieffer, Daniel Scott

    2016-04-01

    Rockfalls are one of major cause of landslide fatalities around the world. The present work discusses the reliability of integrated monitoring of displacements in a rockfall within the Alpine region (Salzburg Land - Austria), taking into account also the effect of the ongoing climate change. Due to the unpredictability of the frequency and magnitude, that threatens human lives and infrastructure, frequently it is necessary to implement an efficient monitoring system. For this reason, during the last decades, integrated monitoring systems of unstable slopes were widely developed and used (e.g., extensometers, cameras, remote sensing, etc.). In this framework, Remote Sensing techniques, such as GBInSAR technique (Groung-Based Interferometric Synthetic Aperture Radar), have emerged as efficient and powerful tools for deformation monitoring. GBInSAR measurements can be useful to achieve an early warning system using surface deformation parameters as ground displacement or inverse velocity (for semi-empirical forecasting methods). In order to check the reliability of GBInSAR and to monitor the evolution of landslide, it is very important to integrate different techniques. Indeed, a multi-instrumental approach is essential to investigate movements both in surface and in depth and the use of different monitoring techniques allows to perform a cross analysis of the data and to minimize errors, to check the data quality and to improve the monitoring system. During 2013, an intense and complete monitoring campaign has been conducted on the Ingelsberg landslide. By analyzing both historical temperature series (HISTALP) recorded during the last century and those from local weather stations, temperature values (Autumn-Winter, Winter and Spring) are clearly increased in Bad Hofgastein area as well as in Alpine region. As consequence, in the last decades the rockfall events have been shifted from spring to summer due to warmer winters. It is interesting to point out that

  20. Happier Together: Integrating a Wellness Application into a Social Network Site

    NASA Astrophysics Data System (ADS)

    Munson, Sean A.; Lauterbach, Debra; Newman, Mark W.; Resnick, Paul

    What are the benefits and drawbacks of integrating health and wellness interventions into existing online social network websites? In this paper, we report on a case study of deploying the Three Good Things positive psychology exercise as a Facebook application. Our experience shows that embedding a wellness intervention in an existing social website is a viable option. In particular, we find adherence rates on par with or better than many other Internet-based wellness interventions. We also gained insights about users' privacy and audience concerns that inform the design of social network-based wellness applications. Participants did not want all of their entries to be shared with all their Facebook friends, both because they did not want others to know some things and because they did not want to clutter others' newsfeeds. Users found it compelling, however, to interact with their friends around some "Good Things" they had posted.

  1. Insights Into Contamination Control For The Shuttle Payload Integration Facility (SPIF) At The Eastern Launch Site (ELS)

    NASA Astrophysics Data System (ADS)

    Pugel, Nancy J.

    1982-02-01

    The Shuttle Payload Integration Facility (SPIF) is a payload processing facility at the Eastern Launch Site (ELS), Cape Canaveral Air Force Station (CCAFS) which has been designed to accommodate assembly, test, and checkout operations for a number of Shuttle payloads, many of which are contamination sensitive. In general, the SPIF was designed to meet class 100,000, per Fed. Std. 209B (Reference 1), cleanliness requirements and operate as a class 100,000 clean area. However, due to the expansiveness of the building (which includes several airlocks, a transfer aisle, and integration cells), the variety of hardware to be processed through the facility (payloads, upper states, and support equipment), and the variety of operations to be performed for these hardware, many different contamination control methods must be carefully integrated and implemented to maintain an overall clean environment. In instances where the operation being performed is not generally compatible with the clean environment, uniaue and innovative contamination control methods must be developed with respect to ease of implementation as well as effectiveness of contamination control.

  2. Site planning and integration fiscal year 1999 multi-year work plan (MYWP) update for WBS 1.8.2.1

    SciTech Connect

    SCHULTZ, E.A.

    1998-10-01

    The primary mission of the Site Planning and Integration (SP and I) project is to assist Fluor Daniel Project Direction to ensure that all work performed under the Project Hanford Management Contract (PHMC) is adequately planned, executed, controlled, and that performance is measured and reported in an integrated fashion. Furthermore, SP and I is responsible for the development, implementation, and management of systems and processes that integrate technical, schedule, and cost baselines for PHMC work.

  3. Integrated metagenomics and field measurements of polygon features at the NGEE-Arctic Barrow site

    NASA Astrophysics Data System (ADS)

    Tas, N.; Wu, Y.; Smith, L. J.; Ulrich, C.; Kneafsey, T. J.; Torn, M. S.; Hubbard, S. S.; Wullschleger, S. D.; Jansson, J.

    2013-12-01

    Arctic soils contain an estimated 12-42% of terrestrial carbon, most of which is sequestered in permafrost. High latitudes have experienced the greatest regional warming in recent decades and observations suggest that permafrost degradation is now commonly observed in the region. With increasing global temperatures, permafrost soils are becoming a potential source of greenhouse gas (GHG) emissions. Because of widespread permafrost thaw much of the soil organic matter may be available for rapid mineralization by microorganisms in the soil. Yet little is known about the vulnerability of permafrost and the potential response of soil microorganisms to availability of new carbon sources. On the Alaskan North Slope the collapse and rise of soil due to formation of ice wedges and permafrost thaw create distinct features called polygons. As part of the U.S. Department of Energy (DOE) Next Generation Ecosystem Experiment (NGEE) in the Arctic, we aimed to determine the distribution of microbial populations across a range of polygon features and to correlate the microbial data to GHG flux data. To determine the microbial community distribution and metabolic potential, we collected seasonally thawed active layer soil samples along two polygon transects (Site 0 and AB), including high-centered, transitional and low-centered polygons. Illumina HiSeq technology was used to sequence 16SrRNA genes and metagenomes from these active layer soils. The sequence data was correlated to GHG flux measurements and to environmental data from the site, including geophysical and geochemical soil characteristics. Both the microbial communities and the flux measurements varied along the polygon transect. Each polygon had a distinct microbial community structure; however, these microbial communities shared many metabolic capabilities. For example, many genes involved in degradation of chitin could be found all three polygons. Functional genes involved in methanogenesis and CH4-flux measurements

  4. Hydro-mechanical simulations of well abandonment at the Ketzin pilot site for CO2 storage verify wellbore system integrity

    NASA Astrophysics Data System (ADS)

    Unger, Victoria; Kempka, Thomas

    2015-04-01

    In geological underground utilisation, operating and abandoned wells have been identified as a main potential leakage pathways for reservoir fluids. In the scope of the well abandonment procedure currently carried out at the Ketzin pilot site for CO2 storage in Germany, a hydro-mechanical model was built to carry out a coupled analysis of the integrity in the entire wellbore system. The main aim of the present study was to assess the impacts of stress changes associated with CO2 injection as well as the cement backfill undertaken in the scope of well abandonment. A numerical model comprising cement sheaths, steel casings, tubing, multiple packers and wellbore annuli was implemented to enable a detailed representation of the entire wellbore system. The numerical model grid has a horizontal discretisation of 5 m x 5 m to focus on near wellbore effects, whereby element sizes increase with increasing distance from the wellbore. Vertical grid discretisation uses a tartan grid type over the entire model thickness of 1,500 m to ensure a sufficient discretisation of all wellbore system elements as well as of the reservoir unit. The total number of elements amounts to 210,672. Mechanical model parameters were taken from geological, drilling, logging and laboratory test data based on Ketzin pilot site-specific information as well as related literature (Kempka et al., 2014). The coupled calculations were performed using an elasto-plastic constitutive law, whereby an initial simulation run ensured a static mechanical equilibrium to represent the initial state before the start of CO2 injection. Thereto, gravitational load of the overburden rocks and pore pressure distribution following available well logs were integrated for initial model parameterisation including a normal faulting stress regime defined by a horizontal to vertical total stress ratio of 0.85. A correction accounting for the temperature and pressure dependent CO2 density was carried out in advance of each

  5. Increased chromatin fragmentation and reduced acrosome integrity in spermatozoa of red deer from lead polluted sites.

    PubMed

    Castellanos, Pilar; del Olmo, Enrique; Fernández-Santos, M Rocío; Rodríguez-Estival, Jaime; Garde, J Julián; Mateo, Rafael

    2015-02-01

    Vertebrates are constantly exposed to a diffuse pollution of heavy metals existing in the environment, but in some cases, the proximity to emission sources like mining activity increases the risk of developing adverse effects of these pollutants. Here we have studied lead (Pb) levels in spermatozoa and testis, and chromatin damage and levels of endogenous antioxidant activity in spermatozoa of red deer (Cervus elaphus) from a Pb mining area (n=37) and a control area (n=26). Deer from the Pb-polluted area showed higher Pb levels in testis parenchyma, epididymal cauda and spermatozoa, lower values of acrosome integrity, higher activity of glutathione peroxidase (GPx) and higher values of DNA fragmentation (X-DFI) and stainability (HDS) in sperm than in the control area. These results indicate that mining pollution can produce damage on chromatin and membrane spermatozoa in wildlife. The study of chromatin fragmentation has not been studied before in spermatozoa of wildlife species, and the sperm chromatin structure assay (SCSA) has been revealed as a successful tool for this purpose in species in which the amount of sperm that can be collected is very limited.

  6. An integrated methodology on the suitability of offshore sites for wind farm development

    NASA Astrophysics Data System (ADS)

    Patlakas, Platon; Galanis, George; Péray, Marie; Filipot, Jean-François; Kalogeri, Christina; Spyrou, Christos; Diamantis, Dimitris; Kallos, Gerorge

    2016-04-01

    During, the last decades the potential and interest in wind energy investments has been constantly increasing in the European countries. As technology changes rapidly, more and more areas can be identified as suitable for energy applications. Offshore wind farms perfectly illustrate how new technologies allow to build bigger, more efficient and resistant in extreme conditions wind power plants. The current work proposes an integrated methodology to determine the suitability of an offshore marine area for the development of wind farm structures. More specifically, the region of interest is evaluated based both on the natural resources, connected to the local environmental characteristics, and potential constrains set by anthropogenic or other activities. State of the art atmospheric and wave models and a 10-year hindcast database are utilized in conjunction with local information for a number of potential constrains, leading to a 5-scale suitability index for the whole area. In this way, sub regions are characterized, at a high resolution mode, as poorly or highly suitable for wind farm development, providing a new tool for technical/research teams and decision makers. In addition, extreme wind and wave conditions and their 50-years return period are analyzed and used to define the safety level of the wind farms structural characteristics.

  7. THE INTEGRATION OF ENGINEERED AND INSTITUTIONAL CONTROLS: A CASE STUDY APPROACH WITH LESSONS LEARNED FROM PREVIOUSLY CLOSED SITES

    SciTech Connect

    Kevin M. Kostelnik; James H. Clarke; Jerry L. Harbour

    2005-02-01

    Environmental remediation efforts that are underway at hundreds of contaminated sites in the United States will not be able to remediate large portions of those sites to conditions that would permit unrestricted access. Rather, large volumes of waste materials, contaminated soils and cleanup residuals will have to be isolated either in place or in new, often on-site, disposal cells with long term monitoring, maintenance and institutional control needs. The challenge continues to be to provide engineering systems and controls that can ensure the protection of public health and the environment over very long time horizons (hundreds to perhaps thousands of years) with minimal intervention. Effective long term management of legacy hazardous and nuclear waste requires an integrated approach that addresses both the engineered containment and control system itself and the institutional controls and other responsibilities that are needed. Decisions concerning system design, monitoring and maintenance, and the institutional controls that will be employed are best done through a "risk-nformed, performance-based" approach. Such an approach should incorporate an analysis of potential "failure" modes and consequences for all important system features, together with lessons learned from experience with systems already in place. The authors will present the preliminary results of a case study approach that included several sites where contamination isolation systems including institutional controls have been implemented. The results are being used together with failure trees and logic diagrams that have been developed for both the engineered barriers and the institutional controls. The use of these analytical tools to evaluate the potential for different levels of failure and associated consequences will be discussed. Of special interest is the robustness of different approaches to providing long-term protection through redundancy and defense in depth.

  8. SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics

    PubMed Central

    Chen, Dana; Orenstein, Yaron; Golodnitsky, Rada; Pellach, Michal; Avrahami, Dorit; Wachtel, Chaim; Ovadia-Shochat, Avital; Shir-Shapira, Hila; Kedmi, Adi; Juven-Gershon, Tamar; Shamir, Ron; Gerber, Doron

    2016-01-01

    Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression. PMID:27628341

  9. SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics.

    PubMed

    Chen, Dana; Orenstein, Yaron; Golodnitsky, Rada; Pellach, Michal; Avrahami, Dorit; Wachtel, Chaim; Ovadia-Shochat, Avital; Shir-Shapira, Hila; Kedmi, Adi; Juven-Gershon, Tamar; Shamir, Ron; Gerber, Doron

    2016-01-01

    Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression. PMID:27628341

  10. Performance Assessment of a Low-Level Radioactive Waste Disposal Site using GoldSim Integrated Systems Model

    NASA Astrophysics Data System (ADS)

    Merrell, G.; Singh, A.; Tauxe, J.; Perona, R.; Dornsife, W.; grisak, G. E.; Holt, R. M.

    2011-12-01

    Texas Commission on Environmental Quality has approved licenses for four landfills at the Waste Control Specialists (WCS) site located in Andrews County, West Texas. The site includes a hazardous waste landfill and three landfills for radioactive waste. An updated performance assessment is necessary prior to acceptance of waste at the landfills. The updated performance assessment a) provides for more realistic and flexible dose modeling capabilities, b) addresses all plausible release and accident scenarios as they relate to the performance objectives, c) includes impact of climate and hydrologic scenarios that may impact long-term performance of the landfill, d) addresses impact of cover naturalization and degradation on the landfill, and e) incorporates uncertainty and sensitivity analysis for critical parameters. For the updated performance assessment, WCS has developed an integrated systems level performance assessment model using the GoldSim platform. GoldSim serves as a model for integrating all of the major components of a performance assessment, which include the radionuclide source term, facility design, environmental transport pathways, exposure scenarios, and radiological doses. Unlike many computer models that are based on first principles, GoldSim is a systems level model that can be used to integrate and abstract more complex sub-models into one system. This can then be used to assess the results into a unified model of the disposal system and environment. In this particular application, the GoldSim model consists of a) hydrogeologic model that simulates flow and transport through the Dockum geologic unit that underlies all of the waste facilities, b) waste cells that represent the containment unit and simulate degradation of waste forms, radionuclide leaching, and partitioning into the liquid and vapor phase within the waste unit, c) a cover system model that simulates upward diffusive transport from the underground repository to the atmosphere. In

  11. Munitions integrity and corrosion features observed during the HUMMA deep-sea munitions disposal site investigations

    NASA Astrophysics Data System (ADS)

    Silva, Jeff A. K.; Chock, Taylor

    2016-06-01

    An evaluation of the current condition of sea-disposed military munitions observed during the 2009 Hawaii Undersea Military Munitions Assessment Project investigation is presented. The 69 km2 study area is located south of Pearl Harbor, Oahu, Hawaii, and is positioned within a former deep-sea disposal area designated as Hawaii-05 or HI-05 by the United States Department of Defense. HI-05 is known to contain both conventional and chemical munitions that were sea-disposed between 1920 and 1951. Digital images and video reconnaissance logs collected during six remotely operated vehicle and 16 human-occupied vehicle surveys were used to classify the integrity and state of corrosion of the 1842 discarded military munitions (DMM) objects encountered. Of these, 5% (or 90 individual DMM objects) were found to exhibit a mild-moderate degree of corrosion. The majority (66% or 1222 DMM objects) were observed to be significantly corroded, but visually intact on the seafloor. The remaining 29% of DMM encountered were found to be severely corroded and breached, with their contents exposed. Chemical munitions were not identified during the 2009 investigation. In general, identified munitions known to have been constructed with thicker casings were better preserved. Unusual corrosion features were also observed, including what are termed here as 'corrosion skirts' that resembled the flow and cementation of corrosion products at and away from the base of many munitions, and 'corrosion pedestal' features resembling a combination of cemented corrosion products and seafloor sediments that were observed to be supporting munitions above the surface of the seafloor. The origin of these corrosion features could not be determined due to the lack of physical samples collected. However, a microbial-mediated formation hypothesis is presented, based on visual analysis, which can serve as a testable model for future field programs.

  12. Assessing recreation impacts to cliffs in Shenandoah National Park: Integrating visitor observation with trail and recreation site measurements

    USGS Publications Warehouse

    Wood, K.T.; Lawson, S.R.; Marion, J.L.

    2006-01-01

    The rock outcrops and cliffs of Shenandoah National Park provide habitat for several rare and endangered plant and animal species, including the federally endangered Shenandoah Salamander (Plethodon shenandoah; Ludwig et al., 1993). The location of the well-known park tour road, Skyline Drive, along the ridgeline provides exceptional access to many outcrops and cliffs throughout the park for a large number of the park?s 1.2 million annual visitors. Consequently, visitor use of cliff areas has led to natural resource impacts, including marked decreases in size and vigor of known rare plant populations. Despite the clear ecological value and potential threats to the natural resources at cliff areas, managers possess little information on visitor use of cliff sites and presently have no formal planning document to guide management. Thus, a park wide study of cliff sites was initiated during the 2005 visitor use season. As part of this research effort, our study used an integrative approach to study recreational use and visitor-caused resource impacts at one of the more heavily visited cliff sites in the park: Little Stony Man Cliffs (LSMC). In particular, this study integrated data from resource impact measurements and visitor use observation to help assess the effects of recreational use on the natural resources of LSMC. Procedures derived from campsite and trail impact studies were used to measure and characterize the amount of visitor-caused resource impacts on LSMC (Marion & Leung, 2001; Marion, 1995). Visitor use observations were conducted on top of LSMC to document and characterize the type and amount of recreational use the cliffs receive and the behaviors of recreationists that may contribute to cliff-top resource impacts. Resource impact measurement data show trampling disturbance present at LSMC, characterized by vegetation loss, exposed soil, and root exposure. Documentation of informal trails, soil erosion, tree damage, and tree stumps provide further

  13. Integrated methodology for assessing the HCH groundwater pollution at the multi-source contaminated mega-site Bitterfeld/Wolfen.

