Sample records for rt env shiv

  1. Topical nonnucleoside reverse transcriptase inhibitor MC 1220 partially prevents vaginal RT-SHIV infection of macaques.

    PubMed

    Stolte-Leeb, Nicole; Loddo, Roberta; Antimisiaris, Sophia; Schultheiss, Tina; Sauermann, Ulrike; Franz, Monika; Mourtas, Spyridon; Parsy, Christophe; Storer, Richard; La Colla, Paolo; Stahl-Hennig, Christiane

    2011-09-01

    The availability of an effective vaginal microbicide would be a major step toward containment of HIV transmission as well as allowing women self-protection against HIV infection. Here we evaluated the efficacy of vaginal application of the potent nonnucleoside reverse transcriptase inhibitor (NNRTI) MC 1220 against vaginal challenge of macaques with RT-SHIV, a chimeric simian immunodeficiency virus (SIV) containing the reverse transcriptase (RT) gene of HIV-1. Challenge infection of monkeys with RT-SHIV currently represents the only nonhuman primate model available to test the anti-HIV-1 effects of NNRTIs. Two different gel formulations containing different MC 1220 concentrations were evaluated for efficacy in female rhesus macaques exposed to RT-SHIV. Five groups of five animals each were treated with two different gel compositions containing no drug, 0.1% or 0.5% MC 1220, followed by vaginal RT-SHIV challenge 30 min later. One animal in each group treated with the low concentration of MC 1220 as well as one control animal remained uninfected after vaginal challenge. By contrast, three of the animals receiving 0.5% MC 1220 remained uninfected, suggesting a threshold of the drug. Despite being negative for plasma viral RNA and absence of seroconversion, almost all uninfected animals exhibited SIV-specific T cells, either in the periphery or in lymph nodes draining the portal of virus entry. Our results make MC 1220 a promising compound for further development as a topical microbicide and warrant additional testing with improved formulation, long-lasting vaginal delivery systems, or even combinations with other inhibitors. PMID:21332419

  2. MIV-150-Containing Intravaginal Rings Protect Macaque Vaginal Explants against SHIV-RT Infection

    PubMed Central

    Ouattara, Louise A.; Barnable, Patrick; Mawson, Paul; Seidor, Samantha; Zydowsky, Thomas M.; Kizima, Larisa; Rodriguez, Aixa; Fernández-Romero, José A.; Cooney, Michael L.; Roberts, Kevin D.; Gettie, Agegnehu; Blanchard, James; Robbiani, Melissa

    2014-01-01

    Recent studies demonstrated that intravaginal rings (IVRs) containing 100 mg of the nonnucleoside reverse transcriptase inhibitor (NNRTI) MIV-150 significantly protect macaques against a chimeric simian-human immunodeficiency virus that expresses the HIV-1 HxB2 reverse transcriptase (SHIV-RT) when present before and after vaginal challenge. The objectives of this study were to (i) evaluate the pharmacodynamics (PD) of MIV-150 in vaginal fluids (VF) and in ectocervical and vaginal tissues following 100-mg MIV-150 IVR exposure and to (ii) gain more insight whether pharmacokinetics (PK) of MIV-150 can predict PD. MIV-150 in VF collected at 1 day and 14 days post-MIV-150 IVR insertion inhibited ex vivo SHIV-RT infection in vaginal biopsy specimens from untreated animals (not carrying IVRs) in a dose-dependent manner. Previous PK studies demonstrated a significant increase of ectocervical and vaginal tissue MIV-150 concentrations 14 days versus 1 day post-IVR insertion, with the highest increase in vaginal tissue. Therefore, we tested PD of MIV-150 in tissues 14 days post-MIV-150 IVR insertion. Ex vivo SHIV-RT infection of vaginal, but not ectocervical, tissues collected 14 days post-MIV-150 IVR insertion was significantly inhibited compared to infection at the baseline (prior to MIV-150 IVR exposure). No changes in vaginal and ectocervical tissue infection were observed after placebo IVR exposure. Overall, these data underscore the use of the ex vivo macaque explant challenge models to evaluate tissue and VF PK/PD of candidate microbicides before in vivo animal efficacy studies. The data support further development of MIV-150-containing IVRs. PMID:24614384

  3. Enhanced Antiretroviral Therapy in Rhesus Macaques Improves RT-SHIV Viral Decay Kinetics

    PubMed Central

    North, Thomas W.; Villalobos, Andradi; Hurwitz, Selwyn J.; Deere, Jesse D.; Higgins, Joanne; Chatterjee, Payel; Tao, Sijia; Kauffman, Robert C.; Luciw, Paul A.; Kohler, James J.

    2014-01-01

    Using an established nonhuman primate model, rhesus macaques were infected intravenously with a chimeric simian immunodeficiency virus (SIV) consisting of SIVmac239 with the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase from clone HXBc2 (RT-SHIV). The impacts of two enhanced (four- and five-drug) highly active antiretroviral therapies (HAART) on early viral decay and rebound were determined. The four-drug combination consisted of an integrase inhibitor, L-870-812 (L-812), together with a three-drug regimen comprising emtricitabine [(?)-FTC], tenofovir (TFV), and efavirenz (EFV). The five-drug combination consisted of one analog for each of the four DNA precursors {using TFV, (?)-FTC, (?)-?-d-(2R,4R)-1,3-dioxolane-2,6-diaminopurine (amdoxovir [DAPD]), and zidovudine (AZT)}, together with EFV. A cohort treated with a three-drug combination of (?)-FTC, TFV, and EFV served as treated controls. Daily administration of a three-, four-, or five-drug combination of antiretroviral agents was initiated at week 6 or 8 after inoculation and continued up to week 50, followed by a rebound period. Plasma samples were collected routinely, and drug levels were monitored using liquid chromatography-tandem mass spectrometry (LC–MS-MS). Viral loads were monitored with a standard TaqMan quantitative reverse transcriptase PCR (qRT-PCR) assay. Comprehensive analyses of replication dynamics were performed. RT-SHIV infection in rhesus macaques produced typical viral infection kinetics, with untreated controls establishing persistent viral loads of >104 copies of RNA/ml. RT-SHIV loads at the start of treatment (V0) were similar in all treated cohorts (P > 0.5). All antiretroviral drug levels were measureable in plasma. The four-drug and five-drug combination regimens (enhanced HAART) improved suppression of the viral load (within 1 week; P < 0.01) and had overall greater potency (P < 0.02) than the three-drug regimen (HAART). Moreover, rebound viremia occurred rapidly following cessation of any treatment. The enhanced HAART (four- or five-drug combination) showed significant improvement in viral suppression compared to the three-drug combination, but no combination was sufficient to eliminate viral reservoirs. PMID:24777106

  4. Exposure to MIV-150 from a High-Dose Intravaginal Ring Results in Limited Emergence of Drug Resistance Mutations in SHIV-RT Infected Rhesus Macaques

    PubMed Central

    Hsu, Mayla; Keele, Brandon F.; Aravantinou, Meropi; Krawczyk, Noa; Seidor, Samantha; Abraham, Ciby J.; Zhang, Shimin; Rodriguez, Aixa; Kizima, Larisa; Derby, Nina; Jean-Pierre, Ninochka; Mizenina, Olga; Gettie, Agegnehu; Grasperge, Brooke; Blanchard, James; Piatak, Michael J.; Lifson, Jeffrey D.; Fernández-Romero, José A.; Zydowsky, Thomas M.; Robbiani, Melissa

    2014-01-01

    When microbicides used for HIV prevention contain antiretroviral drugs, there is concern for the potential emergence of drug-resistant HIV following use in infected individuals who are either unaware of their HIV infection status or who are aware but still choose to use the microbicide. Resistant virus could ultimately impact their responsiveness to treatment and/or result in subsequent transmission of drug-resistant virus. We tested whether drug resistance mutations (DRMs) would emerge in macaques infected with simian immunodeficiency virus expressing HIV reverse transcriptase (SHIV-RT) after sustained exposure to the potent non-nucleoside reverse transcriptase inhibitor (NNRTI) MIV-150 delivered via an intravaginal ring (IVR). We first treated 4 SHIV-RT-infected animals with daily intramuscular injections of MIV-150 over two 21 day (d) intervals separated by a 7 d drug hiatus. In all 4 animals, NNRTI DRMs (single and combinations) were detected within 14 d and expanded in proportion and diversity with time. Knowing that we could detect in vivo emergence of NNRTI DRMs in response to MIV-150, we then tested whether a high-dose MIV-150 IVR (loaded with >10 times the amount being used in a combination microbicide IVR in development) would select for resistance in 6 infected animals, modeling use of this prevention method by an HIV-infected woman. We previously demonstrated that this MIV-150 IVR provides significant protection against vaginal SHIV-RT challenge. Wearing the MIV-150 IVR for 56 d led to only 2 single DRMs in 2 of 6 animals (430 RT sequences analyzed total, 0.46%) from plasma and lymph nodes despite MIV-150 persisting in the plasma, vaginal fluids, and genital tissues. Only wild type virus sequences were detected in the genital tissues. These findings indicate a low probability for the emergence of DRMs after topical MIV-150 exposure and support the advancement of MIV-150-containing microbicides. PMID:24586674

  5. Persistence of Viral Reservoirs in Multiple Tissues after Antiretroviral Therapy Suppression in a Macaque RT-SHIV Model

    PubMed Central

    Franks, Tamera; Kiser, Rebecca; Coalter, Vicky; Smedley, Jeremy; Piatak, Michael; Mellors, John W.; Lifson, Jeffrey D.; Ambrose, Zandrea

    2013-01-01

    Although antiretroviral therapy (ART) can suppress HIV-1 replication sufficiently to eliminate measurable plasma viremia, infected cells remain and ensure viral recrudescence after discontinuation of ART. We used a macaque model of HIV-1/AIDS to evaluate the location of infected cells during ART. Twelve macaques were infected with RT-SHIVmne, a SIV containing HIV-1 reverse transcriptase, conferring sensitivity to non-nucleoside reverse transcriptase inhibitors (NNRTIs). Ten to fourteen weeks post-infection, 6 animals were treated with 3 or 4 antiretroviral drugs for 17-20 weeks; 6 control animals remained untreated. Viral DNA (vDNA) and RNA (vRNA) were measured in peripheral blood mononuclear cells (PBMC) and at necropsy in multiple tissues by quantitative PCR and RT-PCR. The majority of virally infected cells were located in lymphoid tissues with variable levels in the gastrointestinal tract of both treated and untreated animals. Tissue viral DNA levels correlated with week 1 plasma viremia, suggesting that tissues that harbor proviral DNA are established within the first week of infection. PBMC vDNA levels did not correlate with plasma viremia or tissue levels of vDNA. vRNA levels were high in lymphoid and gastrointestinal tissues of the untreated animals; animals on ART had little vRNA expressed in tissues and virus could not be cultured from lymph node resting CD4+ cells after 17-20 weeks on ART, indicating little or no ongoing viral replication. Strategies for eradication of HIV-1 will need to target residual virus in ART suppressed individuals, which may not be accurately reflected by frequencies of infected cells in blood. PMID:24367650

  6. Sequential emergence and clinical implications of viral mutants with K70E and K65R mutation in reverse transcriptase during prolonged tenofovir monotherapy in rhesus macaques with chronic RT-SHIV infection

    PubMed Central

    Van Rompay, Koen KA; Johnson, Jeffrey A; Blackwood, Emily J; Singh, Raman P; Lipscomb, Jonathan; Matthews, Timothy B; Marthas, Marta L; Pedersen, Niels C; Bischofberger, Norbert; Heneine, Walid; North, Thomas W

    2007-01-01

    Background We reported previously on the emergence and clinical implications of simian immunodeficiency virus (SIVmac251) mutants with a K65R mutation in reverse transcriptase (RT), and the role of CD8+ cell-mediated immune responses in suppressing viremia during tenofovir therapy. Because of significant sequence differences between SIV and HIV-1 RT that affect drug susceptibilities and mutational patterns, it is unclear to what extent findings with SIV can be extrapolated to HIV-1 RT. Accordingly, to model HIV-1 RT responses, 12 macaques were inoculated with RT-SHIV, a chimeric SIV containing HIV-1 RT, and started on prolonged tenofovir therapy 5 months later. Results The early virologic response to tenofovir correlated with baseline viral RNA levels and expression of the MHC class I allele Mamu-A*01. For all animals, sensitive real-time PCR assays detected the transient emergence of K70E RT mutants within 4 weeks of therapy, which were then replaced by K65R mutants within 12 weeks of therapy. For most animals, the occurrence of these mutations preceded a partial rebound of plasma viremia to levels that remained on average 10-fold below baseline values. One animal eventually suppressed K65R viremia to undetectable levels for more than 4 years; sequential experiments using CD8+ cell depletion and tenofovir interruption demonstrated that both CD8+ cells and continued tenofovir therapy were required for sustained suppression of viremia. Conclusion This is the first evidence that tenofovir therapy can select directly for K70E viral mutants in vivo. The observations on the clinical implications of the K65R RT-SHIV mutants were consistent with those of SIVmac251, and suggest that for persons infected with K65R HIV-1 both immune-mediated and drug-dependent antiviral activities play a role in controlling viremia. These findings suggest also that even in the presence of K65R virus, continuation of tenofovir treatment as part of HAART may be beneficial, particularly when assisted by antiviral immune responses. PMID:17417971

  7. Development of sensitive single-round pol or env RT-PCR assays to screen for XMRV in multiple sample types

    PubMed Central

    Tang, Ning; Frank, Andrea; Leckie, Gregor; Hackett, John; Simmons, Graham; Busch, Michael; Abravaya, Klara

    2013-01-01

    The potential association between xenotropic murine leukemia virus-related virus (XMRV) and prostate cancer and chronic fatigue syndrome (CFS) has been much debated. To help resolve the potential role of XMRV in human disease, it is critical to develop sensitive and accurate reverse transcriptase (RT)-PCR assays to screen for the virus. Single-round RT-PCR assays were developed on the automated m2000™ system for detection of the pol or env regions of XMRV in whole blood, plasma, urine cell pellets and urogenital swab samples. Assay performance was assessed by testing two blinded panels, one comprised of whole blood and the other of plasma spiked with serial dilutions of XMRV-infected tissue culture cells and supernatant, respectively, prepared by the Blood XMRV Scientific Research Working Group (SRWG). For both whole blood and plasma panel testing, the assays showed excellent specificity and sensitivity as compared to the other tests included in the SRWG phase I study. Analytical specificity of the assays was also evaluated. Neither pol nor env PCR assays detected a panel of potential cross-reactive microorganisms, although some cross-reaction was observed with mouse genomic DNA. Screening of 196 normal human blood donor plasma, 214 HIV-1 seropositive plasma, 20 formalin-fixed paraffin-embedded (FFPE) prostate cancer specimens, 4 FFPE benign prostate specimens, 400 urine pellets from prostate cancer patients, 166 urine pellets from non-prostate cancer patients, and 135 cervical swab specimens, detected no samples as unequivocally XMRV positive. PMID:22057262

  8. Development of sensitive single-round pol or env RT-PCR assays to screen for XMRV in multiple sample types.

    PubMed

    Tang, Ning; Frank, Andrea; Leckie, Gregor; Hackett, John; Simmons, Graham; Busch, Michael; Abravaya, Klara

    2012-01-01

    The potential association between xenotropic murine leukemia virus-related virus (XMRV) and prostate cancer and chronic fatigue syndrome (CFS) has been much debated. To help resolve the potential role of XMRV in human disease, it is critical to develop sensitive and accurate reverse transcriptase (RT)-PCR assays to screen for the virus. Single-round RT-PCR assays were developed on the automated m2000™ system for detection of the pol or env regions of XMRV in whole blood, plasma, urine cell pellets and urogenital swab samples. Assay performance was assessed by testing two blinded panels, one comprised of whole blood and the other of plasma spiked with serial dilutions of XMRV-infected tissue culture cells and supernatant, respectively, prepared by the Blood XMRV Scientific Research Working Group (SRWG). For both whole blood and plasma panel testing, the assays showed excellent specificity and sensitivity as compared to the other tests included in the SRWG phase I study. Analytical specificity of the assays was also evaluated. Neither pol nor env PCR assays detected a panel of potential cross-reactive microorganisms, although some cross-reaction was observed with mouse genomic DNA. Screening of 196 normal human blood donor plasma, 214 HIV-1 seropositive plasma, 20 formalin-fixed paraffin-embedded (FFPE) prostate cancer specimens, 4 FFPE benign prostate specimens, 400 urine pellets from prostate cancer patients, 166 urine pellets from non-prostate cancer patients, and 135 cervical swab specimens, detected no samples as unequivocally XMRV positive. PMID:22057262

  9. Analysis of immunoglobulin transcripts and hypermutation following SHIV(AD8) infection and protein-plus-adjuvant immunization.

    PubMed

    Francica, Joseph R; Sheng, Zizhang; Zhang, Zhenhai; Nishimura, Yoshiaki; Shingai, Masashi; Ramesh, Akshaya; Keele, Brandon F; Schmidt, Stephen D; Flynn, Barbara J; Darko, Sam; Lynch, Rebecca M; Yamamoto, Takuya; Matus-Nicodemos, Rodrigo; Wolinsky, David; Nason, Martha; Valiante, Nicholas M; Malyala, Padma; De Gregorio, Ennio; Barnett, Susan W; Singh, Manmohan; O'Hagan, Derek T; Koup, Richard A; Mascola, John R; Martin, Malcolm A; Kepler, Thomas B; Douek, Daniel C; Shapiro, Lawrence; Seder, Robert A

    2015-01-01

    Developing predictive animal models to assess how candidate vaccines and infection influence the ontogenies of Envelope (Env)-specific antibodies is critical for the development of an HIV vaccine. Here we use two nonhuman primate models to compare the roles of antigen persistence, diversity and innate immunity. We perform longitudinal analyses of HIV Env-specific B-cell receptor responses to SHIV(AD8) infection and Env protein vaccination with eight different adjuvants. A subset of the SHIV(AD8)-infected animals with higher viral loads and greater Env diversity show increased neutralization associated with increasing somatic hypermutation (SHM) levels over time. The use of adjuvants results in increased ELISA titres but does not affect the mean SHM levels or CDR H3 lengths. Our study shows how the ontogeny of Env-specific B cells can be tracked, and provides insights into the requirements for developing neutralizing antibodies that should facilitate translation to human vaccine studies. PMID:25858157

  10. Passive immunization of macaques with polyclonal anti-SHIV IgG against a heterologous tier 2 SHIV: outcome depends on IgG dose

    PubMed Central

    2014-01-01

    Background A key goal for HIV-1 envelope immunogen design is the induction of cross-reactive neutralizing antibodies (nAbs). As AIDS vaccine recipients will not be exposed to strains exactly matching any immunogens due to multiple HIV-1 quasispecies circulating in the human population worldwide, heterologous SHIV challenges are essential for realistic vaccine efficacy testing in primates. We assessed whether polyclonal IgG, isolated from rhesus monkeys (RMs) with high-titer nAbs (termed SHIVIG), could protect RMs against the R5-tropic tier-2 SHIV-2873Nip, which was heterologous to the viruses or HIV-1 envelopes that had elicited SHIVIG. Results SHIVIG demonstrated binding to HIV Gag, Tat, and Env of different clades and competed with the broadly neutralizing antibodies b12, VRC01, 4E10, and 17b. SHIVIG neutralized tier 1 and tier 2 viruses, including SHIV-2873Nip. NK-cell depletion decreased the neutralizing activity of SHIVIG 20-fold in PBMC assays. Although SHIVIG neutralized SHIV-2873Nip in vitro, this polyclonal IgG preparation failed to prevent acquisition after repeated intrarectal low-dose virus challenges, but at a dose of 400 mg/kg, it significantly lowered peak viremia (P?=?0.001). Unexpectedly, single-genome analysis revealed a higher number of transmitted variants at the low dose of 25 mg/kg, implying increased acquisition at low SHIVIG levels. In vitro, SHIVIG demonstrated complement-mediated Ab-dependent enhancement of infection (C’-ADE) at concentrations similar to those observed in plasmas of RMs treated with 25 mg/kg of SHIVIG. Conclusion Our primate model data suggest a dual role for polyclonal anti-HIV-1 Abs depending on plasma levels upon virus encounter. PMID:24444350

  11. An Intravaginal Ring That Releases the NNRTI MIV-150 Reduces SHIV Transmission in Macaques

    PubMed Central

    Rodriguez, Aixa; Kizima, Larisa; Menon, Radhika; Goldman, Daniel; Kenney, Jessica; Aravantinou, Meropi; Seidor, Samantha; Gettie, Agegnehu; Blanchard, James; Piatak, Michael; Lifson, Jeffrey D.; Fernández-Romero, José A.; Robbiani, Melissa; Zydowsky, Thomas M.

    2015-01-01

    Microbicides may prevent HIV and sexually transmitted infections (STIs) in women; however, determining the optimal means of delivery of active pharmaceutical ingredients remains a major challenge. We previously demonstrated that a vaginal gel containing the non-nucleoside reverse transcriptase inhibitor MIV-150 partially protected macaques from SHIV-RT (simian/HIV reverse transcriptase) infection, and the addition of zinc acetate rendered the gel significantly protective. We test the activity of MIV-150 without the addition of zinc acetate when delivered from either ethylene vinyl acetate (EVA) or silicone intravaginal rings (IVRs). MIV-150 was successfully delivered, because it was detected in vaginal fluids and tissues by radioimmunoassay in pharmacokinetic studies. Moreover, EVA IVRs significantly protected macaques from SHIV-RT infection. Our results demonstrate that MIV-150–containing IVRs have the potential to prevent HIV infection and highlight the possible use of IVRs for delivering drugs that block HIV and other STIs. PMID:22956201

  12. Viral evolution in macaques coinfected with CCR5- and CXCR4-tropic SHIVs in the presence or absence of vaccine-elicited anti-CCR5 SHIV neutralizing antibodies.

    PubMed

    Burke, Brian; Derby, Nina R; Kraft, Zane; Saunders, Cheryl J; Dai, Chuanbin; Llewellyn, Nicholas; Zharkikh, Irina; Vojtech, Lucia; Zhu, Tuofu; Srivastava, Indresh K; Barnett, Susan W; Stamatatos, Leonidas

    2006-11-25

    Macaques were immunized with SF162 Env-based gp140 immunogens and challenged simultaneously with the CCR5-tropic homologous SHIV(SF162P4) and the CXCR4-tropic heterologous SHIV(SF33A) viruses. Both mock-immunized and immunized animals became dually infected. Prior immunization preferentially reduced the viral replication of the homologous virus during primary infection but the relative replication of the two coinfecting viruses during chronic infection was unaffected by prior immunization, despite the fact that five of six immunized animals maintained a significantly lower overall viral replication that the control animals. Neutralizing antibodies participated in controlling the replication of SHIV(SF162P4), but not that of SHIV(SF33A). Dual infection resulted in the emergence and predominance within the circulating CCR5 virus pool, of a variant with a distinct neutralization phenotype. The signature of this variant was the presence of three amino acid changes in gp120, two of which were located in the receptor and coreceptor binding sites. Also, a significant fraction of the viruses circulating in the blood, as early as two weeks post-infection, was recombinants and prior immunization did not prevent their emergence. These findings provide new insights into the dynamic interaction of CCR5- and CXCR4-tropic HIV isolates that are potentially relevant in better understanding HIV-mediated pathogenesis. PMID:16920175

  13. Protective Efficacy of a Global HIV-1 Mosaic Vaccine Against Heterologous SHIV Challenges in Rhesus Monkeys

    PubMed Central

    Barouch, Dan H.; Stephenson, Kathryn E.; Borducchi, Erica N.; Smith, Kaitlin; Stanley, Kelly; McNally, Anna G.; Liu, Jinyan; Abbink, Peter; Maxfield, Lori F.; Seaman, Michael S.; Dugast, Anne-Sophie; Alter, Galit; Ferguson, Melissa; Li, Wenjun; Earl, Patricia L.; Moss, Bernard; Giorgi, Elena E.; Szinger, James J.; Eller, Leigh Anne; Billings, Erik A.; Rao, Mangala; Tovanabutra, Sodsai; Sanders-Buell, Eric; Weijtens, Mo; Pau, Maria G.; Schuitemaker, Hanneke; Robb, Merlin L.; Kim, Jerome H.; Korber, Bette T.; Michael, Nelson L.

    2013-01-01

    SUMMARY The global diversity of HIV-1 represents a critical challenge facing HIV-1 vaccine development. HIV-1 mosaic antigens are bioinformatically optimized immunogens designed for improved coverage of HIV-1 diversity. However, the protective efficacy of global HIV-1 vaccine antigens has not previously been evaluated. Here we demonstrate the capacity of bivalent HIV-1 mosaic antigens to protect rhesus monkeys against acquisition of heterologous challenges with the difficult-to-neutralize simian-human immunodeficiency virus SHIV-SF162P3. Adenovirus/poxvirus and adenovirus/adenovirus vector-based vaccines expressing HIV-1 mosaic Env, Gag, and Pol afforded a significant reduction in the per-exposure acquisition risk following repetitive, intrarectal SHIV-SF162P3 challenges. Protection against acquisition of infection was correlated with vaccine-elicited binding, neutralizing, and functional non-neutralizing antibodies. These data demonstrate the protective efficacy of HIV-1 mosaic antigens and suggest a potential strategy towards the development of a global HIV-1 vaccine. Moreover, our findings suggest that the coordinated activity of multiple antibody functions may contribute to protection against difficult-to-neutralize viruses. PMID:24243013

  14. Variations in the Biological Functions of HIV-1 Clade C Envelope in a SHIV-Infected Rhesus Macaque during Disease Progression

    PubMed Central

    Tso, For Yue; Abrahamyan, Levon; Hu, Shiu-Lok; Ruprecht, Ruth M.; Wood, Charles

    2013-01-01

    A better understanding of how the biological functions of the HIV-1 envelope (Env) changes during disease progression may aid the design of an efficacious anti-HIV-1 vaccine. Although studies from patient had provided some insights on this issue, the differences in the study cohorts and methodology had make it difficult to reach a consensus of the variations in the HIV-1 Env functions during disease progression. To this end, an animal model that can be infected under controlled environment and reflect the disease course of HIV-1 infection in human will be beneficial. Such an animal model was previously demonstrated by the infection of macaque with SHIV, expressing HIV-1 clade C Env V1-V5 region. By using this model, we examined the changes in biological functions of Env in the infected animal over the entire disease course. Our data showed an increase in the neutralization resistance phenotype over time and coincided with the decrease in the net charges of the V1-V5 region. Infection of PBMC with provirus expressing various Env clones, isolated from the infected animal over time, showed a surprisingly better replicative fitness for viruses expressing the Env from early time point. Biotinylation and ELISA data also indicated a decrease of cell-surface-associated Env and virion-associated gp120 content with disease progression. This decrease did not affect the CD4-binding capability of Env, but were positively correlated with the decrease of Env fusion ability. Interestingly, some of these changes in biological functions reverted to the pre-AIDS level during advance AIDS. These data suggested a dynamic relationship between the Env V1-V5 region with the host immune pressure. The observed changes of biological functions in this setting might reflect and predict those occurring during natural disease progression in human. PMID:23840566

  15. GagPol-specific CD4+ T-cells increase the antibody response to Env by intrastructural help

    PubMed Central

    2013-01-01

    Background Immunization of rhesus macaques against Gag of SIV resulted in a more rapid appearance of Env antibodies after infection with SIV or SHIV challenge viruses although the vaccines lacked an Env component. We therefore explored whether T helper cells specific for internal HIV proteins could provide intrastructural help for Env-specific B cells and thus increase the Env antibody response. Results Mice were immunized by adenoviral vector or DNA vaccines against GagPol and then boosted with virus-like particles (VLP) containing GagPol and Env. Env-specific antibody levels after the VLP booster immunizations were significantly higher in GagPol-immunized mice than in mock-vaccinated controls. Adoptive transfer of CD4+ T cells from GagPol-immunized mice also enhanced the Env antibody response to VLP immunization in the recipient mice. Depending on the presence of VLPs, co-cultivation of CD4+ T cells from GagPol-primed mice with BCR transgenic B cells specific for a protein presented on the surface of the VLPs also resulted in the activation of the B and T cells. Conclusions Our study indicates that GagPol-specific T helper cells may provide intrastructural help for Env antibody responses. This cross-talk between immune responses directed against different components of the retroviral particle may be relevant for the immunopathogenesis of retroviral infections and allow to improve virus like particle vaccine approaches against HIV. PMID:24156704

  16. 2005 Nature Publishing Group Protection of macaques from vaginal SHIV

    E-print Network

    Cai, Long

    © 2005 Nature Publishing Group Protection of macaques from vaginal SHIV challenge by vaginally delivered inhibitors of virus­cell fusion Ronald S. Veazey1 , Per Johan Klasse2 , Susan M. Schader2 , Qinxue. Shattock3 , Martin S. Springer6 & John P. Moore2 Human immunodeficiency virus type 1 (HIV-1) continues

  17. Comparison of the Effects of Pathogenic Simian Human Immunodeficiency Virus Strains SHIV-89.6P and SHIV-KU2 in Cynomolgus Macaques

    PubMed Central

    PAWAR, SANTOSH N.; MATTILA, JOSHUA T.; STURGEON, TIMOTHY J.; LIN, PHILANA LING; NARAYAN, OPENDRA; MONTELARO, RONALD C.; FLYNN, JOANNE L.

    2012-01-01

    Factors explaining why human immunodeficiency virus (HIV) enhances the risk of reactivated tuberculosis (TB) are poorly understood. Unfortunately, experimental models of HIV-induced reactivated TB are lacking. We examined whether cynomolgus macaques, which accurately model latent TB in humans, could be used to model pathogenesis of HIV infection in the lungs and associated lymph nodes. These experiments precede studies modeling the effects of HIV infection on latent TB. We infected two groups of macaques with chimeric simian–human immunodeficiency viruses (SHIV-89.6P and SHIV-KU2) and followed viral titers and immunologic parameters including lymphocytes numbers and phenotype in the blood, bronchoalveolar lavage cells, and lymph nodes over the course of infection. Tissues from the lungs, liver, kidney, spleen, and lymph nodes were similarly examined at necropsy. Both strains produced dramatic CD4+ T cell depletion. Plasma titers were not different between viruses, but we found more SHIV-89.6P in the lungs. Both viruses induced similar patterns of cell activation markers. SHIV-89.6P induced more IFN-? expression than SHIV-KU2. These results indicate SHIV-89.6P and SHIV-KU2 infect cynomolgus macaques and may be used to accurately model effects of HIV infection on latent TB. PMID:18366326

  18. The potential for using flax ( Linum usitatissimum L.) shiv as a lignocellulosic raw material for particleboard

    Microsoft Academic Search

    Antonios N. Papadopoulos; Jamie R. B. Hague

    2003-01-01

    Single-layer experimental particleboards were made from various wood chip\\/flax shiv mixtures bonded with urea formaldehyde resin. Flax particles were characterised by having higher length to thickness and length to width ratios and lower bulk density than industrial wood chip particles. Partial substitution of wood by flax shiv resulted in the deterioration of all key board properties. This was attributed to

  19. Protective effects of nef-deleted SHIV or that having IFN? against disease induced with a pathogenic virus early after vaccination

    Microsoft Academic Search

    Y. Enose; M. Kita; T. Yamamoto; H. Suzuki; A. Miyake; R. Horiuchi; K. Ibuki; K. Kaneyasu; T. Kuwata; E. Takahashi; K. Shinohara; T. Miura; M. Hayami

    2004-01-01

    Summary. To clarify the involvement of primitive non-specific immune responses in the protective effects of a live, attenuated virus, each two rhesus macaques were intravenously immunized with an attenuated chimeric simian and human immunodeficiency virus (SHIV) in which the nef gene was deleted (SHIV-NI) or a SHIV having human IFN-? inserted into the deleted nef region (SHIV IFN-?). These immunized

  20. Spliced human endogenous retroviral HERV-H env transcripts in T-cell leukaemia cell lines and normal leukocytes: alternative splicing pattern of HERV-H transcripts

    Microsoft Academic Search

    Mats Lindeskog; Jonas Blomberg

    The majority of human endogenous retroviral HERV-H elements in the human genome have large deletions in pol and lack most of env, 5-10% are more or less complete with a potentially immuno- suppressive transmembrane protein-encoding env region. Spliced HERV-H env transcripts were detec- ted in T-cell leukaemia cell lines and lymphocytes from healthy blood donors by using RT-PCR. The transcripts

  1. SHIV162P3 Infection of Rhesus Macaques Given Maraviroc Gel Vaginally Does Not Involve Resistant Viruses

    Microsoft Academic Search

    Athe M. N. Tsibris; Urboshi Pal; Allison L. Schure; Ronald S. Veazey; Kevin J. Kunstman; Timothy J. Henrich; P. J. Klasse; Steven M. Wolinsky; Daniel R. Kuritzkes; John P. Moore

    2011-01-01

    Maraviroc (MVC) gels are effective at protecting rhesus macaques from vaginal SHIV transmission, but breakthrough infections can occur. To determine the effects of a vaginal MVC gel on infecting SHIV populations in a macaque model, we analyzed plasma samples from three rhesus macaques that received a MVC vaginal gel (day 0) but became infected after high-dose SHIV-162P3 vaginal challenge. Two

  2. A pilot study comparing the development of EIAV Env-specific antibodies induced by DNA/recombinant vaccinia-vectored vaccines and an attenuated Chinese EIAV vaccine.