    PubMed

    Wycisk, Peter; Stollberg, Reiner; Neumann, Christian; Gossel, Wolfgang; Weiss, Holger; Weber, Roland

    2013-04-01

    A large-scale groundwater contamination characterises the Pleistocene groundwater system of the former industrial and abandoned mining region Bitterfeld/Wolfen, Eastern Germany. For more than a century, local chemical production and extensive lignite mining caused a complex contaminant release from local production areas and related dump sites. Today, organic pollutants (mainly organochlorines) are present in all compartments of the environment at high concentration levels. An integrated methodology for characterising the current situation of pollution as well as the future fate development of hazardous substances is highly required to decide on further management and remediation strategies. Data analyses have been performed on regional groundwater monitoring data from about 10 years, containing approximately 3,500 samples, and up to 180 individual organic parameters from almost 250 observation wells. Run-off measurements as well as water samples were taken biweekly from local creeks during a period of 18 months. A kriging interpolation procedure was applied on groundwater analytics to generate continuous distribution patterns of the nodal contaminant samples. High-resolution geological 3-D modelling serves as a database for a regional 3-D groundwater flow model. Simulation results support the future fate assessment of contaminants. A first conceptual model of the contamination has been developed to characterise the contamination in regional surface waters and groundwater. A reliable explanation of the variant hexachlorocyclohexane (HCH) occurrence within the two local aquifer systems has been derived from the regionalised distribution patterns. Simulation results from groundwater flow modelling provide a better understanding of the future pollutant migration paths and support the overall site characterisation. The presented case study indicates that an integrated assessment of large-scale groundwater contaminations often needs more data than only from local

  14. OPERATIONS REVIEW OF THE SAVANNAH RIVER SITE INTEGRATED SALT DISPOSITION PROCESS - 11327

    SciTech Connect

    Peters, T.; Poirier, M.; Fondeur, F.; Fink, S.; Brown, S.; Geeting, M.

    2011-02-07

    The Savannah River Site (SRS) is removing liquid radioactive waste from its Tank Farm. To treat waste streams that are low in Cs-137, Sr-90, and actinides, SRS developed the Actinide Removal Process and implemented the Modular Caustic Side Solvent Extraction (CSSX) Unit (MCU). The Actinide Removal Process contacts salt solution with monosodium titanate to sorb strontium and select actinides. After monosodium titanate contact, the resulting slurry is filtered to remove the monosodium titanate (and sorbed strontium and actinides) and entrained sludge. The filtrate is transferred to the MCU for further treatment to remove cesium. The solid particulates removed by the filter are concentrated to {approx} 5 wt %, washed to reduce the sodium concentration, and transferred to the Defense Waste Processing Facility for vitrification. The CSSX process extracts the cesium from the radioactive waste using a customized solvent to produce a Decontaminated Salt Solution (DSS), and strips and concentrates the cesium from the solvent with dilute nitric acid. The DSS is incorporated in grout while the strip acid solution is transferred to the Defense Waste Processing Facility for vitrification. The facilities began radiological processing in April 2008 and started processing of the third campaign ('MarcoBatch 3') of waste in June 2010. Campaigns to date have processed {approx}1.2 million gallons of dissolved saltcake. Savannah River National Laboratory (SRNL) personnel performed tests using actual radioactive samples for each waste batch prior to processing. Testing included monosodium titanate sorption of strontium and actinides followed by CSSX batch contact tests to verify expected cesium mass transfer. This paper describes the tests conducted and compares results from facility operations. The results include strontium, plutonium, and cesium removal, cesium concentration, and organic entrainment and recovery data. Additionally, the poster describes lessons learned during operation

  15. Dr.VIS v2.0: an updated database of human disease-related viral integration sites in the era of high-throughput deep sequencing.

    PubMed

    Yang, Xiaobo; Li, Ming; Liu, Qi; Zhang, Yabing; Qian, Junyan; Wan, Xueshuai; Wang, Anqiang; Zhang, Haohai; Zhu, Chengpei; Lu, Xin; Mao, Yilei; Sang, Xinting; Zhao, Haitao; Zhao, Yi; Zhang, Xiaoyan

    2015-01-01

    Dr.VIS is a database of human disease-related viral integration sites (VIS). The number of VIS has grown rapidly since Dr.VIS was first released in 2011, and there is growing recognition of the important role that viral integration plays in the development of malignancies. The updated database version, Dr.VIS v2.0 (http://www.bioinfo.org/drvis or bminfor.tongji.edu.cn/drvis_v2), represents 25 diseases, covers 3340 integration sites of eight oncogenic viruses in human chromosomes and provides more accurate information about VIS from high-throughput deep sequencing results obtained mainly after 2012. Data of VISes for three newly identified oncogenic viruses for 14 related diseases have been added to this 2015 update, which has a 5-fold increase of VISes compared to Dr.VIS v1.0. Dr.VIS v2.0 has 2244 precise integration sites, 867 integration regions and 551 junction sequences. A total of 2295 integration sites are located near 1730 involved genes. Of the VISes, 1153 are detected in the exons or introns of genes, with 294 located up to 5 kb and a further 112 located up to 10 kb away. As viral integration may alter chromosome stability and gene expression levels, characterizing VISes will contribute toward the discovery of novel oncogenes, tumor suppressor genes and tumor-associated pathways. PMID:25355513

  16. Lentiviral vector platform for improved erythropoietin expression concomitant with shRNA mediated host cell elastase down regulation.

    PubMed

    Dhamne, Hemant; Chande, Ajit G; Mukhopadhyaya, Robin

    2014-01-01

    Lentiviral vector (LV) mediated gene transfer holds great promise to develop stable cell lines for sustained transgene expression providing a valuable alternative to the conventional plasmid transfection based recombinant protein production methods. We report here making a third generation HIV-2 derived LV containing erythropoietin (EPO) gene expression cassette to generate a stable HEK293 cell line secreting EPO constitutively. A high producer cell clone was obtained by limiting dilution and was adapted to serum free medium. The suspension adapted cell clone stably produced milligram per liter quantities of EPO. Subsequent host metabolic engineering using lentiviral RNAi targeted to block an endogenous candidate protease elastase, identified through an in silico approach, resulted in appreciable augmentation of EPO expression above the original level. This study of LV based improved glycoprotein expression with host cell metabolic engineering for stable production of protein therapeutics thus exemplifies the versatility of LV and is of significant future biopharmaceutical importance.

  17. Lentiviral vector platform for improved erythropoietin expression concomitant with shRNA mediated host cell elastase down regulation.

    PubMed

    Dhamne, Hemant; Chande, Ajit G; Mukhopadhyaya, Robin

    2014-01-01

    Lentiviral vector (LV) mediated gene transfer holds great promise to develop stable cell lines for sustained transgene expression providing a valuable alternative to the conventional plasmid transfection based recombinant protein production methods. We report here making a third generation HIV-2 derived LV containing erythropoietin (EPO) gene expression cassette to generate a stable HEK293 cell line secreting EPO constitutively. A high producer cell clone was obtained by limiting dilution and was adapted to serum free medium. The suspension adapted cell clone stably produced milligram per liter quantities of EPO. Subsequent host metabolic engineering using lentiviral RNAi targeted to block an endogenous candidate protease elastase, identified through an in silico approach, resulted in appreciable augmentation of EPO expression above the original level. This study of LV based improved glycoprotein expression with host cell metabolic engineering for stable production of protein therapeutics thus exemplifies the versatility of LV and is of significant future biopharmaceutical importance. PMID:24325878

  18. Pseudo attP sites in favor of transgene integration and expression in cultured porcine cells identified by Streptomyces phage phiC31 integrase.

    PubMed

    Bi, Yanzhen; Liu, Ximei; Zhang, Long; Shao, Changwei; Ma, Zhuo; Hua, Zaidong; Zhang, Liping; Li, Li; Hua, Wenjun; Xiao, Hongwei; Wei, Qingxin; Zheng, Xinmin

    2013-09-08

    Phage PhiC31 integrase integrates attB-containing plasmid into pseudo attP site in eukaryotic genomes in a unidirectional site-specific manner and maintains robust transgene expression. Few studies, however, explore its potential in livestock. This study aims to discover the molecular basis of PhiC31 integrase-mediated site-specific recombination in pig cells. We show that PhiC31 integrase can mediate site-specific transgene integration into the genome of pig kidney PK15 cells. Intramolecular recombination in pig PK15 cell line occurred at maximum frequency of 82% with transiently transfected attB- and attP-containing plasmids. An optimal molar ratio of pCMV-Int to pEGFP-N1-attB at 5:1 was observed for maximum number of cell clones under drug selection. Four candidate pseudo attP sites were identified by TAIL-PCR from those cell clones with single-copy transgene integration. Two of them gave rise to higher integration frequency occurred at 33%. 5' and 3' junction PCR showed that transgene integration mediated by PhiC31 integrase was mono-allelic. Micro- deletion and insertion were observed by sequencing the integration border, indicating that double strand break was induced by the recombination. We then constructed rescue reporter plasmids by ABI-REC cloning of the four pseudo attP sites into pBCPB + plasmid. Transfection of these rescue plasmids and pCMV-Int resulted in expected intramolecular recombination between attB and pseudo attP sites. This proved that the endogenous pseudo attP sites were functional substrates for PhiC31 integrase-mediated site-specific recombination. Two pseudo attP sites maintained robust extracellular and intracellular EGFP expression. Alamar blue assay showed that transgene integration into these specific sites had little effect on cell proliferation. This is the first report to document the potential use of PhiC31 integrase to mediate site-specific recombination in pig cells. Our work established an ideal model to study the position

  19. An integrated experimental program to understanding leakage from geologic carbon sequestration sites across scales

    NASA Astrophysics Data System (ADS)

    Clarens, A. F.; Wang, S.; Liang, B.; Peters, C. A.; Fitts, J. P.; Deng, H.; Ellis, B. R.

    2012-12-01

    angle decreased during the CO2 phase transition from supercritical or liquid to gas. These results suggest complex and nonlinear effects from wetting during leakage events. At intermediate scales, column experiments are underway in a 1 m column and a 10 m column is under construction. At Princeton, experimental work on fractured carbonate-rich caprocks has shown that preferential dissolution of calcite leads to significant alterations of fracture geometry. The evolution of fracture hydrodynamic properties, however, is more complex due to heterogeneous mineral distribution. Single- and multi-phase Computational Fluid Dynamics (CFD) simulations have been conducted to quantify changes in permeability and relative permeability due to geochemical alterations. Also, CFD calculations generate the detailed maps of velocity fields needed to study the interactions between fluid dynamics and mineral heterogeneity, which ultimately determine reaction rates. At the bench-scale, experiments are underway to study CO2 properties and reactions in porous and fractured sedimentary rocks. Inferences are drawn with the benefit of a suite of imaging methods. These experimental and modeling efforts are being integrated to isolate relevant physical and geochemical processes to generate the fundamental understanding needed to interpret field-scale observations.

  20. B-cell reconstitution after lentiviral vector–mediated gene therapy in patients with Wiskott-Aldrich syndrome

    PubMed Central

    Castiello, Maria Carmina; Scaramuzza, Samantha; Pala, Francesca; Ferrua, Francesca; Uva, Paolo; Brigida, Immacolata; Sereni, Lucia; van der Burg, Mirjam; Ottaviano, Giorgio; Albert, Michael H.; Grazia Roncarolo, Maria; Naldini, Luigi; Aiuti, Alessandro; Villa, Anna; Bosticardo, Marita

    2015-01-01

    Background Wiskott-Aldrich syndrome (WAS) is a severe X-linked immunodeficiency characterized by microthrombocytopenia, eczema, recurrent infections, and susceptibility to autoimmunity and lymphomas. Hematopoietic stem cell transplantation is the treatment of choice; however, administration of WAS gene–corrected autologous hematopoietic stem cells has been demonstrated as a feasible alternative therapeutic approach. Objective Because B-cell homeostasis is perturbed in patients with WAS and restoration of immune competence is one of the main therapeutic goals, we have evaluated reconstitution of the B-cell compartment in 4 patients who received autologous hematopoietic stem cells transduced with lentiviral vector after a reduced-intensity conditioning regimen combined with anti-CD20 administration. Methods We evaluated B-cell counts, B-cell subset distribution, B cell–activating factor and immunoglobulin levels, and autoantibody production before and after gene therapy (GT). WAS gene transfer in B cells was assessed by measuring vector copy numbers and expression of Wiskott-Aldrich syndrome protein. Results After lentiviral vector-mediated GT, the number of transduced B cells progressively increased in the peripheral blood of all patients. Lentiviral vector-transduced progenitor cells were able to repopulate the B-cell compartment with a normal distribution of B-cell subsets both in bone marrow and the periphery, showing a WAS protein expression profile similar to that of healthy donors. In addition, after GT, we observed a normalized frequency of autoimmune-associated CD19+CD21−CD35− and CD21low B cells and a reduction in B cell–activating factor levels. Immunoglobulin serum levels and autoantibody production improved in all treated patients. Conclusions We provide evidence that lentiviral vector-mediated GT induces transgene expression in the B-cell compartment, resulting in ameliorated B-cell development and functionality and contributing to immunologic

  1. Intercellular delivery of a herpes simplex virus VP22 fusion protein from cells infected with lentiviral vectors

    PubMed Central

    Lai, Zhennan; Han, Ina; Zirzow, Gregory; Brady, Roscoe O.; Reiser, Jakob

    2000-01-01

    Effective gene therapy depends on the efficient transfer of therapeutic genes and their protein products to target cells. Lentiviral vectors appear promising for virus-mediated gene delivery and long-term expression in nondividing cells. The herpes simplex virus type 1 tegument protein VP22 has recently been shown to mediate intercellular transport of proteins, raising the possibility that it may be helpful in a setting where the global delivery of therapeutic proteins is desired. To investigate the effectiveness of lentiviral vectors to deliver genes encoding proteins fused to VP22, and to test whether the system is sufficiently potent to allow protein delivery from transduced cells in vitro and in vivo, fusion constructs of VP22 and the enhanced green fluorescent protein (EGFP) were prepared and delivered into target cells by using HIV-1-based lentiviral vectors. To follow the spread of VP22-EGFP to other cells, transduced COS-7 cells were coplated with a number of different cell types, including brain choroid plexus cells, human endothelial cells, H9 cells, and HeLa cells. We found that VP22-EGFP fusion proteins were transported from transduced cells to recipient cells and that such fusion proteins accumulated in the nucleus and in the cytoplasm of such cells. To determine the ability to deliver fusion proteins in vivo, we injected transduced H9 cells as well as the viral vector directly into the brain of mice. We present evidence that VP22-EGFP fusion proteins were transported effectively from lentivirus transduced cells in vivo. We also show that the VP22-EGFP fusion protein encoded by the lentivirus is transported between cells. Our data indicate that such fusion proteins are present in the nucleus and in the cytoplasm of neighboring cells. Therefore, lentiviral vectors may provide a potent biological system for delivering genes encoding therapeutic proteins fused to VP22. PMID:11027330

  2. Integrated GlycoProteome Analyzer (I-GPA) for Automated Identification and Quantitation of Site-Specific N-Glycosylation

    PubMed Central

    Park, Gun Wook; Kim, Jin Young; Hwang, Heeyoun; Lee, Ju Yeon; Ahn, Young Hee; Lee, Hyun Kyoung; Ji, Eun Sun; Kim, Kwang Hoe; Jeong, Hoi Keun; Yun, Ki Na; Kim, Yong-Sam; Ko, Jeong-Heon; An, Hyun Joo; Kim, Jae Han; Paik, Young-Ki; Yoo, Jong Shin

    2016-01-01

    Human glycoproteins exhibit enormous heterogeneity at each N-glycosite, but few studies have attempted to globally characterize the site-specific structural features. We have developed Integrated GlycoProteome Analyzer (I-GPA) including mapping system for complex N-glycoproteomes, which combines methods for tandem mass spectrometry with a database search and algorithmic suite. Using an N-glycopeptide database that we constructed, we created novel scoring algorithms with decoy glycopeptides, where 95 N-glycopeptides from standard α1-acid glycoprotein were identified with 0% false positives, giving the same results as manual validation. Additionally automated label-free quantitation method was first developed that utilizes the combined intensity of top three isotope peaks at three highest MS spectral points. The efficiency of I-GPA was demonstrated by automatically identifying 619 site-specific N-glycopeptides with FDR ≤ 1%, and simultaneously quantifying 598 N-glycopeptides, from human plasma samples that are known to contain highly glycosylated proteins. Thus, I-GPA platform could make a major breakthrough in high-throughput mapping of complex N-glycoproteomes, which can be applied to biomarker discovery and ongoing global human proteome project. PMID:26883985

  3. Integrated GlycoProteome Analyzer (I-GPA) for Automated Identification and Quantitation of Site-Specific N-Glycosylation.

    PubMed

    Park, Gun Wook; Kim, Jin Young; Hwang, Heeyoun; Lee, Ju Yeon; Ahn, Young Hee; Lee, Hyun Kyoung; Ji, Eun Sun; Kim, Kwang Hoe; Jeong, Hoi Keun; Yun, Ki Na; Kim, Yong-Sam; Ko, Jeong-Heon; An, Hyun Joo; Kim, Jae Han; Paik, Young-Ki; Yoo, Jong Shin

    2016-01-01

    Human glycoproteins exhibit enormous heterogeneity at each N-glycosite, but few studies have attempted to globally characterize the site-specific structural features. We have developed Integrated GlycoProteome Analyzer (I-GPA) including mapping system for complex N-glycoproteomes, which combines methods for tandem mass spectrometry with a database search and algorithmic suite. Using an N-glycopeptide database that we constructed, we created novel scoring algorithms with decoy glycopeptides, where 95 N-glycopeptides from standard α1-acid glycoprotein were identified with 0% false positives, giving the same results as manual validation. Additionally automated label-free quantitation method was first developed that utilizes the combined intensity of top three isotope peaks at three highest MS spectral points. The efficiency of I-GPA was demonstrated by automatically identifying 619 site-specific N-glycopeptides with FDR ≤ 1%, and simultaneously quantifying 598 N-glycopeptides, from human plasma samples that are known to contain highly glycosylated proteins. Thus, I-GPA platform could make a major breakthrough in high-throughput mapping of complex N-glycoproteomes, which can be applied to biomarker discovery and ongoing global human proteome project. PMID:26883985

  4. Breeding of transgenic cattle for human coagulation factor IX by a combination of lentiviral system and cloning.

    PubMed

    Monzani, P S; Sangalli, J R; De Bem, T H C; Bressan, F F; Fantinato-Neto, P; Pimentel, J R V; Birgel-Junior, E H; Fontes, A M; Covas, D T; Meirelles, F V

    2013-02-28

    Recombinant coagulation factor IX must be produced in mammalian cells because FIX synthesis involves translational modifications. Human cell culture-based expression of human coagulation factor IX (hFIX) is expensive, and large-scale production capacity is limited. Transgenic animals may greatly increase the yield of therapeutic proteins and reduce costs. In this study, we used a lentiviral system to obtain transgenic cells and somatic cell nuclear transfer (SCNT) to produce transgenic animals. Lentiviral vectors carrying hFIX driven by 3 bovine β-casein promoters were constructed. Bovine epithelial mammary cells were transduced by lentivirus, selected with blasticidin, plated on extracellular matrix, and induced by lactogenic hormones; promoter activity was evaluated by quantitative PCR. Transcriptional activity of the 5.335-kb promoter was 6-fold higher than the 3.392- and 4.279-kb promoters, which did not significantly differ. Transgenic bovine fibroblasts were transduced with lentivirus carrying the 5.335-kb promoter and used as donor cells for SCNT. Cloned transgenic embryo production yielded development rates of 28.4%, similar to previous reports on cloned non-transgenic embryos. The embryos were transferred to recipient cows (N = 21) and 2 births of cloned transgenic cattle were obtained. These results suggest combination of the lentiviral system and cloning may be a good strategy for production of transgenic cattle.

  5. Robust Lentiviral Gene Delivery But Limited Transduction Capacity of Commonly Used Adeno-Associated Viral Serotypes in Xenotransplanted Human Skin.

    PubMed

    Jakobsen, Maria; Askou, Anne Louise; Stenderup, Karin; Rosada, Cecilia; Dagnæs-Hansen, Frederik; Jensen, Thomas G; Corydon, Thomas J; Mikkelsen, Jacob Giehm; Aagaard, Lars

    2015-08-01

    Skin is an easily accessible organ, and therapeutic gene transfer to skin remains an attractive alternative for the treatment of skin diseases. Although we have previously documented potent lentiviral gene delivery to human skin, vectors based on adeno-associated virus (AAV) rank among the most promising gene delivery tools for in vivo purposes. Thus, we compared the potential usefulness of various serotypes of recombinant AAV vectors and lentiviral vectors for gene transfer to human skin in a xenotransplanted mouse model. Vector constructs encoding firefly luciferase were packaged in AAV capsids of serotype 1, 2, 5, 6, 8, and 9 and separately administered by intradermal injection in human skin transplants. For all serotypes, live bioimaging demonstrated low levels of transgene expression in the human skin graft, and firefly luciferase expression was observed primarily in neighboring tissue outside of the graft. In contrast, gene delivery by intradermally injected lentiviral vectors was efficient and led to extensive and persistent firefly luciferase expression within the human skin graft only. The study demonstrates the limited capacity of single-stranded AAV vectors of six commonly used serotypes for gene delivery to human skin in vivo. PMID:26204415

  6. Lung endothelial HO-1 targeting in vivo using lentiviral miRNA regulates apoptosis and autophagy during oxidant injury

    PubMed Central

    Zhang, Yi; Jiang, Ge; Sauler, Maor; Lee, Patty J.

    2013-01-01

    The lung endothelium is a major target for inflammatory and oxidative stress. Heme oxygenase-1 (HO-1) induction is a crucial defense mechanism during oxidant challenges, such as hyperoxia. The role of lung endothelial HO-1during hyperoxia in vivo is not well defined. We engineered lentiviral vectors with microRNA (miRNA) sequences controlled by vascular endothelium cadherin (VE-cad) to study the specific role of lung endothelial HO-1. Wild-type (WT) murine lung endothelial cells (MLECs) or WT mice were treated with lentivirus and exposed to hyperoxia (95% oxygen). We detected HO-1 knockdown (∼55%) specifically in the lung endothelium. MLECs and lungs showed approximately a 2-fold increase in apoptosis and ROS generation after HO-1 silencing. We also demonstrate for the first time that silencing endothelial HO-1 has the same effect on lung injury and survival as silencing HO-1 in multiple lung cell types and that HO-1 regulates caspase 3 activation and autophagy in endothelium during hyperoxia. These studies demonstrate the utility of endothelial-targeted gene silencing in vivo using lentiviral miRNA constructs to assess gene function and that endothelial HO-1 is an important determinant of survival during hyperoxia.—Zhang, Y., Jiang, G., Sauler, M., Lee, P. J. Lung endothelial HO-1 targeting in vivo using lentiviral miRNA regulates apoptosis and autophagy during oxidant injury. PMID:23771928

  7. Lentiviral vector-mediated over-expression of Sox9 protected chondrocytes from IL-1β induced degeneration and apoptosis

    PubMed Central

    Lu, Huading; Zeng, Chun; Chen, Mingwei; Lian, Liyi; Dai, Yuhu; Zhao, Huiqing

    2015-01-01

    To explore whether the over-expression of Sry-related HMG box (Sox9) in degenerative chondrocytes is able to improve cell regeneration and protects cells from inflammation induced apoptosis, we generated a Sox9 over-expressing vector delivery system in which the Sox9 gene was inserted into a lentiviral vector. After infecting mouse chondrocytes with the Sox9-encoding vector, we observed a high level of gene transduction efficiency and achieved a high level of Sox9 expression in the infected chondrocytes. To explore whether over-expression of Sox9 is able to induce cell regeneration and improve cell survival, we induced Sox9 over-expression by lentiviral vector infection 48 hours before IL-1β treatment. The cells were infected with the reporter gene GFP-encoded lentiviral vector as a negative control or left uninfected. 48-hours after IL-1β treatment, the chrondrocytes treated with IL-1β alone, underwent a degenerative process, with elevated expression of MMP-3, MMP-13, ADAMTS-5 and ALP, but the cell specific anabolic proteins collagen II and aggrecan were significantly suppressed. The cells infected with the GFP reporter vector had no increased regeneration after IL-1β treatment. The results indicated that Sox9 is an important chondrocyte transcription factor, promoting chondrocyte regeneration and cell survival, which were mediated through affecting multiple cell differentiation as well as anti-apoptotic signaling pathways. PMID:26617711

  8. Cleavage of Hemagglutinin-Bearing Lentiviral Pseudotypes and Their Use in the Study of Influenza Virus Persistence

    PubMed Central

    Sawoo, Olivier; Dublineau, Amélie; Batéjat, Christophe; Zhou, Paul; Manuguerra, Jean-Claude; Leclercq, India

    2014-01-01

    Influenza A viruses (IAVs) are a major cause of infectious respiratory human diseases and their transmission is dependent upon the environment. However, the role of environmental factors on IAV survival outside the host still raises many questions. In this study, we used lentiviral pseudotypes to study the influence of the hemagglutinin protein in IAV survival. High-titered and cleaved influenza-based lentiviral pseudoparticles, through the use of a combination of two proteases (HAT and TMPRSS2) were produced. Pseudoparticles bearing hemagglutinin proteins derived from different H1N1, H3N2 and H5N1 IAV strains were subjected to various environmental parameters over time and tested for viability through single-cycle infectivity assays. We showed that pseudotypes with different HAs have different persistence profiles in water as previously shown with IAVs. Our results also showed that pseudotypes derived from H1N1 pandemic virus survived longer than those derived from seasonal H1N1 virus from 1999, at high temperature and salinity, as previously shown with their viral counterparts. Similarly, increasing temperature and salinity had a negative effect on the survival of the H3N2 and H5N1 pseudotypes. These results showed that pseudotypes with the same lentiviral core, but which differ in their surface glycoproteins, survived differently outside the host, suggesting a role for the HA in virus stability. PMID:25166303

  9. Optimization of lentiviral vector transduction into peripheral blood mononuclear cells in combination with the fibronectin fragment CH-296 stimulation.

    PubMed

    Chono, Hideto; Goto, Yumi; Yamakawa, Satoko; Tanaka, Shinya; Tosaka, Yasuhiro; Nukaya, Ikuei; Mineno, Junichi

    2011-03-01

    Large scale T-cell expansion and efficient gene transduction are required for adoptive T-cell gene therapy. Based on our previous observations, human peripheral blood mononuclear cells (PBMCs) can be expanded efficiently while conserving a naïve phenotype by stimulating with both recombinant human fibronectin fragment (CH-296) and anti-CD3 monoclonal antibodies. In this article, we explored the possibility of using this co-stimulation method to generate engineered T cells using lentiviral vector. Human PBMCs were stimulated with anti-CD3 together with immobilized CH-296 or anti-CD28 antibody as well as anti-CD3/anti-CD28 conjugated beads and transduced with lentiviral vector simultaneously. Co-stimulation with CH-296 gave superior transduction efficiency than with anti-CD28. Next, PBMCs were stimulated and transduced with anti-CD3/CH-296 or with anti-CD3/CD28 beads. T-cell expansion, gene transfer efficiencies and immunophenotypes were analysed. Stimulation with anti-CD3/CH-296 resulted in more than 10-times higher cell expansion and higher gene transfer efficiency with conservation of the naïve phenotype compared with anti-CD3/CD28 stimulation method. Thus, lentiviral transduction with anti-CD3/CH-296 co-stimulation is an efficient way to generate large numbers of genetically modified T cells and may be suitable for many gene therapy protocols that use adoptive T-cell transfer therapy.

  10. Quantitative analysis of recombination between YFP and CFP genes of FRET biosensors introduced by lentiviral or retroviral gene transfer.

    PubMed

    Komatsubara, Akira T; Matsuda, Michiyuki; Aoki, Kazuhiro

    2015-01-01

    Biosensors based on the principle of Förster (or fluorescence) resonance energy transfer (FRET) have been developed to visualize spatio-temporal dynamics of signalling molecules in living cells. Many of them adopt a backbone of intramolecular FRET biosensor with a cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) as donor and acceptor, respectively. However, there remains the difficulty of establishing cells stably expressing FRET biosensors with a YFP and CFP pair by lentiviral or retroviral gene transfer, due to the high incidence of recombination between YFP and CFP genes. To address this, we examined the effects of codon-diversification of YFP on the recombination of FRET biosensors introduced by lentivirus or retrovirus. The YFP gene that was fully codon-optimized to E.coli evaded the recombination in lentiviral or retroviral gene transfer, but the partially codon-diversified YFP did not. Further, the length of spacer between YFP and CFP genes clearly affected recombination efficiency, suggesting that the intramolecular template switching occurred in the reverse-transcription process. The simple mathematical model reproduced the experimental data sufficiently, yielding a recombination rate of 0.002-0.005 per base. Together, these results show that the codon-diversified YFP is a useful tool for expressing FRET biosensors by lentiviral or retroviral gene transfer. PMID:26290434

  11. Establishment of an improved high-efficiency thermal asymmetric interlaced PCR for identification of genomic integration sites mediated by phiC31 integrase.

    PubMed

    Zhou, Zaiwei; Ma, Haiyan; Qu, Lijuan; Xie, Fei; Ma, Qingwen; Ren, Zhaorui

    2012-03-01

    Streptomyces phage phiC31 integrase is widely used to mediate the integration of exogenous genes into host genomes for gene therapy and genomic modification, as it autonomously performs efficient, unidirectional, site-specific integration into pseudo attP sites of the host genome. Although pseudo attP sites are rarely found within exons, it is necessary to map their precise locations to avoid the risk of insertion mutagenesis. High-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR) is a technique that has been developed to recover genomic sequences that flank insertion tags. We have found, however, that this technique is poorly efficient, as it amplifies many non-specific targets and frequently does not generate sufficient product for downstream analysis. Therefore, we have modified the hiTAIL-PCR procedure and re-designed the random primers. As a result, both the amount and specificity of the reaction product were enhanced for each integration site. Restriction analysis of known sequences within the integrated vector, which co-amplified with the flanking genomic sequences, validated 90% of these bands for sequencing. In contrast, only 30% of the bands produced by previous hiTAIL-PCR could be validated. Compared with the original hiTAIL-PCR, our improved hiTAIL-PCR procedure identified phiC31 integration sites more accurately and efficiently.

  12. RD2-MolPack-Chim3, a Packaging Cell Line for Stable Production of Lentiviral Vectors for Anti-HIV Gene Therapy

    PubMed Central

    Stornaiuolo, Anna; Piovani, Bianca Maria; Bossi, Sergio; Zucchelli, Eleonora; Corna, Stefano; Salvatori, Francesca; Mavilio, Fulvio; Bordignon, Claudio; Rizzardi, Gian Paolo

    2013-01-01

    Abstract Over the last two decades, several attempts to generate packaging cells for lentiviral vectors (LV) have been made. Despite different technologies, no packaging clone is currently employed in clinical trials. We developed a new strategy for LV stable production based on the HEK-293T progenitor cells; the sequential insertion of the viral genes by integrating vectors; the constitutive expression of the viral components; and the RD114-TR envelope pseudotyping. We generated the intermediate clone PK-7 expressing constitutively gag/pol and rev genes and, by adding tat and rd114-tr genes, the stable packaging cell line RD2-MolPack, which can produce LV carrying any transfer vector (TV). Finally, we obtained the RD2-MolPack-Chim3 producer clone by transducing RD2-MolPack cells with the TV expressing the anti-HIV transgene Chim3. Remarkably, RD114-TR pseudovirions have much higher potency when produced by stable compared with transient technology. Most importantly, comparable transduction efficiency in hematopoietic stem cells (HSC) is obtained with 2-logs less physical particles respect to VSV-G pseudovirions produced by transient transfection. Altogether, RD2-MolPack technology should be considered a valid option for large-scale production of LV to be used in gene therapy protocols employing HSC, resulting in the possibility of downsizing the manufacturing scale by about 10-fold in respect to transient technology. PMID:23767932

  13. RD2-MolPack-Chim3, a packaging cell line for stable production of lentiviral vectors for anti-HIV gene therapy.

    PubMed

    Stornaiuolo, Anna; Piovani, Bianca Maria; Bossi, Sergio; Zucchelli, Eleonora; Corna, Stefano; Salvatori, Francesca; Mavilio, Fulvio; Bordignon, Claudio; Rizzardi, Gian Paolo; Bovolenta, Chiara

    2013-08-01

    Over the last two decades, several attempts to generate packaging cells for lentiviral vectors (LV) have been made. Despite different technologies, no packaging clone is currently employed in clinical trials. We developed a new strategy for LV stable production based on the HEK-293T progenitor cells; the sequential insertion of the viral genes by integrating vectors; the constitutive expression of the viral components; and the RD114-TR envelope pseudotyping. We generated the intermediate clone PK-7 expressing constitutively gag/pol and rev genes and, by adding tat and rd114-tr genes, the stable packaging cell line RD2-MolPack, which can produce LV carrying any transfer vector (TV). Finally, we obtained the RD2-MolPack-Chim3 producer clone by transducing RD2-MolPack cells with the TV expressing the anti-HIV transgene Chim3. Remarkably, RD114-TR pseudovirions have much higher potency when produced by stable compared with transient technology. Most importantly, comparable transduction efficiency in hematopoietic stem cells (HSC) is obtained with 2-logs less physical particles respect to VSV-G pseudovirions produced by transient transfection. Altogether, RD2-MolPack technology should be considered a valid option for large-scale production of LV to be used in gene therapy protocols employing HSC, resulting in the possibility of downsizing the manufacturing scale by about 10-fold in respect to transient technology.

  14. A Modular Lentiviral and Retroviral Construction System to Rapidly Generate Vectors for Gene Expression and Gene Knockdown In Vitro and In Vivo

    PubMed Central

    Geiling, Benjamin; Vandal, Guillaume; Posner, Ada R.; de Bruyns, Angeline; Dutchak, Kendall L.; Garnett, Samantha; Dankort, David

    2013-01-01

    The ability to express exogenous cDNAs while suppressing endogenous genes via RNAi represents an extremely powerful research tool with the most efficient non-transient approach being accomplished through stable viral vector integration. Unfortunately, since traditional restriction enzyme based methods for constructing such vectors are sequence dependent, their construction is often difficult and not amenable to mass production. Here we describe a non-sequence dependent Gateway recombination cloning system for the rapid production of novel lentiviral (pLEG) and retroviral (pREG) vectors. Using this system to recombine 3 or 4 modular plasmid components it is possible to generate viral vectors expressing cDNAs with or without inhibitory RNAs (shRNAmirs). In addition, we demonstrate a method to rapidly produce and triage novel shRNAmirs for use with this system. Once strong candidate shRNAmirs have been identified they may be linked together in tandem to knockdown expression of multiple targets simultaneously or to improve the knockdown of a single target. Here we demonstrate that these recombinant vectors are able to express cDNA and effectively knockdown protein expression using both cell culture and animal model systems. PMID:24146852

  15. Integrating nonlinear site effects in broadband ground motion models: Observations and simulations in the Los Angeles basin

    NASA Astrophysics Data System (ADS)

    Assimaki, D.; Steidl, J.; Li, W.