    PubMed

    Meng, Qinglai; Lin, Yuezhi; Ma, Jian; Ma, Yan; Zhao, Liping; Li, Shenwei; Yang, Kai; Zhou, Jianhua; Shen, Rongxian; Zhang, Xiaoyan; Shao, Yiming

    2012-12-01

    Data from successful attenuated lentiviral vaccine studies indicate that fully mature Env-specific antibodies characterized by high titer, high avidity, and the predominant recognition of conformational epitopes are associated with protective efficacy. Although vaccination with a DNA prime/recombinant vaccinia-vectored vaccine boost strategy has been found to be effective in some trials with non-human primate/simian/human immunodeficiency virus (SHIV) models, it remains unclear whether this vaccination strategy could elicit mature equine infectious anemia virus (EIAV) Env-specific antibodies, thus protecting vaccinated horses against EIAV infection. Therefore, in this pilot study we vaccinated horses using a strategy based on DNA prime/recombinant Tiantan vaccinia (rTTV)-vectored vaccines encoding EIAV env and gag genes, and observed the development of Env-specific antibodies, neutralizing antibodies, and p26-specific antibodies. Vaccination with DNA induced low titer, low avidity, and the predominant recognition of linear epitopes by Env-specific antibodies, which was enhanced by boosting vaccinations with rTTV vaccines. However, the maturation levels of Env-specific antibodies induced by the DNA/rTTV vaccines were significantly lower than those induced by the attenuated vaccine EIAV(FDDV). Additionally, DNA/rTTV vaccines did not elicit broadly neutralizing antibodies. After challenge with a virulent EIAV strain, all of the vaccinees and control horses died from EIAV disease. These data indicate that the regimen of DNA prime/rTTV vaccine boost did not induce mature Env-specific antibodies, which might have contributed to immune protection failure. PMID:23171359

  3. Primate immune responses to HIV-1 Env formulated in the saponin-based adjuvant AbISCO-100 in the presence or absence of TLR9 co-stimulation.

    PubMed

    Martinez, Paola; Sundling, Christopher; O'Dell, Sijy; Mascola, John R; Wyatt, Richard T; Karlsson Hedestam, Gunilla B

    2015-01-01

    Protein-based vaccines require adjuvants to achieve optimal responses. Toll-like receptor (TLR) 9 agonists were previously shown to improve responses to protein-based vaccines, such as the Hepatitis B virus vaccine formulated in alum. Here, we used CpG-C together with the clinically relevant saponin-based adjuvant AbISCO-100/Matrix-M (AbISCO), to assess if TLR9 co-stimulation would quantitatively or qualitatively modulate HIV-1 envelope glycoprotein (Env)-specific B and T cell responses in rhesus macaques. The macaques were inoculated with soluble Env trimers in AbISCO, with or without the addition of CpG-C, using an interval similar to the Hepatitis B virus vaccine. Following a comprehensive evaluation of antigen-specific responses in multiple immune compartments, we show that the Env-specific circulating IgG, memory B cells and plasma cells displayed similar kinetics and magnitude in the presence or absence of CpG-C and that there was no apparent difference between the two groups in the elicited HIV-1 neutralizing antibody titers or antigen-specific CD4+ T cell responses. Importantly, the control of SHIV viremia was significantly improved in animals from both Env-immunized groups relative to adjuvant alone controls, demonstrating the potential of AbISCO to act as a stand-alone adjuvant for Env-based vaccines. PMID:25762407

  4. Raj JainThe Ohio State University RajJain,ShivKalyanraman,RamViswanathan

    E-print Network

    Jain, Raj

    Raj JainThe Ohio State University RajJain,ShivKalyanraman,RamViswanathan DepartmentofComputerandInformationSci. TheOhioStateUniversity Columbus,OH43210 Jain@ACM.Org #12;Raj JainThe Ohio State University Features Scheme Simulation results Overview #12;Raj JainThe Ohio State University Design Features Congestion

  5. Raj JainThe Ohio State University Raj Jain, Shiv Kalyanaraman, Ram Viswanathan

    E-print Network

    Jain, Raj

    Raj JainThe Ohio State University Raj Jain, Shiv Kalyanaraman, Ram Viswanathan Department of CIS The Ohio State University Columbus, OH 43210 Jain@ACM.Org #12;Raj JainThe Ohio State University Why BECN's cause confusion How t28Fix it Overview #12;Raj JainThe Ohio State University Backward Explicit

  6. Raj JainThe Ohio State University Raj Jain, Shiv Kalyanraman, Ram Viswanathan

    E-print Network

    Jain, Raj

    Raj JainThe Ohio State University Raj Jain, Shiv Kalyanraman, Ram Viswanathan Department of Computer and Information Sci. The Ohio State University Columbus,OH43210 Jain@ACM.Org #12;Raj JainThe Ohio exist. #12;Raj JainThe Ohio State University When is the system overloaded? What control is the feedback

  7. Postexposure protection of macaques from vaginal SHIV infection by topical integrase inhibitors.

    PubMed

    Dobard, Charles; Sharma, Sunita; Parikh, Urvi M; West, Rolieria; Taylor, Andrew; Martin, Amy; Pau, Chou-Pong; Hanson, Debra L; Lipscomb, Jonathan; Smith, James; Novembre, Francis; Hazuda, Daria; Garcia-Lerma, J Gerardo; Heneine, Walid

    2014-03-12

    Coitally delivered microbicide gels containing antiretroviral drugs are important for HIV prevention. However, to date, microbicides have contained entry or reverse transcriptase inhibitors that block early steps in virus infection and thus need to be given as a preexposure dose that interferes with sexual practices and may limit compliance. Integrase inhibitors block late steps after virus infection and therefore are more suitable for post-coital dosing. We first determined the kinetics of strand transfer in vitro and confirmed that integration begins about 6 hours after infection. We then used a repeat-challenge macaque model to assess efficacy of vaginal gels containing integrase strand transfer inhibitors when applied before or after simian/human immunodeficiency virus (SHIV) challenge. We showed that gel containing the strand transfer inhibitor L-870812 protected two of three macaques when applied 30 min before SHIV challenge. We next evaluated the efficacy of 1% raltegravir gel and demonstrated its ability to protect macaques when applied 3 hours after SHIV exposure (five of six protected; P < 0.05, Fisher's exact test). Breakthrough infections showed no evidence of drug resistance in plasma or vaginal secretions despite continued gel dosing after infection. We documented rapid vaginal absorption reflecting a short pharmacological lag time and noted that vaginal, but not plasma, virus load was substantially reduced in the breakthrough infection after raltegravir gel treatment. We provide a proof of concept that topically applied integrase inhibitors protect against vaginal SHIV infection when administered shortly before or 3 hours after virus exposure. PMID:24622515

  8. Incorporation of chimeric HIV-SIV-Env and modified HIV-Env proteins into HIV pseudovirions

    SciTech Connect

    Devitt, Gerard [Forschungsschwerpunkt Infektion und Krebs, F020, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg (Germany); Emerson, Vanessa [Forschungsschwerpunkt Infektion und Krebs, F020, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg (Germany); Holtkotte, Denise [Forschungsschwerpunkt Infektion und Krebs, F020, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg (Germany); Pfeiffer, Tanya [Forschungsschwerpunkt Infektion und Krebs, F020, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg (Germany); Pisch, Thorsten [Forschungsschwerpunkt Infektion und Krebs, F020, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg (Germany); Bosch, Valerie [Forschungsschwerpunkt Infektion und Krebs, F020, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg (Germany)]. E-mail: v.bosch@dkfz.de

    2007-05-10

    Low level incorporation of the viral glycoprotein (Env) into human immunodeficiency virus (HIV) particles is a major drawback for vaccine strategies against HIV/AIDS in which HIV particles are used as immunogen. Within this study, we have examined two strategies aimed at achieving higher levels of Env incorporation into non-infectious pseudovirions (PVs). First, we have generated chimeric HIV/SIV Env proteins containing the truncated C-terminal tail region of simian immunodeficiency virus (SIV)mac239-Env767{sup stop}, which mediates strongly increased incorporation of SIV-Env into SIV particles. In a second strategy, we have employed a truncated HIV-Env protein (Env-Tr752{sup N750K}) which we have previously demonstrated to be incorporated into HIV virions, generated in infected T-cells, to a higher level than that of Wt-HIV-Env. Although the chimeric HIV/SIV Env proteins were expressed at the cell surface and induced increased levels of cell-cell fusion in comparison to Wt-HIV-Env, they did not exhibit increased incorporation into either HIV-PVs or SIV-PVs. Only Env-Tr752{sup N750K} exhibited significantly higher (threefold) levels of incorporation into HIV-PVs, an improvement, which, although not dramatic, is worthwhile for the large-scale preparation of non-infectious PVs for vaccine studies aimed at inducing Env humoral responses.

  9. Characterization of immune responses elicited in macaques immunized sequentially with chimeric VEE/SIN alphavirus replicon particles expressing SIVGag and/or HIVEnv and with recombinant HIVgp140Env protein.

    PubMed

    Xu, Rong; Srivastava, Indresh K; Greer, Catherine E; Zarkikh, Irina; Kraft, Zane; Kuller, Larene; Polo, John M; Barnett, Susan W; Stamatatos, Leonidas

    2006-10-01

    In the present study, macaques were coimmunized with VEErep/SINenv chimeric alphavirus replicon particles expressing SIVp55Gag and HIVDeltaV2gp140Env or only with replicon particles expressing HIVDeltaV2gp140Env. All animals were subsequently immunized with recombinant trimeric HIVDeltaV2gp140Env protein. During alphavirus immunization, anti-SIVGag and anti-HIVEnv-specific interferon (IFN)-gamma responses, as well as high titers of anti-HIVEnv binding (gp120 but not gp41 specific) and anti-HIV neutralizing antibodies, were generated. The subsequent immunization with recombinant HIVDeltaV2gp140 enhanced the neutralizing antibody titers and Env-specific IFN-gamma responses. Following intravenous challenge with the R5- tropic SHIV(SF162P4) virus, significantly lower primary plasma viremia levels were recorded in the immunized animals, as compared to control animals immunized with replicon particles expressing influenza virus HA. Our results show that this method of immunization elicits both strong cellular immunity and neutralizing antibodies in primates and, thus, merits further investigation. PMID:17067273

  10. Conditional transduction of Salmonella typhimurium envB mutations.

    PubMed Central

    Antón, D N

    1987-01-01

    Joint transduction of the argR and envB genes was observed, at a frequency of 24.5%, when four envB strains were transduced to tetracycline resistance (Tetr) with bacteriophage P22 grown on an argR372::Tn10 envB+ donor. When round-cell argR372::Tn10 derivatives of those envB strains were used as donors, two of them did not produce envB transductants in wild-type LT2 and other envB+ recipients, even though large numbers of Tetr transductants were obtained. This apparent exclusion of envB mutations did not occur when mecillinam-resistant derivatives of those envB+ strains were used as recipients. Mutations conferring partial resistance to mecillinam were found, unlinked to the argR-envB region, in three of the four envB strains studied; envB+ derivatives of the four strains were competent to accept envB mutations excluded by wild-type recipients. It is suggested that some envB mutations are lethal in the absence of suppressor mutations, some of which increase resistance to mecillinam. Images PMID:3549704

  11. Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys.

    PubMed

    Barouch, Dan H; Whitney, James B; Moldt, Brian; Klein, Florian; Oliveira, Thiago Y; Liu, Jinyan; Stephenson, Kathryn E; Chang, Hui-Wen; Shekhar, Karthik; Gupta, Sanjana; Nkolola, Joseph P; Seaman, Michael S; Smith, Kaitlin M; Borducchi, Erica N; Cabral, Crystal; Smith, Jeffrey Y; Blackmore, Stephen; Sanisetty, Srisowmya; Perry, James R; Beck, Matthew; Lewis, Mark G; Rinaldi, William; Chakraborty, Arup K; Poignard, Pascal; Nussenzweig, Michel C; Burton, Dennis R

    2013-11-14

    Human immunodeficiency virus type 1 (HIV-1)-specific monoclonal antibodies with extraordinary potency and breadth have recently been described. In humanized mice, combinations of monoclonal antibodies have been shown to suppress viraemia, but the therapeutic potential of these monoclonal antibodies has not yet been evaluated in primates with an intact immune system. Here we show that administration of a cocktail of HIV-1-specific monoclonal antibodies, as well as the single glycan-dependent monoclonal antibody PGT121, resulted in a rapid and precipitous decline of plasma viraemia to undetectable levels in rhesus monkeys chronically infected with the pathogenic simian-human immunodeficiency virus SHIV-SF162P3. A single monoclonal antibody infusion afforded up to a 3.1 log decline of plasma viral RNA in 7?days and also reduced proviral DNA in peripheral blood, gastrointestinal mucosa and lymph nodes without the development of viral resistance. Moreover, after monoclonal antibody administration, host Gag-specific T-lymphocyte responses showed improved functionality. Virus rebounded in most animals after a median of 56?days when serum monoclonal antibody titres had declined to undetectable levels, although, notably, a subset of animals maintained long-term virological control in the absence of further monoclonal antibody infusions. These data demonstrate a profound therapeutic effect of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys as well as an impact on host immune responses. Our findings strongly encourage the investigation of monoclonal antibody therapy for HIV-1 in humans. PMID:24172905

  12. ENVE 417 HYDRAULIC DESIGN TOPIC SYLLABUS

    E-print Network

    Clark, Shirley E.

    design for an assigned neighborhood. Use the software to modify the design as needed. (EPANET available, SSOs and Biological Transformation in Sewers Sewer Appurtenances, Sanitary Sewer Design Sanitary SewerENVE 417 HYDRAULIC DESIGN TOPIC SYLLABUS Current Catalog Data: Design of water and waste water

  13. A Long-Acting Integrase Inhibitor Protects Female Macaques from Repeated High-Dose Intravaginal SHIV Challenge

    PubMed Central

    Andrews, Chasity D.; Yueh, Yun Lan; Spreen, William R.; St. Bernard, Leslie; Boente-Carrera, Mar; Rodriguez, Kristina; Gettie, Agegnehu; Russell-Lodrigue, Kasi; Blanchard, James; Ford, Susan; Mohri, Hiroshi; Cheng-Mayer, Cecilia; Hong, Zhi; Ho, David D.; Markowitz, Martin

    2015-01-01

    GSK1265744 long-acting (GSK744 LA) is a strand-transfer inhibitor of HIV/SIV integrase and was shown to be an effective pre-exposure prophylaxis agent in a low-dose intrarectal SHIV rhesus macaque challenge model. Here, we examined the pharmacokinetics and efficacy of GSK744 LA as PrEP against repeat high-dose intravaginal SHIV challenge in female rhesus macaques treated with Depo-Provera which promotes viral transmission vaginally. When Depo-Provera-treated female rhesus macaques were dosed with 50 mg/kg of GSK744 LA monthly, systemic and tissue drug concentrations were lower than previously observed in male rhesus macaques. GSK744 concentrations were 5-fold lower on average in cervical tissues than rectal tissues. Eight female rhesus macaques were treated with GSK744 LA at week 0, and four female rhesus macaques served as controls. All animals received a high dose challenge of SHIV162P3 at week 1. No infection was detected in GSK744 LA-treated rhesus macaques, whereas viremia was detected 1 to 2 weeks after SHIV challenge in all control animals. The GSK744 LA-treated rhesus macaques were given a second administration of drug at week 4 and further challenged at weeks 5 and 7. GSK744 LA treatment protected 6 of 8 female rhesus macaques against three high-dose SHIV challenges, whereas all control animals became infected after the first challenge (P = 0.0003, log-rank test). These results support further clinical development of GSK744 LA for pre-exposure prophylaxis. PMID:25589630

  14. Retroviral Env Glycoprotein Trafficking and Incorporation into Virions

    PubMed Central

    Murakami, Tsutomu

    2012-01-01

    Together with the Gag protein, the Env glycoprotein is a major retroviral structural protein and is essential for forming infectious virus particles. Env is synthesized, processed, and transported to certain microdomains at the plasma membrane and takes advantage of the same host machinery for its trafficking as that used by cellular glycoproteins. Incorporation of Env into progeny virions is probably mediated by the interaction between Env and Gag, in some cases with the additional involvement of certain host factors. Although several general models have been proposed to explain the incorporation of retroviral Env glycoproteins into virions, the actual mechanism for this process is still unclear, partly because structural data on the Env protein cytoplasmic tail is lacking. This paper presents the current understanding of the synthesis, trafficking, and virion incorporation of retroviral Env proteins. PMID:22811910

  15. Immune mechanisms associated with protection from vaginal SIV challenge in rhesus monkeys infected with virulence-attenuated SHIV 89.6

    E-print Network

    Miller, C J

    2005-01-01

    immune responses to vaginal herpes infection in mice [44,infections [6, 59]. Progesterone-dependent thinning of the vaginalinfection with virulence attenuated-simian–human immunode?ciency virus (SHIV) 89.6 provides protection against vaginal

  16. Floating JMaRT

    E-print Network

    Guillaume Bossard; Stefanos Katmadas

    2015-05-30

    We define a new partially solvable system of equations that parametrises solutions to six-dimensional N=(1,0) ungauged supergravity coupled to tensor multiplets. We obtain this system by applying a series of dualities on the known floating brane system, imposing that it allows for the JMaRT solution. We construct an explicit multi-centre solution generalising the JMaRT solution, with an arbitrary number of additional BPS centres on a line. We describe explicitly the embedding of the JMaRT solution in this system in five dimensions.

  17. Floating JMaRT

    E-print Network

    Bossard, Guillaume

    2014-01-01

    We define a new partially solvable system of equations that parametrises solutions to six-dimensional N=(1,0) ungauged supergravity coupled to tensor multiplets. We obtain this system by applying a series of dualities on the known floating brane system, imposing that it allows for the JMaRT solution. We construct an explicit multi-centre solution generalising the JMaRT solution, with an arbitrary number of additional BPS centres on a line. We describe explicitly the embedding of the JMaRT solution in this system in five dimensions.

  18. Aaron Shepard's RT Page

    NSDL National Science Digital Library

    Shepard, Aaron.

    1996-01-01

    Aaron Shepard, author of Stories on Stage: Scripts for Reader's Theater (H.W. Wilson, 1993), has provided this web site as a way to broaden interest in the reader's theater (RT) genre. Using minimal (or no) sets, props, and costumes, RT performances are opportunities for students to participate in short dramatic adaptations of prose or dramatic works. Of the RT scripts available on the site, several are original and several are adaptations of well-known short stories. There are twelve scripts for grade, middle, and high school, and five for college classes.

  19. Floating JMaRT

    NASA Astrophysics Data System (ADS)

    Bossard, Guillaume; Katmadas, Stefanos

    2015-04-01

    We define a new partially solvable system of equations that parametrises solutions to six-dimensional ungauged supergravity coupled to tensor multiplets. We obtain this system by applying a series of dualities on the known floating brane system, imposing that it allows for the JMaRT solution. We construct an explicit multi-centre solution generalising the JMaRT solution, with an arbitrary number of additional BPS centres on a line. We describe explicitly the embedding of the JMaRT solution in this system in five dimensions.

  20. Therapeutic Efficacy of Potent Neutralizing HIV-1-Specific Monoclonal Antibodies in SHIV-Infected Rhesus Monkeys

    PubMed Central

    Barouch, Dan H.; Whitney, James B.; Moldt, Brian; Klein, Florian; Oliveira, Thiago Y.; Liu, Jinyan; Stephenson, Kathryn E.; Chang, Hui-Wen; Shekhar, Karthik; Gupta, Sanjana; Nkolola, Joseph P.; Seaman, Michael S.; Smith, Kaitlin M.; Borducchi, Erica N.; Cabral, Crystal; Smith, Jeffrey Y.; Blackmore, Stephen; Sanisetty, Srisowmya; Perry, James R.; Beck, Matthew; Lewis, Mark G.; Rinaldi, William; Chakraborty, Arup K.; Poignard, Pascal; Nussenzweig, Michel C.; Burton, Dennis R.

    2014-01-01

    HIV-1-specific monoclonal antibodies (mAbs) with extraordinary potency and breadth have recently been described. In humanized mice, combinations of mAbs have been shown to suppress viremia, but the therapeutic potential of these mAbs has not yet been evaluated in primates with an intact immune system. Here we show that administration of a cocktail of HIV-1-specific mAbs, as well as the single glycan-dependent mAb PGT121, resulted in a rapid and precipitous decline of plasma viremia to undetectable levels in rhesus monkeys chronically infected with the pathogenic virus SHIV-SF162P3. A single mAb infusion afforded up to a 3.1 log decline of plasma viral RNA in 7 days and also reduced proviral DNA in peripheral blood, gastrointestinal mucosa, and lymph nodes without the development of viral resistance. Moreover, following mAb administration, host Gag-specific T lymphocyte responses exhibited improved functionality. Virus rebounded in the majority of animals after a median of 56 days when serum mAb titers had declined to undetectable levels, although a subset of animals maintained long-term virologic control in the absence of further mAb infusions. These data demonstrate a profound therapeutic effect of potent neutralizing HIV-1-specific mAbs in SHIV-infected rhesus monkeys as well as an impact on host immune responses. Our findings strongly encourage the investigation of mAb therapy for HIV-1 in humans. PMID:24172905

  1. Passive transfer of modest titers of potent and broadly neutralizing anti-HIV monoclonal antibodies block SHIV infection in macaques

    PubMed Central

    Shingai, Masashi; Donau, Olivia K.; Plishka, Ronald J.; Buckler-White, Alicia; Mascola, John R.; Nabel, Gary J.; Nason, Martha C.; Montefiori, David; Moldt, Brian; Poignard, Pascal; Diskin, Ron; Bjorkman, Pamela J.; Eckhaus, Michael A.; Klein, Florian; Mouquet, Hugo; Cetrulo Lorenzi, Julio Cesar; Gazumyan, Anna; Burton, Dennis R.; Nussenzweig, Michel C.

    2014-01-01

    It is widely appreciated that effective human vaccines directed against viral pathogens elicit neutralizing antibodies (NAbs). The passive transfer of anti–HIV-1 NAbs conferring sterilizing immunity to macaques has been used to determine the plasma neutralization titers, which must be present at the time of exposure, to prevent acquisition of SIV/HIV chimeric virus (SHIV) infections. We administered five recently isolated potent and broadly acting anti-HIV neutralizing monoclonal antibodies (mAbs) to rhesus macaques and challenged them intrarectally 24 h later with either of two different R5-tropic SHIVs. By combining the results obtained from 60 challenged animals, we determined that the protective neutralization titer in plasma preventing virus infection in 50% of the exposed monkeys was relatively modest (?1:100) and potentially achievable by vaccination. PMID:25155019

  2. Lymphocyte Activation during Acute Simian/Human Immunodeficiency Virus SHIV89.6PD Infection in Macaques†

    PubMed Central

    Wallace, Marianne; Waterman, Paul M.; Mitchen, Jacque L.; Djavani, Mahmoud; Brown, Charles; Trivedi, Parul; Horejsh, Douglas; Dykhuizen, Marta; Kitabwalla, Moiz; Pauza, C. David

    1999-01-01

    Host-virus interactions control disease progression in human immunodeficiency virus-infected human beings and in nonhuman primates infected with simian or simian/human immunodeficiency viruses (SHIV). These interactions evolve rapidly during acute infection and are key to the mechanisms of viral persistence and AIDS. SHIV89.6PD infection in rhesus macaques can deplete CD4+ T cells from the peripheral blood, spleen, and lymph nodes within 2 weeks after exposure and is a model for virulent, acute infection. Lymphocytes isolated from blood and tissues during the interval of acute SHIV89.6PD infection have lost the capacity to proliferate in response to phytohemagglutinin (PHA). T-cell unresponsiveness to mitogen occurred within 1 week after mucosal inoculation yet prior to massive CD4+ T-cell depletion and extensive virus dissemination. The lack of mitogen response was due to apoptosis in vitro, and increased activation marker expression on circulating T cells in vivo coincided with the appearance of PHA-induced apoptosis in vitro. Inappropriately high immune stimulation associated with rapid loss of mature CD4+ T cells suggested that activation-induced cell death is a mechanism for helper T-cell depletion in the brief period before widespread virus dissemination. Elevated levels of lymphocyte activation likely enhance SHIV89.6PD replication, thus increasing the loss of CD4+ T cells and diminishing the levels of virus-specific immunity that remain after acute infection. The level of surviving immunity may dictate the capacity to control virus replication and disease progression. We describe this level of immune competence as the host set point to show its pivotal role in AIDS pathogenesis. PMID:10559340

  3. Call title : FP7-ENV-2010 Call identifier: FP7-ENV-2010

    E-print Network

    Milano-Bicocca, Università

    called: ACTIVITY/ AREA TOPICS CALLED FUNDING SCHEMES ACTIVITY 6.1. CLIMATE CHANGE, POLLUTION AND RISKS pollution and health risks of modern office buildings Collaborative Project (small or medium-scale focused research project) ENV.2010.1.2.2-2 Human health and environmental effects of exposure to pharmaceuticals

  4. ENVS 340: Topics in Pollution: Gulf Oil Spill Spring 2011

    E-print Network

    ENVS 340: Topics in Pollution: Gulf Oil Spill Spring 2011 ENVS 340 Topics in Pollution: Gulf Oil Oil Spill based on scientific research. Our report is due ~May 8. Our first goal is to determine Spill BIOL 378 Environmental Toxicology Instructor: Dr. Susan Allen-Gil Office: CNS 253 Phone: 274

  5. ENVS 404/196: Internship Syllabus Contact Information

    E-print Network

    1 ENVS 404/196: Internship Syllabus Contact Information Peg Boulay, Internship Coordinator/Academic Advisor 242 Columbia Hall 346-5945 boulay@uoregon.edu Purpose of this Course The ENVS Internship Program for environmentally-focused work experience. A well-designed internship will allow you to develop your professional

  6. Longitudinal study to assess the safety and efficacy of a live-attenuated SHIV vaccine in long term immunized rhesus macaques

    SciTech Connect

    Yankee, Thomas M. [Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, 3025 WHW - MS 3029, 3901 Rainbow Boulevard, Kansas City, KS 66160 (United States)], E-mail: tyankee@kumc.edu; Sheffer, Darlene; Liu Zhengian; Dhillon, Sukhbir; Jia Fenglan; Chebloune, Yahia [Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, 3025 WHW - MS 3029, 3901 Rainbow Boulevard, Kansas City, KS 66160 (United States); Stephens, Edward B. [Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, 3025 WHW - MS 3029, 3901 Rainbow Boulevard, Kansas City, KS 66160 (United States); Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160 (United States); Narayan, Opendra [Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, 3025 WHW - MS 3029, 3901 Rainbow Boulevard, Kansas City, KS 66160 (United States)

    2009-01-05

    Live-attenuated viruses derived from SIV and SHIV have provided the most consistent protection against challenge with pathogenic viruses, but concerns regarding their long-term safety and efficacy have hampered their clinical usefulness. We report a longitudinal study in which we evaluated the long-term safety and efficacy of {delta}vpuSHIV{sub PPC}, a live virus vaccine derived from SHIV{sub PPC}. Macaques were administered two inoculations of {delta}vpuSHIV{sub PPC}, three years apart, and followed for eight years. None of the five vaccinated macaques developed an AIDS-like disease from the vaccine. At eight years, macaques were challenged with pathogenic SIV and SHIV. None of the four macaques with detectable cellular-mediated immunity prior to challenge had detectable viral RNA in the plasma. This study demonstrates that multiple inoculations of a live vaccine virus can be used safely and can significantly extend the efficacy of the vaccine, as compared to a single inoculation, which is efficacious for approximately three years.

  7. Presence of env-like sequences in Quercus suber retrotransposons.

    PubMed

    Carvalho, M; Ribeiro, T; Viegas, W; Morais-Cecilio, L; Rocheta, M

    2010-01-01

    The main difference between LTR retrotransposons and retroviruses is the presence of the envelope (env) gene in the latter, downstream of the pol gene. The env gene is involved in their infectious capacity. Here we report the presence of env-like sequences in the genome of Quercus suber (cork oak), one of the most economically important Portuguese species. These gene sequences were isolated through DNA amplification between RNaseH conserved motifs and 3' LTR, based on the structure of copia retrotransposons. Phylogenetic analysis revealed that almost all the clones isolated are clustered with Cyclops-2, a Ty3-gypsy element identified in Pisum sativum, except one clustered with gypsy and copia retroelements found in different species. This suggests the existence of a potential ancestral sequence of the env gene, prior to the separation of Ty3-gypsy and Ty1-copia retrotransposons. Additionally, the isolated env-like sequences showed 26-39% of homology with env-like sequences characterized in viruses. The origin of env-like sequences in retrotransposons from host plant taxa is discussed. PMID:21063063

  8. ANTIBODY MEDIATED IMMUNOTHERAPY OF MACAQUES CHRONICALLY INFECTED WITH SHIV SUPPRESSES VIREMIA

    PubMed Central

    Shingai, Masashi; Nishimura, Yoshiaki; Klein, Florian; Mouquet, Hugo; Donau, Olivia K.; Plishka, Ronald; Buckler-White, Alicia; Piatak, Michael; Lifson, Jeffrey D.; Dimitrov, Dimiter; Nussenzweig, Michel C.; Martin, Malcolm A.

    2014-01-01

    Neutralizing antibodies (NAbs) can confer immunity to primate lentiviruses by blocking infection in macaque models of AIDS1–4. However, earlier studies of anti-HIV 1 NAbs administered to infected individuals or humanized mice, reported poor control of virus replication and the rapid emergence of resistant variants 5–7. A new generation of anti-HIV 1 monoclonal antibodies (mAbs), possessing extraordinary potency and breadth of neutralizing activity, has recently been isolated from infected individuals 8. These NAbs target different regions of the HIV 1 envelope glycoprotein including the CD4 binding site (bs), glycans located in the V1/V2, V3, and V4 regions, and the membrane proximal external region of gp419–14. We have examined two of the new antibodies, directed to the CD4 bs and the V3 region (3BNC117 and 10-1074 respectively) for their ability to block infection and suppress viremia in macaques infected with the R5 tropic SHIVAD8 virus, which emulates many of the pathogenic and immunogenic properties of HIV 1 during infections of rhesus macaques15,16. Either antibody alone can potently block virus acquisition. When administered individually to recently infected monkeys, the 10-1074 antibody caused a rapid decline in virus loads to undetectable levels for 4 to 7 days, followed by virus rebound during which neutralization resistant variants became detectable. When administered together, a single treatment rapidly suppressed plasma viremia for 3 to 5 weeks in some long-term chronically SHIV infected animals with low CD4+ T cell levels. A second cycle of anti-HIV 1 mAb therapy, administered to two previously treated animals, successfully controlled virus rebound. These results suggest that immunotherapy or a combination of immunotherapy plus conventional antiretroviral drugs might be useful as a treatment for chronically HIV-1 infected individuals experiencing immune dysfunction. PMID:24172896

  9. A single amino acid substitution within the transmembrane domain of the human immunodeficiency virus type 1 Vpu protein renders simian-human immunodeficiency virus (SHIV{sub KU-1bMC33}) susceptible to rimantadine

    SciTech Connect

    Hout, David R. [Department of Anatomy and Cell Biology, University of Kansas Medical Center 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Gomez, Lisa M. [Department of Anatomy and Cell Biology, University of Kansas Medical Center 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Pacyniak, Erik [Department of Anatomy and Cell Biology, University of Kansas Medical Center 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Miller, Jean-Marie [Department of Anatomy and Cell Biology, University of Kansas Medical Center 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Hill, M. Sarah [Department of Anatomy and Cell Biology, University of Kansas Medical Center 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Stephens, Edward B. [Department of Anatomy and Cell Biology, University of Kansas Medical Center 3901 Rainbow Blvd., Kansas City, KS 66160 (United States)]. E-mail: estephen@kumc.edu

    2006-05-10

    Previous studies from our laboratory have shown that the transmembrane domain (TM) of the Vpu protein of human immunodeficiency virus type 1 (HIV-1) contributes to the pathogenesis of SHIV{sub KU-1bMC33} in macaques and that the TM domain of Vpu could be replaced with the M2 protein viroporin from influenza A virus. Recently, we showed that the replacement of the TM domain of Vpu with that of the M2 protein of influenza A virus resulted in a virus (SHIV{sub M2}) that was sensitive to rimantadine [Hout, D.R., Gomez, M.L., Pacyniak, E., Gomez, L.M., Inbody, S.H., Mulcahy, E.R., Culley, N., Pinson, D.M., Powers, M.F., Wong, S.W., Stephens, E.B., 2006. Substitution of the transmembrane domain of Vpu in simian human immunodeficiency virus (SHIV{sub KU-1bMC33}) with that of M2 of influenza A results in a virus that is sensitive to inhibitors of the M2 ion channel and is pathogenic for pig-tailed macaques. Virology 344, 541-558]. Based on previous studies of the M2 protein which have shown that the His-X-X-X-Trp motif within the M2 is essential to the function of the M2 proton channel, we have constructed a novel SHIV in which the alanine at position 19 of the TM domain was replaced with a histidine residue resulting in the motif His-Ile-Leu-Val-Trp. The SHIV{sub VpuA19H} replicated with similar kinetics as the parental SHIV{sub KU-1bMC33} and pulse-chase analysis revealed that the processing of viral proteins was similar to SHIV{sub KU-1bMC33}. This SHIV{sub VpuA19H} virus was found to be more sensitive to the M2 ion channel blocker rimantadine than SHIV{sub M2}. Electron microscopic examination of SHIV{sub VpuA19H}-infected cells treated with rimantadine revealed an accumulation of viral particles at the cell surface and within intracellular vesicles, which was similar to that previously observed to SHIV{sub M2}-infected cells treated with rimantadine. These data indicate that the Vpu protein of HIV-1 can be converted into a rimantadine-sensitive ion channel with the alteration of one amino acid and provide additional evidence that drugs targeting the Vpu TM/ion channel can be effective anti-HIV-1 drugs.