    2006-12-01

    Site-specific ground response analyses to strong seismic motion are currently required for the design of new components of the civil infrastructure on deep and/or soft sedimentary deposits, which prevail in many urban areas of moderate to high seismic risk in the US such as the Los Angeles basin. In these cases, it is necessary to arrive at realistic predictions of the nonlinear soil behavior, which require elaborate analyses to be employed that are associated, however, with considerable cost and effort. Currently, uncertainties exist regarding the methodology to be employed, the level of sophistication required that determines the number of input parameters, and the development of these parameters for implementation. These difficulties, further aggravated by the lack of well-documented validation studies, have thus far prohibited the integration of nonlinear analysis procedures in broadband ground motion simulations. We here present the parametric investigation of recorded and simulated ground motion time-histories for selected sites in the Los Angeles basin, conducted to examine the variability in ground response estimation as a function of the employed nonlinear soil model complexity, and the extent of geotechnical data availability in the near-surface. For this purpose, weak motion waveform inversion is first employed at selected sites in the basin, in absence of the necessary detailed low-strain dynamic soil property distribution in the near surface. Successively, the corresponding one-dimensional (1D) crustal velocity profiles are depicted at these locations based on the SCEC Community Velocity Model, and synthetic ground motion simulations are conducted for the rupture of a wide range of strike-slip fault geometries by means of the hybrid low/high-frequency method with correlated random source parameters. The lack of multiple strong motion seismic data at these sites necessitates the use of simulated ground motion time-histories for the generation of a

  16. A Lentiviral Vector Expressing Japanese Encephalitis Virus-like Particles Elicits Broad Neutralizing Antibody Response in Pigs

    PubMed Central

    Souque, Philippe; Frenkiel, Marie-Pascale; Paulous, Sylvie; Garcìa-Nicolàs, Obdulio; Summerfield, Artur; Charneau, Pierre; Desprès, Philippe

    2015-01-01

    Background Japanese encephalitis virus (JEV) is the major cause of viral encephalitis in Southeast Asia. Vaccination of domestic pigs has been suggested as a “one health” strategy to reduce viral disease transmission to humans. The efficiency of two lentiviral TRIP/JEV vectors expressing the JEV envelope prM and E glycoproteins at eliciting protective humoral response was assessed in a mouse model and piglets. Methodology/Principal Findings A gene encoding the envelope proteins prM and E from a genotype 3 JEV strain was inserted into a lentiviral TRIP vector. Two lentiviral vectors TRIP/JEV were generated, each expressing the prM signal peptide followed by the prM protein and the E glycoprotein, the latter being expressed either in its native form or lacking its two C-terminal transmembrane domains. In vitro transduction of cells with the TRIP/JEV vector expressing the native prM and E resulted in the efficient secretion of virus-like particles of Japanese encephalitis virus. Immunization of BALB/c mice with TRIP/JEV vectors resulted in the production of IgGs against Japanese encephalitis virus, and the injection of a second dose one month after the prime injection greatly boosted antibody titers. The TRIP/JEV vectors elicited neutralizing antibodies against JEV strains belonging to genotypes 1, 3, and 5. Immunization of piglets with two doses of the lentiviral vector expressing JEV virus-like particles led to high titers of anti-JEV antibodies, that had efficient neutralizing activity regardless of the JEV genotype tested. Conclusions/Significance Immunization of pigs with the lentiviral vector expressing JEV virus-like particles is particularly efficient to prime antigen-specific humoral immunity and trigger neutralizing antibody responses against JEV genotypes 1, 3, and 5. The titers of neutralizing antibodies elicited by the TRIP/JEV vector are sufficient to confer protection in domestic pigs against different genotypes of JEV and this could be of a great

  17. Editing T cell specificity towards leukemia by zinc-finger nucleases and lentiviral gene transfer

    PubMed Central

    Lombardo, Angelo; Magnani, Zulma; Liu, Pei-Qi; Reik, Andreas; Chu, Victoria; Paschon, David E.; Zhang, Lei; Kuball, Jurgen; Camisa, Barbara; Bondanza, Attilio; Casorati, Giulia; Ponzoni, Maurilio; Ciceri, Fabio; Bordignon, Claudio; Greenberg, Philip D.; Holmes, Michael C.; Gregory, Philip D.; Naldini, Luigi; Bonini, Chiara

    2016-01-01

    The transfer of high-avidity T-cell receptor (TCR) genes isolated from rare tumor-specific lymphocytes into polyclonal T cells is an attractive cancer immunotherapy strategy. However, TCR gene transfer results in competition for surface expression and inappropriate pairing between the exogenous and endogenous TCR chains, resulting in suboptimal activity and potentially harmful unpredicted specificities. We designed zinc-finger nucleases (ZFNs) promoting the disruption of endogenous TCR β and α chain genes. ZFN-treated lymphocytes lacked CD3/TCR surface expression and expanded with IL-7 and IL-15. Upon lentiviral transfer of a TCR for the WT1 tumor antigen, these TCR-edited cells expressed the new TCR at high levels, were easily expanded to near-purity, and proved superior in specific antigen recognition to matched TCR-transferred cells. In contrast to TCR-transferred cells, TCR edited lymphocytes did not mediate off-target reactivity while maintaining anti-tumor activity in vivo, thus demonstrating that complete editing of T-cell specificity generate tumor-specific lymphocytes with improved biosafety profile. PMID:22466705

  18. Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants

    PubMed Central

    Greenwood, Edward JD; Matheson, Nicholas J; Wals, Kim; van den Boomen, Dick JH; Antrobus, Robin; Williamson, James C; Lehner, Paul J

    2016-01-01

    Viruses manipulate host factors to enhance their replication and evade cellular restriction. We used multiplex tandem mass tag (TMT)-based whole cell proteomics to perform a comprehensive time course analysis of >6500 viral and cellular proteins during HIV infection. To enable specific functional predictions, we categorized cellular proteins regulated by HIV according to their patterns of temporal expression. We focussed on proteins depleted with similar kinetics to APOBEC3C, and found the viral accessory protein Vif to be necessary and sufficient for CUL5-dependent proteasomal degradation of all members of the B56 family of regulatory subunits of the key cellular phosphatase PP2A (PPP2R5A-E). Quantitative phosphoproteomic analysis of HIV-infected cells confirmed Vif-dependent hyperphosphorylation of >200 cellular proteins, particularly substrates of the aurora kinases. The ability of Vif to target PPP2R5 subunits is found in primate and non-primate lentiviral lineages, and remodeling of the cellular phosphoproteome is therefore a second ancient and conserved Vif function. DOI: http://dx.doi.org/10.7554/eLife.18296.001 PMID:27690223

  19. Lentiviral vectors in gene therapy: their current status and future potential.

    PubMed

    Escors, David; Breckpot, Karine

    2010-04-01

    The concept of gene therapy originated in the mid twentieth century and was perceived as a revolutionary technology with the promise to cure almost any disease of which the molecular basis was understood. Since then, several gene vectors have been developed and the feasibility of gene therapy has been shown in many animal models of human disease. However, clinical efficacy could not be demonstrated until the beginning of the new century in a small-scale clinical trial curing an otherwise fatal immunodeficiency disorder in children. This first success, achieved after retroviral therapy, was later overshadowed by the occurrence of vector-related leukemia in a significant number of the treated children, demonstrating that the future success of gene therapy depends on our understanding of vector biology. This has led to the development of later-generation vectors with improved efficiency, specificity, and safety. Amongst these are HIV-1 lentivirus-based vectors (lentivectors), which are being increasingly used in basic and applied research. Human gene therapy clinical trials are currently underway using lentivectors in a wide range of human diseases. The intention of this review is to describe the main scientific steps leading to the engineering of HIV-1 lentiviral vectors and place them in the context of current human gene therapy.

  20. Role of Transgene Regulation in Ex Vivo Lentiviral Correction of Artemis Deficiency

    PubMed Central

    Multhaup, Megan M.; Podetz-Pedersen, Kelly M.; Karlen, Andrea D.; Olson, Erik R.; Gunther, Roland; Somia, Nikunj V.; Blazar, Bruce R.; Cowan, Morton J.

    2015-01-01

    Abstract Artemis is a single-stranded endonuclease, deficiency of which results in a radiation-sensitive form of severe combined immunodeficiency (SCID-A) most effectively treated by allogeneic hematopoietic stem cell (HSC) transplantation and potentially treatable by administration of genetically corrected autologous HSCs. We previously reported cytotoxicity associated with Artemis overexpression and subsequently characterized the human Artemis promoter with the intention to provide Artemis expression that is nontoxic yet sufficient to support immunodevelopment. Here we compare the human Artemis promoter (APro) with the moderate-strength human phosphoglycerate kinase (PGK) promoter and the strong human elongation factor-1α (EF1α) promoter to regulate expression of Artemis after ex vivo lentiviral transduction of HSCs in a murine model of SCID-A. Recipient animals treated with the PGK-Artemis vector exhibited moderate repopulation of their immune compartment, yet demonstrated a defective proliferative T lymphocyte response to in vitro antigen stimulation. Animals treated with the EF1α-Artemis vector displayed high levels of T lymphocytes but an absence of B lymphocytes and deficient lymphocyte function. In contrast, ex vivo transduction with the APro-Artemis vector supported effective immune reconstitution to wild-type levels, resulting in fully functional T and B lymphocyte responses. These results demonstrate the importance of regulated Artemis expression in immune reconstitution of Artemis-deficient SCID. PMID:25738323

  1. Lentiviral vectors in gene therapy: their current status and future potential

    PubMed Central

    Escors, David; Breckpot, Karine

    2010-01-01

    Summary The concept of gene therapy originated in the mid 20th century and was perceived as a revolutionary technology with the promise to cure almost any disease of which the molecular basis was understood. Since then, several gene vectors have been developed, and the feasibility of gene therapy shown in many animal models of human disease. However, clinical efficacy could not be demonstrated until the beginning of the new century in a small-scale clinical trial curing an otherwise fatal immunodeficiency disorder in children. This first success – achieved after retroviral therapy - was later on overshadowed by the occurrence of vector-related leukaemia in a significant number of the treated children, demonstrating that the future success of gene therapy depends on our understanding of vector biology. This has led to the development of later generation vectors with improved efficiency, specificity and safety. Amongst these are HIV-1 lentivirus-based vectors (lentivectors), which are being increasingly used in basic and applied research. Human gene therapy clinical trials are currently under way using lentivectors in a wide range of human diseases. The intention of this review is to describe the main scientific steps leading to the engineering of HIV-1 lentiviral vectors, and place them in the context of current human gene therapy. PMID:20143172

  2. Optimizing Glioblastoma Temozolomide Chemotherapy Employing Lentiviral-based Anti-MGMT shRNA Technology

    PubMed Central

    Viel, Thomas; Monfared, Parisa; Schelhaas, Sonja; Fricke, Inga B; Kuhlmann, Michael T; Fraefel, Cornel; Jacobs, Andreas H

    2013-01-01

    Despite treatments combining surgery, radiation-, and chemotherapy, patients affected by glioblastoma (GBM) have a limited prognosis. Addition of temozolomide (TMZ) to radiation therapy is the standard therapy in clinical application, but effectiveness of TMZ is limited by the tumor's overexpression of the DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT). The goal of this study was to use the highly specific and efficient RNA interference (RNAi) pathway to modulate MGMT expression to increase TMZ efficiency in chemotherapy resistant GBM. Using lentiviral-based anti-MGMT small hairpin RNA (shRNA) technology we observed a specific inhibition of the MGMT expression in GBM cell lines as well as in subcutaneous tumors. Tumor growth inhibition was observed following TMZ treatment of xenografts with low MGMT expression in contrast to xenografts with high MGMT expression. Bioluminescence imaging (BLI) measurements indicated that luciferase and shRNA-expressing lentiviruses were able to efficiently transduce the GBM xenografts in vivo. Treatment combining injection of a lentivirus expressing an anti-MGMT shRNA and TMZ induced a reduction of the size of the tumors, in contrast with treatment combining the lentivirus expressing the control shRNA and TMZ. Our data suggest that anti-MGMT shRNA therapy could be used in combination with TMZ chemotherapy in order to improve the treatment of resistant GBM. PMID:23319055

  3. Use of a Closed Culture System to Improve the Safety of Lentiviral Vector Production.

    PubMed

    Wu, Tao; Bour, Gaëtan; Durand, Sarah; Lindner, Véronique; Gossé, Francine; Zona, Laetitia; Certoux, Jean-Marie; Diana, Michele; Baumert, Thomas F; Marescaux, Jacques; Mutter, Didier; Pessaux, Patrick; Robinet, Eric

    2015-12-01

    We evaluated the possibility of introducing a combination of six oncogenes into primary porcine hepatocytes (PPH) using a lentiviral vector (LV)-mediated gene transfer in order to develop a porcine hepatocellular carcinoma model based on autologous transplantation of ex vivo-transformed hepatocytes. The six oncogenes were introduced into three plasmids, hence enabling the production of LVs encoding a luciferase reporter gene and hTERT+p53(DD), cyclinD1+CDK4(R24C), and c-myc(T58A)+HRas(G21V) genes, respectively. In order to improve the protection of the laboratory personnel manipulating such LVs, we used a compact cell culture cassette (CliniCell(®) device) as a closed cell culture system. We demonstrated that the CliniCell device allows to produce LVs, through plasmid transfection of 293T cells, and, after transfer to a second cassette, to transduce PPH with a similar efficacy as conventional open cell culture systems such as flasks or Petri dishes. Additionally, it is possible to cryopreserve at -80°C the transduced cells, directly in the CliniCell device used for the transduction. In conclusion, the use of a closed culture system for the safe handling of oncogene-encoding LVs lays the foundation for the development of porcine tumor models based on the autologous transplantation of ex vivo-transformed primary cells. PMID:26467420

  4. Visualization of DC-SIGN-mediated entry pathway of engineered lentiviral vectors in target cells.

    PubMed

    Liu, Yarong; Tai, April; Joo, Kye-Il; Wang, Pin

    2013-01-01

    Dendritic cells (DCs) are potent antigen-presenting cells and therefore have enormous potential as vaccine targets. We have previously developed an engineered lentiviral vector (LV) that is pseudotyped with a mutated Sindbis virus glycoprotein (SVGmu), which is capable of targeting DCs through Dendritic Cell-specific ICAM3-grabbing Nonintegrin (DC-SIGN), a receptor that is predominantly expressed by DCs. In this study, we aimed to elucidate the internalization and trafficking mechanisms of this viral vector system through direct visualization of GFP-Vpr-tagged viral particles in target DCs, which was further corroborated by drug inhibition and dominant-negative mutants of cellular proteins that regulate the endocytic traffic. We demonstrated that our engineered LVs enter the cell via receptor-mediated clathrin- and dynamin-dependent endocytosis. Microtubule networks were also involved in a productive infection. Viral vector fusion was low-pH-dependent and occurred in the early endosomal stage of the intracellular transport. Autophagy was also examined for its effect on transduction efficiency, and we observed that enhanced autophage activity reduced vector infectivity, while suppressed autophagy boosted transduction efficiency. This study shed some light on the internalization and trafficking mechanisms of DC-directed LVs and offers some strategies to further improve the efficiency of LV-mediated gene therapy.

  5. Design of a regulated lentiviral vector for hematopoietic stem cell gene therapy of globoid cell leukodystrophy

    PubMed Central

    Ungari, Silvia; Montepeloso, Annita; Morena, Francesco; Cocchiarella, Fabienne; Recchia, Alessandra; Martino, Sabata; Gentner, Bernhard; Naldini, Luigi; Biffi, Alessandra

    2015-01-01

    Globoid cell leukodystrophy (GLD) is a demyelinating lysosomal storage disease due to the deficiency of the galactocerebrosidase (GALC) enzyme. The favorable outcome of hematopoietic stem and progenitor cell (HSPC)-based approaches in GLD and other similar diseases suggests HSPC gene therapy as a promising therapeutic option for patients. The path to clinical development of this strategy was hampered by a selective toxicity of the overexpressed GALC in the HSPC compartment. Here, we presented the optimization of a lentiviral vector (LV) in which miR-126 regulation was coupled to codon optimization of the human GALC cDNA to obtain a selective and enhanced enzymatic activity only upon transduced HSPCs differentiation. The safety of human GALC overexpression driven by this LV was extensively demonstrated in vitro and in vivo on human HSPCs from healthy donors. No perturbation in the content of proapoptotic sphingolipids, gene expression profile, and capability of engraftment and mutlilineage differentiation in chimeric mice was observed. The therapeutic potential of this LV was then assessed in a severe GLD murine model that benefited from transplantation of corrected HSPCs with longer survival and ameliorated phenotype as compared to untreated siblings. This construct has thus been selected as a candidate for clinical translation. PMID:26509184

  6. Design of a regulated lentiviral vector for hematopoietic stem cell gene therapy of globoid cell leukodystrophy.

    PubMed

    Ungari, Silvia; Montepeloso, Annita; Morena, Francesco; Cocchiarella, Fabienne; Recchia, Alessandra; Martino, Sabata; Gentner, Bernhard; Naldini, Luigi; Biffi, Alessandra

    2015-01-01

    Globoid cell leukodystrophy (GLD) is a demyelinating lysosomal storage disease due to the deficiency of the galactocerebrosidase (GALC) enzyme. The favorable outcome of hematopoietic stem and progenitor cell (HSPC)-based approaches in GLD and other similar diseases suggests HSPC gene therapy as a promising therapeutic option for patients. The path to clinical development of this strategy was hampered by a selective toxicity of the overexpressed GALC in the HSPC compartment. Here, we presented the optimization of a lentiviral vector (LV) in which miR-126 regulation was coupled to codon optimization of the human GALC cDNA to obtain a selective and enhanced enzymatic activity only upon transduced HSPCs differentiation. The safety of human GALC overexpression driven by this LV was extensively demonstrated in vitro and in vivo on human HSPCs from healthy donors. No perturbation in the content of proapoptotic sphingolipids, gene expression profile, and capability of engraftment and mutlilineage differentiation in chimeric mice was observed. The therapeutic potential of this LV was then assessed in a severe GLD murine model that benefited from transplantation of corrected HSPCs with longer survival and ameliorated phenotype as compared to untreated siblings. This construct has thus been selected as a candidate for clinical translation.