  10. Demonstration results for the standard ENV 12924.

    PubMed

    Louwerse, Kees

    2002-01-01

    Within the working programme of CEN/TC251 (Health Informatics), a standard for Security Categorisation and Protection for Healthcare Information Systems has been developed. This document was formally adopted in 1997 by CEN as pre-standard CEN ENV 12924. A demonstration and implementation effort, which was to be effected in principle at one location, was planned and executed as part of the MEDSEC project. The standard CEN ENV 12924 contains a security categorisation model for information systems in Healthcare, distinguishing six categories, plus some refinements. For each category it specifies the required protection measures. The project task consisted of demonstrating and implementing the standard (as far as possible within a limited period) in a real life situation, and providing feedback on these results to the CEN organisation. To this end, the categorisation scheme, as specified in the standard, was applied to a large part of the information (sub)-systems in the Leiden University Medical Centre. A set of ten sub-systems was then selected for a more detailed investigation. The actual protection status for each sub-system was evaluated on the basis of the recommended protection profiles specified in the standard. For each of the relevant recommendations in the standard, its status was recorded, and remarks were added on its relevance, feasibility, etc. These detailed data have been gathered in separate reports for each sub-system. These reports evidently are confidential, in view of protection of the hospital's information security. A similar, though more limited exercise has been done at Magdeburg University Hospital (UHM), in order to be able to allow for possible differences in local situations. A thorough comparison of results for different hospitals was beyond the scope of the project, however. From the overall picture we have tried to draw conclusions on the quality, completeness and applicability of the standard, as well as on the actual level of protection of the systems. As a by-product of the investigation, for all systems out of the small group, implementation plans have been specified to bring the protection in the various (sub)-systems on a higher level, where necessary. Subsequently, these plans have been realised to a large extent. To facilitate the bookkeeping of the results, we have used the SIDERO model, resulting from the SEISMED project. This model has been enhanced, for this purpose, with the recommendations from this standard. A brief description of this database model has been included in Appendix B. As an overall conclusion, we may state that the standard has proven to be a very useful instrument, providing a good basis for a security review of the types of Healthcare information systems which are encountered in a hospital environment. Some suggestions have been presented, for amending recommendations that were found too unpractical or too heavy in the circumstances considered. Also, we suggest to add one category to the set of six which is being used now. Furthermore, the use of a 'bookkeeping tool' (like e.g. SIDERO) is strongly recommended. PMID:15458164

  11. Highly potent HIV-specific antibody neutralization in vitro translates into effective protection against mucosal SHIV challenge in vivo.

    PubMed

    Moldt, Brian; Rakasz, Eva G; Schultz, Niccole; Chan-Hui, Po-Ying; Swiderek, Kristine; Weisgrau, Kimberly L; Piaskowski, Shari M; Bergman, Zachary; Watkins, David I; Poignard, Pascal; Burton, Dennis R

    2012-11-13

    Most animal studies using passive administration of HIV broadly neutralizing monoclonal antibodies (bnMAbs) have associated protection against high-dose mucosal viral challenge with relatively high serum concentrations of antibody. We recently identified several bnMAbs remarkable for their in vitro potency against HIV. Of these bnMAbs, PGT121 is one of the most broad and potent antibodies isolated to date and shows 10- to 100-fold higher neutralizing activity than previously characterized bnMAbs. To evaluate the protective potency of PGT121 in vivo, we performed a protection study in rhesus macaques. Animals were i.v. administered 5 mg/kg, 1 mg/kg, or 0.2 mg/kg PGT121 24 h before being vaginally challenged with a single high dose of chimeric simian-human immunodeficiency virus (SHIV)(SF162P3). Sterilizing immunity was achieved in all animals administered 5 mg/kg and 1 mg/kg and three of five animals administered 0.2 mg/kg PGT121, with corresponding average antibody serum concentrations of 95 µg/mL, 15 µg/mL, and 1.8 µg/mL, respectively. The results suggest that a protective serum concentration for PGT121 is in the single-digit µg/mL for SHIV(SF162P3), showing that PGT121 can mediate sterilizing immunity at serum concentrations that are significantly lower than those observed in previous studies and that may be achievable through vaccination with the development of a suitable immunogen. PMID:23100539

  12. Antibodies to CD4-induced sites in HIV gp120 correlate with the control of SHIV challenge in macaques vaccinated with subunit immunogens

    PubMed Central

    DeVico, Anthony; Fouts, Timothy; Lewis, George K.; Gallo, Robert C.; Godfrey, Karla; Charurat, Manhattan; Harris, Ilia; Galmin, Lindsey; Pal, Ranajit

    2007-01-01

    Epitopes located in and around the coreceptor binding site of HIV-1 envelope glycoprotein (gp120) exhibit enhanced exposure after attachment to the CD4 receptor and comprise some of the most conserved and functionally important residues on the viral envelope. Therefore, antibody responses to these epitopes [designated as CD4-induced (CD4i)] should be highly cross-reactive and potentially useful for HIV vaccine development. To address this question, rhesus macaques were vaccinated with subunit immunogens designed to raise humoral responses against CD4i epitopes and challenged rectally with SHIV162P3, which encodes a heterologous envelope versus the immunogen. We found that animals vaccinated with a rhesus full-length single-chain (rhFLSC) complex exhibited significantly accelerated clearance of plasma viremia and an absence of long-term tissue viremia compared with unvaccinated control animals. Such control of infection correlated with stronger responses to CD4i epitopes in the rhFLSC-vaccinated animals, compared with macaques immunized with gp120, cross-linked gp120–CD4 complexes, or soluble CD4 alone. These responses were strongly boosted in the rhFLSC-vaccinated animals by SHIV162P3 infection. The control of infection was not associated with anti-CD4 responses, overall anti-gp120-binding titers, or neutralizing activity measured in conventional assays. Vaccine-naive animals also developed anti-CD4i epitope responses after simian/ human immunodeficiency virus (SHIV) challenge, which appeared later than the overall anti-gp120 responses and in concert with the decline of viremia to a low set point. Collectively, these data suggest that antibodies to CD4i epitopes may play a role in controlling SHIV infection and provide insights for HIV vaccine development. PMID:17956985

  13. Appreciating HIV-1 diversity: subtypic differences in ENV

    SciTech Connect

    Gnanakaran, S [Los Alamos National Laboratory; Shen, Tongye [Los Alamos National Laboratory; Lynch, Rebecca M [NON LANL; Derdeyn, Cynthia A [NON LANL

    2008-01-01

    Human immunodeficiency virus type 1 (HIV-1) group M is responsible for the current AIDS pandemic and exhibits exceedingly high levels of viral genetic diversity around the world, necessitating categorization of viruses into distinct lineages, or subtypes. These subtypes can differ by around 35% in the envelope (Env) glycoproteins of the virus, which are displayed on the surface of the virion and are targets for both neutralizing antibody and cell-mediated immune responses. This diversity reflects the remarkable ability of the virus to adapt to selective pressures, the bulk of which is applied by the host immune response, and represents a serious obstacle for developing an effective vaccine with broad coverage. Thus, it is important to understand the underlying biological consequences of inter-subtype diversity. Recent studies have revealed that the HIV-1 subtypes exhibit phenotypic differences that result from subtle differences in Env structure, particularly within the highly immunogenic V3 domain, which participates directly in viral entry. This review will therefore explore current research that describes subtypic differences in Env at the genetic and phenotypic level, focusing in particular on V3, and highlighting recent discoveries about the unique features of subtype C Env, which is the most prevalent subtype globally.

  14. ENVS 404: Internship Syllabus Contact Information: Internship Coordinator

    E-print Network

    1 ENVS 404: Internship Syllabus Contact Information: Internship Coordinator Peg Boulay Environmental Leadership Program Co-Director, Internship Coordinator and Academic Adviser 242 Columbia Hall 541-346-5945 boulay@uoregon.edu Note: The Internship Coordinator position may also be filled by a Graduate Teaching

  15. The Nonnucleoside Reverse Transcription Inhibitor MIV-160 Delivered from an Intravaginal Ring, But Not from a Carrageenan Gel, Protects Against Simian/Human Immunodeficiency Virus-RT Infection

    PubMed Central

    Aravantinou, Meropi; Singer, Rachel; Derby, Nina; Calenda, Giulia; Mawson, Paul; Abraham, Ciby J.; Menon, Radhika; Seidor, Samantha; Goldman, Daniel; Kenney, Jessica; Villegas, Guillermo; Gettie, Agegnehu; Blanchard, James; Lifson, Jeffrey D.; Piatak, Michael; Fernández-Romero, José A.; Zydowsky, Thomas M.; Teleshova, Natalia

    2012-01-01

    Abstract We previously showed that a carrageenan (CG) gel containing 50??M MIV-150 (MIV-150/CG) reduced vaginal simian/human immunodeficiency virus (SHIV)-RT infection of macaques (56%, p>0.05) when administered daily for 2 weeks with the last dose given 8?h before challenge. Additionally, when 100?mg of MIV-150 was loaded into an intravaginal ring (IVR) inserted 24?h before challenge and removed 2 weeks after challenge, >80% protection was observed (p<0.03). MIV-160 is a related NNRTI with a similar IC50, greater aqueous solubility, and a shorter synthesis. To objectively compare MIV-160 with MIV-150, herein we evaluated the antiviral effects of unformulated MIV-160 in vitro as well as the in vivo protection afforded by MIV-160 delivered in CG (MIV-160/CG gel) and in an IVR under regimens used with MIV-150 in earlier studies. Like MIV-150, MIV-160 exhibited potent antiviral activity against SHIV-RT in macaque vaginal explants. However, formulated MIV-160 exhibited divergent effects in vivo. The MIV-160/CG gel offered no protection compared to CG alone, whereas the MIV-160 IVRs protected significantly. Importantly, the results of in vitro release studies of the MIV-160/CG gel and the MIV-160 IVR suggested that in vivo efficacy paralleled the amount of MIV-160 released in vitro. Hundreds of micrograms of MIV-160 were released daily from IVRs while undetectable amounts of MIV-160 were released from the CG gel. Our findings highlight the importance of testing different modalities of microbicide delivery to identify the optimal formulation for efficacy in vivo. PMID:22816564

  16. Polymorphisms in the HIV-1 gp41 env gene, natural resistance to enfuvirtide (T-20) and pol resistance among pregnant Brazilian women.

    PubMed

    Reis, Mônica Nogueira da Guarda; de Alcântara, Keila Correa; Cardoso, Ludimila Paula Vaz; Stefani, Mariane Martins Araújo

    2014-01-01

    The selective pressure of antiretroviral drugs (ARVs) targeting HIV-1 pol can promote drug resistance mutations in other genomic regions, such as env. Drug resistance among women should be monitored to avoid horizontal and mother-to-child transmission. To describe natural resistance to T-20 (enfuvirtide), gp41 env polymorphisms, mutations in pol and HIV-1 subtypes, 124 pregnant women were recruited. For 98 patients, the gp41 env, protease (PR) and reverse transcriptase (RT) fragments were sequenced. The patients were ARV naïve (n?=?30), taking mother-to-child transmission prophylaxis (n?=?50), or being treated with highly active ARV therapy/HAART (n?=?18). The Stanford and IAS/USA databases and other sources were used to analyze PR/RT, gp41 env resistance mutations. The HIV-1 genetic diversity was analyzed by REGA/phylogenetic analyses. The patients' median age was 25 years (range, 16-42), 18.4% had AIDS. The frequency of natural resistance to T-20 (N42D, L44M, and R46M-low-impact mutations) was 6.1% (6/98); 20.4% (20/98) had compensatory mutations in HR2. The prevalence of transmitted drug resistance in the pol was 13.3% (4/30), and the prevalence of secondary drug resistance was 33.3% (6/18). Two patients were infected with multidrug resistant/MDR viruses. The analysis of HIV-1 subtypes (PR/RT/gp41) revealed that 61.2% (60/98) were subtype B, 12.2% (12/98) were subtype C, 4.1% (4/98) were subtype F1, and 22.4% (22/98) were possible recombinants (BF1?=?20.4%; BC?=?2%). Natural resistance to T-20 was not associated with pol resistance or previous ARV use. The high rate of secondary resistance, including MDR, indicates that the number of women that may need T-20 salvage therapy may be higher than anticipated. PMID:24037943

  17. Structure and immune recognition of trimeric prefusion HIV-1 Env

    PubMed Central

    Pancera, Marie; Zhou, Tongqing; Druz, Aliaksandr; Georgiev, Ivelin S.; Soto, Cinque; Gorman, Jason; Huang, Jinghe; Acharya, Priyamvada; Chuang, Gwo-Yu; Ofek, Gilad; Stewart-Jones, Guillaume B. E.; Stuckey, Jonathan; Bailer, Robert T.; Joyce, M. Gordon; Louder, Mark K.; Tumba, Nancy; Yang, Yongping; Zhang, Baoshan; Cohen, Myron S.; Haynes, Barton F.; Mascola, John R.; Morris, Lynn; Munro, James B.; Blanchard, Scott C.; Mothes, Walther; Connors, Mark; Kwong, Peter D.

    2015-01-01

    The HIV-1-envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a postfusion state. As the sole viral antigen on the HIV-1-virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5-Å resolution for an HIV-1-Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the prefusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Prefusion gp41 encircles N- and C-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry likely involve opening the clasp and expelling the termini. N-linked glycosylation and sequence-variable regions cover the prefusion closed spike: we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation. PMID:25296255

  18. Isolation and characterization of monoclonal antibodies elicited by trimeric HIV1 Env gp140 protein immunogens

    Microsoft Academic Search

    Nina R. Derby; Sean Gray; Elizabeth Wayner; Dwayne Campogan; Giorgos Vlahogiannis; Zane Kraft; Susan W. Barnett; Indresh K. Srivastava; Leonidas Stamatatos

    2007-01-01

    Eleven anti-HIV Env monoclonal antibodies (MAbs) were isolated from mice immunized with soluble Env proteins derived from the clade B Env, SF162, or ?V2 (a derivative of SF162 lacking the V2 loop). All six anti-gp120 MAbs studied, neutralized SF162 and their activities were dependent by the glycosylation patterns of the V1, V2 or V3 loops. Only one anti-gp120 MAb (an

  19. Expression of Human Endogenous Retrovirus env Genes in the Blood of Breast Cancer Patients

    PubMed Central

    Rhyu, Dong-Won; Kang, Yun-Jeong; Ock, Mee-Sun; Eo, Jung-Woo; Choi, Yung-Hyun; Kim, Wun-Jae; Leem, Sun-Hee; Yi, Joo-Mi; Kim, Heui-Soo; Cha, Hee-Jae

    2014-01-01

    Human endogenous retroviruses (HERV) env proteins have been recently reported to be significantly up-regulated in certain cancers. Specifically, mRNA and protein levels of HERV-K (HML-2) are up-regulated in the blood plasma or serum of breast cancer patients. Here, we collected blood samples of 49 breast cancer patients and analyzed mRNA expressions of various HERVs env genes including HERV-R, HERV-H, HERV-K, and HERV-P by real-time PCR. The expression of env genes were significantly increased in the blood of primary breast cancer patients but were decreased in patients undergoing chemotherapy to a similar level with benign patients. When we compared the group currently undergoing chemotherapy and those patients undergoing chemotherapy simultaneously with radiotherapy, HERVs env genes were reduced more in the chemotherapy only group, suggesting that chemotherapy is more effective in reducing HERV env gene expression than is radiotherapy. Among chemotherapy groups, HERV env gene expression was the lowest in the taxotere- or taxol-treated group, suggesting that taxotere and taxol can reduce HERVs env expression. These data suggest the potential to use HERVs env genes as a diagnosis marker for primary breast cancer, and further studies are needed to identify the mechanism and physiological significance of the reduction of HERV env gene expression during chemotherapy. PMID:24964007

  20. UV-inactivated vaccinia virus (VV) in a multi-envelope DNA-VV-protein (DVP) HIV-1 vaccine protects macaques from lethal challenge with heterologous SHIV

    PubMed Central

    Jones, Bart G; Sealy, Robert E; Zhan, Xiaoyan; Freiden, Pamela J; Surman, Sherri L; Blanchard, James L.; Hurwitz, Julia L

    2012-01-01

    The pandemic of HIV-1 has continued for decades, yet there remains no licensed vaccine. Previous research has demonstrated the effectiveness of a multi-envelope, multi-vectored HIV-1 vaccine in a macaque-SHIV model, illustrating a potential means of combating HIV-1. Specifically, recombinant DNA, vaccinia virus (VV) and purified protein (DVP) delivery systems were used to vaccinate animals with dozens of antigenically-distinct HIV-1 envelopes for induction of immune breadth. The vaccinated animals controlled disease following challenge with a heterologous SHIV. This demonstration suggested that the antigenic cocktail vaccine strategy, which has succeeded in several other vaccine fields (e.g. pneumococcus), might also succeed against HIV-1. The strategy remains untested in an advanced clinical study, in part due to safety concerns associated with the use of replication-competent VV. To address this concern, we designed a macaque study in which psoralen/ultraviolet light-inactivated VV (UV VV) was substituted for replication-competent VV in the multi-envelope DVP protocol. Control animals received a vaccine encompassing no VV, or no vaccine. All VV vaccinated animals generated an immune response toward VV, and all vaccinated animals generated an immune response toward HIV-1 envelope. After challenge with heterologous SHIV 89.6P, animals that received replication-competent VV or UV VV experienced similar outcomes. They exhibited reduced peak viral loads, maintenance of CD4+ T cell counts and improved survival compared to control animals that received no VV or no vaccine; there were 0/15 deaths among all animals that received VV and 5/9 deaths among controls. Results define a practical means of improving VV safety, and encourage advancement of a promising multi-envelope DVP HIV-1 vaccine candidate. PMID:22425790

  1. Transcriptional and functional studies of Human Endogenous Retrovirus envelope EnvP(b) and EnvV genes in human trophoblasts.

    PubMed

    Vargas, Amandine; Thiery, Maxime; Lafond, Julie; Barbeau, Benoit

    2012-03-30

    HERV (Human Endogenous Retrovirus)-encoded envelope proteins are implicated in the development of the placenta. Indeed, Syncytin-1 and -2 play a crucial role in the fusion of human trophoblasts, a key step in placentation. Other studies have identified two other HERV env proteins, namely EnvP(b) and EnvV, both expressed in the placenta. In this study, we have fully characterized both env transcripts and their expression pattern and have assessed their implication in trophoblast fusion. Through RACE analyses, standard spliced transcripts were detected, while EnvV transcripts demonstrated alternative splicing at its 3' end. Promoter activity and expression of both genes were induced in forskolin-stimulated BeWo cells and in primary trophoblasts. Although we have confirmed the fusogenic activity of EnvP(b), overexpression or silencing experiments revealed no impact of this protein on trophoblast fusion. Our results demonstrate that both env genes are expressed in human trophoblasts but are not required for syncytialization. PMID:22277806

  2. SimEnvVis: A Climate Data Visualization Wizard

    NASA Astrophysics Data System (ADS)

    Heitzler, Magnus; Nocke, Thomas

    2013-04-01

    To efficiently make sense of complex climate data, climate scientists need to choose and utilize appropriate analysis tools in respect to specific sets of tasks. Among these, visual analysis tools, like those originating from the field of visual analytics, efficiently support to communicate such information by directly addressing human visual perception. However, climate scientists often are not aware of or not familiar with the large variety of available visual analysis tools or are underestimating their potential benefit for common research tasks and thus reducing the probability to use most suitable ones and therefore impairing the knowledge discovery process. To address this problem, SimEnvVis was developed as an easy-to-use wizard-based software system guiding the user step-by-step in choosing most appropriate visualization and visual analytics tools from a large and easily extendable repository consisting of script-based and interactive tools with different application foci (spatial, temporal or abstract data) and supported techniques (e.g. glyphs, isocontours, stream visualization). Considering the analysis context (e.g. data characteristics, user preferences and analysis tasks) SimEnvVis automatically evaluates the attached tools using a combination of a vector-based and a rule-based mechanism. Based on the users decision, the selected visual analysis tool is launched using a template which is dynamically parameterized by taking into account the analysis context. By displaying the session history in different modes as well as providing the possibility to start SimEnvVis in first-time-user mode to reduce GUI complexity and hide tools which are under development the wizard is in particular useful for novice users. This way, SimEnvVis increases the probability for the usage of appropriate visual analysis tools, lowers the obstacles of familiarization with them and therefore accelerates the knowledge discovery process as well as positively contributes to the quality of its results. With this contribution, we provide a description of the wizard as well as visual analysis use cases to illustrate its application.

  3. Nucleotide sequencing of an apparent proviral copy of env mRNA defines determinants of expression of the mouse mammary tumor virus env gene.

    PubMed Central

    Majors, J E; Varmus, H E

    1983-01-01

    To extend our understanding of the organization and expression of the mouse mammary tumor virus genome, we determined the nucleotide sequence of large regions of a cloned mouse mammary tumor virus strain C3H provirus that appears to be a DNA copy of env mRNA. In conjunction with analysis of several additional clones of integrated and unintegrated mouse mammary tumor virus DNAs, we came to the following conclusions: (i) the mRNA for env is generated by splicing mechanisms that recognize conventional eucaryotic signals at donor and acceptor sites with a leader of at least 289 bases in length; (ii) the first of three possible initiation codons for translation of env follows the splice junction by a single nucleotide and produces a signal peptide of 98 amino acids; (iii) the amino terminal sequence of the major virion glycoprotein gp52env is confirmed by nucleotide sequencing and is encoded by a sequence beginning 584 nucleotides from the 5' end of env mRNA; (iv) the final 17 amino acids at the carboxyl terminus of the primary product of env are encoded within the long terminal repeat by the 51 bases at the 5' end of the U3 domain; and (v) bases 2 through 4 at the 5' end of the long terminal repeat constitute an initiation codon that commences an open reading frame capable of directing the synthesis of a 36-kilodalton protein. PMID:6312081

  4. Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus

    PubMed Central

    Hughes, Joseph; Biek, Roman; Litster, Annette; Willett, Brian J.; Hosie, Margaret J.

    2015-01-01

    Analysing the evolution of feline immunodeficiency virus (FIV) at the intra-host level is important in order to address whether the diversity and composition of viral quasispecies affect disease progression. We examined the intra-host diversity and the evolutionary rates of the entire env and structural fragments of the env sequences obtained from sequential blood samples in 43 naturally infected domestic cats that displayed different clinical outcomes. We observed in the majority of cats that FIV env showed very low levels of intra-host diversity. We estimated that env evolved at a rate of 1.16×10?3 substitutions per site per year and demonstrated that recombinant sequences evolved faster than non-recombinant sequences. It was evident that the V3–V5 fragment of FIV env displayed higher evolutionary rates in healthy cats than in those with terminal illness. Our study provided the first evidence that the leader sequence of env, rather than the V3–V5 sequence, had the highest intra-host diversity and the highest evolutionary rate of all env fragments, consistent with this region being under a strong selective pressure for genetic variation. Overall, FIV env displayed relatively low intra-host diversity and evolved slowly in naturally infected cats. The maximum evolutionary rate was observed in the leader sequence of env. Although genetic stability is not necessarily a prerequisite for clinical stability, the higher genetic stability of FIV compared with human immunodeficiency virus might explain why many naturally infected cats do not progress rapidly to AIDS. PMID:25535323

  5. Mutational analysis of the linker region of EnvZ, an osmosensor in Escherichia coli.

    PubMed Central

    Park, H; Inouye, M

    1997-01-01

    EnvZ, a transmembrane signal transducer, is composed of a periplasmic sensor domain, transmembrane domains, and a cytoplasmic signaling domain. Between the second transmembrane domain and the cytoplasmic signaling domain there is a linker domain consisting of approximately 50 residues. In this study, we investigated the functional role of the EnvZ linker domain with respect to signal transduction. Amino acid sequence alignment of linker regions among various bacterial signal transducer proteins does not show a high sequence identity but suggests a common helix 1-loop-helix 2 structure. Among several mutations introduced in the EnvZ linker region, it was found that hydrophobic-to-charged amino acid substitutions in helix 1 and helix 2 and deletions in helix 1, loop, and helix 2 (delta14, delta8, and delta7) resulted in constitutive OmpC expression. In the linker mutant EnvZ x delta7, both kinase and phosphatase activities were significantly reduced but the ratio of kinase to phosphatase activity increased, consistent with the constitutive OmpC expression. In contrast, the purified cytoplasmic fragment of EnvZ x delta7 possessed both kinase and phosphatase activities at levels similar to those of the cytoplasmic fragment of wild-type EnvZ. In addition, the linker mutations had no direct effect on EnvZ C-terminal dimerization. These results together with previous data suggest that the linker region is not directly involved in EnvZ enzymatic activities and that it may have a crucial role in propagating a conformational change to ensure correct positioning of two EnvZ molecules within a dimer during the transmembrane signaling. PMID:9209057

  6. env Gene of chicken RNA tumor viruses: extent of conservation in cellular and viral genomes.

    PubMed

    Fujita, D J; Tal, J; Varmus, H E; Bishop, J M

    1978-09-01

    The env gene of avian sarcoma-leukosis viruses codes for envelope glycoproteins that determine viral host range, antigenic specificity, and interference patterns. We used molecular hybridization to analyze the natural distribution and possible origins of the nucleotide sequences that encode env; our work exploited the availability of radioactive DNA (cDNA(gp)) complementary to most or all of env. env sequences were detectable in the DNAs of chickens which synthesized an env gene product (chick helper factor positive) encoded by an endogenous viral gene and also in the DNAs of chickens which synthesized little or no env gene product (chick helper factor negative). env sequences were not detectable in DNAs from Japanese quail, ring-necked pheasant, golden pheasant, duck, squab, salmon sperm, or calf thymus. The detection of sequences closely related to viral env only in chicken DNA contrasts sharply with the demonstration that the transforming gene (src) of avian sarcoma viruses has readily detectable homologues in the DNAs of all avian species tested [D. Stehelin, H. E. Varmus, J. M. Bishop, and P. K. Vogt, Nature (London) 260: 170-173, 1976] and in the DNAs of other vertebrates (D. Spector, personal communication). Thermal denaturation studies on duplexes formed between cDNA(gp) and chicken DNA and also between cDNA(gp) and RNAs of subgroup A to E viruses derived from chickens indicated that these duplexes were well matched. In contrast, cDNA(gp) did not form stable hybrids with RNAs of viruses which were isolated from ring-necked and golden pheasants. We conclude that substantial portions of nucleotide sequences within the env genes of viruses of subgroups A to E are closely related and that these genes probably have a common, perhaps cellular, evolutionary origin. PMID:212576

  7. Interinstrument Reliability of the RT3 Accelerometer

    ERIC Educational Resources Information Center

    Reneman, Michiel

    2010-01-01

    The objective of this study was to assess the interinstrument reliability of six RT3 accelerometers for measuring physical activities. Each of the six healthy participants, mean age 36.1 years (SD 9.4), carried six RT3 accelerometers (same type and same producer) simultaneously placed ventrally at the waist belt. The participants performed three…

  8. P20-08. Glycosylation: an important factor in Env diversity

    E-print Network

    Desaire, Heather; Haynes, Barton F.; Go, Eden P.; Liao, Hua-Xin; Sutherland, Laura L.; Chang, Qing; Zhang, Ying; Irungu, Janet W.; Alam, M. S.

    2009-10-22

    . Env glycans shield immunogenic epitopes, and incorporation of gly- cans provides the virus with mechanisms of immune escape. In addition, at least one broadly neutralizing anti- body, 2G12, has as its target a conformational glycan epitope...

  9. Secretion of a murine retroviral Env associated with resistance to infection

    Microsoft Academic Search

    Abdallah Nihrane; Irina Lebedeva; Myung Soo Lyu; Kazunobu Fujita; Jonathan Silver

    1997-01-01

    Fv4 is an endogenous defective murine leukaemia virus (MuLV) which expresses high levels of an envelope protein (Env) closely related to that of the ecotropic class of MuLVs. Mice bearing the natural Fv4 gene or a transgenic version are resistant to infection by ecotropic MuLVs. Fv4 mice secrete the surface peptide (SU) of the Fv4 Env in their serum and

  10. Differential binding of neutralizing and non-neutralizing antibodies to native-like soluble HIV-1 Env trimers, uncleaved Env proteins, and monomeric subunits

    PubMed Central

    2014-01-01

    Background The trimeric envelope glycoproteins (Env) on the surface of HIV-1 virions are the targets for neutralizing antibodies (NAbs). No candidate HIV-1 immunogen has yet induced potent, broadly active NAbs (bNAbs). Part of the explanation may be that previously tested Env proteins inadequately mimic the functional, native Env complex. Trimerization and the proteolytic processing of Env precursors into gp120 and gp41 profoundly alter antigenicity, but soluble cleaved trimers are too unstable to serve as immunogens. By introducing stabilizing mutations (SOSIP), we constructed soluble, cleaved Env trimers derived from the HIV-1 subtype A isolate BG505 that resemble native Env spikes on virions both structurally and antigenically. Results We used surface plasmon resonance (SPR) to quantify antibody binding to different forms of BG505 Env: the proteolytically cleaved SOSIP.664 trimers, cleaved gp120-gp41ECTO protomers, and gp120 monomers. Non-NAbs to the CD4-binding site bound only marginally to the trimers but equally well to gp120-gp41ECTO protomers and gp120 monomers, whereas the bNAb VRC01, directed to the CD4bs, bound to all three forms. In contrast, bNAbs to V1V2 glycan-dependent epitopes bound preferentially (PG9 and PG16) or exclusively (PGT145) to trimers. We also explored the antigenic consequences of three different features of SOSIP.664 gp140 trimers: the engineered inter-subunit disulfide bond, the trimer-stabilizing I559P change in gp41ECTO, and proteolytic cleavage at the gp120-gp41ECTO junction. Each of these three features incrementally promoted native-like trimer antigenicity. We compared Fab and IgG versions of bNAbs and validated a bivalent model of IgG binding. The NAbs showed widely divergent binding kinetics and degrees of binding to native-like BG505 SOSIP.664. High off-rate constants and low stoichiometric estimates of NAb binding were associated with large amounts of residual infectivity after NAb neutralization of the corresponding BG505.T332N pseudovirus. Conclusions The antigenicity and structural integrity of cleaved BG505 SOSIP.664 trimers render these proteins good mimics of functional Env spikes on virions. In contrast, uncleaved gp140s antigenically resemble individual gp120-gp41ECTO protomers and gp120 monomers, but not native trimers. Although NAb binding to functional trimers may thus be both necessary and sufficient for neutralization, the kinetics and stoichiometry of the interaction influence the neutralizing efficacy of individual NAbs. PMID:24884783

  11. RT-2 observations of Solar flares

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Sandip Kumar; Rao, A. R.; Agrawal, V. K.; Nandi, Anuj; Debnath, D.; Kotoch, T. B.; Sreekumar, S.; Kotov, Yury; Arkhangelsky, Andrey; Buslov, A. S.; Oreshnikov, E. M.; Yurov, Vitaly; Tyshkevich, V.; Manoharan, P. K.; Shaheda Begum, S.

    The RT-2 detectors onboard the Coronas-Photon satellite have detected several solar flares from February to November 2009. RT-2 includes a pair of low background Phoswich scientillation detectors of good sensitivity and provides a good opportunity to study faint solar hard X-ray flares during the solar minimum. We present the detection of Quasi-Periodic Pulsations in a solar flare and also provide an estimate of the number distribution of solar flares during the solar minimum.

  12. Molecular identification of erythrocytic necrosis virus (ENV) from the blood of Pacific herring (Clupea pallasii)

    USGS Publications Warehouse

    Emmenegger, Eveline J.; Glenn, Jolene A.; Winton, James R.; Batts, William N.; Gregg, Jacob L.; Hershberger, Paul K.

    2014-01-01

    Viral erythrocytic necrosis (VEN) is a condition affecting the red blood cells of more than 20 species of marine and anadromous fishes in the North Atlantic and North Pacific Oceans. Among populations of Pacific herring (Clupea pallasii) on the west coast of North America the disease causes anemia and elevated mortality in periodic epizootics. Presently, VEN is diagnosed by observation of typical cytoplasmic inclusion bodies in stained blood smears from infected fish. The causative agent, erythrocytic necrosis virus (ENV), is unculturable and a presumed iridovirus by electron microscopy. In vivo amplification of the virus in pathogen-free laboratory stocks of Pacific herring with subsequent virus concentration, purification, DNA extraction, and high-throughput sequencing were used to obtain genomic ENV sequences. Fragments with the highest sequence identity to the family Iridoviridae were used to design four sets of ENV-specific polymerase chain reaction (PCR) primers. Testing of blood and tissue samples from experimentally and wild infected Pacific herring as well as DNA extracted from other amphibian and piscine iridoviruses verified the assays were specific to ENV with a limit of detection of 0.0003 ng. Preliminary phylogenetic analyses of a 1448 bp fragment of the putative DNA polymerase gene supported inclusion of ENV in a proposed sixth genus of the family Iridoviridae that contains other erythrocytic viruses from ectothermic hosts. This study provides the first molecular evidence of ENV's inclusion within the Iridoviridae family and offers conventional PCR assays as a means of rapidly surveying the ENV-status of wild and propagated Pacific herring stocks.