  7. Vectofusin-1, a new viral entry enhancer, strongly promotes lentiviral transduction of human hematopoietic stem cells.

    PubMed

    Fenard, David; Ingrao, Dina; Seye, Ababacar; Buisset, Julien; Genries, Sandrine; Martin, Samia; Kichler, Antoine; Galy, Anne

    2013-05-07

    Gene transfer into hCD34(+) hematopoietic stem/progenitor cells (HSCs) using human immunodeficiency virus type 1 (HIV-1)-based lentiviral vectors (LVs) has several promising therapeutic applications. Yet, efficiency, safety, and cost of LV gene therapy could be ameliorated by enhancing target cell transduction levels and reducing the amount of LV used on the cells. Several transduction enhancers already exist such as fibronectin fragments and cationic compounds, but all present limitations. In this study, we describe a new transduction enhancer called Vectofusin-1, which is a short cationic peptide, active on several LV pseudotypes. Vectofusin-1 is used as a soluble additive to safely increase the frequency of transduced HSCs and to augment the level of transduction to one or two copies of vector per cell in a vector dose-dependent manner. Vectofusin-1 acts at the entry step by promoting the adhesion and the fusion between viral and cellular membranes. Vectofusin-1 is therefore a promising additive that could significantly ameliorate hCD34(+) cell-based gene therapy.Molecular Therapy-Nucleic Acids (2013) 2, e90; doi:10.1038/mtna.2013.17; published online 7 May 2013.

  8. Stable and Efficient Gene Transfer into the Retina Using an HIV-Based Lentiviral Vector

    NASA Astrophysics Data System (ADS)

    Miyoshi, Hiroyuki; Takahashi, Masayo; Gage, Fred H.; Verma, Inder M.

    1997-09-01

    The development of methods for efficient gene transfer to terminally differentiated retinal cells is important to study the function of the retina as well as for gene therapy of retinal diseases. We have developed a lentiviral vector system based on the HIV that can transduce terminally differentiated neurons of the brain in vivo. In this study, we have evaluated the ability of HIV vectors to transfer genes into retinal cells. An HIV vector containing a gene encoding the green fluorescent protein (GFP) was injected into the subretinal space of rat eyes. The GFP gene under the control of the cytomegalovirus promoter was efficiently expressed in both photoreceptor cells and retinal pigment epithelium. However, the use of the rhodopsin promoter resulted in expression predominantly in photoreceptor cells. Most successfully transduced eyes showed that photoreceptor cells in >80% of the area of whole retina expressed the GFP. The GFP expression persisted for at least 12 weeks with no apparent decrease. The efficient gene transfer into photoreceptor cells by HIV vectors will be useful for gene therapy of retinal diseases such as retinitis pigmentosa.

  9. Role of transgene regulation in ex vivo lentiviral correction of artemis deficiency.

    PubMed

    Multhaup, Megan M; Podetz-Pedersen, Kelly M; Karlen, Andrea D; Olson, Erik R; Gunther, Roland; Somia, Nikunj V; Blazar, Bruce R; Cowan, Morton J; McIvor, R Scott

    2015-04-01

    Artemis is a single-stranded endonuclease, deficiency of which results in a radiation-sensitive form of severe combined immunodeficiency (SCID-A) most effectively treated by allogeneic hematopoietic stem cell (HSC) transplantation and potentially treatable by administration of genetically corrected autologous HSCs. We previously reported cytotoxicity associated with Artemis overexpression and subsequently characterized the human Artemis promoter with the intention to provide Artemis expression that is nontoxic yet sufficient to support immunodevelopment. Here we compare the human Artemis promoter (APro) with the moderate-strength human phosphoglycerate kinase (PGK) promoter and the strong human elongation factor-1α (EF1α) promoter to regulate expression of Artemis after ex vivo lentiviral transduction of HSCs in a murine model of SCID-A. Recipient animals treated with the PGK-Artemis vector exhibited moderate repopulation of their immune compartment, yet demonstrated a defective proliferative T lymphocyte response to in vitro antigen stimulation. Animals treated with the EF1α-Artemis vector displayed high levels of T lymphocytes but an absence of B lymphocytes and deficient lymphocyte function. In contrast, ex vivo transduction with the APro-Artemis vector supported effective immune reconstitution to wild-type levels, resulting in fully functional T and B lymphocyte responses. These results demonstrate the importance of regulated Artemis expression in immune reconstitution of Artemis-deficient SCID. PMID:25738323

  10. Identification of a Tc1-like transposon integration site in the genome of the flounder (Platichthys flesus): a novel use of an inverse PCR method.

    PubMed

    Poćwierz-Kotus, Anita; Burzyński, Artur; Wenne, Roman

    2010-03-01

    The inverse PCR method has been developed and applied employed for the identification of the integration sites of the Tc1-like transposons in the genome of the flounder, Platichthys flesus. One Tc1-like insertion instance was recognized and characterized, demonstrating an efficiency of the method for determining of transposon integration sites. The similarity of the sequence flanking transposon (SFT) to reverse transcriptase sequences (RVT) was demonstrated. It is likely that the insertion took place within currently degenerated LINE (long interspersed nuclear elements) retrotransposon.

  11. Tropical forest response to elevated CO2: Model-experiment integration at the AmazonFACE site.

    NASA Astrophysics Data System (ADS)

    Fleischer, K.

    2015-12-01

    The terrestrial biosphere's response to current and future elevated atmospheric carbon dioxide (eCO2) is a large source of uncertainty in future projections of the C cycle, climate and ecosystem functioning. In particular, the sensitivity of tropical rainforest ecosystems to eCO­2 is largely unknown even though the importance of tropical forests for biodiversity, carbon storage and regional and global climate feedbacks is unambiguously recognized. The AmazonFACE (Free-Air Carbon Enrichment) project will be the first ecosystem scale eCO2 experiment undertaken in the tropics, as well as the first to be undertaken in a mature forest. AmazonFACE provides the opportunity to integrate ecosystem modeling with experimental observations right from the beginning of the experiment, harboring a two-way exchange, i.e. models provide hypotheses to be tested, and observations deliver the crucial data to test and improve ecosystem models. We present preliminary exploration of observed and expected process responses to eCO2 at the AmazonFACE site from the dynamic global vegetation model LPJ-GUESS, highlighting opportunities and pitfalls for model integration of tropical FACE experiments. The preliminary analysis provides baseline hypotheses, which are to be further developed with a follow-up multiple model inter-comparison. The analysis builds on the recently undertaken FACE-MDS (Model-Data Synthesis) project, which was applied to two temperate FACE experiments and exceeds the traditional focus on comparing modeled end-target output. The approach has proven successful in identifying well (and less well) represented processes in models, which are separated for six clusters also here; (1) Carbon fluxes, (2) Carbon pools, (3) Energy balance, (4) Hydrology, (5) Nutrient cycling, and (6) Population dynamics. Simulation performance of observed conditions at the AmazonFACE site (a.o. from Manaus K34 eddy flux tower) will highlight process-based model deficiencies, and aid the separation

  12. Integration of landslide hazard maps into probabilistic risk assessment in context of global changes: an alpine test site

    NASA Astrophysics Data System (ADS)

    Vandromme, Rosalie; Desramaut, Nicolas; Baills, Audrey; Fontaine, Mélanie; Hohmann, Audrey; Grandjean, Gilles; Sedan, Olivier; Puissant, Anne; Malet, Jean-Philippe

    2013-04-01

    The aim of this work is to develop a methodology to integrate global changes scenarios into quantitative risk assessment. This paper describes a methodology to take into account effects of changing climate on landslides activity and impacts of social changes on exposure to provide a complete evaluation of risk for given scenarios. This approach is applied for demonstration purpose on a southern alpine test site. Mechanical approaches represent a solution to quantify landslide susceptibility and to model hazard on unprecedented conditions, as it is likely to occur. However, as the quantity and the quality of data are generally very heterogeneous at a regional scale, it is necessary to take into account their uncertainty in the analysis. In this perspective, a new hazard modeling method has been developed and integrated in a GIS-based software called ALICE®. To go further, climate change scenarios have been computed for the alpine test site (Barcelonnette area, France) using the REMO-COSMO-LM. From the precipitation time series, a daily index of the soil water content has been computed thanks to a reservoir-based model (GARDENIA®). Hence, the program classifies hazard zones depending on the several spatial data (lithological, DEM, etc…) and different hydrological contexts varying in time. The probabilistically initiated landslides are then propagated thank to a semi-empirical model (BORA) to provide real hazard maps. Different scenarios of land-use have been developed using an automate cellular model to cover the probable range of development of potential elements at risks in the future. These exposure maps are then combined with the aforementioned hazard maps to obtain risk maps for the different periods and the different land-use development scenarios. Potential evolutions of landslide risks are then evaluated, with a general increase in the 7 communes. This methodology also allows the analysis of the contributions of both considered global changes (climate and

  13. Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial.

    PubMed

    Wang, Gary P; Berry, Charles C; Malani, Nirav; Leboulch, Philippe; Fischer, Alain; Hacein-Bey-Abina, Salima; Cavazzana-Calvo, Marina; Bushman, Frederic D

    2010-06-01

    X-linked severe-combined immunodeficiency (SCID-X1) has been treated by therapeutic gene transfer using gammaretroviral vectors, but insertional activation of proto-oncogenes contributed to leukemia in some patients. Here we report a longitudinal study of gene-corrected progenitor cell populations from 8 patients using 454 pyrosequencing to map vector integration sites, and extensive resampling to allow quantification of clonal abundance. The number of transduced cells infused into patients initially predicted the subsequent diversity of circulating cells. A capture-recapture analysis was used to estimate the size of the gene-corrected cell pool, revealing that less than 1/100th of the infused cells had long-term repopulating activity. Integration sites were clustered even at early time points, often near genes involved in growth control, and several patients harbored expanded cell clones with vectors integrated near the cancer-implicated genes CCND2 and HMGA2, but remain healthy. Integration site tracking also documented that chemotherapy for adverse events resulted in successful control. The longitudinal analysis emphasizes that key features of transduced cell populations--including diversity, integration site clustering, and expansion of some clones--were established early after transplantation. The approaches to sequencing and bioinformatics analysis reported here should be widely useful in assessing the outcome of gene therapy trials.

  14. Earthquake Monitoring at 9° 50'N on the East Pacific Rise RIDGE 2000 Integrated Studies Site

    NASA Astrophysics Data System (ADS)

    Tolstoy, M.; Waldhauser, F.; Kim, W.

    2004-12-01

    In the fall of 2003 nine ocean bottom seismometers (OBSs) were deployed from the R/V Keldysh within the `bull's-eye' region of the R2K ISS at 9° 49'N - 9° 51'N on the East Pacific Rise as part of the Ridge 2000 Integrated Studies Site. These instruments were recovered using the R/V Atlantis in April 2004, and twelve more were deployed to take their place for a second year of monitoring (with three years total planned). During the turn-around cruise, two short temporary deployments (~4-8 days), of an additional 3 OBSs each, were accomplished to provide very dense instrument spacing (a few 100 m) around specific vents where in situ chemical monitoring was taking place (Luther et al.). Good data were collected on seven of the nine long deployment and six short deployment OBSs. We will present early results from analysis of these data including an estimate of the level of activity observed through-out the seven month period of the first deployment, and preliminary epicenters. Data will also be shown from the short temporary deployments. Early analysis of these data indicates an event rate of ~8 events per day for events where arrivals are apparent on at least three instruments, and may therefore expect to be located. Also notable in these data are pulses and prolonged periods of what appear to be tremor. This tremor is not generally coherent or synchronous from station to station and is therefore likely a very localized phenomena associated with hydrothermal fluid flow. The exceptionally well characterized and monitored seafloor at this site will allow for unprecedented correlation of observed seismic activity with local biology, geology, geochemical and hydrothermal monitoring. In addition, past and future detailed geophysical imaging of this area will provide an excellent context for observed faulting and fracturing.

  15. Integrated GPR and ERT as Enhanced Detection for Subsurface Historical Structures Inside Babylonian Houses Site, Uruk City, Southern Iraq

    NASA Astrophysics Data System (ADS)

    Al-Khersan, Emad H.; Al-Ani, Jassim M. T.; Abrahem, Salah N.

    2016-03-01

    Uruk archaeological site, which located in Al-Muthanna Governorate southern Iraq, was investigated by integrated geophysical methods, ground penetration radar (GPR) and electric resistivity tomography (ERT) to image the historical buried structures. The GPR images show large radar attributes characterized by its continuous reflections having different widths. GPR attributes at shallower depth are mainly representing the upper part of Babylonian Houses that can often be found throughout the study area. In addition, radargrams characterized objects such as buried items, buried trenches and pits which were mainly concentrated near the surface. The ERT results show the presence of several anomalies at different depths generally having low resistivities. It is clear that the first upper zone can be found throughout the whole area and it may represent the top zone of the Babylonian houses. This zone is characterized by its dry clay and sandy soil containing surface broken bricks and slag mixed with core boulders. The second one underneath the top shows a prominent lower resistivity zone. It is probably caused by the moisture content that reduces the resistivity. The thickness of this zone is not equal at all parts of the site. The third deeper zone typically represents the archaeological walls. Most of the main anomalies perhaps referred to the buried clay brick walls. The map of the archaeological anomalies distribution and 3D view of the foundations at the study area using GPR and ERT techniques clearly show the characteristics of the Babylonian remains. A contour map and 3D view of Uruk show that the archaeological anomalies are concentrated mainly at the NE part of the district with higher values of wall height that range between 6 and 8 m and reach to more than 10 m. At the other directions, there are fewer walls with lower heights of 4-6 m and reach in some places the wall foot.

  16. Site-specific integration of the temperate bacteriophage phi adh into the Lactobacillus gasseri chromosome and molecular characterization of the phage (attP) and bacterial (attB) attachment sites.

    PubMed Central

    Raya, R R; Fremaux, C; De Antoni, G L; Klaenhammer, T R

    1992-01-01

    The temperate bacteriophage phi adh integrates its genome into the chromosomal DNA of Lactobacillus gasseri ADH by a site-specific recombination process. Southern hybridization analysis of BclI-digested genomic DNA from six relysogenized derivatives of the prophage-cured strain NCK102 displayed phage-chromosomal junction fragments identical to those of the lysogenic parent. The phi adh attachment site sequence, attP, was located within a 365-bp EcoRI-HindIII fragment of phage phi adh. This fragment was cloned and sequenced. DNA sequence analysis revealed striking features common to the attachment sites of other site-specific recombination systems: five direct repeats of the sequence TGTCCCTTTT(C/T) and a 14-bp inverted repeat. Oligonucleotides derived from the sequence of the attP-containing fragment enabled us to amplify predicted junction fragment sequences and thus to identify attL, attR, and attB. The core region was defined as the 16-bp sequence TACACTTCTTAGGAGG. Phage-encoded functions essential for site-specific insertion of phage phi adh were located in a 4.5-kb BclI fragment. This fragment was cloned in plasmid pSA34 to generate the insertional vector pTRK182. Plasmid pTRK182 was introduced into L. gasseri NCK102 by electroporation. Hybridization analysis showed that a single copy of pTRK182 had integrated at the attB site of the NCK102 erythromycin-resistant transformants. This is the first site-specific recombination system described in lactobacilli, as well as the first attP-based site-specific integration vector constructed for L. gasseri ADH. Images PMID:1512192

  17. Unusual site-specific DNA integration into the highly active pseudo-attB of the Streptomyces albus J1074 genome.

    PubMed

    Bilyk, Bohdan; Luzhetskyy, Andriy

    2014-06-01

    The φC31-encoded recombination system has become a widely used tool for genetic analysis of streptomycetes, gene therapy and generation of transgenic animals. However, the application of this system, even in the context of its natural host genus, Streptomyces, may require a specific approach for each species. In this study, we have identified a novel pseudo-attB site, called pseB4, for integration of vectors using the φC31 system. More than 90 % of clones contained two copies of pSET152- or pOJ436-based cosmids, after their introduction into S. albus. The efficiency of the integration of φC31-based vectors into pseB4 is therefore comparable to that of the integration into attB. Moreover, in contrast with integration into the native attB, integration into pseB4 is not polar and does not require a complementary sequence in the TT-core region. Furthermore, an analysis of conjugation frequency revealed mutual inhibition of plasmid integration into either site when both the attB and pseB4 sites were present in the genome.

  18. Phase Preference by Active, Acetate-Utilizing Bacteria at the Rifle, CO Integrated Field Research Challenge Site

    SciTech Connect

    Kerkhof, L.; Williams, K.H.; Long, P.E.; McGuinness, L.

    2011-02-21

    Previous experiments at the Rifle, Colorado Integrated Field Research Challenge (IFRC) site demonstrated that field-scale addition of acetate to groundwater reduced the ambient soluble uranium concentration. In this report, sediment samples collected before and after acetate field addition were used to assess the active microbes via {sup 13}C acetate stable isotope probing on 3 phases [coarse sand, fines (8-approximately 150 {micro}m), groundwater (0.2-8 {micro}m)] over a 24-day time frame. TRFLP results generally indicated a stronger signal in {sup 13}C-DNA in the 'fines' fraction compared to the sand and groundwater. Before the field-scale acetate addition, a Geobacter-like group primarily synthesized {sup 13}C-DNA in the groundwater phase, an alpha Proteobacterium primarily grew on the fines/sands, and an Acinetobacter sp. and Decholoromonas-like OTU utilized much of the {sup 13}C acetate in both groundwater and particle-associated phases. At the termination of the field-scale acetate addition, the Geobacter-like species was active on the solid phases rather than the groundwater, while the other bacterial groups had very reduced newly synthesized DNA signal. These findings will help to delineate the acetate utilization patterns of bacteria in the field and can lead to improved methods for stimulating distinct microbial populations in situ.

  19. An integrated, peptide-based approach to site-specific protein immobilization for detection of biomolecular interactions.

    PubMed

    Kruis, Ilmar C; Löwik, Dennis W P M; Boelens, Wilbert C; van Hest, Jan C M; Pruijn, Ger J M

    2016-09-21

    We have developed an integrated solution for the site-specific immobilization of proteins on a biosensor surface, which may be widely applicable for high throughput analytical purposes. The gold surface of a biosensor was coated with an anti-fouling layer of zwitterionic peptide molecules from which leucine zipper peptides protrude. Proteins of interest, the autoantigenic proteins La and U1A, were immobilized via a simple incubation procedure by using the complementary leucine zipper sequence as a genetically fused binding tag. This tag forms a strong coiled-coil interaction that is stable during multiple consecutive measurements and under common regeneration conditions. Visualization of the immobilized proteins of interest via antibody binding with multiplex surface plasmon resonance imaging demonstrated 2.5 times higher binding responses than when these proteins were randomly attached to the surface via the commonly applied activated ester-mediated coupling. The proteins could also be immobilized in a leucine zipper-dependent manner directly from complex mixtures like bacterial lysates, eliminating the need for laborious purification steps. This method allows the production of uniform functional protein arrays by control over immobilized protein orientation and geometry and is compatible with high-throughput procedures.

  20. Management of comments on DOE`s Site Characterization Plan (SCP) and integration with the planned geotechnical program

    SciTech Connect

    Bjerstedt, T.W.; Gil, A.V.; Baird, F.A.

    1991-12-31

    The US DOE has committed to respond to comments on the SCP throughout the site characterization process. As of January 1990 DOE has received 4,574 comments on both the SCP/Consultation Draft and the statutory SCP. Of these, 2,662 responses have been completed and returned to the originators. Many comments are programmatic in nature and express diverse concerns beyond the scope of the SCP. DOE uses a three-tiered process in responding to comments that integrated technical and management responsibilities. The process defines specific roles in developing, reviewing, and concurring on responses. Commitments or open-items can be generated in DOE responses to comments, which are tracked on a relational database. Major changes reflected in the Secretary of Energy`s 1989 reassessment of the high-level waste program were advocated in comments on the SCP. Most DOE commitments, however, deal with consideration of recommendations contained in SCP comments relevant to low-levels of technical planning detail (SCP Study Plans). Commitments are discharged when referred to the appropriate quality-affecting or management process whereupon their merits can be evaluated.

  1. Induction of lactogenesis in transgenic virgin pigs: evidence for gene and integration site-specific hormonal regulation.

    PubMed

    Shamay, A; Pursel, V G; Wall, R J; Hennighausen, L

    1992-02-01

    Five month-old transgenic female pigs from three lines carrying the mouse whey acidic protein (WAP) gene and nontransgenic female littermates were implanted with slow-release estrogen and progesterone pellets. Histological analysis of biopsies taken at the time of implantation and 4 weeks later revealed that mammary alveolar development had occurred upon hormonal stimulation in vivo. beta-Casein and beta-lactoglobulin mRNA was found in all induced animals, and WAP mRNA was detected in two of the three transgenic pigs. Differential hormonal regulation between the transgenes in the three lines and also between endogenous milk protein genes was observed in induced mammary tissue cultured in vitro. In the presence of insulin, hydrocortisone, and PRL, beta-casein and WAP mRNA levels increased in all transgenic pigs. In contrast, beta-lactoglobulin mRNA had reached or exceeded lactational levels in response to the in vivo induction, and no further increase was observed in vitro. This suggests that the regulation of the beta-lactoglobulin gene is distinct from that of beta-casein and WAP. Differences were also observed during pregnancy; whereas beta-lactoglobulin gene expression was induced in early pregnancy, a time when PRL levels are low, WAP mRNA levels increased sharply around parturition. Finally, the observation that hormonal regulation of WAP transgenes greatly differed between the three lines suggests that chromatin surrounding the integration site can modify the response of transcription elements. PMID:1569963

  2. Proviral integration site for Moloney murine leukemia virus (PIM) kinases promote human T helper 1 cell differentiation.

    PubMed

    Tahvanainen, Johanna; Kyläniemi, Minna K; Kanduri, Kartiek; Gupta, Bhawna; Lähteenmäki, Hanna; Kallonen, Teemu; Rajavuori, Anna; Rasool, Omid; Koskinen, Päivi J; Rao, Kanury V S; Lähdesmäki, Harri; Lahesmaa, Riitta

    2013-02-01

    The differentiation of human primary T helper 1 (Th1) cells from naïve precursor cells is regulated by a complex, interrelated signaling network. The identification of factors regulating the early steps of Th1 cell polarization can provide important insight in the development of therapeutics for many inflammatory and autoimmune diseases. The serine/threonine-specific proviral integration site for Moloney murine leukemia virus (PIM) kinases PIM1 and PIM2 have been implicated in the cytokine-dependent proliferation and survival of lymphocytes. We have established that the third member of this family, PIM3, is also expressed in human primary Th cells and identified a new function for the entire PIM kinase family in T lymphocytes. Although PIM kinases are expressed more in Th1 than Th2 cells, we demonstrate here that these kinases positively influence Th1 cell differentiation. Our RNA interference results from human primary Th cells also suggest that PIM kinases promote the production of IFNγ, the hallmark cytokine produced by Th1 cells. Consistent with this, they also seem to be important for the up-regulation of the critical Th1-driving factor, T box expressed in T cells (T-BET), and the IL-12/STAT4 signaling pathway during the early Th1 differentiation process. In summary, we have identified PIM kinases as new regulators of human primary Th1 cell differentiation, thus providing new insights into the mechanisms controlling the selective development of human Th cell subsets. PMID:23209281

  3. Integration of Fish and Wildlife Data with Geobased and Remotely Sensed Land Use/land Cover Data: a Demonstration Using Sites in Pennsylvania. [Berwick and Lancaster

    NASA Technical Reports Server (NTRS)

    Cushwa, C. T.; Laroche, G.; Dubrock, C. W.

    1982-01-01

    The U.S. Fish and Wildlife Service developed a statewide fish and wildlife data base for the Pennsylvania Game Commission that includes 125 categories of information on each of the 844 species. This species data base is integrated with geobased and remotely-sensed land use/land cover data from two sites in Pennsylvania. One site is an energy development project; the other is a high-energy use area. Analyses using the combined animal and land use data bases can be demonstrated for a variety of land use/land cover types at both sites. The ability to make "what if" analysis prior to project implementation is presented.

  4. High-titer lentiviral vectors stimulate fetal calf serum-specific human CD4 T-cell responses: implications in human gene therapy.

    PubMed

    Bao, L; Guo, H; Huang, X; Tammana, S; Wong, M; McIvor, R S; Zhou, X

    2009-06-01

    Human immunodeficiency virus-1-derived lentiviral vectors have been increasingly used for gene delivery in both pre-clinical and clinical models. Numerous studies have shown that dendritic cells (DC) transduced with concentrated lentiviral vectors can induce primary T-cell responses to viral and tumor antigens. In this study, we attempted to generate influenza hemagglutinin-specific CD4 T cells using lentiviral vectors containing the signal sequence and human lysosome-associated membrane protein to target hemagglutinin to the major histocompatibility complex class II processing pathway. Autologous dendritic cells were generated in serum-free medium and transduced with concentrated, high-titer lentiviruses to stimulate autologous T cells. Unexpectedly, we failed to generate influenza hemagglutinin-specific CD4 T cells rather than T cells specific for fetal calf serum (FCS). By limiting dilution, we established several FCS-specific CD4 T-cell clones restricted by human leukocyte antigen-DR1 and human leukocyte antigen-DR4. Lentiviruses produced in human serum-adapted 293 cells or in serum-free medium were unable to sensitize dendritic cells for recognition by FCS-specific CD4 T-cell clones. Our results indicate that residual FCS in concentrated lentiviral pellets is, in part, responsible for its immunogenicity. These FCS-specific CD4 T cells may be useful in testing clinical grade lentiviral vectors for the presence of contaminating FCS.

  5. Generation and usage of aequorin lentiviral vectors for Ca(2+) measurement in sub-cellular compartments of hard-to-transfect cells.

    PubMed

    Lim, Dmitry; Bertoli, Alessandro; Sorgato, M Catia; Moccia, Francesco

    2016-05-01

    Targeted aequorin-based Ca(2+) probes represent an unprecedented tool for the reliable measurement of Ca(2+) concentration and dynamics in different sub-cellular compartments. The main advantages of aequorin are its proteinaceous nature, which allows attachment of a signal peptide for targeting aequorin to virtually any sub-cellular compartment; its low Ca(2+)-binding capacity; the wide range of Ca(2+) concentrations that can be measured, ranging from sub-micromolar to millimolar; its robust performance in aggressive environments, e.g., the strong acidic pH of the lysosomal lumen. Lentiviral vectors represent a popular tool to transduce post-mitotic or hard-to-transfect cells both in vitro and in vivo. Furthermore, it has great potential for gene therapy. Last generation lentiviral vectors represent a perfect compromise for combining large insert size, ease of production and handling, and high degree of biosafety. Here, we describe strategies for cloning aequorin probes - targeted to the cytosol, sub-plasma membrane cytosolic domains, the mitochondrial matrix, and the endoplasmic reticulum lumen - into lentiviral vectors. We describe methods for the production of lentiviral particles, and provide examples of measuring Ca(2+) dynamics by such aequorin-encoding lentiviral vectors in sub-cellular compartments of hard-to-transfect cells, including immortalized striatal neurons, primary cerebellar granule neurons and endothelial progenitor cells, which provide suitable in vitro models for the study of different human diseases. PMID:26992273

  6. Reduction of liver macrophage transduction by pseudotyping lentiviral vectors with a fusion envelope from Autographa californica GP64 and Sendai virus F2 domain

    PubMed Central

    Markusic, David M; van Til, Niek P; Hiralall, Johan K; Elferink, Ronald PJ Oude; Seppen, Jurgen

    2009-01-01

    Background Lentiviral vectors are well suited for gene therapy because they can mediate long-term expression in both dividing and nondividing cells. However, lentiviral vectors seem less suitable for liver gene therapy because systemically administered lentiviral vectors are preferentially sequestered by liver macrophages. This results in a reduction of available virus and might also increase the immune response to the vector and vector products. Reduction of macrophage sequestration is therefore essential for efficient lentiviral liver gene therapy. Results Fusions were made of Autographa californica GP64 and the hepatocyte specific Sendai Virus envelope proteins. Lentiviral vectors were produced with either wild type GP64, Sendai-GP64, or both wild type GP64 and Sendai-GP64 and tested in vitro and in vivo for hepatocyte and macrophage gene transfer. Sendai-GP64 pseudotyped vectors showed specific gene transfer to HepG2 hepatoma cells, with no detectable transduction of HeLa cervical carcinoma cells, and a decreased affinity for RAW mouse macrophages. Co-expression of wild type GP64 and Sendai-GP64 resulted in improved viral titers while retaining increased affinity for HepG2 cells. In vivo, the Sendai-GP64 vectors also showed decreased transduction of murine liver macrophages. Conclusion We demonstrate reduced macrophage transduction in vitro and in vivo with GP64/Sendai chimeric envelope proteins. PMID:19811629

  7. Fitness cost implications of phiC31-mediated site-specific integrations in target-site strains of the Mexican fruit fly, Anastrepha ludens (Diptera: Tephritidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Site-specific recombination technologies are powerful new tools for the manipulation of genomic DNA in insects that can improve transgenesis strategies such as targeting transgene insertions, allowing transgene cassette exchange and DNA mobilization for transgene stabilization. However, understandin...

  8. Stable hydrogen and oxygen isotope ratios for selected sites of the National Oceanic and Atmospheric Administration's Atmospheric Integrated Research Monitoring Network (AIRMoN)

    USGS Publications Warehouse

    Coplen, Tyler B.; Huang, Richard

    2000-01-01

    Increasingly, hydrologic studies require information on the isotopic composition of natural waters. This report presents stable hydrogen (δ2H) and oxygen isotope ratios (δ180) of precipitation samples from seven selected sites of the National Oceanic and Atmospheric Administration's Atmospheric Integrated Research Monitoring Network (AIRMoN) collected during the years 1992-1994.

  9. 49 CFR 40.43 - What steps must operators of collection sites take to protect the security and integrity of urine...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... following before each collection to deter tampering with specimens: (1) Secure any water sources or... 49 Transportation 1 2013-10-01 2013-10-01 false What steps must operators of collection sites take to protect the security and integrity of urine collections? 40.43 Section 40.43 Transportation...

  10. Integrated geophysical and LIDAR surveys at the archaeological site of Ancient Epomanduodurum, Mandeure-Mathay (Doubs, Eastern France).

    NASA Astrophysics Data System (ADS)

    Thivet, M.; Bossuet, G.; Laplaige, C.

    2009-04-01

    For several years, some integrated geophysical studies were carried out at Mandeure-Mathay (Franche-Comté Region, Eastern France) for the archaeological evaluation of ancient Epomanduodurum. It's a site of a major scientific interest for understanding the territorial structure of earliest agglomerations in the Eastern Gaul at the end of the Iron Age and during the Roman period. As regards its size, urban equipment, monuments and function, the ancient town is considered as the second behind the civitas capital of Sequani, Besançon-Vesontio. It is located in the Doubs valley, where the plain of Alsace opens into the marches of Burgundy, in a traffic zone between the Vosges and the Jura. This location allows transit between the Rhône valley and the Rhein plain, through Saône and Doubs valleys. This geographical situation was a significant factor in the creation of the late Iron Age settlement, later to turn into a major Gallo-roman town. The whole site includes urban centre and two artisan suburbs. The buried ruins are extended moreover 500 hectares outside and inside a meander of the river. The first "well-organized" research done on the site goes back as far as the end of the 18th Century. However, it is only round the beginning of the 19th century that major constructions such as the theatre (1820) and the sanctuary (1880) were uncovered. The status and the influence of Latenian sanctuary, located in the centre part of a great monumental complex of Early Augustan period, played probably an important role in the emergence of this foreground agglomeration. From the beginning of the survey, in 2001, high resolution and no invasive geophysical methods have been performed on large scale both on the terrace and in the floodplain. Automatic Resistivity Profiling (ARP) and magnetic mapping were taken in grids covering respective areas of 60 and 40 hectares. Ground penetrating radar was occasionally used to confirm the detection of specific anthropogenic anomalies

  11. Stable Expression of Lentiviral Antigens by Quality-Controlled Recombinant Mycobacterium bovis BCG Vectors.

    PubMed

    Hart, Bryan E; Asrican, Rose; Lim, So-Yon; Sixsmith, Jaimie D; Lukose, Regy; Souther, Sommer J R; Rayasam, Swati D G; Saelens, Joseph W; Chen, Ching-Ju; Seay, Sarah A; Berney-Meyer, Linda; Magtanong, Leslie; Vermeul, Kim; Pajanirassa, Priyadharshini; Jimenez, Amanda E; Ng, Tony W; Tobin, David M; Porcelli, Steven A; Larsen, Michelle H; Schmitz, Joern E; Haynes, Barton F; Jacobs, William R; Lee, Sunhee; Frothingham, Richard

    2015-07-01

    The well-established safety profile of the tuberculosis vaccine strain, Mycobacterium bovis bacille Calmette-Guérin (BCG), makes it an attractive vehicle for heterologous expression of antigens from clinically relevant pathogens. However, successful generation of recombinant BCG strains possessing consistent insert expression has encountered challenges in stability. Here, we describe a method for the development of large recombinant BCG accession lots which stably express the lentiviral antigens, human immunodeficiency virus (HIV) gp120 and simian immunodeficiency virus (SIV) Gag, using selectable leucine auxotrophic complementation. Successful establishment of vaccine stability stems from stringent quality control criteria which not only screen for highly stable complemented BCG ΔleuCD transformants but also thoroughly characterize postproduction quality. These parameters include consistent production of correctly sized antigen, retention of sequence-pure plasmid DNA, freeze-thaw recovery, enumeration of CFU, and assessment of cellular aggregates. Importantly, these quality assurance procedures were indicative of overall vaccine stability, were predictive for successful antigen expression in subsequent passaging both in vitro and in vivo, and correlated with induction of immune responses in murine models. This study has yielded a quality-controlled BCG ΔleuCD vaccine expressing HIV gp120 that retained stable full-length expression after 10(24)-fold amplification in vitro and following 60 days of growth in mice. A second vaccine lot expressed full-length SIV Gag for >10(68)-fold amplification in vitro and induced potent antigen-specific T cell populations in vaccinated mice. Production of large, well-defined recombinant BCG ΔleuCD lots can allow confidence that vaccine materials for immunogenicity and protection studies are not negatively affected by instability or differences between freshly grown production batches. PMID:25924766

  12. Scaffold-mediated lentiviral transduction for functional tissue engineering of cartilage.

    PubMed

    Brunger, Jonathan M; Huynh, Nguyen P T; Guenther, Caitlin M; Perez-Pinera, Pablo; Moutos, Franklin T; Sanchez-Adams, Johannah; Gersbach, Charles A; Guilak, Farshid

    2014-03-01

    The ability to develop tissue constructs with matrix composition and biomechanical properties that promote rapid tissue repair or regeneration remains an enduring challenge in musculoskeletal engineering. Current approaches require extensive cell manipulation ex vivo, using exogenous growth factors to drive tissue-specific differentiation, matrix accumulation, and mechanical properties, thus limiting their potential clinical utility. The ability to induce and maintain differentiation of stem cells in situ could bypass these steps and enhance the success of engineering approaches for tissue regeneration. The goal of this study was to generate a self-contained bioactive scaffold capable of mediating stem cell differentiation and formation of a cartilaginous extracellular matrix (ECM) using a lentivirus-based method. We first showed that poly-L-lysine could immobilize lentivirus to poly(ε-caprolactone) films and facilitate human mesenchymal stem cell (hMSC) transduction. We then demonstrated that scaffold-mediated gene delivery of transforming growth factor β3 (TGF-β3), using a 3D woven poly(ε-caprolactone) scaffold, induced robust cartilaginous ECM formation by hMSCs. Chondrogenesis induced by scaffold-mediated gene delivery was as effective as traditional differentiation protocols involving medium supplementation with TGF-β3, as assessed by gene expression, biochemical, and biomechanical analyses. Using lentiviral vectors immobilized on a biomechanically functional scaffold, we have developed a system to achieve sustained transgene expression and ECM formation by hMSCs. This method opens new avenues in the development of bioactive implants that circumvent the need for ex vivo tissue generation by enabling the long-term goal of in situ tissue engineering. PMID:24550481

  13. Intraosseous delivery of lentiviral vectors targeting factor VIII expression in platelets corrects murine hemophilia A.