  13. Molecular identification of erythrocytic necrosis virus (ENV) from the blood of Pacific herring (Clupea pallasii).

    PubMed

    Emmenegger, Eveline J; Glenn, Jolene A; Winton, James R; Batts, William N; Gregg, Jacob L; Hershberger, Paul K

    2014-11-01

    Viral erythrocytic necrosis (VEN) is a condition affecting the red blood cells of more than 20 species of marine and anadromous fishes in the North Atlantic and North Pacific Oceans. Among populations of Pacific herring (Clupea pallasii) on the west coast of North America the disease causes anemia and elevated mortality in periodic epizootics. Presently, VEN is diagnosed by observation of typical cytoplasmic inclusion bodies in stained blood smears from infected fish. The causative agent, erythrocytic necrosis virus (ENV), is unculturable and a presumed iridovirus by electron microscopy. In vivo amplification of the virus in pathogen-free laboratory stocks of Pacific herring with subsequent virus concentration, purification, DNA extraction, and high-throughput sequencing were used to obtain genomic ENV sequences. Fragments with the highest sequence identity to the family Iridoviridae were used to design four sets of ENV-specific polymerase chain reaction (PCR) primers. Testing of blood and tissue samples from experimentally and wild infected Pacific herring as well as DNA extracted from other amphibian and piscine iridoviruses verified the assays were specific to ENV with a limit of detection of 0.0003 ng. Preliminary phylogenetic analyses of a 1448 bp fragment of the putative DNA polymerase gene supported inclusion of ENV in a proposed sixth genus of the family Iridoviridae that contains other erythrocytic viruses from ectothermic hosts. This study provides the first molecular evidence of ENV's inclusion within the Iridoviridae family and offers conventional PCR assays as a means of rapidly surveying the ENV-status of wild and propagated Pacific herring stocks. PMID:25263493

  14. Substitution of the transmembrane domain of Vpu in simian-human immunodeficiency virus (SHIV{sub KU1bMC33}) with that of M2 of influenza A results in a virus that is sensitive to inhibitors of the M2 ion channel and is pathogenic for pig-tailed macaques

    SciTech Connect

    Hout, David R. [Department of Anatomy and Cell Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Gomez, Melissa L. [Department of Anatomy and Cell Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Pacyniak, Erik [Department of Anatomy and Cell Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Gomez, Lisa M. [Department of Anatomy and Cell Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Fegley, Barbara [Department of Anatomy and Cell Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Mulcahy, Ellyn R. [Department of Anatomy and Cell Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Hill, M. Sarah [Department of Anatomy and Cell Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Culley, Nathan [Laboratory Animal Resources, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Pinson, David M. [Department of Laboratory Medicine and Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Nothnick, Warren [Department of Obstetrics and Gynecology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States); Powers, Michael F.; Wong, Scott W. [Vaccine and Gene Therapy Institute, Oregon National Primate Research Center, Oregon University for the Health Sciences, Beaverton, OR 97003 (United States); Stephens, Edward B. [Department of Anatomy and Cell Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160 (United States)]. E-mail: estephen@kumc.edu

    2006-01-20

    The Vpu protein of human immunodeficiency virus type 1 has been shown to shunt the CD4 receptor molecule to the proteasome for degradation and to enhance virus release from infected cells. The exact mechanism by which the Vpu protein enhances virus release is currently unknown but some investigators have shown that this function is associated with the transmembrane domain and potential ion channel properties. In this study, we determined if the transmembrane domain of Vpu could be functionally substituted with that of the prototypical viroporin, the M2 protein of influenza A virus. We constructed chimeric vpu gene in which the transmembrane domain of Vpu was replaced with that of the M2 protein of influenza. This chimeric vpu gene was substituted for the vpu gene in the genome of a pathogenic simian human immunodeficiency virus, SHIV{sub KU-1bMC33}. The resulting virus, SHIV{sub M2}, synthesized a Vpu protein that had a slightly different M{sub r} compared to the parental SHIV{sub KU-1bMC33}, reflecting the different sizes of the two Vpu proteins. The SHIV{sub M2} was shown to replicate with slightly reduced kinetics when compared to the parental SHIV{sub KU-1bMC33} but electron microscopy revealed that the site of maturation was similar to the parental virus SHIV{sub KU1bMC33}. We show that the replication and spread of SHIV{sub M2} could be blocked with the antiviral drug rimantadine, which is known to target the M2 ion channel. Our results indicate a dose dependent inhibition of SHIV{sub M2} with 100 {mu}M rimantadine resulting in a >95% decrease in p27 released into the culture medium. Rimantadine did not affect the replication of the parental SHIV{sub KU-1bMC33}. Examination of SHIV{sub M2}-infected cells treated with 50 {mu}M rimantadine revealed numerous viral particles associated with the cell plasma membrane and within intracytoplasmic vesicles, which is similar to HIV-1 mutants lacking a functional vpu. To determine if SHIV{sub M2} was as pathogenic as the parental SHIV{sub KU-1bMC33} virus, two pig-tailed macaques were inoculated and followed for up to 8 months. Both pig-tailed macaques developed severe CD4{sup +} T cell loss within 1 month of inoculation, high viral loads, and histological lesions consistent with lymphoid depletion similar to the parental SHIV{sub KU-1bMC33}. Taken together, these results indicate for the first time that the TM domain of the Vpu protein can be functionally substituted with the TM of M2 of influenza A virus, and shows that compounds that target the TM domain of Vpu protein of HIV-1 could serve as novel anti-HIV-1 drugs.

  15. Biodegradation of Bis(2-Chloroethyl) Ether by Xanthobacter sp. Strain ENV481?

    PubMed Central

    McClay, Kevin; Schaefer, Charles E.; Vainberg, Simon; Steffan, Robert J.

    2007-01-01

    Degradation of bis(2-chloroethyl) ether (BCEE) was observed to occur in two bacterial strains. Strain ENV481, a Xanthobacter sp. strain, was isolated by enrichment culturing of samples from a Superfund site located in the northeastern United States. The strain was able to grow on BCEE or 2-chloroethylethyl ether as the sole source of carbon and energy. BCEE degradation in strain ENV481 was facilitated by sequential dehalogenation reactions resulting in the formation of 2-(2-chloroethoxy)ethanol and diethylene glycol (DEG), respectively. 2-Hydroxyethoxyacetic acid was detected as a product of DEG catabolism by the strain. Degradation of BCEE by strain ENV481 was independent of oxygen, and the strain was not able to grow on a mixture of benzene, ethylbenzene, toluene, and xylenes, other prevalent contaminants at the site. Another bacterial isolate, Pseudonocardia sp. strain ENV478 (S. Vainberg et al., Appl. Environ. Microbiol. 72:5218-5224, 2006), degraded BCEE after growth on tetrahydrofuran or propane but was not able to grow on BCEE as a sole carbon source. BCEE degradation by strain ENV478 appeared to be facilitated by a monooxygenase-mediated O-dealkylation mechanism, and it resulted in the accumulation of 2-chloroacetic acid that was not readily degraded by the strain. PMID:17873075

  16. Complex determinants of macrophage tropism in env of simian immunodeficiency virus.

    PubMed Central

    Mori, K; Ringler, D J; Kodama, T; Desrosiers, R C

    1992-01-01

    Macrophage-tropic virus variants evolved during the course of infection of individual rhesus monkeys with cloned, non-macrophagetropic simian immunodeficiency virus. Specific changes in the envelope gene (env) were found to be primarily responsible for the dramatic increase in the ability of the virus to replicate in macrophages. Cloned viruses differing at nine amino acid positions in env exhibited a more than 100-fold difference in replicative capacity for primary cultures of rhesus monkey alveolar macrophages. At least five of the nine amino acid changes contributed to macrophage tropism. These determinants were distributed across the full length of env, including both the gp120 and gp41 products of the env gene. Furthermore, the emergence of macrophagetropic variants in vivo was associated with specific pathologic manifestations in which the macrophage is the major infected cell type. Thus, major determinants of macrophage tropism reside in env, they can be complex in nature, and the presence of macrophage-tropic virus variants in vivo can influence the disease course and disease manifestations. PMID:1548752

  17. Isolation and characterization of monoclonal antibodies elicited by trimeric HIV-1 Env gp140 protein immunogens

    PubMed Central

    Derby, Nina R.; Gray, Sean; Wayner, Elizabeth; Campogan, Dwayne; Vlahogiannis, Giorgos; Kraft, Zane; Barnett, Susan W.; Srivastava, Indresh K.; Stamatatos, Leonidas

    2007-01-01

    Eleven anti-HIV Env monoclonal antibodies (MAbs) were isolated from mice immunized with soluble Env proteins derived from the clade B Env, SF162, or ?V2 (a derivative of SF162 lacking the V2 loop). All six anti-gp120 MAbs studied, neutralized SF162 and their activities were dependent by the glycosylation patterns of the V1, V2 or V3 loops. Only one anti-gp120 MAb (an anti-V3 MAb) displayed cross-neutralizing activity, which was influenced by the type of V1 loop present on the target heterologous viruses. None of the five anti-gp41 MAbs studied displayed anti-SF162 neutralizing activity. Our studies indicate that the current limitation of soluble HIV Env gp140 immunogens to elicit robust cross-reactive neutralizing antibody responses is not only due to the elicitation of high titers of homologous antibodies, but also due to the elicitation of antibodies whose epitopes are naturally occluded, or not present, on the virion-associated Env. PMID:17560621

  18. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 Env trimer

    PubMed Central

    Lyumkis, Dmitry; Julien, Jean-Philippe; de Val, Natalia; Cupo, Albert; Potter, Clinton S.; Klasse, Per Johan; Burton, Dennis R.; Sanders, Rogier W.; Moore, John P.; Carragher, Bridget; Wilson, Ian A.; Ward, Andrew B.

    2014-01-01

    The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly neutralizing antibodies (bnAbs), Env is a focus for rational vaccine design. We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble SOSIP gp140 trimer in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 Å resolution. The structure reveals the spatial arrangement of Env components, including the V1/V2, V3, HR1 and HR2 domains, and shielding glycans. The structure also provides insights into trimer assembly, gp120-gp41 interactions, and the CD4bs epitope cluster for bnAbs, which covers a more extensive area and defines a more complex site of vulnerability than previously described. PMID:24179160

  19. Direct evidence for intracellular anterograde co-transport of M-PMV Gag and Env on microtubules

    PubMed Central

    Pereira, Lara E.; Clark, Jasmine; Grznarova, Petra; Wen, Xiaoyun; LaCasse, Rachel; Ruml, Tomas; Spearman, Paul

    2014-01-01

    The intracellular transport of Mason-Pfizer monkey virus (M-PMV) assembled capsids from the pericentriolar region to the plasma membrane (PM) requires trafficking of envelope glycoprotein (Env) to the assembly site via the recycling endosome. However, it is unclear if Env-containing vesicles play a direct role in trafficking capsids to the PM. Using live cell microscopy, we demonstrate, for the first time, anterograde co-transport of Gag and Env. Nocodazole disruption of microtubules had differential effects on Gag and Env trafficking, with pulse-chase assays showing a delayed release of Env-deficient virions. Particle tracking demonstrated an initial loss of linear movement of GFP-tagged capsids and mCherry-tagged Env, followed by renewed movement of Gag but not Env at 4 h post-treatment. Thus, while delayed capsid trafficking can occur in the absence of microtubules, efficient anterograde transport of capsids appears to be mediated by microtubule-associated Env-containing vesicles. PMID:24418544

  20. Terminal amino acid sequences and proteolytic cleavage sites of mouse mammary tumor virus env gene products.

    PubMed Central

    Henderson, L E; Sowder, R; Smythers, G; Oroszlan, S

    1983-01-01

    The mature envelope glycoproteins of mouse mammary tumor virus (gp52 and gp36) were isolated by reversed-phase high-pressure liquid chromatography. The N-terminal amino acid sequence of gp36 was determined for 28 residues. The C-terminal amino acid sequences of gp52 and gp36 were determined by carboxypeptidase digestion. The N-terminal amino acid sequence of gp52 has been reported previously (L. O. Arthur et al., J. Virol. 41:414-422, 1982). These data were aligned with the predicted amino acid sequence of the env gene product obtained by translation of the DNA sequence (S. M. S. Redmond and C. Dickson, Eur. Mol. Biol. Org. J. 2:125-131, 1983). The amino acid sequences of the mature viral proteins were in agreement with the predicted amino acid sequence of the env gene product over the regions of alignment. This alignment showed the sites of proteolytic cleavages of the env gene product leading to the mature viral envelope glycoproteins. The N-terminal amino acid sequence of gp52 starts at residue 99 of the predicted structure indicating proteolytic cleavage of a signal peptide. A dipeptide (Lys-Arg) is excised between the C-terminus of gp52 and the N-terminus of gp36. The C-terminal amino acid sequence of gp36 is identical to the sequence predicted by the codons immediately preceding the termination codon for the env gene product. The data show that there is no proteolytic processing at the C-terminal of the murine mammary tumor virus env gene product and that the env gene coding region extends into the long terminal repeat. Images PMID:6310154

  1. RT-level fast fault simulator

    Microsoft Academic Search

    Krzysztof Sapiecha

    In this paper a new fast fault simulation technique is presented for calculation of fault propagation through HLPs (High Level Primitives). ROTDDs (Reduced Ordered Ternary Decision Diagrams) are used to describe HLP modules. The technique is implemented in the HTDD RT- level fault simulator. The simulator is evaluated with some ITC99 benchmarks. A hypothesis is proved that a test set

  2. Conservation Biology-BIOL 21200/ENVS 21200 Course Information and Policies

    E-print Network

    Conservation Biology- BIOL 21200/ENVS 21200 Course Information and Policies General Info Time: Tu will periodically collaborate with members of the Conservation Psychology course to share perspectives and understanding of various issues in conservation biology. Our objectives during laboratories will be develop

  3. ENV-3A40: The Human Geography of Climate Change Semester 2, 2012/2013

    E-print Network

    Hulme, Mike

    1 ENV-3A40: The Human Geography of Climate Change Semester 2, 2012/2013 Convenor: Professor Mike Hulme Other contributors: guests Summary The risks and opportunities associated with climate change and policy discourse around climate change. In recent years, the creative arts have represented the idea

  4. Receptor-Induced Thiolate Couples Env Activation to Retrovirus Fusion and Infection

    Microsoft Academic Search

    Jason G. Smith; James M. Cunningham

    2007-01-01

    According to current models of retrovirus infection, receptor binding to the surface subunit (SU) of the envelope glycoprotein (Env) triggers a conformational change in the transmembrane subunit (TM) that mediates virus fusion to cell membranes. To understand how this occurs, we investigated the role of the receptor Tva in avian leukosis virus-A (ALV-A) infection. We find that Tva binding induced

  5. CD4-induced activation in a soluble HIV-1 Env trimer.

    PubMed

    Guttman, Miklos; Garcia, Natalie K; Cupo, Albert; Matsui, Tsutomu; Julien, Jean-Philippe; Sanders, Rogier W; Wilson, Ian A; Moore, John P; Lee, Kelly K

    2014-07-01

    The HIV envelope glycoprotein (Env) trimer undergoes receptor-induced conformational changes that drive fusion of the viral and cellular membranes. Env conformational changes have been observed using low-resolution electron microscopy, but only large-scale rearrangements have been visible. Here, we use hydrogen-deuterium exchange and oxidative labeling to gain a more precise understanding of the unliganded and CD4-bound forms of soluble Env trimers (SOSIP.664), including their glycan composition. CD4 activation induces the reorganization of bridging sheet elements, V1/V2 and V3, much of the gp120 inner domain, and the gp41 fusion subunit. Two CD4 binding site-targeted inhibitors have substantially different effects: NBD-556 partially mimics CD4-induced destabilization of the V1/V2 and V3 crown, whereas BMS-806 only affects regions around the gp120/gp41 interface. The structural information presented here increases our knowledge of CD4- and small molecule-induced conformational changes in Env and the allosteric pathways that lead to membrane fusion. PMID:24931470

  6. HIV1 encodes a sequence overlapping env gp41 with highly significant similarity to

    E-print Network

    Kececioglu, John

    HIV­1 encodes a sequence overlapping env gp41 with highly significant similarity to selenium, paralleling the loss of CD4+ T cells, has been widely documented in HIV­1 infections. As recently reviewed (1 HIV patients, and children as well as adults [2, 3, 4, 5, 6, 7]. The observations of a number

  7. Regulation of ompC and ompF expression in Escherichia coli in the absence of envZ.

    PubMed Central

    Forst, S; Delgado, J; Ramakrishnan, G; Inouye, M

    1988-01-01

    The expression of the genes encoding the major outer membrane porin proteins OmpF and OmpC in Escherichia coli is regulated by ompR, which encodes the transcriptional activator protein OmpR, and envZ, which encodes a receptorlike protein located in the inner membrane. To examine the role of EnvZ in the expression of the osmoregulated porin genes, we analyzed the production of OmpF and OmpC in cells that lack envZ function. We show that EnvZ is required for the maximal production of OmpC in cells grown in minimal medium but is not essential for the efficient induction of OmpC that occurs during a shift to a high-osmolarity medium. In contrast, the production of OmpF in cells that lack envZ function was similar to that of the parent strain, whereas OmpF repression during a shift to a high-osmolarity medium was incomplete in the absence of EnvZ. These results are discussed in the context of the putative role of EnvZ in the expression of ompF and ompC. Images PMID:2846509

  8. How Can HIV-Type-1-Env Immunogenicity Be Improved to Facilitate Antibody-Based Vaccine Development?

    PubMed Central

    Sanders, Rogier W.; Cerutti, Andrea; Moore, John P.

    2012-01-01

    Abstract No vaccine candidate has induced antibodies (Abs) that efficiently neutralize multiple primary isolates of HIV-1. Preexisting high titers of neutralizing antibodies (NAbs) are essential, because the virus establishes infection before anamnestic responses could take effect. HIV-1 infection elicits Abs against Env, Gag, and other viral proteins, but of these only a subset of the anti-Env Abs can neutralize the virus. Whereas the corresponding proteins from other viruses form the basis of successful vaccines, multiple large doses of HIV-1 Env elicit low, transient titers of Abs that are not protective in humans. The inaccessibility of neutralization epitopes hinders NAb induction, but Env may also subvert the immune response by interacting with receptors on T cells, B cells, monocytes, macrophages, and dendritic cells. Here, we discuss evidence from immunizations of different species with various modified Env constructs. We also suggest how the divergent Ab responses to Gag and Env during infection may reflect differences in B cell regulation. Drawing on these analyses, we outline strategies for improving Env as a component of a vaccine aimed at inducing strong and sustained NAb responses. PMID:21495876

  9. Antigenic properties of a transport-competent influenza HA/HIV Env chimeric protein

    SciTech Connect

    Ye Ling [Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Room 3086 Rollins Research Center, Atlanta, GA 30322 (United States); Sun Yuliang [Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Room 3086 Rollins Research Center, Atlanta, GA 30322 (United States); Lin Jianguo [Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Room 3086 Rollins Research Center, Atlanta, GA 30322 (United States); Bu Zhigao [Harbin Veterinary Research Institute, CAAS, 427 Maduan Street, Nangang District, Harbin 150001 (China); Wu Qingyang [Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Room 3086 Rollins Research Center, Atlanta, GA 30322 (United States); Jiang, Shibo [New York Blood Center, 310 E. 67 Street, New York, NY 10021 (United States); Steinhauer, David A. [Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Room 3086 Rollins Research Center, Atlanta, GA 30322 (United States); Compans, Richard W. [Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Room 3086 Rollins Research Center, Atlanta, GA 30322 (United States); Yang Chinglai [Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Room 3086 Rollins Research Center, Atlanta, GA 30322 (United States)]. E-mail: chyang@emory.edu

    2006-08-15

    The transmembrane subunit (gp41) of the HIV Env glycoprotein contains conserved neutralizing epitopes which are not well-exposed in wild-type HIV Env proteins. To enhance the exposure of these epitopes, a chimeric protein, HA/gp41, in which the gp41 of HIV-1 89.6 envelope protein was fused to the C-terminus of the HA1 subunit of the influenza HA protein, was constructed. Characterization of protein expression showed that the HA/gp41 chimeric proteins were expressed on cell surfaces and formed trimeric oligomers, as found in the HIV Env as well as influenza HA proteins. In addition, the HA/gp41 chimeric protein expressed on the cell surface can also be cleaved into 2 subunits by trypsin treatment, similar to the influenza HA. Moreover, the HA/gp41 chimeric protein was found to maintain a pre-fusion conformation. Interestingly, the HA/gp41 chimeric proteins on cell surfaces exhibited increased reactivity to monoclonal antibodies against the HIV Env gp41 subunit compared with the HIV-1 envelope protein, including the two broadly neutralizing monoclonal antibodies 2F5 and 4E10. Immunization of mice with a DNA vaccine expressing the HA/gp41 chimeric protein induced antibodies against the HIV gp41 protein and these antibodies exhibit neutralizing activity against infection by an HIV SF162 pseudovirus. These results demonstrate that the construction of such chimeric proteins can provide enhanced exposure of conserved epitopes in the HIV Env gp41 and may represent a novel vaccine design strategy for inducing broadly neutralizing antibodies against HIV.

  10. p1 RJM 4/05/07 CY3E2 Env FB Sys 2005 Exam Dr Richard Mitchell 2007

    E-print Network

    Mitchell, Richard

    p1 RJM 4/05/07 CY3E2 ­ Env FB Sys ­ 2005 Exam © Dr Richard Mitchell 2007 CY3E2 2005 Exam 3. Host values of H and S. [6] #12;p2 RJM 4/05/07 CY3E2 ­ Env FB Sys ­ 2005 Exam © Dr Richard Mitchell 2007 S +- ++ +- -- -- dS/dt=0 dH/dt=0 9 H 10 S -+ 5 2 5 2 #12;p3 RJM 4/05/07 CY3E2 ­ Env FB Sys ­ 2005 Exam © Dr Richard

  11. Cytotoxic T cells and neutralizing antibodies induced in rhesus monkeys by virus-like particle HIV vaccines in the absence of protection from SHIV infection.

    PubMed

    Wagner, R; Teeuwsen, V J; Deml, L; Notka, F; Haaksma, A G; Jhagjhoorsingh, S S; Niphuis, H; Wolf, H; Heeney, J L

    1998-05-25

    HIV Pr55gag has in the absence of other viral components the capacity to self assemble in budding noninfectious virus-like particles (VLP). The immunological spectrum of the HIV-1IIIB gag-derived VLP was expanded either by stable anchoring of chimeric modified gp 120 on the surface of the VLP (type 1) or by replacing sequences of the Pr55gag precursor by the V3 loop and a linear portion of the CD4 binding domain (type 2). This noninfectious antigen delivery system was evaluated for immunogenicity and efficacy in rhesus macaques without adjuvants. Intramuscular immunization with both types of VLP induced high titers of gag-specific antibodies ranging from 1/8000 to 1/510,000 for type 1 VLP and from 1/4000 to 1/16,000 for type 2 VLP. Only animals immunized with type 1 VLP developed substantial endpoint titers of env-specific antibodies (1/2000-1/32,000) with a neutralizing capacity at serum dilutions of 1/32-1/128. Gag- and env-specific cytotoxic T lymphocyte (CTL) activity was induced by both types of VLP at similar levels. Four weeks after the last immunization animals were challenged intravenously with 20 MID50 of the cell free homologous envelope simian/HIV-1IIIB chimeric challenge stock Despite HIV-1-specific neutralizing and CTL responses, all vaccinated animals became infected. PMID:9614868

  12. Simian-Human Immunodeficiency Virus SHIV89.6-Induced Protection against Intravaginal Challenge with Pathogenic SIVmac239 Is Independent of the Route of Immunization and Is Associated with a Combination of Cytotoxic T-Lymphocyte and Alpha Interferon Responses

    PubMed Central

    Abel, Kristina; Compton, Lara; Rourke, Tracy; Montefiori, David; Lu, Ding; Rothaeusler, Kristina; Fritts, Linda; Bost, Kristen; Miller, Christopher J.

    2003-01-01

    Attenuated primate lentivirus vaccines provide the most consistent protection against challenge with pathogenic simian immunodeficiency virus (SIV). Thus, they provide an excellent model to examine the influence of the route of immunization on challenge outcome and to study vaccine-induced protective anti-SIV immune responses. In the present study, rhesus macaques were immunized with live nonpathogenic simian-human immunodeficiency virus (SHIV) 89.6 either intravenously or mucosally (intranasally or intravaginally) and then challenged intravaginally with pathogenic SIVmac239. The route of immunization did not affect mucosal challenge outcome after a prolonged period of systemic infection with the nonpathogenic vaccine virus. Further, protection from the SIV challenge was associated with the induction of multiple host immune effector mechanisms. A comparison of immune responses in vaccinated-protected and vaccinated-unprotected animals revealed that vaccinated-protected animals had higher frequencies of SIV Gag-specific cytotoxic T lymphocytes and gamma interferon (IFN-?)-secreting cells during the acute phase postchallenge. Vaccinated-protected animals also had a more pronounced increase in peripheral blood mononuclear cell IFN-? mRNA levels than did the vaccinated-unprotected animals in the first few weeks after challenge. Thus, innate as well as cellular anti-SIV immune responses appeared to contribute to the SHIV89.6-induced protection against intravaginal challenge with pathogenic SIVmac239. PMID:12584336

  13. HIV-1 tat promotes integrin-mediated HIV transmission to dendritic cells by binding Env spikes and competes neutralization by anti-HIV antibodies.

    PubMed

    Monini, Paolo; Cafaro, Aurelio; Srivastava, Indresh K; Moretti, Sonia; Sharma, Victoria A; Andreini, Claudia; Chiozzini, Chiara; Ferrantelli, Flavia; Cossut, Maria R Pavone; Tripiciano, Antonella; Nappi, Filomena; Longo, Olimpia; Bellino, Stefania; Picconi, Orietta; Fanales-Belasio, Emanuele; Borsetti, Alessandra; Toschi, Elena; Schiavoni, Ilaria; Bacigalupo, Ilaria; Kan, Elaine; Sernicola, Leonardo; Maggiorella, Maria T; Montin, Katy; Porcu, Marco; Leone, Patrizia; Leone, Pasqualina; Collacchi, Barbara; Palladino, Clelia; Ridolfi, Barbara; Falchi, Mario; Macchia, Iole; Ulmer, Jeffrey B; Buttò, Stefano; Sgadari, Cecilia; Magnani, Mauro; Federico, Maurizio P M; Titti, Fausto; Banci, Lucia; Dallocchio, Franco; Rappuoli, Rino; Ensoli, Fabrizio; Barnett, Susan W; Garaci, Enrico; Ensoli, Barbara

    2012-01-01

    Use of Env in HIV vaccine development has been disappointing. Here we show that, in the presence of a biologically active Tat subunit vaccine, a trimeric Env protein prevents in monkeys virus spread from the portal of entry to regional lymph nodes. This appears to be due to specific interactions between Tat and Env spikes that form a novel virus entry complex favoring R5 or X4 virus entry and productive infection of dendritic cells (DCs) via an integrin-mediated pathway. These Tat effects do not require Tat-transactivation activity and are blocked by anti-integrin antibodies (Abs). Productive DC infection promoted by Tat is associated with a highly efficient virus transmission to T cells. In the Tat/Env complex the cysteine-rich region of Tat engages the Env V3 loop, whereas the Tat RGD sequence remains free and directs the virus to integrins present on DCs. V2 loop deletion, which unshields the CCR5 binding region of Env, increases Tat/Env complex stability. Of note, binding of Tat to Env abolishes neutralization of Env entry or infection of DCs by anti-HIV sera lacking anti-Tat Abs, which are seldom present in natural infection. This is reversed, and neutralization further enhanced, by HIV sera containing anti-Tat Abs such as those from asymptomatic or Tat-vaccinated patients, or by sera from the Tat/Env vaccinated monkeys. Thus, both anti-Tat and anti-Env Abs are required for efficient HIV neutralization. These data suggest that the Tat/Env interaction increases HIV acquisition and spreading, as a mechanism evolved by the virus to escape anti-Env neutralizing Abs. This may explain the low effectiveness of Env-based vaccines, which are also unlikely to elicit Abs against new Env epitopes exposed by the Tat/Env interaction. As Tat also binds Envs from different clades, new vaccine strategies should exploit the Tat/Env interaction for both preventative and therapeutic interventions. PMID:23152803

  14. Elicitation of both anti HIV-1 Env humoral and cellular immunities by replicating vaccinia prime Sendai virus boost regimen and boosting by CD40Lm.

    PubMed

    Zhang, Xianfeng; Sobue, Tomoyoshi; Isshiki, Mao; Makino, Shun-ichi; Inoue, Makoto; Kato, Kazunori; Shioda, Tatsuo; Ohashi, Takashi; Sato, Hirotaka; Komano, Jun; Hanabusa, Hideji; Shida, Hisatoshi

    2012-01-01

    For protection from HIV-1 infection, a vaccine should elicit both humoral and cell-mediated immune responses. A novel vaccine regimen and adjuvant that induce high levels of HIV-1 Env-specific T cell and antibody (Ab) responses was developed in this study. The prime-boost regimen that used combinations of replication-competent vaccinia LC16m8? (m8?) and Sendai virus (SeV) vectors expressing HIV-1 Env efficiently produced both Env-specific CD8(+) T cells and anti-Env antibodies, including neutralizing antibodies (nAbs). These results sharply contrast with vaccine regimens that prime with an Env expressing plasmid and boost with the m8? or SeV vector that mainly elicited cellular immunities. Moreover, co-priming with combinations of m8?s expressing Env or a membrane-bound human CD40 ligand mutant (CD40Lm) enhanced Env-specific CD8(+) T cell production, but not anti-Env antibody production. In contrast, priming with an m8? that coexpresses CD40Lm and Env elicited more anti-Env Abs with higher avidity, but did not promote T cell responses. These results suggest that the m8? prime/SeV boost regimen in conjunction with CD40Lm expression could be used as an immunization platform for driving both potent cellular and humoral immunities against pathogens such as HIV-1. PMID:23236521

  15. Virion Instability of Human Immunodeficiency Virus Type 1 Reverse Transcriptase (RT) Mutated in the Protease Cleavage Site between RT p51 and the RT RNase H Domain

    Microsoft Academic Search

    Michael E. Abram; Michael A. Parniak

    2005-01-01

    Each of the human immunodeficiency virus type 1 (HIV-1) pol-encoded enzymes, protease (PR), reverse transcriptase (RT), and integrase (IN), is active only as a dimer (or higher-order oligomer in the case of IN), but only RT comprises subunits of different masses. RT is a heterodimer of 66-kDa and 51-kDa subunits. The latter is formed by HIV PR-catalyzed cleavage of p66

  16. HIV-1 Nef Responsiveness is Determined by Env Variable Regions Involved in Trimer Association and Correlates with Neutralization Sensitivity

    PubMed Central

    Usami, Yoshiko; Göttlinger, Heinrich

    2013-01-01

    SUMMARY HIV-1 Nef and the unrelated MLV glycoGag similarly enhance the infectivity of HIV-1 virions. We now show that the effects of Nef and glycoGag are similarly determined by variable regions of HIV-1 gp120 that control Env trimer association and neutralization sensitivity. Whereas neutralization-sensitive X4-tropic Env proteins conferred high responsiveness to Nef and glycoGag, particles bearing neutralization-resistant R5-tropic Envs were considerably less affected. The profoundly different Nef/glycoGag-responsiveness of a neutralization-resistant and a neutralization-sensitive R5-tropic Env could be switched by exchanging their gp120 V1/V2 regions, which also switches their neutralization sensitivity. Within V1/V2, the same determinants governed Nef/glycoGag-responsiveness and neutralization sensitivity, indicating that these phenotypes are mechanistically linked. The V1/V2 and V3 regions, which form an apical trimer-association domain, together determined the Nef- and glycoGag-responsiveness of an X4-tropic Env. Our results suggest that Nef and glycoGag counteract the inactivation of Env spikes with relatively unstable apical trimer-association domains. PMID:24209751

  17. La Fory, 1000 m env. Ar^ete S, Les singes

    E-print Network

    La Fory, 1000 m env. Ar^ete S, Les singes La voie Les singes suit une ´echine rocheuse peu raide en sangles pour relier les points d'as- surance des relais. Coinceurs inutiles. Acc`es Martigny (471 m prise le 23 septembre 2011) #12;La Fory - Acc`es par Bovernier I (ViaMichelin) #12;La Fory - Acc`es par

  18. HIV ENV glycoprotein-mediated bystander apoptosis depends on expression of the CCR5 co-receptor at the cell surface and ENV fusogenic activity.

    PubMed

    Joshi, Anjali; Nyakeriga, Alice M; Ravi, Revathi; Garg, Himanshu

    2011-10-21

    HIV-1 infections lead to a progressive depletion of CD4 cells culminating in AIDS. The coreceptor usage by HIV varies from CCR5 (R5) tropic early in infection to CXCR4 (X4) tropic in later infections. Although the coreceptor switch from R5 to X4 tropic HIV is well associated with progression to AIDS, the role of CCR5 in disease progression especially in patients infected exclusively with R5 isolates throughout the disease remains enigmatic. To better understand the role of CCR5 and R5 tropic HIV envelope in AIDS pathogenesis, we asked whether the levels of CCR5 and/or HIV Env-mediated fusion determine apoptosis of bystander cells. We generated CD4(+) T cell lines expressing varying levels of CCR5 on the cell surface to show that CCR5 expression levels correlate with bystander apoptosis induction. The mechanism of apoptosis involved caspase-3 activation and mitochondrial depolarization and was dependent on gp41 fusion activity as confirmed by fusion-restricted gp41 point mutants and use of the fusion inhibitor T20. Interestingly, lower levels of CCR5 were able to support virus replication in the absence of bystander apoptosis. Our findings suggest that R5 HIV-1-mediated bystander apoptosis is dependent on both CCR5 expression levels as well as fusogenic activity of the Env glycoprotein. PMID:21859712

  19. Structure and immune recognition of trimeric pre-fusion HIV-1 Env.

    PubMed

    Pancera, Marie; Zhou, Tongqing; Druz, Aliaksandr; Georgiev, Ivelin S; Soto, Cinque; Gorman, Jason; Huang, Jinghe; Acharya, Priyamvada; Chuang, Gwo-Yu; Ofek, Gilad; Stewart-Jones, Guillaume B E; Stuckey, Jonathan; Bailer, Robert T; Joyce, M Gordon; Louder, Mark K; Tumba, Nancy; Yang, Yongping; Zhang, Baoshan; Cohen, Myron S; Haynes, Barton F; Mascola, John R; Morris, Lynn; Munro, James B; Blanchard, Scott C; Mothes, Walther; Connors, Mark; Kwong, Peter D

    2014-10-23

    The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation. PMID:25296255

  20. Aerobic Biodegradation of N-Nitrosodimethylamine by the Propanotroph Rhodococcus ruber ENV425?

    PubMed Central

    Fournier, Diane; Hawari, Jalal; Halasz, Annamaria; Streger, Sheryl H.; McClay, Kevin R.; Masuda, Hisako; Hatzinger, Paul B.