    PubMed

    Wang, Xuefeng; Shin, Simon C; Chiang, Andy F J; Khan, Iram; Pan, Dao; Rawlings, David J; Miao, Carol H

    2015-04-01

    Intraosseous (IO) infusion of lentiviral vectors (LVs) for in situ gene transfer into bone marrow may avoid specific challenges posed by ex vivo gene delivery, including, in particular, the requirement of preconditioning. We utilized IO delivery of LVs encoding a GFP or factor VIII (FVIII) transgene directed by ubiquitous promoters (a MND or EF-1α-short element; M-GFP-LV, E-F8-LV) or a platelet-specific, glycoprotein-1bα promoter (G-GFP-LV, G-F8-LV). A single IO infusion of M-GFP-LV or G-GFP-LV achieved long-term and efficient GFP expression in Lineage(-)Sca1(+)c-Kit(+) hematopoietic stem cells and platelets, respectively. While E-F8-LV produced initially high-level FVIII expression, robust anti-FVIII immune responses eliminated functional FVIII in circulation. In contrast, IO delivery of G-F8-LV achieved long-term platelet-specific expression of FVIII, resulting in partial correction of hemophilia A. Furthermore, similar clinical benefit with G-F8-LV was achieved in animals with pre-existing anti-FVIII inhibitors. These findings further support platelets as an ideal FVIII delivery vehicle, as FVIII, stored in α-granules, is protected from neutralizing antibodies and, during bleeding, activated platelets locally excrete FVIII to promote clot formation. Overall, a single IO infusion of G-F8-LV was sufficient to correct hemophilia phenotype for long term, indicating that this approach may provide an effective means to permanently treat FVIII deficiency. PMID:25655313

  14. Intraosseous Delivery of Lentiviral Vectors Targeting Factor VIII Expression in Platelets Corrects Murine Hemophilia A

    PubMed Central

    Wang, Xuefeng; Shin, Simon C; Chiang, Andy F J; Khan, Iram; Pan, Dao; Rawlings, David J; Miao, Carol H

    2015-01-01

    Intraosseous (IO) infusion of lentiviral vectors (LVs) for in situ gene transfer into bone marrow may avoid specific challenges posed by ex vivo gene delivery, including, in particular, the requirement of preconditioning. We utilized IO delivery of LVs encoding a GFP or factor VIII (FVIII) transgene directed by ubiquitous promoters (a MND or EF-1α-short element; M-GFP-LV, E-F8-LV) or a platelet-specific, glycoprotein-1bα promoter (G-GFP-LV, G-F8-LV). A single IO infusion of M-GFP-LV or G-GFP-LV achieved long-term and efficient GFP expression in Lineage-Sca1+c-Kit+ hematopoietic stem cells and platelets, respectively. While E-F8-LV produced initially high-level FVIII expression, robust anti-FVIII immune responses eliminated functional FVIII in circulation. In contrast, IO delivery of G-F8-LV achieved long-term platelet-specific expression of FVIII, resulting in partial correction of hemophilia A. Furthermore, similar clinical benefit with G-F8-LV was achieved in animals with pre-existing anti-FVIII inhibitors. These findings further support platelets as an ideal FVIII delivery vehicle, as FVIII, stored in α-granules, is protected from neutralizing antibodies and, during bleeding, activated platelets locally excrete FVIII to promote clot formation. Overall, a single IO infusion of G-F8-LV was sufficient to correct hemophilia phenotype for long term, indicating that this approach may provide an effective means to permanently treat FVIII deficiency. PMID:25655313

  15. Structural basis of lentiviral subversion of a cellular protein degradation pathway

    NASA Astrophysics Data System (ADS)

    Schwefel, David; Groom, Harriet C. T.; Boucherit, Virginie C.; Christodoulou, Evangelos; Walker, Philip A.; Stoye, Jonathan P.; Bishop, Kate N.; Taylor, Ian A.

    2014-01-01

    Lentiviruses contain accessory genes that have evolved to counteract the effects of host cellular defence proteins that inhibit productive infection. One such restriction factor, SAMHD1, inhibits human immunodeficiency virus (HIV)-1 infection of myeloid-lineage cells as well as resting CD4+ T cells by reducing the cellular deoxynucleoside 5'-triphosphate (dNTP) concentration to a level at which the viral reverse transcriptase cannot function. In other lentiviruses, including HIV-2 and related simian immunodeficiency viruses (SIVs), SAMHD1 restriction is overcome by the action of viral accessory protein x (Vpx) or the related viral protein r (Vpr) that target and recruit SAMHD1 for proteasomal degradation. The molecular mechanism by which these viral proteins are able to usurp the host cell's ubiquitination machinery to destroy the cell's protection against these viruses has not been defined. Here we present the crystal structure of a ternary complex of Vpx with the human E3 ligase substrate adaptor DCAF1 and the carboxy-terminal region of human SAMHD1. Vpx is made up of a three-helical bundle stabilized by a zinc finger motif, and wraps tightly around the disc-shaped DCAF1 molecule to present a new molecular surface. This adapted surface is then able to recruit SAMHD1 via its C terminus, making it a competent substrate for the E3 ligase to mark for proteasomal degradation. The structure reported here provides a molecular description of how a lentiviral accessory protein is able to subvert the cell's normal protein degradation pathway to inactivate the cellular viral defence system.

  16. Complete correction of murine Artemis immunodeficiency by lentiviral vector-mediated gene transfer.

    PubMed

    Mostoslavsky, Gustavo; Fabian, Attila J; Rooney, Sean; Alt, Frederick W; Mulligan, Richard C

    2006-10-31

    Artemis gene mutations are responsible for the development of a severe combined immunodeficiency [radiation-sensitive (RS) SCID] characterized by a severe B and T cell deficiency and a normal natural killer cell population. To establish the feasibility of a gene therapy approach to the treatment of RS-SCID, we generated a series of lentiviral vectors expressing human Artemis from different promoters and used them to transduce highly purified hematopoietic stem cells (HSCs) from Artemis knockout mice. HSCs transduced by the different viruses were transplanted into either lethally irradiated Rag-1-deficient animals or Artemis knockout mice treated with a nonmyeloablative dose of Busulfan. In both models, transplantation of HSCs transduced by a vector that used a murine phosphoglycerate kinase (PGK) promoter led to a complete functional correction of the immunodeficiency. Corrected animals displayed rescue of mature B cells with normal levels of serum immunoglobulins, together with complete rescue of the T cell compartment as evidenced by the presence of mature T lymphocytes in peripheral blood as well as normal values of thymocytes in thymus. Those B and T cells were capable of activation, as shown both by in vitro stimulation responses and in vivo after immune challenge. Overall, the results indicate that a gene therapy approach for RS-SCID involving the transplantation of genetically modified HSCs is indeed feasible. Furthermore, our studies suggest the possibility that nonmyeloablative conditioning regimens might be effectively used to promote engraftment of genetically modified cells in the case of diseases where standard irradiation-based myeloablative bone marrow transplantation protocols may prove problematic. PMID:17062750

  17. Generation of multi-functional antigen-specific human T-cells by lentiviral TCR gene transfer.

    PubMed

    Perro, M; Tsang, J; Xue, S-A; Escors, D; Cesco-Gaspere, M; Pospori, C; Gao, L; Hart, D; Collins, M; Stauss, H; Morris, E C

    2010-06-01

    T-cell receptor (TCR) gene transfer is an attractive strategy to generate antigen-specific T-cells for adoptive immunotherapy of cancer and chronic viral infection. However, current TCR gene transfer protocols trigger T-cell differentiation into terminally differentiated effector cells, which likely have reduced ability to mediate disease protection in vivo. We have developed a lentiviral gene transfer strategy to generate TCR-transduced human T-cells without promoting T-cell differentiation. We found that a combination of interleukin-15 (IL15) and IL21 facilitated lentiviral TCR gene transfer into non-proliferating T-cells. The transduced T-cells showed redirection of antigen specificity and produced IL2, IFNgamma and TNFalpha in a peptide-dependent manner. A significantly higher proportion of the IL15/IL21-stimulated T-cells were multi-functional and able to simultaneously produce all three cytokines (P<0.01), compared with TCR-transduced T-cells generated by conventional anti-CD3 plus IL2 stimulation, which primarily secreted only one cytokine. Similarly, IL15/IL21 maintained high levels of CD62L and CD28 expression in transduced T-cells, whereas anti-CD3 plus IL2 accelerated the loss of CD62L/CD28 expression. The data demonstrate that the combination of lentiviral TCR gene transfer together with IL15/IL21 stimulation can efficiently redirect the antigen specificity of resting primary human T-cells and generate multi-functional T-cells.

  18. Lentiviral-mediated transfer of CDNF promotes nerve regeneration and functional recovery after sciatic nerve injury in adult rats

    SciTech Connect

    Cheng, Lei; Liu, Yi; Zhao, Hua; Zhang, Wen; Guo, Ying-Jun; Nie, Lin

    2013-10-18

    Highlights: •CDNF was successfully transfected by a lentiviral vector into the distal sciatic nerve. •CDNF improved S-100, NF200 expression and nerve regeneration after sciatic injury. •CDNF improved the remyelination and thickness of the regenerated sciatic nerve. •CDNF improved gastrocnemius muscle weight and sciatic functional recovery. -- Abstract: Peripheral nerve injury is often followed by incomplete and unsatisfactory functional recovery and may be associated with sensory and motor impairment of the affected limb. Therefore, a novel method is needed to improve the speed of recovery and the final functional outcome after peripheral nerve injuries. This report investigates the effect of lentiviral-mediated transfer of conserved dopamine neurotrophic factor (CDNF) on regeneration of the rat peripheral nerve in a transection model in vivo. We observed notable overexpression of CDNF protein in the distal sciatic nerve after recombinant CDNF lentiviral vector application. We evaluated sciatic nerve regeneration after surgery using light and electron microscopy and the functional recovery using the sciatic functional index and target muscle weight. HE staining revealed better ordered structured in the CDNF-treated group at 8 weeks post-surgery. Quantitative analysis of immunohistochemistry of NF200 and S-100 in the CDNF group revealed significant improvement of axonal and Schwann cell regeneration compared with the control groups at 4 weeks and 8 weeks after injury. The thickness of the myelination around the axons in the CDNF group was significantly higher than in the control groups at 8 weeks post-surgery. The CDNF group displayed higher muscle weights and significantly increased sciatic nerve index values. Our findings suggest that CDNF gene therapy could provide durable and stable CDNF protein concentration and has the potential to enhance peripheral nerve regeneration, morphological and functional recovery following nerve injury, which suggests a

  19. Generation of multi-functional antigen-specific human T-cells by lentiviral TCR gene transfer.

    PubMed

    Perro, M; Tsang, J; Xue, S-A; Escors, D; Cesco-Gaspere, M; Pospori, C; Gao, L; Hart, D; Collins, M; Stauss, H; Morris, E C

    2010-06-01

    T-cell receptor (TCR) gene transfer is an attractive strategy to generate antigen-specific T-cells for adoptive immunotherapy of cancer and chronic viral infection. However, current TCR gene transfer protocols trigger T-cell differentiation into terminally differentiated effector cells, which likely have reduced ability to mediate disease protection in vivo. We have developed a lentiviral gene transfer strategy to generate TCR-transduced human T-cells without promoting T-cell differentiation. We found that a combination of interleukin-15 (IL15) and IL21 facilitated lentiviral TCR gene transfer into non-proliferating T-cells. The transduced T-cells showed redirection of antigen specificity and produced IL2, IFNgamma and TNFalpha in a peptide-dependent manner. A significantly higher proportion of the IL15/IL21-stimulated T-cells were multi-functional and able to simultaneously produce all three cytokines (P<0.01), compared with TCR-transduced T-cells generated by conventional anti-CD3 plus IL2 stimulation, which primarily secreted only one cytokine. Similarly, IL15/IL21 maintained high levels of CD62L and CD28 expression in transduced T-cells, whereas anti-CD3 plus IL2 accelerated the loss of CD62L/CD28 expression. The data demonstrate that the combination of lentiviral TCR gene transfer together with IL15/IL21 stimulation can efficiently redirect the antigen specificity of resting primary human T-cells and generate multi-functional T-cells. PMID:20164855

  20. Innocuous full-length botulinum neurotoxin targets and promotes the expression of lentiviral vectors in central and autonomic neurons.

    PubMed

    O'Leary, V B; Ovsepian, S V; Raghunath, A; Huo, Q; Lawrence, G W; Smith, L; Dolly, J O

    2011-07-01

    Fragments of botulinum neurotoxin (BoNT) have been explored as potential targeting moieties and carriers of biomolecules into neurons, although with lower binding and translocation efficiency compared with intact proteins. This study exploits a detoxified recombinant form of full-length BoNT/B (BoTIM/B) fused with core streptavidin (CS-BoTIM/B) for lentiviral targeting to central and autonomic neurons. CS-BoTIM/B underwent an activity-dependent entry into cultured spinal cord neurons. Coupling CS-BoTIM/B to biotinylated lentivirus-encoding green fluorescent protein (GFP) endowed considerable neuron selectivity to the vector as evident from the preferential expression of the reporter in neurons co-cultured with skeletal muscle cells. CS-BoTIM/B-guided lentiviral transduction with the expression of a SNARE protein, SNAP-25 (S25), rendered non-susceptible to proteolysis by three BoNT serotypes, yielded a sizable decrease in cleaved S25 upon exposure of spinal cord neurons to these toxins. This was accompanied by synaptic transmission being spared from blockade by BoNT/A or BoNT/E, reflecting adequate translation and functional competence of recombinant multi-toxin-resistant S25. The augmented neurotropism conveyed on the lentivirus by CS-BoTIM/B was also demonstrated in vivo through enhanced expression of a reporter in intramural ganglionic neurons in the rat trachea, after injection of the targeted GFP-encoding lentivirus. Thus, a novel and realistic prospect for gene therapy of peripheral neuropathies is offered in this study through lentiviral targeting to neurons by CS-BoTIM/B.

  1. Full scale field test of the in situ air stripping process at the Savannah River integrated demonstration test site

    SciTech Connect

    Looney, B.B.; Hazen, T.C.; Kaback, D.S.; Eddy, C.A.

    1991-06-29

    Under sponsorship from the US Department of Energy, technical personnel from the Savannah River Laboratory (SRL) and other DOE laboratories, universities and private industry have completed a full scale demonstration of environmental remediation using horizontal wells. This demonstration was performed as Phase I of an Integrated Demonstration Project designed to evaluate innovative remediation technologies for environmental restoration of sites contaminated with organic contaminants. The demonstration utilized two directionally drilled horizontal wells to deliver gases and extract contaminants from the subsurface. The resulting in situ air stripping process was designed to remediate soils and sediments above and below the water table as well as groundwater contaminated with volatile organic contaminants. The 139 day long test successfully removed volatile chlorinated solvents from the subsurface using the two horizontal wells. One well, approximately 300 ft (90m) long and 165 ft (50m) deep drilled below a contaminant plume in the groundwater, was used to inject air and strip the contaminants from the groundwater. A second horizontal well, approximately 175 ft (53m) long and 75 ft (23m) deep in the vadose zone, was used to extract residual contamination in the vadose zone along with the material purged from the groundwater. Pretest and posttest characterization data and monitoring data during the demonstration were collected to aid in interpretation of the test and to provide the information needed for future environmental restoration that employ directionally drilled wells as extraction or delivery systems. Contaminant concentration data and microbiological monitoring data are summarized in this report; the characterization data and geophysical monitoring data are documented in a series of related project reports.

  2. Integrating smart-phone based momentary location tracking with fixed site air quality monitoring for personal exposure assessment.

    PubMed

    Su, Jason G; Jerrett, Michael; Meng, Ying-Ying; Pickett, Melissa; Ritz, Beate

    2015-02-15

    Epidemiological studies investigating relationships between environmental exposures from air pollution and health typically use residential addresses as a single point for exposure, while environmental exposures in transit, at work, school or other locations are largely ignored. Personal exposure monitors measure individuals' exposures over time; however, current personal monitors are intrusive and cannot be operated at a large scale over an extended period of time (e.g., for a continuous three months) and can be very costly. In addition, spatial locations typically cannot be identified when only personal monitors are used. In this paper, we piloted a study that applied momentary location tracking services supplied by smart phones to identify an individual's location in space-time for three consecutive months (April 28 to July 28, 2013) using available Wi-Fi networks. Individual exposures in space-time to the traffic-related pollutants Nitrogen Oxides (NOX) were estimated by superimposing an annual mean NOX concentration surface modeled using the Land Use Regression (LUR) modeling technique. Individual's exposures were assigned to stationary (including home, work and other stationary locations) and in-transit (including commute and other travel) locations. For the individual, whose home/work addresses were known and the commute route was fixed, it was found that 95.3% of the time, the individual could be accurately identified in space-time. The ambient concentration estimated at the home location was 21.01 ppb. When indoor/outdoor infiltration, indoor sources of air pollution and time spent outdoors were taken into consideration, the individual's cumulative exposures were 28.59 ppb and 96.49 ppb, assuming a respective indoor/outdoor ratio of 1.33 and 5.00. Integrating momentary location tracking services with fixed-site field monitoring, plus indoor-outdoor air exchange calibration, makes exposure assessment of a very large population over an extended time period

  3. A robust transfection reagent for the transfection of CHO and HEK293 cells and production of recombinant proteins and lentiviral particles - PTG1.