    2009-01-01

    The propanotroph Rhodococcus ruber ENV425 was observed to rapidly biodegrade N-nitrosodimethylamine (NDMA) after growth on propane, tryptic soy broth, or glucose. The key degradation intermediates were methylamine, nitric oxide, nitrite, nitrate, and formate. Small quantities of formaldehyde and dimethylamine were also detected. A denitrosation reaction, initiated by hydrogen atom abstraction from one of the two methyl groups, is hypothesized to result in the formation of n-methylformaldimine and nitric oxide, the former of which decomposes in water to methylamine and formaldehyde and the latter of which is then oxidized further to nitrite and then nitrate. Although the strain mineralized more than 60% of the carbon in [14C]NDMA to 14CO2, growth of strain ENV425 on NDMA as a sole carbon and energy source could not be confirmed. The bacterium was capable of utilizing NDMA, as well as the degradation intermediates methylamine and nitrate, as sources of nitrogen during growth on propane. In addition, ENV425 reduced environmentally relevant microgram/liter concentrations of NDMA to <2 ng/liter in batch cultures, suggesting that the bacterium may have applications for groundwater remediation. PMID:19542346

  1. Characterization of BIV Env core: implication for mechanism of BIV-mediated cell fusion.

    PubMed

    Li, Shu; Zhu, Jieqing; Peng, Yu; Cui, Shanshan; Wang, Chunping; Gao, George F; Tien, Po

    2005-04-01

    Entry of lentiviruses, such as human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV), requires folding of two heptad repeat regions (HR1 and HR2) of gp41 into a trimer-of-hairpins, which subsequently brings virus and cell membrane into fusion. This motif is a generalized feature of viral fusion proteins and has been exploited in generating antiviral fusion agents. In the present paper, we report structural characters of Env protein from another lentivirus, bovine immunodeficiency virus (BIV), which contributes to a good animal model of HIV. BIV HR1 and HR2 regions are predicted by two different programs and expressed separately or conjointly in Escherichia coli. Biochemical and biophysical analyses show that the predicted HRs of BIV Env can form a stable trimer-of-hairpins or six-helix bundle just like that formed by feline immunodeficiency virus Env. Cell fusion assay demonstrates that the HR2 peptide of BIV can efficiently inhibit the virus-mediated cell fusion. PMID:15737628

  2. Intelligence and RT: A Modified Hick Paradigm and a New RT Paradigm.

    ERIC Educational Resources Information Center

    Neubauer, Aljoscha C.

    1991-01-01

    The relationship between speed of information processing (SIP) and psychometric intelligence was investigated by giving 60 college students (22 males and 38 females) 2 choice reaction time (RT) tests (modified Hick paradigm) and Raven's Advanced Progressive Matrices. Results support an association between intelligence and SIP. (SLD)

  3. Reverse Transcriptase (RT) Inhibition of PCR at Low Concentrations of Template and Its Implications for Quantitative RT-PCR

    PubMed Central

    Chandler, Darrell P.; Wagnon, Christina A.; Bolton, Harvey

    1998-01-01

    Numerous instances of reverse transcriptase (RT) inhibition of the PCR were observed while developing nonquantitative uncoupled RT-PCR techniques for detecting nitrogenase and ammonia monooxygenase gene expression in situ. The inhibitory effect of RT on the PCR was removed with increasing template concentrations beyond 105 to 106 copies. Including T4 gene 32 protein during the reverse transcription phase of the RT-PCR reaction increased the RT-PCR product yield by as much as 483%; if gene 32 protein was introduced after reverse transcription but prior to the PCR phase, no improvement in product yield was observed. Addition of 1 ?g of exogenous calf thymus DNA or yeast tRNA did little to relieve RT inhibition of the PCR on both genomic DNA and mRNA templates. These results suggest that RT inhibition of the PCR is mediated through direct interaction with the specific primer-template combination (DNA and RNA) and point to specific assay modifications for estimating the extent of RT inhibition and counteracting some of the inhibitory effect. Furthermore, the working hypothesis of RT inhibition below a 105 to 106 copy threshold has important implications for quantitative RT-PCR studies. In particular, competitive, quantitative RT-PCR systems will consistently underestimate the actual RNA concentration. Hence, enumerations of RNA templates below 105 to 106 copies will be relative to an internal standard and will not be an absolute measure of RNA abundance in situ. PMID:9464406

  4. GPG-NH2 acts via the metabolite ?HGA to target HIV1 Env to the ER-associated protein degradation pathway

    Microsoft Academic Search

    Alenka Jejcic; Stefan Höglund; Anders Vahlne

    2010-01-01

    ABSTRACT: BACKGROUND: The synthetic peptide glycyl-prolyl-glycine amide (GPG-NH2) was previously shown to abolish the ability of HIV-1 particles to fuse with the target cells, by reducing the content of the viral envelope glycoprotein (Env) in progeny HIV-1 particles. The loss of Env was found to result from GPG-NH2 targeting the Env precursor protein gp160 to the ER-associated protein degradation (ERAD)

  5. Towards magnetic resonance imaging guided radiation therapy (MRIgRT)

    Microsoft Academic Search

    Teodor Marius Stanescu

    2008-01-01

    The goal of this work is to address key aspects of the magnetic resonance imaging guided radiation therapy (MRIgRT) process of cancer sites. MRIgRT is implemented by using a system comprised of a magnetic resonance imaging (MRI) scanner coupled with a radiation source, in our case a radiotherapy accelerator (Linac). The potential benefits of MRIgRT are the real-time tracking of

  6. RT systems overview JS sep 2006 simons@astron.nl

    E-print Network

    Peletier, Reynier

    Basic Detection Techniques Radio Telescope SystemsRadio Telescope Systems anan overviewoverview #12;RT systems overview JS sep 2006 OverviewOverview Radio frequency radiation Basic telescope system Radio imaging Antenna properties Noise characterisation of a radio telescope #12;RT systems overview JS sep 2006

  7. Antigenic and 3D structural characterization of soluble X4 and hybrid X4-R5 HIV-1 Env trimers

    PubMed Central

    2014-01-01

    Background HIV-1 is decorated with trimeric glycoprotein spikes that enable infection by engaging CD4 and a chemokine coreceptor, either CCR5 or CXCR4. The variable loop 3 (V3) of the HIV-1 envelope protein (Env) is the main determinant for coreceptor usage. The predominant CCR5 using (R5) HIV-1 Env has been intensively studied in function and structure, whereas the trimeric architecture of the less frequent, but more cytopathic CXCR4 using (X4) HIV-1 Env is largely unknown, as are the consequences of sequence changes in and near V3 on antigenicity and trimeric Env structure. Results Soluble trimeric gp140 Env constructs were used as immunogenic mimics of the native spikes to analyze their antigenic properties in the context of their overall 3D structure. We generated soluble, uncleaved, gp140 trimers from a prototypic T-cell line-adapted (TCLA) X4 HIV-1 strain (NL4-3) and a hybrid (NL4-3/ADA), in which the V3 spanning region was substituted with that from the primary R5 isolate ADA. Compared to an ADA (R5) gp140, the NL4-3 (X4) construct revealed an overall higher antibody accessibility, which was most pronounced for the CD4 binding site (CD4bs), but also observed for mAbs against CD4 induced (CD4i) epitopes and gp41 mAbs. V3 mAbs showed significant binding differences to the three constructs, which were refined by SPR analysis. Of interest, the NL4-3/ADA construct with the hybrid NL4-3/ADA CD4bs showed impaired CD4 and CD4bs mAb reactivity despite the presence of the essential elements of the CD4bs epitope. We obtained 3D reconstructions of the NL4-3 and the NL4-3/ADA gp140 trimers via electron microscopy and single particle analysis, which indicates that both constructs inherit a propeller-like architecture. The first 3D reconstruction of an Env construct from an X4 TCLA HIV-1 strain reveals an open conformation, in contrast to recently published more closed structures from R5 Env. Exchanging the X4 V3 spanning region for that of R5 ADA did not alter the open Env architecture as deduced from its very similar 3D reconstruction. Conclusions 3D EM analysis showed an apparent open trimer configuration of X4 NL4-3 gp140 that is not modified by exchanging the V3 spanning region for R5 ADA. PMID:24884925

  8. Silencing of endogenous envelope genes in human choriocarcinoma cells shows that envPb1 is involved in heterotypic cell fusions

    PubMed Central

    Bjerregaard, Bolette; Kjeldbjerg, Anders L.; Pedersen, Finn Skou; Larsson, Lars-Inge; Rossi, John J.

    2012-01-01

    Syncytin-1 and envPb1 are two conserved envelope genes in the human genome encoded by single loci from the HERV-W and -Pb families, respectively. To characterize the role of these envelope proteins in cell–cell fusion, we have developed lentiviral vectors that express short hairpin RNAs for stable knockdown of syncytin-1 and envPb1. Analysis of heterotypic fusion activity between trophoblast-derived choriocarcinoma BeWo cells, in which syncytin-1 and envPb1 are specifically silenced, and endothelial cells demonstrated that both syncytin-1 and envPb1 are important to fusion. The ability to fuse cells makes syncytin-1 and envPb1 attractive candidate molecules in therapy against cancer. Our available vectors may help eventually to decipher roles for these genes in human health and/or disease. PMID:22573740

  9. Structural insights into key sites of vulnerability on HIV-1 Env and Influenza HA

    PubMed Central

    Julien, Jean-Philippe; Lee, Peter S.; Wilson, Ian A.

    2012-01-01

    Summary Human immunodeficiency virus-1 (HIV-1) envelope protein (Env) and influenza hemagglutinin (HA) are the surface glycoproteins responsible for viral entry into host cells, the first step in the virus life cycle necessary to initiate infection. These glycoproteins exhibit a high degree of sequence variability and glycosylation, which are used as strategies to escape host immune responses. Nonetheless, antibodies with broadly neutralizing activity against these viruses have been isolated that have managed to overcome these barriers. Here, we review recent advances in the structural characterization of these antibodies with their viral antigens that defines a few sites of vulnerability on these viral spikes. These broadly neutralizing antibodies tend to focus their recognition on the sites of similar function between the two viruses: the receptor binding site and membrane fusion machinery. However, some sites of recognition are unique to the virus neutralized, such as the dense shield of oligomannose carbohydrates on HIV-1 Env. These observations are discussed in the context of structure-based design strategies to aid in vaccine design or development of antivirals. PMID:23046130

  10. Potential Of VIRAC* RT-32 And RT-16 Antennas To Serve As Satellite Ground Station

    NASA Astrophysics Data System (ADS)

    Bleiders, M.; Trokss, J.; Elerts, M.

    2015-02-01

    The basic application of RT-32 and RT-16 parabolic antennas is radio astronomy observations, both the radio-telescopes have been upgraded with state-of-the art cryogenic receivers, and now a large-scale modernization of the infrastructure is underway. Since the radio-astronomical observations are not full-time activities, a research work has been done to clear up whether these antennas, besides the mentioned activities, can be used as a satellite ground station. The main goal of this added functionality is to make possible the use of the extremely high reception systems' figure-of-merit thus raising the satellite downlink data rates without increasing the on-board power consumption, which would be particularly important for developers of small satellites. In this paper, the progress in the research project is reported, which includes successful S-band satellite signal reception experiments and possible options as to integration of the related equipment into the system so that both functionalities could successfully coexist. Performance of the existing and the upgraded antenna positioning systems is estimated to determine if the latter are usable even for servicing low-Earth orbiting satellites. In addition, possible options are considered as to upgrading the system with automatic beam tracking capability, which would increase the antenna pointing accuracy even further.

  11. HIV-1 reverse transcriptase mutations that confer decreased in vitro susceptibility to anti-RT DNA aptamer RT1t49 confer cross resistance to other anti-RT aptamers but not to standard RT inhibitors.

    PubMed

    Fisher, Timothy S; Joshi, Pheroze; Prasad, Vinayaka R

    2005-10-01

    RNA and DNA aptamers specific for HIV-1 reverse transcriptase (RT) can inhibit reverse transcription in vitro. RNA aptamers have been shown to potently block HIV-1 replication in culture. We previously reported mutants of HIV-1 RT with substitutions N255D or N265D that display resistance to the DNA aptamer RT1t49. Variant viruses bearing these mutations singly or in combination were compromised for replication. In order to address the wider applicability of such aptamers, HIV-1 RT variants containing the N255D, N265D or both (Dbl) were tested for the extent of their cross-resistance to other DNA/RNA aptamers as well as to other RT inhibitors. Both N265D and Dbl RTs were resistant to most aptamers tested. N255D mutant displayed mild resistance to two of the DNA aptamers, little change in sensitivity to three and hypersensitivity to one. Although all mutants displayed wild type-like ribonuclease H activity, their activity was compromised under conditions that prevent re-binding. This suggests that the processivity defect caused by these mutations can also affect RNase H function thus contributing further to the replication defect in mutant viruses. These results indicate that mutants conferring resistance to anti-RT aptamers significantly affect many HIV-1 RT enzymatic activities, which could contribute to preventing the development of resistance in vivo. If such mutations were to arise in vivo, our results suggest that variant viruses should remain susceptible to many existing anti-RT inhibitors. This result was tempered by the observation that NRTI-resistance mutations such as K65R can confer resistance to some anti-RT aptamers. PMID:16207371

  12. Predicting Gene Structures from Multiple RT-PCR Tests

    NASA Astrophysics Data System (ADS)

    Ková?, Jakub; Vina?, Tomáš; Brejová, Bro?a

    It has been demonstrated that the use of additional information such as ESTs and protein homology can significantly improve accuracy of gene prediction. However, many sources of external information are still being omitted from consideration. Here, we investigate the use of product lengths from RT-PCR experiments in gene finding. We present hardness results and practical algorithms for several variants of the problem and apply our methods to a real RT-PCR data set in the Drosophila genome. We conclude that the use of RT-PCR data can improve the sensitivity of gene prediction and locate novel splicing variants.

  13. SCIENCE, POLICY & ETHICS MINOR Faculty: Phil Ammirato (Biology), Randall Balmer (Religion), Diane Dittrick (EnvSci), Tim

    E-print Network

    Halpin-Healy, Tim

    SCIENCE, POLICY & ETHICS MINOR Faculty: Phil Ammirato (Biology), Randall Balmer (Religion), Diane Dittrick (EnvSci), Tim Halpin-Healy (Physics), Peter Juviler (Politics/Human Rights), Brian Morton (Biology programs & race science, the Manhattan Project, as well as the Cold War build-up of nuclear arsenals

  14. Exploration of Novel Fuels for Gas Turbine (ENV-406) Modeling of T60 Test Rig with Diesel & Biodiesel Fuels

    E-print Network

    Exploration of Novel Fuels for Gas Turbine (ENV-406) Modeling of T60 Test Rig with Diesel de biodiesel B20. La matrice de test numérique constitue de quatre cas d'écoulement réactifs c20 biodiesel blend. The numerical test matrix consists of four reacting flow cases, and one non

  15. The visna virus genome: evidence for a hypervariable site in the env gene and sequence homology among lentivirus envelope proteins.

    PubMed Central

    Braun, M J; Clements, J E; Gonda, M A

    1987-01-01

    The complete nucleotide sequence of the visna virus 1514 genome was determined. Our sequence confirms the relationship of visna virus and other lentiviruses to human immunodeficiency virus (HIV) both at the level of sequence homology and of genomic organization. Sequence homology is shown to extend to the transmembrane proteins of lentivirus env genes; this homology is strongest in the extracellular domain, suggesting that close structural and functional similarities may also exist among these envelope proteins. Comparison of our data with the sequence of visna virus LV1-1, an antigenic variant derived from strain 1514, demonstrates that the rate of divergence has been about 1.7 x 10(-3) substitutions per nucleotide per year in vivo. This rate is orders of magnitude higher than that for most DNA genomes, but agrees well with estimates of the rate for HIV. A statistically significant cluster of mutations in the env gene appears to represent a hypervariable site and may correspond to the epitope responsible for the antigenic differences between 1514 and LV1-1. Analysis of the potential RNA folding pattern of the visna virus env gene shows that this hypervariable site falls within a region with little potential for intramolecular base pairing. This correlation of hypervariability with lack of RNA secondary structure is strengthened by the fact that it also holds for a hypervariable site in the env gene of HIV. PMID:2824836

  16. Macrophage Entry Mediated by HIV Envs from Brain and Lymphoid Tissues is Determined by the Capacity to use Low CD4 Levels and Overall Efficiency of Fusion

    PubMed Central

    Thomas, Elaine R.; Dunfee, Rebecca L.; Stanton, Jennifer; Bogdan, Derek; Taylor, Joann; Kunstman, Kevin; Bell, Jeanne E.; Wolinsky, Steven M.; Gabuzda, Dana

    2007-01-01

    HIV infects macrophages and microglia in the central nervous system (CNS), which express lower levels of CD4 than CD4+ T cells in peripheral blood. To investigate mechanisms of HIV neurotropism, full-length env genes were cloned from autopsy brain and lymphoid tissues from 4 AIDS patients with HIV-associated dementia (HAD). Characterization of 55 functional Env clones demonstrated that Envs with reduced dependence on CD4 for fusion and viral entry are more frequent in brain compared to lymphoid tissue. Envs that mediated efficient entry into macrophages were frequent in brain, but were also present in lymphoid tissue. For most Envs, entry into macrophages correlated with overall fusion activity at all levels of CD4 and CCR5. gp160 nucleotide sequences were compartmentalized in brain versus lymphoid tissue within each patient. Proline at position 308 in the V3 loop of gp120 was associated with brain compartmentalization in 3 patients, but mutagenesis studies suggested that P308 alone does not contribute to reduced CD4 dependence or macrophage-tropism. These results suggest that HIV adaptation to replicate in the CNS selects for Envs with reduced CD4 dependence and increased fusion activity. Macrophage-tropic Envs are frequent in brain but are also present in lymphoid tissues of AIDS patients with HAD, and entry into macrophages in the CNS and other tissues is dependent on the ability to use low receptor levels and overall efficiency of fusion. PMID:17084877

  17. Macrophage entry mediated by HIV Envs from brain and lymphoid tissues is determined by the capacity to use low CD4 levels and overall efficiency of fusion

    SciTech Connect

    Thomas, Elaine R. [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA (United States); Dunfee, Rebecca L. [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA (United States); Stanton, Jennifer [Northwestern University Medical School, Chicago, IL (United States); Bogdan, Derek [Northwestern University Medical School, Chicago, IL (United States); Taylor, Joann [Northwestern University Medical School, Chicago, IL (United States); Kunstman, Kevin [Northwestern University Medical School, Chicago, IL (United States); Bell, Jeanne E. [Department of Pathology, Western General Hospital, University of Edinburgh, Edinburgh (United Kingdom); Wolinsky, Steven M. [Northwestern University Medical School, Chicago, IL (United States); Gabuzda, Dana [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA (United States) and Department of Neurology, Harvard Medical School, Boston, MA (United States)]. E-mail: dana_gabuzda@dfci.harvard.edu

    2007-03-30

    HIV infects macrophages and microglia in the central nervous system (CNS), which express lower levels of CD4 than CD4+ T cells in peripheral blood. To investigate mechanisms of HIV neurotropism, full-length env genes were cloned from autopsy brain and lymphoid tissues from 4 AIDS patients with HIV-associated dementia (HAD). Characterization of 55 functional Env clones demonstrated that Envs with reduced dependence on CD4 for fusion and viral entry are more frequent in brain compared to lymphoid tissue. Envs that mediated efficient entry into macrophages were frequent in brain but were also present in lymphoid tissue. For most Envs, entry into macrophages correlated with overall fusion activity at all levels of CD4 and CCR5. gp160 nucleotide sequences were compartmentalized in brain versus lymphoid tissue within each patient. Proline at position 308 in the V3 loop of gp120 was associated with brain compartmentalization in 3 patients, but mutagenesis studies suggested that P308 alone does not contribute to reduced CD4 dependence or macrophage-tropism. These results suggest that HIV adaptation to replicate in the CNS selects for Envs with reduced CD4 dependence and increased fusion activity. Macrophage-tropic Envs are frequent in brain but are also present in lymphoid tissues of AIDS patients with HAD, and entry into macrophages in the CNS and other tissues is dependent on the ability to use low receptor levels and overall efficiency of fusion.

  18. Systemic DNA immunization against ovine lentivirus using particle-mediated epidermal delivery and modified vaccinia Ankara encoding the gag and/or env genes.

    PubMed

    Niesalla, H; de Andrés, X; Barbezange, C; Fraisier, C; Reina, R; Arnarson, H; Biescas, E; Mazzei, M; McNeilly, T N; Liu, C; Watkins, C; Perez, M; Carrozza, M L; Bandecchi, P; Solano, C; Crespo, H; Glaria, I; Huard, C; Shaw, D J; de Blas, I; de Andrés, D; Tolari, F; Rosati, S; Suzan-Monti, M; Andrésdottir, V; Torsteinsdottir, S; Petursson, G; Badiola, J; Lujan, L; Pepin, M; Amorena, B; Blacklaws, B; Harkiss, G D

    2009-01-01

    To determine whether systemic immunization with plasmid DNA and virus vector against visna/maedi virus (VMV) would induce protective immune responses, sheep were immunized with VMV gag and/or env sequences using particle-mediated epidermal bombardment and injection of recombinant modified vaccinia Ankara. The results showed that immunization induced both humoral and cell-mediated responses prior to and after virus challenge. The vaccination protocol did not prevent infection, but immunization with the gag gene or a combination of gag and env genes resulted in significantly reduced provirus loads in blood and mediastinal lymph node, respectively. Provirus loads in lung and draining lymph node were unaffected, but p25 expression was undetectable in lungs of animals immunized with a combination of gag and env genes. Analysis of target tissues for lesions at post-mortem showed that immunization with the env gene caused a significant increase in lesion score, while the gag gene or a combination of gag and env genes had no effect. Inclusion of the ovine interferon-gamma gene in the initial priming mixture had minimal effect on immune responses, provirus load, or lesion development, although it resulted in a decreased p25 expression in the lung. The results thus show that systemic immunization with gag or a combination of gag and env genes reduces provirus load in blood and lymphoid tissue, respectively whereas env immunization has no effect on provirus load but increased lesion development. PMID:18984025

  19. HIV-1 Env-Specific Memory and Germinal Center B Cells in C57BL/6 Mice

    PubMed Central

    Soldemo, Martina; Pedersen, Gabriel K.; Hedestam, Gunilla B. Karlsson

    2014-01-01

    Continued efforts to define the immunogenic properties of the HIV-1 envelope glycoproteins (Env) are needed to elicit effective antibody (Ab) responses by vaccination. HIV-1 is a highly neutralization-resistant virus due to conformational and glycan shielding of conserved Ab determinants on the virus spike. Elicitation of broadly neutralizing Abs that bind poorly accessible epitope regions on Env is therefore extremely challenging and will likely require selective targeting of specific sub-determinants. To evaluate such approaches there is a pressing need for in vivo studies in both large and small animals, including mice. Currently, most mouse immunization studies are performed in the BALB/c strain; however, the C57BL/6 strain offers improved possibilities for mechanistic studies due to the availability of numerous knock-out strains on this genetic background. Here, we compared Env immunogenicity in BALB/c and C57BL/6 mice and found that the magnitude of the antigen-specific response was somewhat lower in C57BL/6 than in BALB/c mice by ELISA but not significantly different by B cell ELISpot measurements. We then established protocols for the isolation of single Env-specific memory B cells and germinal center (GC) B cells from immunized C57BL/6 mice to facilitate future studies of the elicited response at the monoclonal Ab level. We propose that these protocols can be used to gain an improved understanding of the early recruitment of Env-specific B cells to the GC as well as the archiving of such responses in the memory B cell pool following immunization. PMID:25198199

  20. Genetic Attributes of Blood-Derived Subtype-C HIV-1 tat and env in India and Neurocognitive Function

    PubMed Central

    Tilghman, Myres W.; Bhattacharya, Jayanta; Deshpande, Suprit; Ghate, Manisha; Espitia, Stephen; Grant, Igor; Marcotte, Thomas D.; Smith, Davey; Mehendale, Sanjay

    2013-01-01

    Genetic elements in HIV-1 subtype B tat and env are associated with neurotoxicity yet less is known about other subtypes. HIV-1 sub-type C tat and env sequences were analyzed to determine viral genetic elements associated with neurocognitive impairment in a large Indian cohort. Population-based sequences of HIV-1 tat (exon 1) and env (C2-V3 coding region) were generated from blood plasma of HIV-infected patients in Pune, India. Participants were classified as cognitively normal or impaired based on neuropsychological assessment. Tests for signature residues, positive and negative selection, entropy, and ambiguous bases were performed using tools available through Los Alamos National Laboratory (http://www.hiv.lanl.gov) and Datamonkey (http://www.datamonkey.org). HIV-1 subtype C tat and env sequences were analyzed for 155 and 160 participants, of which 34–36% were impaired. Two signature residues were unique to impaired participants in exon 1 of tat at codons 29 (arginine) and 68 (proline). Positive selection was noted at codon 29 among normal participants and at codon 68 in both groups. The signature at codon 29 was also a signature for low CD4+ (<200 cells/mm3) counts but remained associated with impairment after exclusion of those with low CD4+ counts. No unique genetic signatures were noted in env. In conclusion, two signature residues were identified in exon 1 of HIV-1 subtype C tat that were associated with neurocognitive impairment in India and not completely accounted for by HIV disease progression. These signatures support a linkage between diversifying selection in HIV-1 subtype C tat and neurocognitive impairment. PMID:24150902

  1. Application of RT-PCR for Indexing Avocado Sunblotch Viroid

    Microsoft Academic Search

    R. J. Schnell; D. N. Kuhn; C. M. Ronning; D. Harkins

    1997-01-01

    Schnell, R. J., Kuhn, D. N., Ronning, C. M., and Harkins, D. 1997. Application of RT-PCR for indexing avocado sunblotch viroid. Plant Dis. 81:1023-1026. A method for the routine detection of avocado sunblotch viroid (ASBVd) in nucleic acid ex- tracts of infected avocado tissues by reverse transcription-polymerase chain reaction (RT-PCR) was developed using ASBVd-specific primers. Amplified cDNA products were analyzed

  2. Mutagenesis of tyrosine and di-leucine motifs in the HIV-1 envelope cytoplasmic domain results in a loss of Env-mediated fusion and infectivity

    PubMed Central

    2011-01-01

    Background The gp41 component of the Human Immunodeficiency Virus (HIV) envelope glycoprotein (Env) contains a long cytoplasmic domain (CD) with multiple highly conserved tyrosine (Y) and dileucine (LL) motifs. Studies suggest that the motifs distal to major endocytosis motif (Y712HRL), located at residues 712-715 of Env, may contribute to Env functionality in the viral life cycle. In order to examine the biological contribution of these motifs in the biosynthesis, transport, and function of Env, we constructed two panels of mutants in which the conserved Y- and LL-motifs were sequentially substituted by alternative residues, either in the presence or absence of Y712. Additional mutants targeting individual motifs were then constructed. Results All mutant Envs, when expressed in the absence of other viral proteins, maintained at least WT levels of Env surface staining by multiple antibodies. The Y712 mutation (Y712C) contributed to at least a 4-fold increase in surface expression for all mutants containing this change. Sequential mutagenesis of the Y- and LL-motifs resulted in a generally progressive decrease in Env fusogenicity. However, additive mutation of dileucine and tyrosine motifs beyond the tyrosine at residue 768 resulted in the most dramatic effects on Env incorporation into virions, viral infectivity, and virus fusion with target cells. Conclusions From the studies reported here, we show that mutations of the Y- and LL-motifs, which effectively eliminate the amphipathic nature of the lytic peptide 2 (LLP2) domain or disrupt YW and LL motifs in a region spanning residues 795-803 (YWWNLLQYW), just C-terminal of LLP2, can dramatically interfere with biological functions of HIV-1 Env and abrogate virus replication. Because these mutant proteins are expressed at the cell surface, we conclude that tyrosine and di-leucine residues within the cytoplasmic domain of gp41 play critical roles in HIV-1 replication that are distinct from that of targeting the plasma membrane. PMID:21569545

  3. A gene therapy model for retrovirus-induced disease with a viral env gene: expression-dependent resistance in immunosuppressed hosts.

    PubMed

    Kitagawa, M; Aizawa, S; Sado, T; Yamaguchi, S; Suzuki, T; Hirokawa, K; Ikeda, H

    2001-11-01

    At the initial stage of retroviral infection, virion envelope glycoprotein (env product) binds to cell surface receptors. Cells infected with retrovirus or into which the env gene was introduced, become resistant to superinfection by other retroviruses with the same receptor specificity, a phenomenon known as receptor interference. We have demonstrated previously that the introduction of an env gene from a truncated endogenous ecotropic murine leukemia virus (MuLV), the Fv-4 resistance (Fv-4r) gene, into the bone marrow hematopoietic cells of Fv-4 sensitive (Fv-4s) mice protected mice from ecotropic retrovirus-induced disease. Using the gene transfer system under the control of the retroviral vector and bone marrow transplantation (BMT), here we could show that the expression of an introduced Fv-4r gene in hematopoietic cells continued for more than 1 year after BMT. To determine the inhibitory mechanism of Fv-4r env gene expression against FLV-infection in this model system, peripheral blood mononuclear cells (PBMCs), or spleen cells from chimeras with various degrees of env-expression, were mixed with green fluorescence protein (GFP)-conjugated Friend MuLV envglycoprotein (GFP-Fr-ENV). The amount of GFP-Fr-ENV bound to these cells inversely correlated with the expression intensity of the transduced env gene indicating the receptor interference effect. Next, to see whether transduction of the Fv-4r gene would protect an immunosuppressed host from FLV-induced leukemogenesis, we generated immunocompromised chimeras by transplanting env-transduced bone marrow cells into a thymectomized host. These chimeras also resisted FLV-induced leukemogenesis, indicating that receptor interference-based gene therapy could become a therapeutic basis for immunodeficiency virus-induced diseases in vivo. PMID:11681421

  4. The avian retrovirus env gene family: molecular analysis of host range and antigenic variants.

    PubMed Central

    Bova, C A; Olsen, J C; Swanstrom, R

    1988-01-01

    The nucleotide sequence of the env gp85-coding domain from two avian sarcoma and leukosis retrovirus isolates was determined to identify host range and antigenic determinants. The predicted amino acid sequence of gp85 from a subgroup D virus isolate of the Schmidt-Ruppin strain of Rous sarcoma virus was compared with the previously reported sequences of subgroup A, B, C, and E avian sarcoma and leukosis retroviruses. Subgroup D viruses are closely related to the subgroup B viruses but have an extended host range that includes the ability to penetrate certain mammalian cells. There are 27 amino acid differences shared between the subgroup D sequence and three subgroup B sequences. At 16 of these sites, the subgroup D sequence is identical to the sequence of one or more of the other subgroup viruses (A, C, and E). The remaining 11 sites are specific to subgroup D and show some clustering in the two large variable regions that are thought to be major determinants of host range. Biological analysis of recombinant viruses containing a dominant selectable marker confirmed the role of the gp85-coding domain in determining the host range of the subgroup D virus in the infection of mammalian cells. We also compared the sequence of the gp85-coding domain from two subgroup A viruses, Rous-associated virus type 1 and a subgroup A virus of the Schmidt-Ruppin strain of Rous sarcoma virus. The comparison revealed 24 nonconservative amino acid changes, of which 6 result in changes in potential glycosylation sites. The positions of 10 amino acid differences are coincident with the positions of 10 differences found between two subgroup B virus env gene sequences. These 10 sites identify seven domains in the sequence which may constitute determinants of type-specific antigenicity. Using a molecular recombinant, we demonstrated that type-specific neutralization of two subgroup A viruses was associated with the gp85-coding domain of the virus. PMID:2824857

  5. Design of Lipid Nanocapsule Delivery Vehicles for Multivalent Display of Recombinant Env Trimers in HIV Vaccination

    PubMed Central

    2015-01-01

    Immunization strategies that elicit antibodies capable of neutralizing diverse virus strains will likely be an important part of a successful vaccine against HIV. However, strategies to promote robust humoral responses against the native intact HIV envelope trimer structure are lacking. We recently developed chemically cross-linked lipid nanocapsules as carriers of molecular adjuvants and encapsulated or surface-displayed antigens, which promoted follicular helper T-cell responses and elicited high-avidity, durable antibody responses to a candidate malaria antigen. To apply this system to the delivery of HIV antigens, Env gp140 trimers with terminal his-tags (gp140T-his) were anchored to the surface of lipid nanocapsules via Ni-NTA-functionalized lipids. Initial experiments revealed that the large (409 kDa), heavily glycosylated trimers were capable of extracting fluid phase lipids from the membranes of nanocapsules. Thus, liquid-ordered and/or gel-phase lipid compositions were required to stably anchor trimers to the particle membranes. Trimer-loaded nanocapsules combined with the clinically relevant adjuvant monophosphoryl lipid A primed high-titer antibody responses in mice at antigen doses ranging from 5 ?g to as low as 100 ng, whereas titers dropped more than 50-fold over the same dose range when soluble trimer was mixed with a strong oil-in-water adjuvant comparator. Nanocapsule immunization also broadened the number of distinct epitopes on the HIV trimer recognized by the antibody response. These results suggest that nanocapsules displaying HIV trimers in an oriented, multivalent presentation can promote key aspects of the humoral response against Env immunogens. PMID:25020048

  6. NASA SPoRT GOES-R Proving Ground Activities

    NASA Technical Reports Server (NTRS)

    Stano, Geoffrey T.; Fuell, Kevin K.; Jedloec, Gary J.

    2010-01-01

    The NASA Short-term Prediction Research and Transition (SPoRT) program is a partner with the GOES-R Proving Ground (PG) helping prepare forecasters understand the unique products to come from the GOES-R instrument suite. SPoRT is working collaboratively with other members of the GOES-R PG team and Algorithm Working Group (AWG) scientists to develop and disseminate a suite of proxy products that address specific forecast problems for the WFOs, Regional and National Support Centers, and other NOAA users. These products draw on SPoRT s expertise with the transition and evaluation of products into operations from the MODIS instrument and the North Alabama Lightning Mapping Array (NALMA). The MODIS instrument serves as an excellent proxy for the Advanced Baseline Imager (ABI) that will be aboard GOES-R. SPoRT has transitioned and evaluated several multi-channel MODIS products. The true and false color products are being used in natural hazard detection by several SPoRT partners to provide better observation of land features, such as fires, smoke plumes, and snow cover. Additionally, many of SPoRT s partners are coastal offices and already benefit from the MODIS sea surface temperature composite. This, along with other surface feature observations will be developed into ABI proxy products for diagnostic use in the forecast process as well as assimilation into forecast models. In addition to the MODIS instrument, the NALMA has proven very valuable to WFOs with access to these total lightning data. These data provide situational awareness and enhanced warning decision making to improve lead times for severe thunderstorm and tornado warnings. One effort by SPoRT scientists includes a lightning threat product to create short-term model forecasts of lightning activity. Additionally, SPoRT is working with the AWG to create GLM proxy data from several of the ground based total lightning networks, such as the NALMA. The evaluation will focus on the vastly improved spatial coverage of the GLM, but with the trade-off of lower resolution compared to the NALMA. In addition to the above tasks, SPoRT will make these data available in the NWS next generation display software, AWIPS II. This has already been successfully completed for the two basic GLM proxies. SPoRT will use these products to train forecasters on the capabilities of GOES-R and foster feedback to develop additional products, visualizations, and requirements beneficial to end users needs. These developments and feedback will be made available to the GOES-R Proving Ground for the upcoming 2010 Spring Program in Norman, Oklahoma.

  7. Impact of viral dose and major histocompatibility complex class IB haplotype on viral outcome in mauritian cynomolgus monkeys vaccinated with Tat upon challenge with simian/human immunodeficiency virus SHIV89.6P.

    PubMed

    Cafaro, Aurelio; Bellino, Stefania; Titti, Fausto; Maggiorella, Maria Teresa; Sernicola, Leonardo; Wiseman, Roger W; Venzon, David; Karl, Julie A; O'Connor, David; Monini, Paolo; Robert-Guroff, Marjorie; Ensoli, Barbara

    2010-09-01

    The effects of the challenge dose and major histocompatibility complex (MHC) class IB alleles were analyzed in 112 Mauritian cynomolgus monkeys vaccinated (n = 67) or not vaccinated (n = 45) with Tat and challenged with simian/human immunodeficiency virus (SHIV) 89.6P(cy243.) In the controls, the challenge dose (10 to 20 50% monkey infectious doses [MID(50)]) or MHC did not affect susceptibility to infection, peak viral load, or acute CD4 T-cell loss, whereas in the chronic phase of infection, the H1 haplotype correlated with a high viral load (P = 0.0280) and CD4 loss (P = 0.0343). Vaccination reduced the rate of infection acquisition at 10 MID(50) (P < 0.0001), and contained acute CD4 loss at 15 MID(50) (P = 0.0099). Haplotypes H2 and H6 were correlated with increased susceptibility (P = 0.0199) and resistance (P = 0.0087) to infection, respectively. Vaccination also contained CD4 depletion (P = 0.0391) during chronic infection, independently of the challenge dose or haplotype. PMID:20554774

  8. Quantitative RT-PCR for measuring gene expression.

    PubMed

    Riedy, M C; Timm, E A; Stewart, C C

    1995-01-01

    Classical Northern blot analysis for measuring mRNA requires too many cells to be practical for cell sorting. Yet, measurement of gene expression in small subsets within a heterogeneous population of cells is often desired. The PCR in combination with prior reverse transcription (RT-PCR) of the mRNA of interest provides a means for measuring gene expression using as few as one cell. When RT-PCR is performed, the reliability of the data can be highly subjective due to the efficiency of both RT and PCR steps. This subjectivity can be eliminated by a technique for quantitating specific RNA molecules using an internal RNA competitive reference standard (RNA-CRS), which is identical to the sequence of interest except for a deletion of 80 bases. Here we illustrate a strategy for quantitative PCR using a RNA-CRS, synthesized solely using nonplasmid-based PCR techniques. The competitive reaction consists of a constant quantity of wild-type mRNA (from 100-1000 cells) added individually to tubes containing a serially decreasing amount of RNA-CRS. The RT-PCR is performed on these samples, then the resulting product is analyzed by gel electrophoresis and densitometry. The procedure for preparing the RNA-CRS and subsequent RT-PCR steps are described in detail. PMID:7702857

  9. Dense display of HIV1 envelope spikes on the lambda phage scaffold does not result in the generation of improved antibody responses to HIV1 Env

    Microsoft Academic Search

    Jonelle Mattiacio; Scott Walter; Matt Brewer; William Domm; Alan E. Friedman; Stephen Dewhurst

    2011-01-01

    The generation of strong, virus-neutralizing antibody responses to the HIV-1 envelope spike (Env) is a major goal in HIV-1 vaccine research. To try to enhance the Env-specific response, we displayed oligomeric gp140 on a virus-like scaffold provided by the lambda phage capsid. To do this, an in vitro complementation system was used to “decorate” phage particles with glycosylated, mammalian cell-derived

  10. Human Ubc9 is involved in intracellular HIV-1 Env stability after trafficking out of the trans-Golgi network in a Gag dependent manner.

    PubMed

    Bohl, Christopher R; Abrahamyan, Levon G; Wood, Charles

    2013-01-01

    The cellular E2 Sumo conjugase, Ubc9 interacts with HIV-1 Gag, and is important for the assembly of infectious HIV-1 virions. In the previous study we demonstrated that in the absence of Ubc9, a defect in virion assembly was associated with decreased levels of mature intracellular Envelope (Env) that affected Env incorporation into virions and virion infectivity. We have further characterized the effect of Ubc9 knockdown on HIV Env processing and assembly. We found that gp160 stability in the endoplasmic reticulum (ER) and its trafficking to the trans-Golgi network (TGN) were unaffected, indicating that the decreased intracellular mature Env levels in Ubc9-depleted cells were due to a selective degradation of mature Env gp120 after cleavage from gp160 and trafficked out of the TGN. Decreased levels of Gag and mature Env were found to be associated with the plasma membrane and lipid rafts, which suggest that these viral proteins were not trafficked correctly to the assembly site. Intracellular gp120 were partially rescued when treated with a combination of lysosome inhibitors. Taken together our results suggest that in the absence of Ubc9, gp120 is preferentially degraded in the lysosomes likely before trafficking to assembly sites leading to the production of defective virions. This study provides further insight in the processing and packaging of the HIV-1 gp120 into mature HIV-1 virions. PMID:23861967

  11. Human Ubc9 Is Involved in Intracellular HIV-1 Env Stability after Trafficking out of the Trans-Golgi Network in a Gag Dependent Manner

    PubMed Central

    Bohl, Christopher R.; Abrahamyan, Levon G.; Wood, Charles

    2013-01-01

    The cellular E2 Sumo conjugase, Ubc9 interacts with HIV-1 Gag, and is important for the assembly of infectious HIV-1 virions. In the previous study we demonstrated that in the absence of Ubc9, a defect in virion assembly was associated with decreased levels of mature intracellular Envelope (Env) that affected Env incorporation into virions and virion infectivity. We have further characterized the effect of Ubc9 knockdown on HIV Env processing and assembly. We found that gp160 stability in the endoplasmic reticulum (ER) and its trafficking to the trans-Golgi network (TGN) were unaffected, indicating that the decreased intracellular mature Env levels in Ubc9-depleted cells were due to a selective degradation of mature Env gp120 after cleavage from gp160 and trafficked out of the TGN. Decreased levels of Gag and mature Env were found to be associated with the plasma membrane and lipid rafts, which suggest that these viral proteins were not trafficked correctly to the assembly site. Intracellular gp120 were partially rescued when treated with a combination of lysosome inhibitors. Taken together our results suggest that in the absence of Ubc9, gp120 is preferentially degraded in the lysosomes likely before trafficking to assembly sites leading to the production of defective virions. This study provides further insight in the processing and packaging of the HIV-1 gp120 into mature HIV-1 virions. PMID:23861967

  12. Life+ EnvEurope DEIMS - improving access to long-term ecosystem monitoring data in Europe

    NASA Astrophysics Data System (ADS)

    Kliment, Tomas; Peterseil, Johannes; Oggioni, Alessandro; Pugnetti, Alessandra; Blankman, David

    2013-04-01

    Long-term ecological (LTER) studies aim at detecting environmental changes and analysing its related drivers. In this respect LTER Europe provides a network of about 450 sites and platforms. However, data on various types of ecosystems and at a broad geographical scale is still not easily available. Managing data resulting from long-term observations is therefore one of the important tasks not only for an LTER site itself but also on the network level. Exchanging and sharing the information within a wider community is a crucial objective in the upcoming years. Due to the fragmented nature of long-term ecological research and monitoring (LTER) in Europe - and also on the global scale - information management has to face several challenges: distributed data sources, heterogeneous data models, heterogeneous data management solutions and the complex domain of ecosystem monitoring with regard to the resulting data. The Life+ EnvEurope project (2010-2013) provides a case study for a workflow using data from the distributed network of LTER-Europe sites. In order to enhance discovery, evaluation and access to data, the EnvEurope Drupal Ecological Information Management System (DEIMS) has been developed. This is based on the first official release of the Drupal metadata editor developed by US LTER. EnvEurope DEIMS consists of three main components: 1) Metadata editor: a web-based client interface to manage metadata of three information resource types - datasets, persons and research sites. A metadata model describing datasets based on Ecological Metadata Language (EML) was developed within the initial phase of the project. A crosswalk to the INSPIRE metadata model was implemented to convey to the currently on-going European activities. Person and research site metadata models defined within the LTER Europe were adapted for the project needs. The three metadata models are interconnected within the system in order to provide easy way to navigate the user among the related resources. 2) Discovery client: provides several search profiles for datasets, persons, research sites and external resources commonly used in the domain, e.g. Catalogue of Life , based on several search patterns ranging from simple full text search, glossary browsing to categorized faceted search. 3) Geo-Viewer: a map client that portrays boundaries and centroids of the research sites as Web Map Service (WMS) layers. Each layer provides a link to both Metadata editor and Discovery client in order to create or discover metadata describing the data collected within the individual research site. Sharing of the dataset metadata with DEIMS is ensured in two ways: XML export of individual metadata records according to the EML schema for inclusion in the international DataOne network, and periodic harvesting of metadata into GeoNetwork catalogue, thus providing catalogue service for web (CSW), which can be invoked by remote clients. The final version of DEIMS will be a pilot implementation for the information system of LTER-Europe, which should establish a common information management framework within the European ecosystem research domain and provide valuable environmental information to other European information infrastructures as SEIS, Copernicus and INSPIRE.

  13. Detection of Acute HIV-1 Infection by RT-LAMP

    PubMed Central

    2015-01-01

    A rapid, cost-effective diagnostic test for the detection of acute HIV-1 infection is highly desired. Isothermal amplification techniques, such as reverse-transcription loop-mediated isothermal amplification (RT-LAMP), exhibit characteristics that are ideal for the development of a rapid nucleic acid amplification test (NAAT) because they are quick, easy to perform and do not require complex, dedicated equipment and laboratory space. In this study, we assessed the ability of the HIV-1 RT-LAMP assay to detect acute HIV infection as compared to a representative rapid antibody test and several FDA-approved laboratory-based assays. The HIV-1 RT-LAMP assay detected seroconverting individuals one to three weeks earlier than a rapid HIV antibody test and up to two weeks earlier than a lab-based antigen/antibody (Ag/Ab) combo enzyme immunoassay (EIA). RT-LAMP was not as sensitive as a lab-based qualitative RNA assay, which could be attributed to the significantly smaller nucleic acid input volume. To our knowledge, this is the first demonstration of detecting acute HIV infection using the RT-LAMP assay. The availability of a rapid NAAT, such as the HIV-1 RT-LAMP assay, at the point of care (POC) or in laboratories that do not have access to large platform NAAT could increase the percentage of individuals who receive an acute HIV infection status or confirmation of their HIV status, while immediately linking them to counseling and medical care. In addition, early knowledge of HIV status could lead to reduced high-risk behavior at a time when individuals are at a higher risk for transmitting the virus. PMID:25993381

  14. AWIPS II Application Development, a SPoRT Perspective

    NASA Technical Reports Server (NTRS)

    Burks, Jason E.; Smith, Matthew; McGrath, Kevin M.

    2014-01-01

    The National Weather Service (NWS) is deploying its next-generation decision support system, called AWIPS II (Advanced Weather Interactive Processing System II). NASA's Short-term Prediction Research and Transition (SPoRT) Center has developed several software 'plug-ins' to extend the capabilities of AWIPS II. SPoRT aims to continue its mission of improving short-term forecasts by providing NASA and NOAA products on the decision support system used at NWS weather forecast offices (WFOs). These products are not included in the standard Satellite Broadcast Network feed provided to WFOs. SPoRT has had success in providing support to WFOs as they have transitioned to AWIPS II. Specific examples of transitioning SPoRT plug-ins to WFOs with newly deployed AWIPS II systems will be presented. Proving Ground activities (GOES-R and JPSS) will dominate SPoRT's future AWIPS II activities, including tool development as well as enhancements to existing products. In early 2012 SPoRT initiated the Experimental Product Development Team, a group of AWIPS II developers from several institutions supporting NWS forecasters with innovative products. The results of the team's spring and fall 2013 meeting will be presented. Since AWIPS II developers now include employees at WFOs, as well as many other institutions related to weather forecasting, the NWS has dealt with a multitude of software governance issues related to the difficulties of multiple remotely collaborating software developers. This presentation will provide additional examples of Research-to-Operations plugins, as well as an update on how governance issues are being handled in the AWIPS II developer community.

  15. MMTV Env encodes an ITAM responsible for transformation of mammary epithelial cells in three-dimensional culture

    Microsoft Academic Search

    Elad Katz; Mohamed H. Lareef; John C. Rassa; Shannon M. Grande; Leslie B. King; Jose Russo; Susan R. Ross; John G. Monroe

    Expression of immunoreceptor tyrosine-based activation motif (ITAM)-containing signaling proteins is normally restricted to hematopoietic tissues. The basal activity of ITAM- containing proteins is mediated through negative regulation by coreceptors restricted to hematopoietic tissues. We have identified an ITAM signaling domain encoded within the env gene of murine mammary tumor virus (MMTV). Three-dimensional structures derived in vitro from murine cells stably

  16. Field evaluation of a gag/env heteroduplex mobility assay for genetic subtyping of small-ruminant lentiviruses.

    PubMed

    Germain, Karine; Croise, Benoit; Valas, Stephen

    2008-08-01

    Small-ruminant lentiviruses (SRLVs) display a high genetic diversity and are currently classified into five genotypes and an increasing number of subtypes. The co-circulation of subtypes in restricted geographical regions, combined with the occurrence of cross-species infection, suggests the need for development of a large-scale screening methodology for rapid monitoring of the prevalence of the various genetic subtypes and their genetic evolution. Here, a heteroduplex mobility assay (HMA) was developed for the rapid identification of group B subtypes. The assay was validated for both the p14 nucleocapsid-coding region of the gag gene and the V1-V2 region of the env gene using a panel of reference standards and was applied to the genetic subtyping of SRLV field isolates from five mixed flocks in France. Subtyping of 75 blood samples using the env HMA revealed a preferential distribution of subtypes B1 and B2 in sheep and goats, despite direct evidence for interspecies transmission of both subtypes. Adding the gag HMA to the env HMA provided evidence for dual infection and putative recombination between subtypes B1 and B2 in five goats, and between groups A and B in one sheep. Phylogenetic analysis revealed that 100 % (23/23) and 96.7 % (30/31) of samples were correctly classified using the gag and env HMAs, respectively. These results indicate that dual infection and recombination may be a significant source of new variation in SRLV and provide a useful tool for the rapid genetic subtyping of SRLV isolates, which could be relevant for the development of more accurate diagnosis of prevalent SRLV strains in different countries. PMID:18632974

  17. stt rt t Prstt st sttr r str r s

    E-print Network

    Paris-Sud XI, Université de

    stt rt t Prstt st sttr r str r s rtr tétqs ë rsté rrr tr strt r t stt rt t r st sttr tr stt Pr t tt sttr str r s r r s s t rs t rtr t rsts sr tq rts s rs rs rtr stt r st rsss r t s s t sr ts t t rtr rs s rtr t str ts t t t t ssts rs rss tr t tr r st sttr

  18. Association between Specific HIV-1 Env Traits and Virologic Control in vivo

    PubMed Central

    Joos, Beda; Rieder, Philip; Fischer, Marek; Kuster, Herbert; Rusert, Peter; Trkola, Alexandra; Pillai, Satish K.; Wong, Joseph K.; Weber, Rainer; Günthard, Huldrych F.

    2014-01-01

    HIV RNA levels are influenced by genetic characteristics of both the host and the virus. Here we applied machine learning techniques to determine if plasma-derived HIV-1 amino acid sequences can be used to predict spontaneous virologic control. We studied the relationship between HIV-1 env genotype and viral load in 20 chronically-infected patients undergoing treatment interruptions (SSITT, Swiss-Spanish Intermittent Treatment Trial) and in 104 primary HIV infected (PHI) patients before antiretroviral therapy (cART) and where applicable also after treatment stop. Extensive longitudinal sampling during the interruptions was performed in nine SSITT patients. Sequences obtained from these nine patients during the first virus rebound were used as a training data set and revealed a strong genetic signature (accuracy 98.6% in cross-validation) associated with control of viremia at levels below 5000 copies/mL of viral RNA maintained for at least two months after the final cART stop. The simple sequence pattern at gp120 positions 268E/358T was confirmed to be predictive of control in the clonal sequences originating from these patients during all subsequent rebounds. Sequences from the remaining 11 SSITT patients with less frequent sampling and from the PHI patients were used for external validation. High sensitivities (71-100%) and negative predictive values (80-100%) but low positive predictive values (12-40%) were achieved in the patient-wise analysis which was based on presence of the genetic pattern in all clones. These results suggest that presence of virus lacking the amino acid pattern 268E/358T is associated with VL >5000 at baseline of PHI and with low probability of spontaneous virologic control after treatment stop. Conversely, however, presence of 268E/358T does not predict control of viremia. These residues in HIV gp120 might affect in vivo HIV-1 fitness either at the level of Env function or influence susceptibility to adaptive or innate immune response. PMID:19524069

  19. Proviral amplification of the Gypsy endogenous retrovirus of Drosophila melanogaster involves env-independent invasion of the female germline.

    PubMed Central

    Chalvet, F; Teysset, L; Terzian, C; Prud'homme, N; Santamaria, P; Bucheton, A; Pélisson, A

    1999-01-01

    Gypsy is an infectious endogenous retrovirus of Drosophila melanogaster. The gypsy proviruses replicate very efficiently in the genome of the progeny of females homozygous for permissive alleles of the flamenco gene. This replicative transposition is correlated with derepression of gypsy expression, specifically in the somatic cells of the ovaries of the permissive mothers. The determinism of this amplification was studied further by making chimeric mothers containing different permissive/restrictive and somatic/germinal lineages. We show here that the derepression of active proviruses in the permissive soma is necessary and sufficient to induce proviral insertions in the progeny, even if the F1 flies derive from restrictive germ cells devoid of active proviruses. Therefore, gypsy endogenous multiplication results from the transfer of some gypsy-encoded genetic material from the soma towards the germen of the mother and its subsequent insertion into the chromosomes of the progeny. This transfer, however, is not likely to result from retroviral infection of the germline. Indeed, we also show here that the insertion of a tagged gypsy element, mutant for the env gene, occurs at high frequency, independently of the production of gypsy Env proteins by any transcomplementing helper. The possible role of the env gene for horizontal transfer to new hosts is discussed. PMID:10228177

  20. A novel rabbit monoclonal antibody platform to dissect the diverse repertoire of antibody epitopes for HIV-1 Env immunogen design.

    PubMed

    Chen, Yuxin; Vaine, Michael; Wallace, Aaron; Han, Dong; Wan, Shengqin; Seaman, Michael S; Montefiori, David; Wang, Shixia; Lu, Shan

    2013-09-01

    The majority of available monoclonal antibodies (MAbs) in the current HIV vaccine field are generated from HIV-1-infected people. In contrast, preclinical immunogenicity studies have mainly focused on polyclonal antibody responses in experimental animals. Although rabbits have been widely used for antibody studies, there has been no report of using rabbit MAbs to dissect the specificity of antibody responses for AIDS vaccine development. Here we report on the production of a panel of 12 MAbs from a New Zealand White (NZW) rabbit that was immunized with an HIV-1 JR-FL gp120 DNA prime and protein boost vaccination regimen. These rabbit MAbs recognized a diverse repertoire of envelope (Env) epitopes ranging from the highly immunogenic V3 region to several previously underappreciated epitopes in the C1, C4, and C5 regions. Nine MAbs showed cross-reactivity to gp120s of clades other than clade B. Increased somatic mutation and extended CDR3 were observed with Ig genes of several molecularly cloned rabbit MAbs. Phylogenic tree analysis showed that the heavy chains of MAbs recognizing the same region on gp120 tend to segregate into an independent subtree. At least three rabbit MAbs showed neutralizing activities with various degrees of breadth and potency. The establishment of this rabbit MAb platform will significantly enhance our ability to test optimal designs of Env immunogens to gain a better understanding of the structural specificity and evolution process of Env-specific antibody responses elicited by candidate AIDS vaccines. PMID:23864612

  1. Effects of different promoters on the virulence and immunogenicity of a HIV-1 Env-expressing recombinant vaccinia vaccine.

    PubMed

    Isshiki, Mao; Zhang, Xianfeng; Sato, Hirotaka; Ohashi, Takashi; Inoue, Makoto; Shida, Hisatoshi

    2014-02-01

    Previously, we developed a vaccination regimen that involves priming with recombinant vaccinia virus LC16m8? (rm8?) strain followed by boosting with a Sendai virus-containing vector. This protocol induced both humoral and cellular immune responses against the HIV-1 envelope protein. The current study aims to optimize this regimen by comparing the immunogenicity and safety of two rm8? strains that express HIV-1 Env under the control of a moderate promoter, p7.5, or a strong promoter, pSFJ1-10. m8?-p7.5-JRCSFenv synthesized less gp160 but showed significantly higher growth potential than m8?-pSFJ-JRCSFenv. The two different rm8? strains induced antigen-specific immunity; however, m8?-pSFJ-JRCSFenv elicited a stronger anti-Env antibody response whereas m8?-p7.5-JRCSFenv induced a stronger Env-specific cytotoxic T lymphocyte response. Both strains were less virulent than the parental m8? strain, suggesting that they would be safe for use in humans. These findings indicate the vaccine can be optimized to induce favorable immune responses (either cellular or humoral), and forms the basis for the rational design of an AIDS vaccine using recombinant vaccinia as the delivery vector. PMID:24370703

  2. Obacunone Represses Salmonella Pathogenicity Islands 1 and 2 in an envZ-Dependent Fashion

    PubMed Central

    Vikram, Amit; Jayaprakasha, Guddadarangavvanahally K.; Jesudhasan, Palmy R.

    2012-01-01

    Obacunone belongs to a class of unique triterpenoids called limonoids, present in Citrus species. Previous studies from our laboratory suggested that obacunone possesses antivirulence activity and demonstrates inhibition of cell-cell signaling in Vibrio harveyi and Escherichia coli O157:H7. The present work sought to determine the effect of obacunone on the food-borne pathogen Salmonella enterica serovar Typhimurium LT2 by using a cDNA microarray. Transcriptomic studies indicated that obacunone represses Salmonella pathogenicity island 1 (SPI1), the maltose transporter, and the hydrogenase operon. Furthermore, phenotypic data for the Caco-2 infection assay and maltose utilization were in agreement with microarray data suggesting repression of SPI1 and maltose transport. Further studies demonstrated that repression of SPI1 was plausibly mediated through hilA. Additionally, obacunone seems to repress SPI2 under SPI2-inducing conditions as well as in Caco-2 infection models. Furthermore, obacunone seems to repress hilA in an EnvZ-dependent fashion. Altogether, the results of the study seems to suggest that obacunone exerts an antivirulence effect on S. Typhimurium and may serve as a lead compound for development of antivirulence strategies for S. Typhimurium. PMID:22843534

  3. Friend virus-specific cytotoxic T lymphocytes recognize both gag and env gene-encoded specificities

    PubMed Central

    1986-01-01

    We have constructed a series of "synthetic" target cell lines for an analysis of the specificity of anti-Friend virus (FV) CTL. Our results show that murine H-2 genes and individual retroviral genes can be stable expressed in Fisher rat embryo (FRE) cells, and that their products have the potential to form target structures recognized by mouse CTL. Cells expressing H-2Db and either the env or gag genes of one component of FV, helper Friend murine leukemia virus (FMuLV), were lysed by anti-FV CTL and by CTL generated against FMuLV alone. Experiments with Db-transfected FRE clones infected only with the replication-defective spleen focus-forming virus (SFFV) component of FV indicate that the SFFV genome also provides specificities recognized by both anti-FV and anti-FMuLV CTL, thus demonstrating the existence of a crossreactive CTL population. An unexpected finding was that anti-FMuLV CTL, but not anti-FV CTL were also able to lyse FRE clones that expressed H-2Kb in either the presence or absence of FV. The use of heterologous cell lines for the construction of synthetic target cells thus offers a useful approach for the analysis of T cell specificity. PMID:2425028

  4. Effects of murine leukemia virus env gene proteins on macrophage-mediated cytotoxicity in vitro

    NASA Technical Reports Server (NTRS)

    Chapes, S. K.; Takemoto, L. J.; Spooner, B. S. (Principal Investigator)

    1991-01-01

    F5b Tumor cells were incubated with concentrated culture supernatants taken from cells resistant (F5m) or sensitive (F5b) to contact-dependent macrophage cytotoxicity. Macrophage cell line B6MP102 and murine peritoneal macrophages killed targets incubated with supernatants taken from sensitive cells but poorly killed cells incubated in supernatants isolated from resistant cells. Membranes from cells resistant to macrophage killing, F5m, were fused into F5b cells. The fused F5b cells were killed significantly less than F5b cells fused with F5b cell membranes or untreated F5b cells. The decreased killing of F5b cells corresponded to increased concentrations of gp70(a) molecules on F5b cells. Affinity purified gp70(a) was added to cytotoxicity assays but failed to inhibit macrophage cytotoxicity. P15E molecules were detectable on both F5b and F5m cells. In addition, a synthetic peptide found to exhibit the inhibitory properties of p15E was added to cytotoxicity assays. P15E synthetic peptide also did not inhibit macrophage cytotoxicity. Therefore, env gene proteins of murine leukemia virus do not appear responsible for inducing tumor cell resistance to activated macrophage contact-dependent cytotoxicity.

  5. Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2.

    PubMed

    Rolland, Morgane; Edlefsen, Paul T; Larsen, Brendan B; Tovanabutra, Sodsai; Sanders-Buell, Eric; Hertz, Tomer; deCamp, Allan C; Carrico, Chris; Menis, Sergey; Magaret, Craig A; Ahmed, Hasan; Juraska, Michal; Chen, Lennie; Konopa, Philip; Nariya, Snehal; Stoddard, Julia N; Wong, Kim; Zhao, Hong; Deng, Wenjie; Maust, Brandon S; Bose, Meera; Howell, Shana; Bates, Adam; Lazzaro, Michelle; O'Sullivan, Annemarie; Lei, Esther; Bradfield, Andrea; Ibitamuno, Grace; Assawadarachai, Vatcharain; O'Connell, Robert J; deSouza, Mark S; Nitayaphan, Sorachai; Rerks-Ngarm, Supachai; Robb, Merlin L; McLellan, Jason S; Georgiev, Ivelin; Kwong, Peter D; Carlson, Jonathan M; Michael, Nelson L; Schief, William R; Gilbert, Peter B; Mullins, James I; Kim, Jerome H

    2012-10-18

    The RV144 trial demonstrated 31% vaccine efficacy at preventing human immunodeficiency virus (HIV)-1 infection. Antibodies against the HIV-1 envelope variable loops 1 and 2 (Env V1 and V2) correlated inversely with infection risk. We proposed that vaccine-induced immune responses against V1/V2 would have a selective effect against, or sieve, HIV-1 breakthrough viruses. A total of 936 HIV-1 genome sequences from 44 vaccine and 66 placebo recipients were examined. We show that vaccine-induced immune responses were associated with two signatures in V2 at amino acid positions 169 and 181. Vaccine efficacy against viruses matching the vaccine at position 169 was 48% (confidence interval 18% to 66%; P = 0.0036), whereas vaccine efficacy against viruses mismatching the vaccine at position 181 was 78% (confidence interval 35% to 93%; P = 0.0028). Residue 169 is in a cationic glycosylated region recognized by broadly neutralizing and RV144-derived antibodies. The predicted distance between the two signature sites (21?±?7?Å) and their match/mismatch dichotomy indicate that multiple factors may be involved in the protection observed in RV144. Genetic signatures of RV144 vaccination in V2 complement the finding of an association between high V1/V2-binding antibodies and reduced risk of HIV-1 acquisition, and provide evidence that vaccine-induced V2 responses plausibly had a role in the partial protection conferred by the RV144 regimen. PMID:22960785

  6. Remains of abutments for Bridge No. 1575 at MD Rt. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Remains of abutments for Bridge No. 1575 at MD Rt. 51 in Spring Gap, Maryland, looking northeast. (Compare with HAER MD-115 photos taken 1988). - Western Maryland Railway, Cumberland Extension, Pearre to North Branch, from WM milepost 125 to 160, Pearre, Washington County, MD

  7. Pmcndlngr 01 the 31rt Conlennw on Declrlonand Control

    E-print Network

    Grossman, Robert

    describing the evolution of the attitude of a rigid body, such as a spacecraft, when the body is modeled to nonlinear control algorithms which require accurate models of the systems to construct suitable feedbackPmcndlngr 01 the 31rt Conlennw on Declrlonand Control Tucaon. Arkona -Dscember 1992 TA7 - 11

  8. ZIP+4 by Route ZIP+4 ADDRESS ROOM DEPARTMENT RT

    E-print Network

    Oklahoma, University of

    (USPS 73069) Page 2 1/13/2009 #12;ZIP+4 by Route ZIP+4 ADDRESS ROOM DEPARTMENT RT 2001 455 W LINDSEY ST 205 Political Science 2 2002 455 W LINDSEY ST 304 Institute for Public Affairs 2 2003 455 W LINDSEY ST 305 Public Administration 2 2004 455 W LINDSEY ST 406 History 2 2005 455 W LINDSEY ST 521 Anthropology

  9. Parallel Picoliter RT-PCR Assays Using Microfluidics

    E-print Network

    Quake, Stephen R.

    Parallel Picoliter RT-PCR Assays Using Microfluidics Joshua S. Marcus,, W. French Anderson The development of microfluidic tools for high-throughput nucleic acid analysis has become a burgeoning area of research in the post-genome era. Here, we have developed a microfluidic chip to perform 72 parallel 450-p

  10. RT-MDD Framework A Practical Approach Marco Costa1

    E-print Network

    da Silva, Alberto Rodrigues

    : Reactive traceability, MDD, QVT, UML, RT-MDD 1 Introduction An information system involves a set of active Rua Alves Redol, Nº 9 1000-029 Lisboa, Portugal alberto.silva@acm.org Abstract. Traceability approach to traceability using MDD as general orientation and QVT as a transformation language

  11. Measurements of the main parameters of the RT70 antenna

    Microsoft Academic Search

    A. M. Aslanyan; A. G. Gulyan; A. N. Kozlov; V. B. Tarasov; R. M. Martirosyan; V. A. Grishmanovskii; B. G. Sergeev

    1984-01-01

    The main electrical characteristics of the RT-70 antenna at wavelengths of 3, 5, 6, and 40 cm were measured by radio-astronomical methods. Analytical expressions for the antenna charateristics as a function of elevation are found from the measurement results and by the method of least squares. Good agreement is obtained between the results of the experimental research and theoretical calculations.