    PubMed

    Gonçalves, Cristine; Gross, Fabian; Guégan, Philippe; Cheradame, Hervé; Midou, Patrick

    2014-11-01

    Bioproduction of recombinant proteins (r-proteins) and recombinant lentiviral particles (r-lentiviral particles) requires robust transfections consisting of efficient protocols that are easy to implement, with good reproducibility for a maximum production of proteins and lentiviral particles in a short time with low cytotoxicity. This study evaluates the capacity of histidinylated polyethyleneimine I (PTG1) to facilitate robust DNA transfection, with low cytotoxicity, of Chinese hamster ovary (CHO) and human embryonic kidney (HEK293T) cells for the production of r-proteins and r-lentiviral particles. We report that PTG1 transfection of cells in suspension with a plasmid DNA encoding enhanced green fluorescent protein leads to 72 and 97% of transfected CHO and HEK293T cells respectively, and does not significantly affect cell viability. PTG1 transfection of 100 mL of CHO-S cell culture in suspension at a cell density of 2 × 10(6) cells /mL resulted in a high level of transfected cells and protein expression after transfection with 0.75 μg/mL plasmid DNA. Transfection with PTG1 is more efficient than LipofectAmine2000™, and gene expression is higher than observed with FreeStyle™ and JetPEI®. Tri-transfection of HEK293T packaging cells leads to the production of a higher level of r-lentiviral particles compared to the calcium phosphate method, and permits two harvests of viral particles within three days. These results show that PTG1 is a powerful new transfection reagent for cell lines frequently used for recombinant protein and lentiviral particle production. PTG1 could be used in protocols for bioproduction of therapeutic proteins such as antibodies for cancer treatments and viral vectors for gene therapy applications. PMID:25215936

  4. Optimized Lentiviral Transduction Protocols by Use of a Poloxamer Enhancer, Spinoculation, and scFv-Antibody Fusions to VSV-G.

    PubMed

    Anastasov, Nataša; Höfig, Ines; Mall, Sabine; Krackhardt, Angela M; Thirion, Christian

    2016-01-01

    Lentiviral vectors (LV) are widely used to successfully transduce cells for research and clinical applications. This optimized LV infection protocol includes a nontoxic poloxamer-based adjuvant combined with antibody-retargeted lentiviral particles. The novel poloxamer P338 demonstrates superior characteristics for enhancing lentiviral transduction over the best-in-class polybrene-assisted transduction. Poloxamer P338 exhibited dual benefits of low toxicity and high efficiency of lentiviral gene delivery into a range of different primary cell cultures. One of the major advantages of P338 is its availability in pharma grade and applicability as cell culture medium additive in clinical protocols. Lentiviral vectors pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G) can be produced to high titers and mediate high transduction efficiencies in vitro. For clinical applications the need for optimized transduction protocols, especially for transduction of primary T and stem cells, is high. The successful use of retronectin, the second lentivirus enhancer available as GMP material, requires the application of specific coating protocols not applicable in all processes, and results in the need of a relatively high multiplicity of infection (MOI) to achieve effective transduction efficiencies for hematopoietic cells (e.g., CD34+ hematopoietic stem cells). Cell specificity of lentiviral vectors was successfully increased by displaying different ratios of scFv-fused VSV-G glycoproteins on the viral envelope. The system has been validated with human CD30+ lymphoma cells, resulting in preferential gene delivery to CD30+ cells, which was increased fourfold in mixed cell cultures, by presenting scFv antibody fragments binding to respective surface markers. A combination of spinoculation and poloxamer-based chemical adjuvant increases the transduction of primary T-cells by greater than twofold. The combination of poloxamer-based and scFv-retargeted LVs increased

  5. Dual promoter lentiviral vector generates transgenic mice expressing E2-CSFV glycoprotein in their milk, but impairs early identification of transgenic embryos.

    PubMed

    Ramos, Oliberto Sánchez; Carratalá, Yanet Prieto; Puerta, Silvia Gómez; Pereira, Natalie C Parra; Amarán, Lester Suárez; Chaves, Silvana P Jimenez; Alonso, Jorge R Toledo

    2011-04-15

    Lentiviral vectors containing the green fluorescent protein gene have been successfully used to select transgenic embryos before transfer to a surrogate mother. However, there are apparently no reports regarding early detection of transgenic embryos using a lentiviral vector carrying an additional transcription unit for tissue-specific expression of a valuable protein. In this study, two HIV-based lentiviral vectors were constructed. The first one contained the green fluorescent protein (GFP) coding sequence driven by the early SV40 promoter (Lv-G), whereas the other contained an additional transcription unit for the expression of E2 glycoprotein from classical swine fever virus, driven by a 1.5 kb αS1casein promoter from water buffalo (Lv-αS1cE2hisG). Microinjection of single-cell mouse embryos with Lv-G lentiviral vector rendered embryos which were GFP-positive, beginning at the four-cell stage. Of 33 mice born, 28 (81%) carried the transgene DNA and 15 (55.5%) were GFP-positive. Microinjection of Lv-αS1cE2hisG lentiviral vector yielded 28 mice born; although 24 (85%) carried the transgene DNA, none were GFP-positive, suggesting that the tissue-specific expression cassette interfered with expression of the ubiquitous trancriptional unit. In Lv-αS1cE2hisG transgenic mice, E2his was expressed in milk as a homodimer (at concentrations ≤ 0.422 mg/mL). This was apparently the first report of expression of a recombinant protein in the milk of transgenic animals generated by lentiviral transgenesis.

  6. Microgravity Characterization of the Hontomín CO2 Storage Site (Spain). Integration with 3D Seismic Results

    NASA Astrophysics Data System (ADS)

    Ayarza, P.; Andres, J.; Alcalde, J.; Martí, D.; Marzán, I.; Martinez-Catalan, J. R.; Carbonell, R.; García Lobón, J. L.; Pérez Estaún, A.

    2014-12-01

    Hontomín hosts the first Spanish CO2storage Technology Development Plant. The area, located in the southern part of Mesozoic Basque-Cantabrian Basin, presents E-W and ESE-WNW faults formed during a Permian-Triassic extensional event. The latter were reactivated during the opening of the Bay of Biscay, while a new set of NNE-SSW faults developed. Fractures were reactivated again during the Alpine compression. The resulting configuration is a dome-like structure that includes the Mesozoic succession (Upper Triassic to Lower Cretaceous) and is crowned by Upper Cretaceous and Eocene rocks lying unconformably. The target injection pointis located at 1500 m depth, within a Jurassic carbonate saline formation. Several multidisciplinary studies have been carried out in Hontomín aiming to obtain a thorough geological characterization. Among these, a microgravity survey, acquired under the umbrella of the CIUDEN foundation, has provided us with a complete 3D image of the site. A 4x4 km2area, coincident with that surveyed by 3D seismic reflection, has been sampled using a dense grid with a station spacing of 100 m. The result is a high resolution Bouguer anomaly gravity map capable of offering insights into the subsurface geology down to the depth of the injection point. The application of mathematical procedures to the data has further enhanced its potential for interpretation. The calculated regional anomaly indicates that the dome structure strikes E-W to ENE-WSW, sub-parallel to a major fault: the South Fault, part of the Ubierna fault system. The resulting residual anomaly enhances a number of NW-SE features that have also been interpreted as faults and that can be observed after performing vertical and horizontal derivatives to the data. Calculation of the Euler solutions confirms the previous results and brings out a new NNW-SSE feature, namely the East Fault. Integration with 3D seismic data suggests that faults affect different levels of the sedimentary sequence

  7. Scalable Electrophysiological Investigation of iPS Cell-Derived Cardiomyocytes Obtained by a Lentiviral Purification Strategy

    PubMed Central

    Friedrichs, Stephanie; Malan, Daniela; Voss, Yvonne; Sasse, Philipp

    2015-01-01

    Disease-specific induced pluripotent stem (iPS) cells can be generated from patients and differentiated into functional cardiomyocytes for characterization of the disease and for drug screening. In order to obtain pure cardiomyocytes for automated electrophysiological investigation, we here report a novel non-clonal purification strategy by using lentiviral gene transfer of a puromycin resistance gene under the control of a cardiac-specific promoter. We have applied this method to our previous reported wild-type and long QT syndrome 3 (LQTS 3)-specific mouse iPS cells and obtained a pure cardiomyocyte population. These cells were investigated by action potential analysis with manual and automatic planar patch clamp technologies, as well as by recording extracellular field potentials using a microelectrode array system. Action potentials and field potentials showed the characteristic prolongation at low heart rates in LQTS 3-specific, but not in wild-type iPS cell-derived cardiomyocytes. Hence, LQTS 3-specific cardiomyocytes can be purified from iPS cells with a lentiviral strategy, maintain the hallmarks of the LQTS 3 disease and can be used for automated electrophysiological characterization and drug screening. PMID:26237021

  8. Factors that influence VSV-G pseudotyping and transduction efficiency of lentiviral vectors-in vitro and in vivo implications.

    PubMed

    Farley, Daniel C; Iqball, Sharifah; Smith, Joanne C; Miskin, James E; Kingsman, Susan M; Mitrophanous, Kyriacos A

    2007-05-01

    Pseudotyping viral vectors with vesicular stomatitis virus glycoprotein (VSV-G) enables the transduction of an extensive range of cell types from different species. We have discovered two important parameters of the VSV-G-pseudotyping phenomenon that relate directly to the transduction potential of lentiviral vectors: (1) the glycosylation status of VSV-G, and (2) the quantity of glycoprotein associated with virions. We measured production-cell and virion-associated quantities of two isoform variants of VSV-G, which differ in their glycosylation status, VSV-G1 and VSV-G2, and assessed the impact of this difference on the efficiency of mammalian cell transduction by lentiviral vectors. The glycosylation of VSV-G at N336 allowed greater maximal expression of VSV-G in HEK293T cells, thus facilitating vector pseudotyping. The transduction of primate cell lines was substantially affected (up to 50-fold) by the degree of VSV-G1 or VSV-G2 incorporation, whereas other cell lines, such as D17 (canine), were less sensitive to virion-associated VSV-G1/2 quantities. These data indicate that the minimum required concentration of virion-associated VSV-G differs substantially between cell species/types. The implications of these data with regard to VSV-G-pseudotyped vector production, titration, and use in host-cell restriction studies, are discussed.

  9. Primary Human Hepatocytes Repopulate Livers of Mice After In Vitro Culturing and Lentiviral-Mediated Gene Transfer

    PubMed Central

    Bierwolf, Jeanette; Volz, Tassilo; Lütgehetmann, Marc; Allweiss, Lena; Riecken, Kristoffer; Warlich, Michael; Fehse, Boris; Kalff, Joerg C.; Dandri, Maura

    2016-01-01

    Cell-based therapies represent a promising alternative to orthotopic liver transplantation. However, therapeutic effects are limited by low cell engraftment rates. We recently introduced a technique creating human hepatocyte spheroids for potential therapeutic application. The aim of this study was to evaluate whether these spheroids are suitable for engraftment in diseased liver tissues. Intrasplenic spheroid transplantation into immunodeficient uPA/SCID/beige mice was performed. Hepatocyte transduction ability prior to transplantation was tested by lentiviral labeling using red-green-blue (RGB) marking. Eight weeks after transplantation, animals were sacrificed and livers were analyzed by immunohistochemistry and immunofluorescence. To investigate human hepatocyte-specific gene expression profiles in mice, quantitative real-time-PCR was applied. Human albumin and alpha-1-antitrypsin concentrations in mouse serum were quantified to assess the levels of human chimerism. Precultured human hepatocytes reestablished their physiological liver tissue architecture and function upon transplantation in mice. Positive immunohistochemical labeling of the proliferating cell nuclear antigen revealed that human hepatocytes retained their in vivo proliferation capacity. Expression profiles of human genes analyzed in chimeric mouse livers resembled levels determined in native human tissue. Extensive vascularization of human cell clusters was detected by demonstration of von Willebrand factor activity. To model gene therapy approaches, lentiviral transduction was performed ex vivo and fluorescent microscopic imaging revealed maintenance of RGB marking in vivo. Altogether, this is the first report demonstrating that cultured and retroviral transduced human hepatocyte spheroids are able to engraft and maintain their regenerative potential in vivo. PMID:27068494

  10. Primary Human Hepatocytes Repopulate Livers of Mice After In Vitro Culturing and Lentiviral-Mediated Gene Transfer.

    PubMed

    Bierwolf, Jeanette; Volz, Tassilo; Lütgehetmann, Marc; Allweiss, Lena; Riecken, Kristoffer; Warlich, Michael; Fehse, Boris; Kalff, Joerg C; Dandri, Maura; Pollok, Joerg-Matthias

    2016-05-01

    Cell-based therapies represent a promising alternative to orthotopic liver transplantation. However, therapeutic effects are limited by low cell engraftment rates. We recently introduced a technique creating human hepatocyte spheroids for potential therapeutic application. The aim of this study was to evaluate whether these spheroids are suitable for engraftment in diseased liver tissues. Intrasplenic spheroid transplantation into immunodeficient uPA/SCID/beige mice was performed. Hepatocyte transduction ability prior to transplantation was tested by lentiviral labeling using red-green-blue (RGB) marking. Eight weeks after transplantation, animals were sacrificed and livers were analyzed by immunohistochemistry and immunofluorescence. To investigate human hepatocyte-specific gene expression profiles in mice, quantitative real-time-PCR was applied. Human albumin and alpha-1-antitrypsin concentrations in mouse serum were quantified to assess the levels of human chimerism. Precultured human hepatocytes reestablished their physiological liver tissue architecture and function upon transplantation in mice. Positive immunohistochemical labeling of the proliferating cell nuclear antigen revealed that human hepatocytes retained their in vivo proliferation capacity. Expression profiles of human genes analyzed in chimeric mouse livers resembled levels determined in native human tissue. Extensive vascularization of human cell clusters was detected by demonstration of von Willebrand factor activity. To model gene therapy approaches, lentiviral transduction was performed ex vivo and fluorescent microscopic imaging revealed maintenance of RGB marking in vivo. Altogether, this is the first report demonstrating that cultured and retroviral transduced human hepatocyte spheroids are able to engraft and maintain their regenerative potential in vivo. PMID:27068494

  11. Lentiviral Delivery of RNAi for In Vivo Lineage-Specific Modulation of Gene Expression in Mouse Lung Macrophages

    PubMed Central

    Wilson, Andrew A; Kwok, Letty W; Porter, Emily L; Payne, Julie G; McElroy, Gregory S; Ohle, Sarah J; Greenhill, Sara R; Blahna, Matthew T; Yamamoto, Kazuko; Jean, Jyh C; Mizgerd, Joseph P; Kotton, Darrell N

    2013-01-01

    Although RNA interference (RNAi) has become a ubiquitous laboratory tool since its discovery 12 years ago, in vivo delivery to selected cell types remains a major technical challenge. Here, we report the use of lentiviral vectors for long-term in vivo delivery of RNAi selectively to resident alveolar macrophages (AMs), key immune effector cells in the lung. We demonstrate the therapeutic potential of this approach by RNAi-based downregulation of p65 (RelA), a component of the pro-inflammatory transcriptional regulator, nuclear factor κB (NF-κB) and a key participant in lung disease pathogenesis. In vivo RNAi delivery results in decreased induction of NF-κB and downstream neutrophilic chemokines in transduced AMs as well as attenuated lung neutrophilia following stimulation with lipopolysaccharide (LPS). Through concurrent delivery of a novel lentiviral reporter vector (lenti-NF-κB-luc-GFP) we track in vivo expression of NF-κB target genes in real time, a critical step towards extending RNAi-based therapy to longstanding lung diseases. Application of this system reveals that resident AMs persist in the airspaces of mice following the resolution of LPS-induced inflammation, thus allowing these localized cells to be used as effective vehicles for prolonged RNAi delivery in disease settings. PMID:23403494

  12. Efficient Downregulation of Multiple mRNA Targets with a Single shRNA-Expressing Lentiviral Vector

    PubMed Central

    Chumakov, Stepan P.; Kravchenko, Julia E.; Prassolov, Vladimir S.; Frolova, Elena I.; Chumakov, Peter M.

    2010-01-01

    Gene silencing based on RNA interference is widely used in fundamental research and in practical applications. However, a commonly incomplete functional suppression represents a serious drawback of this technology. We describe a series of lentiviral vectors each containing a single or multiple shRNA expression cassette(s) driven by a RNA polymerase III specific promoter and localized within the 3′-LTR of the lentiviral DNA backbone. The vectors also contain an antibiotic-resistance gene that allows positive selection of recipient cells. The combined expression of three different shRNAs specific to a single mRNA was shown to improve dramatically the level of mRNA inhibition, while the use of three different RNA polymerase III specific promoters avoids the loss of shRNA expression cassettes through the homologous recombination. The vector system was used for successful simultaneous suppression of three related SESN1, SESN2 and SESN3 genes, which suggests its particular value for testing phenotypes of functionally redundant genes. PMID:20064551

  13. Efficient downregulation of multiple mRNA targets with a single shRNA-expressing lentiviral vector.

    PubMed

    Chumakov, Stepan P; Kravchenko, Julia E; Prassolov, Vladimir S; Frolova, Elena I; Chumakov, Peter M

    2010-05-01

    Gene silencing based on RNA interference is widely used in fundamental research and in practical applications. However, a commonly incomplete functional suppression represents a serious drawback of this technology. We describe a series of lentiviral vectors each containing a single or multiple shRNA-expression cassette(s) driven by a RNA-polymerase III specific promoter and localized within the 3'-LTR of the lentiviral DNA backbone. The vectors also contain an antibiotic-resistance gene that allows positive selection of recipient cells. The combined expression of three different shRNAs specific to a single mRNA was shown to improve dramatically the level of mRNA inhibition, while the use of three different RNA-polymerase III specific promoters avoids the loss of shRNA-expression cassettes through the homologous recombination. The vector system was used for successful simultaneous suppression of three related SESN1, SESN2 and SESN3 genes, which suggests its particular value for testing phenotypes of functionally redundant genes.

  14. Vpx-Independent