  12. Linear-Convex Control and Duality R.T. Rockafellar

    E-print Network

    Goebel, Rafal

    . For simplicity of presentation, but also with control engineering applications in mind, we specialize the keyLinear-Convex Control and Duality R.T. Rockafellar and Rafal Goebel April 2, 2007 Abstract An optimal control problem with linear dynamics and convex but not necessarily quadratic and possibly

  13. Efavirenz Therapy in Rhesus Macaques Infected with a Chimera of Simian Immunodeficiency Virus Containing Reverse Transcriptase from Human Immunodeficiency Virus Type 1

    PubMed Central

    Hofman, Michael J.; Higgins, Joanne; Matthews, Timothy B.; Pedersen, Niels C.; Tan, Chalet; Schinazi, Raymond F.; North, Thomas W.

    2004-01-01

    The specificity of nonnucleoside reverse transcriptase (RT) inhibitors (NNRTIs) for the RT of human immunodeficiency virus type 1 (HIV-1) has prevented the use of simian immunodeficiency virus (SIV) in the study of NNRTIs and NNRTI-based highly active antiretroviral therapy. However, a SIV-HIV-1 chimera (RT-SHIV), in which the RT from SIVmac239 was replaced with the RT-encoding region from HIV-1, is susceptible to NNRTIs and is infectious to rhesus macaques. We have evaluated the antiviral activity of efavirenz against RT-SHIV and the emergence of efavirenz-resistant mutants in vitro and in vivo. RT-SHIV was susceptible to efavirenz with a mean effective concentration of 5.9 ± 4.5 nM, and RT-SHIV variants selected with efavirenz in cell culture displayed 600-fold-reduced susceptibility. The efavirenz-resistant mutants of RT-SHIV had mutations in RT similar to those of HIV-1 variants that were selected under similar conditions. Efavirenz monotherapy of RT-SHIV-infected macaques produced a 1.82-log-unit decrease in plasma viral-RNA levels after 1 week. The virus load rebounded within 3 weeks in one treated animal and more slowly in a second animal. Virus isolated from these two animals contained the K103N and Y188C or Y188L mutations. The RT-SHIV-rhesus macaque model may prove useful for studies of antiretroviral drug combinations that include efavirenz. PMID:15328115

  14. Analytical Jacobian Calculation in RT Model Including Polarization Effect

    NASA Astrophysics Data System (ADS)

    Okabayashi, Y.; Yoshida, Y.; Ota, Y.

    2014-12-01

    The greenhouse gas observing satellite "GOSAT" launched in January 2009 has been observing global distribution of CO2 and CH4. The TANSO-FTS mounted on GOSAT measures the two polarized components (called "P" and "S") of short wavelength infrared (SWIR) spectrum reflected from the earth's surface. In NIES, column-averaged dry air mole fraction of CO2 and CH4 (XCO2 and XCH4) are retrieved from SWIR spectra. However, the observed polarization information is not effectively utilized in the retrieval process due to the large computational cost of a vector RT model, instead the polarization synthesized spectra and a scalar RT model are used in the operational processing. An optical path length modification due to aerosol scattering is known as the major error source for XCO2 and XCH4 retrieval from SWIR spectra. Because the aerosol scattering changes polarization state of light, more accurate or additional aerosol information is expected by using the observed polarization spectra effectively in the retrieval process, which improves the retrieval accuracy of XCO2 and XCH4. In addition, for information content analysis, sensitivity analysis and error analysis, Jacobian matrix is important onto retrieval algorithm design before analyses for actual observed data. However, in the case of using RT model including polarization effect in retrieval process, the computational cost of Jacobian matrix calculations in maximum a posteriori retrieval is significantly large. Efficient calculation of analytical Jacobian is necessary. As a first step, we are implementing an analytical Jacobian calculation function to the vector RT model "Pstar". RT scheme of Pstar is based on hybrid method comprising the discrete ordinate and matrix operator methods. The reflection/transmission matrices and source vectors are obtained for each vertical layer through the discrete ordinate solution, and the vertically inhomogeneous system is constructed using the matrix operator method. Because the delta-M truncation method is used in the Pstar to reduce the computational cost, single scattering component correction called TMS method is implemented. Calculation of analytical Jacobian has to be constructed above the RT scheme. We will show the formulation and some results of the analytical Jacobian implementation at the presentation.

  15. Structural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers

    PubMed Central

    Blattner, Claudia; Lee, Jeong Hyun; Sliepen, Kwinten; Derking, Ronald; Falkowska, Emilia; de la Peña, Alba Torrents; Cupo, Albert; Julien, Jean-Philippe; van Gils, Marit; Lee, Peter S.; Peng, Wenjie; Paulson, James C.; Poignard, Pascal; Burton, Dennis R.; Moore, John P.; Sanders, Rogier W.

    2014-01-01

    Summary All previously characterized broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) target one of four major sites of vulnerability. Here, we define and structurally characterize a unique epitope on Env that is recognized by a recently discovered family of human monoclonal antibodies (PGT151-158). The PGT151 epitope is comprised of residues and glycans at the interface of gp41 and gp120 within a single protomer and glycans from both subunits of a second protomer and represents a neutralizing epitope that is dependent on both gp120 and gp41. As PGT151 binds only to properly formed, cleaved trimers, this distinctive property, and its ability to stabilize Env trimers, has enabled the successful purification of mature, cleaved Env trimers from the cell surface as a complex with PGT151. Here we compare the structural and functional properties of membrane-extracted Env trimers from several clades with those of the soluble, cleaved SOSIP gp140 trimer. PMID:24768348

  16. Diverse Recombinant HIV-1 Envs Fail To Activate B Cells Expressing the Germline B Cell Receptors of the Broadly Neutralizing Anti-HIV-1 Antibodies PG9 and 447-52D

    PubMed Central

    McGuire, Andrew T.; Glenn, Jolene A.; Lippy, Adriana

    2014-01-01

    ABSTRACT Broadly neutralizing antibodies (bNAbs) against HIV-1 are generated during HIV-1-infection but have not yet been elicited by immunization with recombinant forms of the viral envelope glycoprotein (Env; the target of anti-HIV-1 neutralizing antibodies). A particular type of bNAb targets the CD4-binding site (CD4-BS) region of Env. These antibodies are derived from a limited number of VH/VL genes and can bind to and neutralize diverse HIV-1 strains. Recent reports have demonstrated the limited potential of Env to activate B cells expressing the germline B cell receptor (BCR) forms of anti-CD4-BS bNAbs. A potential reason for the lack of elicitation of anti-CD4-BS bNAbs by Env immunogens is the absence of stimulation of naive B cells expressing the germline BCRs of such antibodies. Several bNAbs have been isolated from HIV-1-infected subjects that target other structurally conserved regions of Env. How frequently Env immunogens stimulate the germline BCRs that give rise to bNAbs that target Env regions other than the CD4-BS is not well understood. Here, we investigated the interactions between diverse Envs and the BCRs of known bNAbs targeting not only the CD4-BS but also conserved elements of the second and third variable Env regions. Our results indicate that Env is generally ineffective in engaging germline BCRs of bNAbs irrespective of their epitope target. Potentially, this is the result of viral evolutionary mechanisms adopted to escape broadly neutralizing antibody responses. Our results also suggest that a single Env capable of activating germline BCRs that target distinct Env epitopes will be very difficult to identify or to design. IMPORTANCE Broadly neutralizing antibodies against HIV-1 are thought to be an important component of the immune responses that a successful vaccine should elicit. Broadly neutralizing antibodies are generated by a subset of those infected by HIV-1, but so far, they have not been generated by immunization with recombinant Envelope (Env, the target of anti-HIV-1 neutralizing antibodies). Here, we provide evidence that the inability of Env to elicit the production of broadly neutralizing antibodies is due to the inability of diverse Envs to engage the germline B cell receptor forms of known broadly neutralizing antibodies. PMID:24352455

  17. RT-level TPG Exploiting High-Level Synthesis Information

    Microsoft Academic Search

    Silvia Chiusano; Fulvio Corno; Paolo Prinetto

    1999-01-01

    High-level t est pattern g eneration is today a widely investigated research topic. The present paper proposes a fully automated, simulation-based ATPG system, to address test pattern generation for circuits described at the RT-level. The approach is based on a set of suitable testability metrics, and the test pattern generation phase resorts to Genetic Algorithms. Experiments s how the excellent

  18. Measurement of the main parameters of the RT70 antenna

    Microsoft Academic Search

    A. M. Aslanian; A. G. Gulian; A. N. Kozlov; V. B. Tarasov; R. M. Martirosian; V. A. Grishmanovskii; B. G. Sergeev

    1984-01-01

    Measurements of the main electrical characteristics of the RT-70 radio-telescope antenna (a two-reflector quasi-parabolic Gregory system) were made at wavelengths of 3, 5, 6, and 40 cm using a radio-astronomical technique. Expressions for the elevation-angle dependences of the antenna characteristics are obtained on the basis of the least squares method. Good agreement between experimental and theoretical results is shown. Gravitational

  19. MIT LINCOLN LABORATORY AnnuAl RepoRt

    E-print Network

    Reuter, Martin

    MIT LINCOLN LABORATORY 2009 AnnuAl RepoRt Te c h n o l o g y i n Su p p o r T o f naT i o n a l Se Vice president for Research and Associate provost Dr. L. Rafael Reif provost Dr. Susan Hockfield president MIT Lincoln Laboratory Massachusetts Institute of Technology Dr. Eric D. Evans Director Mr

  20. Regression equations for RT3 activity monitors to estimate energy expenditure in manual wheelchair users.

    PubMed

    Hiremath, Shivayogi V; Ding, Dan

    2011-01-01

    Activity monitors (AMs) can assist persons with Spinal Cord Injury (SCI) who use manual wheelchairs to self-assess regular physical activity to move towards healthier lifestyles. In this study we evaluated the validity of an accelerometer-based RT3 AM in predicting energy expenditure (EE) of manual wheelchair users with SCI. Twenty-four subjects performed four types of physical activities including wheelchair propulsion, arm-ergometry exercise, deskwork, and resting in a laboratory setting. Subjects wore two RT3 AMs: an RT3 around the waist (RT3W) per the manufacturer's instruction and an RT3 on the upper arm (RT3A). Criterion EE was collected by a portable metabolic system. The absolute EE estimation error for the RT3W varied from 21.3%-55.2% for different activities. Two EE prediction equations (general and activity-specific) were developed from 19 randomly selected subjects and validated on the remaining 4 subjects for the RT3A, RT3W, and RT3 AMs combined. The results showed that the general and activity-specific regression equations for the RT3A performed better than the RT3W and similar to the RT3 AMs combined. The general EE equation for RT3A consisted of both the demographic variable weight and accelerometer variables showing it is sensitive to subject parameters and upper extremity movement. The activity-specific EE equations for RT3A showed demographic variable weight to be a significant predictor during resting and deskwork and accelerometer variables along with weight to be significant predictors during propulsion and arm-ergometry. The validation results from the activity-specific equations for the RT3A showed that the absolute EE estimation error varied from 12.2%-38.1%. Future work will recruit more subjects and refine the prediction equations for the RT3 AM to quantify physical activity in MWUs with SCI. PMID:22256036

  1. Enhancing Transport of Hydrogenophaga flava ENV735 for Bioaugmentation of Aquifers Contaminated with Methyl tert-Butyl Ether

    PubMed Central

    Streger, Sheryl H.; Vainberg, Simon; Dong, Hailiang; Hatzinger, Paul B.

    2002-01-01

    The gasoline oxygenate methyl tert-butyl ether (MTBE) has become a widespread contaminant in groundwater throughout the United States. Bioaugmentation of aquifers with MTBE-degrading cultures may be necessary to enhance degradation of the oxygenate in some locations. However, poor cell transport has sometimes limited bioaugmentation efforts in the past. The objective of this study was to evaluate the transport characteristics of Hydrogenophaga flava ENV735, a pure culture capable of growth on MTBE, and to improve movement of the strain through aquifer solids. The wild-type culture moved only a few centimeters in columns of aquifer sediment. An adhesion-deficient variant (H. flava ENV735:24) of the wild-type strain that moved more readily through sediments was obtained by sequential passage of cells through columns of sterile sediment. Hydrophobic and electrostatic interaction chromatography revealed that the wild-type strain is much more hydrophobic than the adhesion-deficient variant. Electrophoretic mobility assays and transmission electron microscopy showed that the wild-type bacterium contains two distinct subpopulations, whereas the adhesion-deficient strain has only a single, homogeneous population. Both the wild-type strain and adhesion-deficient variant degraded MTBE, and both were identified by 16S rRNA analysis as pure cultures of H. flava. The effectiveness of surfactants for enhancing transport of the wild-type strain was also evaluated. Many of the surfactants tested were toxic to ENV735; however, one nonionic surfactant, Tween 20, enhanced cell transport in sand columns. Improving microbial transport may lead to a more effective bioaugmentation strategy for MTBE-contaminated sites where indigenous oxygenate degraders are absent. PMID:12406751

  2. Detection of the human endogenous retrovirus ERV3-encoded Env-protein in human tissues using antibody-based proteomics

    PubMed Central

    Fei, Chen; Atterby, Christina; Edqvist, Per-Henrik; Pontén, Fredrik; Zhang, Wei Wei; Larsson, Erik; Ryan, Frank P

    2014-01-01

    Objectives There is growing evidence to suggest that human endogenous retroviruses (HERVs) have contributed to human evolution, being expressed in development, normal physiology and disease. A key difficulty in the scientific evaluation of this potential viral contribution is the accurate demonstration of virally expressed protein in specific human cells and tissues. In this study, we have adopted the endogenous retrovirus, ERV3, as our test model in developing a reliable high-capacity methodology for the expression of such endogenous retrovirus-coded protein. Design Two affinity-purified polyclonal antibodies to ERV3 Env-encoded protein were generated to detect the corresponding protein expression pattern in specific human cells, tissues and organs. Participants Sampling included normal tissues from 144 individuals ranging from childhood to old age. This included more than forty different tissues and organs and some 216 different cancer tissues representing the twenty commonest forms of human cancer. Setting The Rudbeck Laboratory, Uppsala University and Uppsala University Hospital, Uppsala, Sweden. Main Outcome Measures The potential expression at likely physiological level of the ERV3Env encoded protein in a wide range of human cells, tissues and organs. Results We found that ERV3 encoded Env protein is expressed at substantive levels in placenta, testis, adrenal gland, corpus luteum, Fallopian tubes, sebaceous glands, astrocytes, bronchial epithelium and the ducts of the salivary glands. Substantive expression was also seen in a variety of epithelial cells as well as cells known to undergo fusion in inflammation and in normal physiology, including fused macrophages, myocardium and striated muscle. This contrasted strongly with the low levels expressed in other tissues types. These findings suggest that this virus plays a significant role in human physiology and may also play a possible role in disease. Conclusion This technique can now be extended to the study of other HERV genomes within the human chromosomes that may have contributed to human evolution, physiology and disease. PMID:24262892

  3. HIV-1 Vaccine-Induced C1 and V2 Env-Specific Antibodies Synergize for Increased Antiviral Activities

    PubMed Central

    Pollara, Justin; Bonsignori, Mattia; Moody, M. Anthony; Liu, Pinghuang; Alam, S. Munir; Hwang, Kwan-Ki; Gurley, Thaddeus C.; Kozink, Daniel M.; Armand, Lawrence C.; Marshall, Dawn J.; Whitesides, John F.; Kaewkungwal, Jaranit; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Rerks-Ngarm, Supachai; Robb, Merlin L.; O'Connell, Robert J.; Kim, Jerome H.; Michael, Nelson L.; Montefiori, David C.; Tomaras, Georgia D.; Liao, Hua-Xin; Haynes, Barton F.

    2014-01-01

    ABSTRACT The RV144 ALVAC/AIDSVax HIV-1 vaccine clinical trial showed an estimated vaccine efficacy of 31.2%. Viral genetic analysis identified a vaccine-induced site of immune pressure in the HIV-1 envelope (Env) variable region 2 (V2) focused on residue 169, which is included in the epitope recognized by vaccinee-derived V2 monoclonal antibodies. The ALVAC/AIDSVax vaccine induced antibody-dependent cellular cytotoxicity (ADCC) against the Env V2 and constant 1 (C1) regions. In the presence of low IgA Env antibody levels, plasma levels of ADCC activity correlated with lower risk of infection. In this study, we demonstrate that C1 and V2 monoclonal antibodies isolated from RV144 vaccinees synergized for neutralization, infectious virus capture, and ADCC. Importantly, synergy increased the HIV-1 ADCC activity of V2 monoclonal antibody CH58 at concentrations similar to that observed in plasma of RV144 vaccinees. These findings raise the hypothesis that synergy among vaccine-induced antibodies with different epitope specificities contributes to HIV-1 antiviral antibody responses and is important to induce for reduction in the risk of HIV-1 transmission. IMPORTANCE The Thai RV144 ALVAC/AIDSVax prime-boost vaccine efficacy trial represents the only example of HIV-1 vaccine efficacy in humans to date. Studies aimed at identifying immune correlates involved in the modest vaccine-mediated protection identified HIV-1 envelope (Env) variable region 2-binding antibodies as inversely correlated with infection risk, and genetic analysis identified a site of immune pressure within the region recognized by these antibodies. Despite this evidence, the antiviral mechanisms by which variable region 2-specific antibodies may have contributed to lower rates of infection remain unclear. In this study, we demonstrate that vaccine-induced HIV-1 envelope variable region 2 and constant region 1 antibodies synergize for recognition of virus-infected cells, infectious virion capture, virus neutralization, and antibody-dependent cellular cytotoxicity. This is a major step in understanding how these types of antibodies may have cooperatively contributed to reducing infection risk and should be considered in the context of prospective vaccine design. PMID:24807721

  4. HIV-1 vaccine-induced C1 and V2 Env-specific antibodies synergize for increased antiviral activities.

    PubMed

    Pollara, Justin; Bonsignori, Mattia; Moody, M Anthony; Liu, Pinghuang; Alam, S Munir; Hwang, Kwan-Ki; Gurley, Thaddeus C; Kozink, Daniel M; Armand, Lawrence C; Marshall, Dawn J; Whitesides, John F; Kaewkungwal, Jaranit; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Rerks-Ngarm, Supachai; Robb, Merlin L; O'Connell, Robert J; Kim, Jerome H; Michael, Nelson L; Montefiori, David C; Tomaras, Georgia D; Liao, Hua-Xin; Haynes, Barton F; Ferrari, Guido

    2014-07-01

    The RV144 ALVAC/AIDSVax HIV-1 vaccine clinical trial showed an estimated vaccine efficacy of 31.2%. Viral genetic analysis identified a vaccine-induced site of immune pressure in the HIV-1 envelope (Env) variable region 2 (V2) focused on residue 169, which is included in the epitope recognized by vaccinee-derived V2 monoclonal antibodies. The ALVAC/AIDSVax vaccine induced antibody-dependent cellular cytotoxicity (ADCC) against the Env V2 and constant 1 (C1) regions. In the presence of low IgA Env antibody levels, plasma levels of ADCC activity correlated with lower risk of infection. In this study, we demonstrate that C1 and V2 monoclonal antibodies isolated from RV144 vaccinees synergized for neutralization, infectious virus capture, and ADCC. Importantly, synergy increased the HIV-1 ADCC activity of V2 monoclonal antibody CH58 at concentrations similar to that observed in plasma of RV144 vaccinees. These findings raise the hypothesis that synergy among vaccine-induced antibodies with different epitope specificities contributes to HIV-1 antiviral antibody responses and is important to induce for reduction in the risk of HIV-1 transmission. Importance: The Thai RV144 ALVAC/AIDSVax prime-boost vaccine efficacy trial represents the only example of HIV-1 vaccine efficacy in humans to date. Studies aimed at identifying immune correlates involved in the modest vaccine-mediated protection identified HIV-1 envelope (Env) variable region 2-binding antibodies as inversely correlated with infection risk, and genetic analysis identified a site of immune pressure within the region recognized by these antibodies. Despite this evidence, the antiviral mechanisms by which variable region 2-specific antibodies may have contributed to lower rates of infection remain unclear. In this study, we demonstrate that vaccine-induced HIV-1 envelope variable region 2 and constant region 1 antibodies synergize for recognition of virus-infected cells, infectious virion capture, virus neutralization, and antibody-dependent cellular cytotoxicity. This is a major step in understanding how these types of antibodies may have cooperatively contributed to reducing infection risk and should be considered in the context of prospective vaccine design. PMID:24807721

  5. Mucosal immunization of lactating female rhesus monkeys with a transmitted/founder HIV-1 envelope induces strong Env-specific IgA antibody responses in breast milk.

    PubMed

    Fouda, Genevieve G A; Amos, Joshua D; Wilks, Andrew B; Pollara, Justin; Ray, Caroline A; Chand, Anjali; Kunz, Erika L; Liebl, Brooke E; Whitaker, Kaylan; Carville, Angela; Smith, Shannon; Colvin, Lisa; Pickup, David J; Staats, Herman F; Overman, Glenn; Eutsey-Lloyd, Krissey; Parks, Robert; Chen, Haiyan; Labranche, Celia; Barnett, Susan; Tomaras, Georgia D; Ferrari, Guido; Montefiori, David C; Liao, Hua-Xin; Letvin, Norman L; Haynes, Barton F; Permar, Sallie R

    2013-06-01

    We previously demonstrated that vaccination of lactating rhesus monkeys with a DNA prime/vector boost strategy induces strong T-cell responses but limited envelope (Env)-specific humoral responses in breast milk. To improve vaccine-elicited antibody responses in milk, hormone-induced lactating rhesus monkeys were vaccinated with a transmitted/founder (T/F) HIV Env immunogen in a prime-boost strategy modeled after the moderately protective RV144 HIV vaccine. Lactating rhesus monkeys were intramuscularly primed with either recombinant DNA (n = 4) or modified vaccinia virus Ankara (MVA) poxvirus vector (n = 4) expressing the T/F HIV Env C.1086 and then boosted twice intramuscularly with C.1086 gp120 and the adjuvant MF59. The vaccines induced Env-binding IgG and IgA as well as neutralizing and antibody-dependent cellular cytotoxicity (ADCC) responses in plasma and milk of most vaccinated animals. Importantly, plasma neutralization titers against clade C HIV variants MW965 (P = 0.03) and CAP45 (P = 0.04) were significantly higher in MVA-primed than in DNA-primed animals. The superior systemic prime-boost regimen was then compared to a mucosal-boost regimen, in which animals were boosted twice intranasally with C.1086 gp120 and the TLR 7/8 agonist R848 following the same systemic prime. While the systemic and mucosal vaccine regimens elicited comparable levels of Env-binding IgG antibodies, mucosal immunization induced significantly stronger Env-binding IgA responses in milk (P = 0.03). However, the mucosal regimen was not as potent at inducing functional IgG responses. This study shows that systemic MVA prime followed by either intranasal or systemic protein boosts can elicit strong humoral responses in breast milk and may be a useful strategy to interrupt postnatal HIV-1 transmission. PMID:23596289

  6. Phenotypic studies on recombinant human immunodeficiency virus type 1 (HIV-1) containing CRF01_AE env gene derived from HIV-1-infected patient, residing in central Thailand.

    PubMed

    Utachee, Piraporn; Jinnopat, Piyamat; Isarangkura-Na-Ayuthaya, Panasda; de Silva, U Chandimal; Nakamura, Shota; Siripanyaphinyo, Uamporn; Wichukchinda, Nuanjun; Tokunaga, Kenzo; Yasunaga, Teruo; Sawanpanyalert, Pathom; Ikuta, Kazuyoshi; Auwanit, Wattana; Kameoka, Masanori

    2009-03-01

    Human immunodeficiency virus type 1 (HIV-1) env genes were cloned from blood samples of HIV-1-infected Thai patients, and 35 infectious CRF01_AE envelope glycoprotein (Env)-recombinant viruses were established. In this report, we examined the neutralization susceptibility of these viruses to human monoclonal antibodies, 2G12, IgG1 b12, 2F5 and 4E10, pooled patient plasma, coreceptor antagonists and fusion inhibitor, T-20. The neutralization susceptibility of CRF01_AE Env-recombinant viruses to 2F5, 4E10, patient plasma, coreceptor antagonists and T-20 varied, while most viruses showed low susceptibility to 2G12 and IgG1 b12. Several dual-tropic viruses showed lower susceptibility to 2F5 and 4E10 than CXCR4- or CCR5-tropic viruses. Neutralization susceptibility of the CRF01_AE Env-recombinant virus to pooled patient plasma was negatively correlated with the length of the V1/V2 region or the number of potential N-linked glycosylation sites in conserved regions of gp120. No correlation was found between the coreceptor usage and neutralization susceptibility of the virus to T-20, whereas several dual-tropic viruses showed higher susceptibility to coreceptor antagonists than CXCR4- or CCR5-tropic viruses. We propose that these CRF01_AE Env-recombinant viruses are useful to further study the molecular mechanism of the susceptibility of CRF01_AE Env to neutralizing antibodies and viral entry inhibitors. PMID:19136072

  7. A comparative study of digital RT-PCR and RT-qPCR for quantification of Hepatitis A virus and Norovirus in lettuce and water samples.

    PubMed

    Coudray-Meunier, Coralie; Fraisse, Audrey; Martin-Latil, Sandra; Guillier, Laurent; Delannoy, Sabine; Fach, Patrick; Perelle, Sylvie

    2015-05-18

    Sensitive and quantitative detection of foodborne enteric viruses is classically achieved by quantitative RT-PCR (RT-qPCR). Recently, digital PCR (dPCR) was described as a novel approach to genome quantification without need for a standard curve. The performance of microfluidic digital RT-PCR (RT-dPCR) was compared to RT-qPCR for detecting the main viruses responsible for foodborne outbreaks (human Noroviruses (NoV) and Hepatitis A virus (HAV)) in spiked lettuce and bottled water. Two process controls (Mengovirus and Murine Norovirus) were used and external amplification controls (EAC) were added to examine inhibition of RT-qPCR and RT-dPCR. For detecting viral RNA and cDNA, the sensitivity of the RT-dPCR assays was either comparable to that of RT-qPCR (RNA of HAV, NoV GI, Mengovirus) or slightly (around 1 log10) decreased (NoV GII and MNV-1 RNA and of HAV, NoV GI, NoV GII cDNA). The number of genomic copies determined by dPCR was always from 0.4 to 1.7 log10 lower than the expected numbers of copies calculated by using the standard qPCR curve. Viral recoveries calculated by RT-dPCR were found to be significantly higher than by RT-qPCR for NoV GI, HAV and Mengovirus in water, and for NoV GII and HAV in lettuce samples. The RT-dPCR assay proved to be more tolerant to inhibitory substances present in lettuce samples. This absolute quantitation approach may be useful to standardize quantification of enteric viruses in bottled water and lettuce samples and may be extended to quantifying other human pathogens in food samples. PMID:25725459

  8. Meeting the Needs of Gifted Students within an RtI Framework

    ERIC Educational Resources Information Center

    Coleman, Mary Ruth; Hughes, Claire E.

    2009-01-01

    Response to Intervention (RtI) is sweeping the country, changing the way children's educational needs are recognized and met. RtI was introduced through special education legislation as part of IDEA 2004 and offered an alternative approach for identifying students with learning disabilities (Bender & Shores, 2007). RtI is designed to bring…

  9. Coexpression of the simian immunodeficiency virus Env and Rev proteins by a recombinant human adenovirus host range mutant.

    PubMed Central

    Cheng, S M; Lee, S G; Ronchetti-Blume, M; Virk, K P; Mizutani, S; Eichberg, J W; Davis, A; Hung, P P; Hirsch, V M; Chanock, R M

    1992-01-01

    Recombinant human adenoviruses (Ads) that replicate in the intestinal tract offer a novel, yet practical, means of immunoprophylaxis against a wide variety of viral and bacterial pathogens. For some infectious agents such as human immunodeficiency virus (HIV), the potential for residual infectious material in vaccine preparations must be eliminated. Therefore, recombinant human Ads that express noninfectious HIV or other microbial proteins are attractive vaccine candidates. To test such an approach for HIV, we chose an experimental model of AIDS based on simian immunodeficiency virus (SIV) infection of macaques. Our data demonstrate that the SIV Env gene products are expressed in cultured cells after infection with a recombinant Ad containing both SIV env and rev genes. An E3 deletion vector derived from a mutant of human Ad serotype 5 that efficiently replicates in both human and monkey cells was used to bypass the usual host range restriction of Ad infection. In addition, we show that the SIV rev gene is properly spliced from a single SIV subgenomic DNA fragment and that the Rev protein is expressed in recombinant Ad-SIV-infected human as well as monkey cells. The expression of SIV gene products in suitable live Ad vectors provides an excellent system for studying the regulation of SIV gene expression in cultured cells and evaluating the immunogenicity and protective efficacy of SIV proteins in macaques. Images PMID:1404612

  10. Variability of the env gene in cynomolgus macaques persistently infected with human immunodeficiency virus type 2 strain ben.

    PubMed Central

    Tolle, T; Petry, H; Bachmann, B; Hunsmann, G; Lüke, W

    1994-01-01

    The sequence variability of distinct regions of the proviral env gene of human immunodeficiency virus type 2 strain ben (HIV-2ben) isolated sequentially over 3 to 4 years from six experimentally infected macaques was studied. The regions investigated were homologous to the V1, V2, V3, V4, V5, and V7 hypervariable regions identified in the env genes of HIV-1 and simian immunodeficiency virus SIVmac, respectively. In contrast to findings with HIV-1 and SIVmac, the V1- and V2-homologous regions were found to be highly conserved during the course of the HIV-2ben infection in macaques. The V3-homologous region showed a degree of variation comparable to that of HIV-1 but not of SIV. In the V4-, V5-, and V7-homologous regions, mutation hot spots were detected in most reisolates of the infected monkeys. Most of these mutations occurred during the first 10 weeks after infection. After 50 weeks, new mutations were rarely detected. At most mutation sites, a dynamic equilibrium between the mutated viral isotype and the infecting predominant wild type was present. This equilibrium might prevent an accumulation of mutations in isolates later in the course of infection. PMID:8139054

  11. Nucleotide sequence and structural analysis of the rat RT1.E u and RT1.Aw3 l genes, and of genes related to RT1.O and RT1.C

    Microsoft Academic Search

    Shashikumar K. Salgar; Heinz W. Kunz; Thomas J. Gill

    1995-01-01

    A cDNA library was constructed using mRNA isolated from the R21 strain of rats which have the major histocompatibility complex (MHC) haplotype RT1.AlBlDlEu and the growth and reproduction complex (grc) genotype grc+. The cDNA clones that hybridized with the class I probes pAG64c and pARI.5 and were 1.3–1.7 kilobases were selected. Full-length clones were identified by sequencing partially the 5'

  12. 0-level Vacuum Packaging RT Process for MEMS Resonators

    E-print Network

    Abelé, N; Hibert, C; Casset, F; Ancey, P; Ionescu, A

    2008-01-01

    A new Room Temperature (RT) 0-level vacuum package is demonstrated in this work, using amorphous silicon (aSi) as sacrificial layer and SiO2 as structural layer. The process is compatible with most of MEMS resonators and Resonant Suspended-Gate MOSFET [1] fabrication processes. This paper presents a study on the influence of releasing hole dimensions on the releasing time and hole clogging. It discusses mass production compatibility in terms of packaging stress during back-end plastic injection process. The packaging is done at room temperature making it fully compatible with IC-processed wafers and avoiding any subsequent degradation of the active devices.

  13. HIV-1 Reverse Transcriptase (RT) Polymorphism 172K Suppresses the Effect of Clinically Relevant Drug Resistance Mutations to Both Nucleoside and Non-nucleoside RT Inhibitors*

    PubMed Central

    Hachiya, Atsuko; Marchand, Bruno; Kirby, Karen A.; Michailidis, Eleftherios; Tu, Xiongying; Palczewski, Krzysztof; Ong, Yee Tsuey; Li, Zhe; Griffin, Daniel T.; Schuckmann, Matthew M.; Tanuma, Junko; Oka, Shinichi; Singh, Kamalendra; Kodama, Eiichi N.; Sarafianos, Stefan G.

    2012-01-01

    Polymorphisms have poorly understood effects on drug susceptibility and may affect the outcome of HIV treatment. We have discovered that an HIV-1 reverse transcriptase (RT) polymorphism (RT172K) is present in clinical samples and in widely used laboratory strains (BH10), and it profoundly affects HIV-1 susceptibility to both nucleoside (NRTIs) and non-nucleoside RT inhibitors (NNRTIs) when combined with certain mutations. Polymorphism 172K significantly suppressed zidovudine resistance caused by excision (e.g. thymidine-associated mutations) and not by discrimination mechanism mutations (e.g. Q151M complex). Moreover, it attenuated resistance to nevirapine or efavirenz imparted by NNRTI mutations. Although 172K favored RT-DNA binding at an excisable pre-translocation conformation, it decreased excision by thymidine-associated mutation-containing RT. 172K affected DNA handling and decreased RT processivity without significantly affecting the kcat/Km values for dNTP. Surface plasmon resonance experiments revealed that RT172K decreased DNA binding by increasing the dissociation rate. Hence, the increased zidovudine susceptibility of RT172K results from its increased dissociation from the chain-terminated DNA and reduced primer unblocking. We solved a high resolution (2.15 ?) crystal structure of RT mutated at 172 and compared crystal structures of RT172R and RT172K bound to NNRTIs or DNA/dNTP. Our structural analyses highlight differences in the interactions between ?-helix E (where 172 resides) and the active site ?9-strand that involve the YMDD loop and the NNRTI binding pocket. Such changes may increase dissociation of DNA, thus suppressing excision-based NRTI resistance and also offset the effect of NNRTI resistance mutations thereby restoring NNRTI binding. PMID:22761416

  14. Comparative detection of rotavirus RNA by conventional RT-PCR, TaqMan RT-PCR and real-time nucleic acid sequence-based amplification.

    PubMed

    Mo, Qiu-Hua; Wang, Hai-Bo; Tan, Hua; Wu, Bi-Mei; Feng, Zi-Li; Wang, Qi; Lin, Ji-Can; Yang, Ze

    2015-03-01

    Rotavirus is one of the major viral pathogens leading to diarrhea. Diagnosis has been conducted by either traditional cultural, serological methods or molecular biology techniques, which include RT-PCR and nucleic acid sequence-based amplification (NASBA). However, their differences regarding accuracy and sensitivity remain unknown. In this study, an in-house conventional RT-PCR assay and more importantly, an in-house real-time NASBA (RT-NASBA) were established, and compared with a commercial TaqMan RT-PCR assay. The results showed that all of these methods were able to detect and distinguish rotavirus from other diarrhea viruses with a 100% concordance rate during the course of an evaluation on 20 clinical stool samples. However, RT-NASBA was much quicker than the other two methods. More importantly, the limit of detection of RT-NASBA could reach seven copies per reaction and was one to two logs lower than that of conventional RT-PCR and TaqMan RT-PCR. These results indicate that this in-house assay was more sensitive, and thus could be used as an efficient diagnosis tool for rotavirus. To the best of our knowledge, this is the first direct comparison among three different assays for the detection of rotavirus. These findings would provide implication for the rational selection of diagnosis tool for rotavirus. PMID:25433218

  15. CIRAAnnuAl RepoRt 2005-2006AnnuAl RepoRt 2005-2006 CIRA ANNUAL REPORT FY 05/06

    E-print Network

    Collett Jr., Jeffrey L.

    CIRAAnnuAl RepoRt 2005-2006AnnuAl RepoRt 2005-2006 #12;CIRA ANNUAL REPORT FY 05/06 COOPERATIVE Vice Provost for Graduate Studies Hank Gardner, Colorado State University Interim Vice President;iv #12;INTRODUCTION This report describes research funded in collaboration with NOAA's cooperative

  16. Characterization of Humoral and Cellular Immune Responses Elicited by a Recombinant Adenovirus Serotype 26 HIV-1 Env Vaccine in Healthy Adults (IPCAVD 001)

    PubMed Central

    Barouch, Dan H.; Liu, Jinyan; Peter, Lauren; Abbink, Peter; Iampietro, M. Justin; Cheung, Ann; Alter, Galit; Chung, Amy; Dugast, Anne-Sophie; Frahm, Nicole; McElrath, M. Juliana; Wenschuh, Holger; Reimer, Ulf; Seaman, Michael S.; Pau, Maria G.; Weijtens, Mo; Goudsmit, Jaap; Walsh, Stephen R.; Dolin, Raphael; Baden, Lindsey R.

    2013-01-01

    Background.?Adenovirus serotype 26 (Ad26) has been developed as a novel candidate vaccine vector for human immunodeficiency virus type 1 (HIV-1) and other pathogens. The primary safety and immunogenicity data from the Integrated Preclinical/Clinical AIDS Vaccine Development Program (IPCAVD) 001 trial, the first-in-human evaluation of a prototype Ad26 vector-based vaccine expressing clade A HIV-1 Env (Ad26.ENVA.01), are reported concurrently with this article. Here, we characterize in greater detail the humoral and cellular immune responses elicited by Ad26.ENVA.01 in humans. Methods.?Samples from the IPCAVD 001 trial were used for humoral and cellular immunogenicity assays. Results.?We observed a dose-dependent expansion of the magnitude, breadth, and epitopic diversity of Env-specific binding antibody responses elicited by this vaccine. Antibody-dependent cell-mediated phagocytosis, virus inhibition, and degranulation functional activity were also observed. Env-specific cellular immune responses induced by the vaccine included multiple CD8+ and CD4+ T-lymphocyte memory subpopulations and cytokine secretion phenotypes, although cellular immune breadth was limited. Baseline vector-specific T-lymphocyte responses were common but did not impair Env-specific immune responses in this study. Conclusion.?Ad26.ENVA.01 elicited a broad diversity of humoral and cellular immune responses in humans. These data support the further clinical development of Ad26 as a candidate vaccine vector. Clinical Trials Registration.?NCT00618605. PMID:23125443

  17. Mucosal immunization against ovine lentivirus using PEI-DNA complexes and modified vaccinia Ankara encoding the gag and/or env genes.

    PubMed

    Reina, R; Barbezange, C; Niesalla, H; de Andrés, X; Arnarson, H; Biescas, E; Mazzei, M; Fraisier, C; McNeilly, T N; Liu, C; Perez, M; Carrozza, M L; Bandecchi, P; Solano, C; Crespo, H; Glaria, I; Huard, C; Shaw, D J; de Blas, I; de Andrés, D; Tolari, F; Rosati, S; Suzan-Monti, M; Andrésdottir, V; Torsteinsdottir, S; Petursson, G; Lujan, L; Pepin, M; Amorena, B; Blacklaws, B; Harkiss, G D

    2008-08-18

    Sheep were immunized against Visna/Maedi virus (VMV) gag and/or env genes via the nasopharynx-associated lymphoid tissue (NALT) and lung using polyethylenimine (PEI)-DNA complexes and modified vaccinia Ankara, and challenged with live virus via the lung. env immunization enhanced humoral responses prior to but not after VMV challenge. Systemic T cell proliferative and cytotoxic responses were generally low, with the responses following single gag gene immunization being significantly depressed after challenge. A transient reduction in provirus load in the blood early after challenge was observed following env immunization, whilst the gag gene either alone or in combination with env resulted in significantly elevated provirus loads in lung. However, despite this, a significant reduction in lesion score was observed in animals immunized with the single gag gene at post-mortem. Inclusion of IFN-gamma in the immunization mixture in general had no significant effects. The results thus showed that protective effects against VMV-induced lesions can be induced following respiratory immunization with the single gag gene, though this was accompanied by an increased pulmonary provirus load. PMID:18606204

  18. HIV-1 Receptor Binding Site-Directed Antibodies Using a VH1-2 Gene Segment Orthologue Are Activated by Env Trimer Immunization

    PubMed Central

    Bale, Shridhar; Phad, Ganesh E.; Guenaga, Javier; Wilson, Richard; Soldemo, Martina; McKee, Krisha; Sundling, Christopher; Mascola, John; Li, Yuxing; Wyatt, Richard T.; Karlsson Hedestam, Gunilla B.

    2014-01-01

    Broadly neutralizing antibodies (bNAbs) isolated from chronically HIV-1 infected individuals reveal important information regarding how antibodies target conserved determinants of the envelope glycoprotein (Env) spike such as the primary receptor CD4 binding site (CD4bs). Many CD4bs-directed bNAbs use the same heavy (H) chain variable (V) gene segment, VH1-2*02, suggesting that activation of B cells expressing this allele is linked to the generation of this type of Ab. Here, we identify the rhesus macaque VH1.23 gene segment to be the closest macaque orthologue to the human VH1-2 gene segment, with 92% homology to VH1-2*02. Of the three amino acids in the VH1-2*02 gene segment that define a motif for VRC01-like antibodies (W50, N58, flanking the HCDR2 region, and R71), the two identified macaque VH1.23 alleles described here encode two. We demonstrate that immunization with soluble Env trimers induced CD4bs-specific VH1.23-using Abs with restricted neutralization breadth. Through alanine scanning and structural studies of one such monoclonal Ab (MAb), GE356, we demonstrate that all three HCDRs are involved in neutralization. This contrasts to the highly potent CD4bs-directed VRC01 class of bNAb, which bind Env predominantly through the HCDR2. Also unlike VRC01, GE356 was minimally modified by somatic hypermutation, its light (L) chain CDRs were of average lengths and it displayed a binding footprint proximal to the trimer axis. These results illustrate that the Env trimer immunogen used here activates B cells encoding a VH1-2 gene segment orthologue, but that the resulting Abs interact distinctly differently with the HIV-1 Env spike compared to VRC01. PMID:25166308

  19. HIV-1 Env C2-V4 Diversification in a Slow-Progressor Infant Reveals a Flat but Rugged Fitness Landscape

    PubMed Central

    Smith, S. Abigail; Wood, Charles; West, John T.

    2013-01-01

    Human immunodeficiency virus type-1 (HIV-1) fitness has been associated with virus entry, a process mediated by the envelope glycoprotein (Env). We previously described Env genetic diversification in a Zambian, subtype C infected, slow-progressor child (1157i) in parallel with an evolving neutralizing antibody response. Because of the role the Variable-3 loop (V3) plays in transmission, cell tropism, neutralization sensitivity, and fitness, longitudinally isolated 1157i C2-V4 alleles were cloned into HIV-1NL4-3-eGFP and -DsRed2 infectious molecular clones. The fluorescent reporters allowed for dual-infection competitions between all patient-derived C2-V4 chimeras to quantify the effect of V3 diversification and selection on fitness. ‘Winners’ and ‘losers’ were readily discriminated among the C2-V4 alleles. Exceptional sensitivity for detection of subtle fitness differences was revealed through analysis of two alleles differing in a single synonymous amino acid. However, when the outcomes of N?=?33 competitions were averaged for each chimera, the aggregate analysis showed that despite increasing diversification and divergence with time, natural selection of C2-V4 sequences in this individual did not appear to be producing a ‘survival of the fittest’ evolutionary pattern. Rather, we detected a relatively flat fitness landscape consistent with mutational robustness. Fitness outcomes were then correlated with individual components of the entry process. Env incorporation into particles correlated best with fitness, suggesting a role for Env avidity, as opposed to receptor/coreceptor affinity, in defining fitness. Nevertheless, biochemical analyses did not identify any step in HIV-1 entry as a dominant determinant of fitness. Our results lead us to conclude that multiple aspects of entry contribute to maintaining adequate HIV-1 fitness, and there is no surrogate analysis for determining fitness. The capacity for subtle polymorphisms in Env to nevertheless significantly impact viral fitness suggests fitness is best defined by head-to-head competition. PMID:23638182

  20. Gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of Japanese encephalitis virus

    NASA Astrophysics Data System (ADS)

    Huang, Su-Hua; Yang, Tsuey-Ching; Tsai, Ming-Hong; Tsai, I.-Shou; Lu, Huang-Chih; Chuang, Pei-Hsin; Wan, Lei; Lin, Ying-Ju; Lai, Chih-Ho; Lin, Cheng-Wen

    2008-10-01

    Virus isolation and antibody detection are routinely used for diagnosis of Japanese encephalitis virus (JEV) infection, but the low level of transient viremia in some JE patients makes JEV isolation from clinical and surveillance samples very difficult. We describe the use of gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of JEV from its RNA genome. We tested the effect of gold nanoparticles on four different PCR systems, including conventional PCR, reverse-transcription PCR (RT-PCR), and SYBR green real-time PCR and RT-PCR assays for diagnosis in the acute phase of JEV infection. Gold nanoparticles increased the amplification yield of the PCR product and shortened the PCR time compared to the conventional reaction. In addition, nanogold-based real-time RT-PCR showed a linear relationship between Ct and template amount using ten-fold dilutions of JEV. The nanogold-based RT-PCR and real-time quantitative RT-PCR assays were able to detect low levels (1-10 000 copies) of the JEV RNA genomes extracted from culture medium or whole blood, providing early diagnostic tools for the detection of low-level viremia in the acute-phase infection. The assays described here were simple, sensitive, and rapid approaches for detection and quantitation of JEV in tissue cultured samples as well as clinical samples.

  1. Molecular aspects of the RT/drug interactions. Perspective of dual inhibitors.

    PubMed

    Distinto, Simona; Maccioni, Elias; Meleddu, Rita; Corona, Angela; Alcaro, Stefano; Tramontano, Enzo

    2013-01-01

    The HIV-1 reverse transcriptase (RT) is one of the most attracting targets for the development of early phase infection inhibitors. Although many RT inhibitors have been approved for the treatment of HIV-1 infection, they all target the polymerase function of this enzyme. So far, no drugs are available for the inhibition of the RT associated ribonuclease H function (RNase H), which plays an essential role in the HIV replication cycle. Moreover it should be reported that many of the known RT inhibitors, targeting the polymerase function, enhance the RNase H activity, indicating that, although spatially distinct, a close relation occurs between the two functions. The aim of this review is to summarise the efforts in the design of new inhibitors either characterized by a novel mechanism of action or capable of blocking both RT associated functions, as well as pointing out the main binding features of the known RT inhibitors. PMID:23092286

  2. The RT6 (Art2) family of ADP-ribosyltransferases in rat and mouse

    Microsoft Academic Search

    Rita Bortell; Toshihiro Kanaitsuka; Linda A. Stevens; Joel Moss; John P. Mordes; Aldo A. Rossini; Dale L. Greiner

    1999-01-01

    Recent evidence suggests that a new member of the mono-ADP-ribosyltransferase\\/NAD glycohydrolase family, RT6, may be important in immune regulation. RT6 is expressed in two allelic forms and is present on post-thymic T cells in the rat. RT6-expressing T cells in the rat may have a regulatory role, a conclusion based on their ability to prevent autoimmune diabetes in the BB

  3. Real-time quantification of microRNAs by stem-loop RT-PCR

    Microsoft Academic Search

    Caifu Chen; Dana A. Ridzon; Adam J. Broomer; Zhaohui Zhou; Danny H. Lee; Julie T. Nguyen; Maura Barbisin; Nan Lan Xu; Vikram R. Mahuvakar; Mark R. Andersen; Kai Qin Lao; Kenneth J. Livak; Karl J. Guegler

    2005-01-01

    A novel microRNA (miRNA) quantification method has been developed using stem-loop RT followed by TaqMan PCR analysis. Stem-loop RT primers are better than conventional ones in terms of RT effici- ency and specificity. TaqMan miRNA assays are spe- cific for mature miRNAs and discriminate among related miRNAs that differ by as little as one nucleot- ide. Furthermore, they are not

  4. Nonscan design-for-testability techniques using RT-level design information

    Microsoft Academic Search

    Sujit Dey; Miodrag Potkonjak

    1997-01-01

    This paper presents nonscan design-for-testability (DFT) techniques applicable to register-transfer (RT)-level data path circuits. Knowledge of high-level design information, in the form of the RT-level structure, as well as the functions of the RT-level components is utilized to develop effective nonscan DFT techniques. Instead of conventional techniques of selecting flip-flops (FF's) to make controllable\\/observable, execution units (EXU's) are selected using

  5. Packetized voice transmission using RT-MAC, a wireless real-time medium access control protocol

    Microsoft Academic Search

    Rusty O. Baldwin; Nathaniel J. Davis IV; Scott F. Midkiff; Richard A. Raines

    2001-01-01

    RT-MAC is a simple, elegant, and robust medium access control (MAC) protocol for use in transmitting real-time data in point-to-point ad hoc wireless local area networks (WLANs). Our enhancement of IEEE 802.11, real-time MAC (RT-MAC), dramatically reduces missed deadlines and packet collisions while increasing throughput by selectively discarding packets and sharing station state information. For example, RT-MAC is able to

  6. RT_BUILD: An expert programmer for implementing and simulating Ada real-time control software

    NASA Technical Reports Server (NTRS)

    Lehman, Larry L.; Houtchens, Steve; Navab, Massoud; Shah, Sunil C.

    1986-01-01

    The RT BUILD is an expert control system programmer that creates real-time Ada code from block-diagram descriptions of control systems. Since RT BUILD embodies substantial knowledge about the implementation of real-time control systems, it can perform many, if not most of the functions normally performed by human real-time programmers. Though much basic research was done in automatic programming, RT BUILD appears to be the first application of this research to an important problem in flight control system development. In particular, RT BUILD was designed to directly increase productivity and reliability for control implementations of large complex systems.

  7. Sensitivity and reproducibility of standardized-competitive RT-PCR for transcript quantification and its comparison with real time RT-PCR

    PubMed Central

    Pagliarulo, Vincenzo; George, Ben; Beil, Stephen J; Groshen, Susan; Laird, Peter W; Cai, Jie; Willey, James; Cote, Richard J; Datar, Ram H

    2004-01-01

    Background Probe based detection assays form the mainstay of transcript quantification. Problems with these assays include varying hybridization efficiencies of the probes used for transcript quantification and the expense involved. We examined the ability of a standardized competitive RT-PCR (StaRT PCR) assay to quantify transcripts of 4 cell cycle associated genes (RB, E2F1, CDKN2A and PCNA) in two cell lines (T24 & LD419) and compared its efficacy with the established Taqman real time quantitative RT-PCR assay. We also assessed the sensitivity, reproducibility and consistency of StaRT PCR. StaRT PCR assay is based on the incorporation of competitive templates (CT) in precisely standardized quantities along with the native template (NT) in a PCR reaction. This enables transcript quantification by comparing the NT and CT band intensities at the end of the PCR amplification. The CT serves as an ideal internal control. The transcript numbers are expressed as copies per million transcripts of a control gene such as ?-actin (ACTB). Results The NT and CT were amplified at remarkably similar rates throughout the StaRT PCR amplification cycles, and the coefficient of variation was least (<3.8%) when the NT/CT ratio was kept as close to 1:1 as possible. The variability between the rates of amplification in different tubes subjected to the same StaRT PCR reaction was very low and within the range of experimental noise. Further, StaRT PCR was sensitive enough to detect variations as low as 10% in endogenous actin transcript quantity (p < 0.01 by the paired student's t-test). StaRT PCR correlated well with Taqman real time RT-PCR assay in terms of transcript quantification efficacy (p < 0.01 for all 4 genes by the Spearman Rank correlation method) and the ability to discriminate between cell types and confluence patterns. Conclusion StaRT PCR is thus a reliable and sensitive technique that can be applied to medium-high throughput quantitative transcript measurement. Further, it correlates well with Taqman real time PCR in terms of quantitative and discriminatory ability. This label-free, inexpensive technique may provide the ability to generate prognostically important molecular signatures unique to individual tumors and may enable identification of novel therapeutic targets. PMID:14741054

  8. DETECCIÓN CUANTITATIVA DEL VIRUS PSOROSIS DE CÍTRICOS MEDIANTE RT-PCR TIEMPO REAL QUANTITATIVE DIAGNOSIS OF CITRUS PSOROSIS VIRUS BY REAL TIME RT-PCR

    Microsoft Academic Search

    Gabriela Barragán-Valencia; Alberto Morales-Loredo; M. Genoveva Álvarez-Ojeda; M. Ángeles; Peña-del Río; Isela Quintero-Zapata; Manuel L. Barragán; Nuevo León

    2008-01-01

    Real time RT-PCR is useful for detecting citrus psorosis virus (CPsV) and also permits the evaluation of the viral concentration that can be used to study some aspects of the disease. In this study a protocol of real time RT-PCR was implemented for the quantitative detection of CPsV, for which a group of primers were designed along with a Taqman

  9. Spinal reirradiation after short-course RT for metastatic spinal cord compression

    SciTech Connect

    Rades, Dirk [Department of Radiation Oncology, University Hospital Hamburg-Eppendorf, Hamburg (Germany)]. E-mail: Rades.Dirk@gmx.net; Stalpers, Lukas J.A. [Department of Radiotherapy, Academic Medical Center, Amsterdam (Netherlands); Veninga, Theo [Department of Radiotherapy, Dr. Bernard Verbeeten Institute, Tilburg (Netherlands); Hoskin, Peter J. [Mount Vernon Centre for Cancer Treatment, Northwood, Middlesex (United Kingdom)

    2005-11-01

    Purpose: To investigate the feasibility and effectiveness of reirradiation (re-RT) for in-field recurrence of metastatic spinal cord compression after primary RT with 1 x 8 Gy or 5 x 4 Gy. Methods and Materials: A total of 62 patients, treated with 1 x 8 Gy (n = 34) or 5 x 4 Gy (n = 28) between January 1995 and August 2003, received re-RT for in-field recurrence of metastatic spinal cord compression. The median time to recurrence was 6 months (range, 2-40 months). Re-RT was performed with 1 x 8 Gy (after 1 x 8 Gy or 5 x 4 Gy, n = 34), 5 x 3 Gy (after 1 x 8 Gy or 5 x 4 Gy, n = 15), or 5 x 4 Gy (after 1 x 8 Gy, n = 13). The cumulative biologically effective dose (primary RT plus re-RT) was 80-100 Gy{sub 2}. The median follow-up after re-RT was 8 months (range, 2-42 months). Motor function was evaluated up to 6 months after re-RT. Results: After re-RT, 25 patients (40%) showed improvement of motor function, 28 (45%) had no change, and 9 (15%) had deterioration. Of the 16 previously nonambulatory patients, 6 (38%) regained the ability to walk. No second in-field recurrence in the same spinal region was observed after re-RT. The outcome was not significantly influenced by the radiation schedule. Radiation myelopathy was not observed. Conclusions: Spinal re-RT with 1 x 8 Gy, 5 x 3 Gy, or 5 x 4 Gy for in-field recurrence of metastatic spinal cord compression appears safe and effective. Myelopathy seems unlikely, if the cumulative biologically effective dose is {<=}100 Gy{sub 2}.

  10. Positional identification of RT1-B (HLA-DQ) as susceptibility locus for autoimmune arthritis.

    PubMed

    Haag, Sabrina; Tuncel, Jonatan; Thordardottir, Soley; Mason, Daniel E; Yau, Anthony C Y; Dobritzsch, Doreen; Bäcklund, Johan; Peters, Eric C; Holmdahl, Rikard

    2015-03-15

    Rheumatoid arthritis (RA) is associated with amino acid variants in multiple MHC molecules. The association to MHC class II (MHC-II) has been studied in several animal models of RA. In most cases these models depend on T cells restricted to a single immunodominant peptide of the immunizing Ag, which does not resemble the autoreactive T cells in RA. An exception is pristane-induced arthritis (PIA) in the rat where polyclonal T cells induce chronic arthritis after being primed against endogenous Ags. In this study, we used a mixed genetic and functional approach to show that RT1-Ba and RT1-Bb (RT1-B locus), the rat orthologs of HLA-DQA and HLA-DQB, determine the onset and severity of PIA. We isolated a 0.2-Mb interval within the MHC-II locus of three MHC-congenic strains, of which two were protected from severe PIA. Comparison of sequence and expression variation, as well as in vivo blocking of RT1-B and RT1-D (HLA-DR), showed that arthritis in these strains is regulated by coding polymorphisms in the RT1-B genes. Motif prediction based on MHC-II eluted peptides and structural homology modeling suggested that variants in the RT1-B P1 pocket, which likely affect the editing capacity by RT1-DM, are important for the development of PIA. PMID:25672758

  11. R.T. deSouza, Indiana University Learning about the nuclear symmetry energy

    E-print Network

    de Souza, Romualdo T.

    R.T. deSouza, Indiana University Learning about the nuclear symmetry energy through the lens of isospin transport Indiana University: K. Brown, S.Hudan, RdS Université Laval: M.-O. Frégeau, J. Gauthier, 054607 (2013); ... IsospinEquilibrationvariable #12;R.T. deSouza, Indiana University Isospin Transport

  12. R.T. deSouza, Indiana University Careers in Academia seminar UIUC

    E-print Network

    de Souza, Romualdo T.

    R.T. deSouza, Indiana University Careers in Academia seminar UIUC Acknowledgments ·Students who. of Sociology, Indiana University "Engendering change in the American Educational System with CALM" Outline advice #12;R.T. deSouza, Indiana University Careers in Academia seminar UIUC Only 26% scored high

  13. Thrombolytic efficacy and enzymatic activity of rt-PA-loaded echogenic liposomes.

    PubMed

    Bader, Kenneth B; Bouchoux, Guillaume; Peng, Tao; Klegerman, Melvin E; McPherson, David D; Holland, Christy K

    2015-08-01

    Echogenic liposomes (ELIP), that can encapsulate both recombinant tissue-type plasminogen activator (rt-PA) and microbubbles, are under development to improve the treatment of thrombo-occlusive disease. However, the enzymatic activity, thrombolytic efficacy, and stable cavitation activity generated by this agent has yet to be evaluated and compared to another established ultrasound-enhanced thrombolytic scheme. A spectrophotometric method was used to compare the enzymatic activity of the rt-PA incorporated into ELIP (t-ELIP) to that of rt-PA. An in vitro flow model was employed to measure the thrombolytic efficacy and dose of ultraharmonic emissions from stable cavitation for 120-kHz ultrasound exposure of three treatment schemes: rt-PA, rt-PA and the perfluorocarbon-filled microbubble Definity(®), and t-ELIP. The enzymatic activity of rt-PA incorporated into t-ELIP was 28 % that of rt-PA. Thrombolytic efficacy of t-ELIP or rt-PA and Definity(®) was equivalent when the dose of t-ELIP was adjusted to produce comparable enzymatic activity. Sustained bubble activity was nucleated from Definity but not from t-ELIP exposed to 120-kHz ultrasound. These results emphasize the advantages of encapsulating a thrombolytic and the importance of incorporating an insoluble gas required to promote sustained, stable cavitation activity. PMID:25829338

  14. Symbolic Execution of UML-RT State Machines Technical Report 2011-578

    E-print Network

    Graham, Nick

    Architect Real Time Edition (IBM RSA-RTE) [3]. RoseRT and RSA-RTE use UML-RT [31], a modeling language typically contain action code, i.e., code written in some programming language (IBM RSA-RTE supports C

  15. RT Level Power Analysis y Jianwen Zhu, Poonam Agrawal, Daniel D. Gajski

    E-print Network

    California at Irvine, University of

    RT Level Power Analysis y Jianwen Zhu, Poonam Agrawal, Daniel D. Gajski Department of Information approach, we present in this paper a power analysis technique which is analytical in nature. The rest as interconnections is discussed. Then we present the power analysis techniques at the RT level in Section 3. We

  16. Role-based Trust Management Security Policy Analysis and Correction Environment (RT-SPACE)

    E-print Network

    Niu, Jianwei

    Role-based Trust Management Security Policy Analysis and Correction Environment (RT-SPACE) Mark or position of the United States Air Force, Department of Defense, or the U.S. Gov- ernment. Copyright is held wwinsborough@acm.org ABSTRACT This paper presents RT-SPACE, a tool suite for authoring, verifying

  17. District-Level Considerations in Supporting and Sustaining RtI Implementation

    ERIC Educational Resources Information Center

    O'Connor, Edward P.; Freeman, Elizabeth Witter

    2012-01-01

    Although Response to Intervention (RtI) implementation efforts have been occurring in schools across the country for more than a decade, questions and concerns are emerging, as some schools are not observing significantly improved student achievement or behavior outcomes as expected. In the literature on RtI implementation, most authors indicate…

  18. Advances in Lecture Recognition: The ISL RT-06S Evaluation System Christian Fugen1

    E-print Network

    Schultz, Tanja

    Advances in Lecture Recognition: The ISL RT-06S Evaluation System Christian F¨ugen1 , Matthias W lecture recognition system devel- oped at the Interactive Systems Laboratories (ISL), for individual head recognition, lectures, distant speech, CHIL, RT-06S. 1. Introduction In this paper, we present the ISL's most

  19. Preclinical and early clinical development of GNbAC1, a humanized IgG4 monoclonal antibody targeting endogenous retroviral MSRV-Env protein.

    PubMed

    Curtin, François; Perron, Hervé; Kromminga, Arno; Porchet, Hervé; Lang, Alois B

    2015-01-01

    Monoclonal antibodies (mAbs) play an increasing important role in the therapeutic armamentarium against multiple sclerosis (MS), an inflammatory and degenerative disorder of the central nervous system. Most of the mAbs currently developed for MS are immunomodulators blocking the inflammatory immune process. In contrast with mAbs targeting immune function, GNbAC1, a humanized IgG4 mAb, targets the multiple sclerosis associated retrovirus envelope (MSRV-Env) protein, an upstream factor in the pathophysiology of MS. MSRV-Env protein is of endogenous retroviral origin, expressed in MS brain lesions, and it is pro-inflammatory and toxic to the remyelination process, by preventing the differentiation of oligodendrocyte precursor cells. We present the preclinical and early clinical development results of GNbAC1. The specificity of GNbAC1 for its endogenous retroviral target is described. Efficacy of different mAb versions of GNbAC1 were assessed in MSRV-Env induced experimental allergic encephalitis (EAE), an animal model of MS. Because the target MSRV-Env is not expressed in animals, no relevant animal model exists for a proper in vivo toxicological program. An off-target 2-week toxicity study in mice was thus performed, and it showed an absence of safety risk. Additional in vitro analyses showed an absence of complement or antibody-dependent cytotoxicity as well as a low level of cross-reactivity to human tissues. The first-in-man clinical study in 33 healthy subjects and a long-term clinical study in 10 MS patients showed that GNbAC1 is well tolerated in humans without induction of immunogenicity and that it induces a pharmacodynamic response on MSRV biomarkers. These initial results suggest that the mAb GNbAC1 could be a safe long-term treatment for patients with MS with a unique therapeutic mechanism of action. PMID:25427053

  20. Anti-P30-52 monoclonal antibody cross-reacted to Env V3 and inhibited the viral multiplication of HIV-1-infected MT-4 cells.

    PubMed

    Ota, A; Bautista, A N; Yadav, M L; Ueda, S

    1999-04-01

    It is well known that the anti-p17 antibody titer decreases with the disease progression among human immunodeficiency virus type 1 (HIV-1) carriers. We previously established several murine anti-p17 monoclonal antibodies (MAbs) to investigate the immunological role of p17, and to further characterize these MAbs, we examined the anti-p17 antibody titer in serum of a patient who was a long-term nonprogressor with hemophilia, and found that the antibody for the p17-derivative peptide from amino acid residues 30 to 52 (P30-52) cross-reacted to the third variable region of the envelope glycoprotein of HIV-1, Env V3. In the present study, we primed mice with P30-52 to establish anti-P30-52 MAbs (P30-52 MAbs), and examined their affinity and whether they suppressed the viral multiplication of HIV-1-infected MT-4 (HTLV-1-transformed CD4+ T-cell line) cells, in a TCID50 assay. At the same time, an anti-Env V3 MAb (Env V3 MAb) was also established and examined as above. The IgM-type P30-52 MAb and Env V3 MAb showed heteroclitic binding, and the IgM-type P30-52 MAb inhibited the viral multiplication. We also found that an increase of fragmented DNA of HIV-1-infected MT-4 cells co-cultured with P30-52 MAbs. Because DNA fragmentation is one of the features of programmed cell death, the viral multiplication may be suppressed by the apoptosis of HIV-1-infected MT-4 cells co-cultured with P30-52 MAbs. Though the relationship between cross-reactivity and the inhibition mechanism of multiplication of HIV-1 is unclear, P30-52 of p17 may well be a useful region of viral proteins for the development of therapeutic and vaccination strategies. PMID:10380013

  1. Low pH Is Required for Avian Sarcoma and Leukosis Virus Env-Induced Hemifusion and Fusion Pore Formation but Not for Pore Growth

    Microsoft Academic Search

    G. B. Melikyan; R. J. O. Barnard; R. M. Markosyan; J. A. T. Young; F. S. Cohen

    2004-01-01

    Binding of avian sarcoma and leukosis virus (ASLV) to its cognate receptor on the cell surface causes conformational changes in its envelope protein (Env). It is currently debated whether low pH is required for ASLV infection. To elucidate the role of low pH, we studied the association between ASLV subgroup B (ASLV-B) and liposomes and fusion between effector cells expressing

  2. SLN # PMP SEC COURSE DAY/TIME INSTRUCTOR CR 100 A 21st Century Civil and Env Eng T 230-320 TBA 1

    E-print Network

    SLN # PMP SEC COURSE DAY/TIME INSTRUCTOR CR 100 A 21st Century Civil and Env Eng T 230-320 TBA 1 of Materials Th 830-1020 * 220 AF Intro to Mechanics of Materials Th 10:30-1220 297 A Foreign Study (IS) TBA 3-5 299 A Independent Project TBA 1-5 Junior 307 A Construction Engineering TThF 1030-1220 Muench 5 327

  3. Comparative Efficacy of Recombinant Modified Vaccinia Virus Ankara Expressing Simian Immunodeficiency Virus (SIV) Gag-Pol and/or Env in Macaques Challenged with Pathogenic SIV

    PubMed Central

    Ourmanov, Ilnour; Brown, Charles R.; Moss, Bernard; Carroll, Miles; Wyatt, Linda; Pletneva, Liuobov; Goldstein, Simoy; Venzon, David; Hirsch, Vanessa M.

    2000-01-01

    Prior studies demonstrated that immunization of macaques with simian immunodeficiency virus (SIV) Gag-Pol and Env recombinants of the attenuated poxvirus modified vaccinia virus Ankara (MVA) provided protection from high levels of viremia and AIDS following challenge with a pathogenic strain of SIV (V. M. Hirsch et al., J. Virol. 70:3741–3752, 1996). This MVA-SIV recombinant expressed relatively low levels of the Gag-Pol portion of the vaccine. To optimize protection, second-generation recombinant MVAs that expressed high levels of either Gag-Pol (MVA-gag-pol) or Env (MVA-env), alone or in combination (MVA-gag-pol-env), were generated. A cohort of 24 macaques was immunized with recombinant or nonrecombinant MVA (four groups of six animals) and was challenged with 50 times the dose at which 50% of macaques are infected with uncloned pathogenic SIVsmE660. Although all animals became infected postchallenge, plasma viremia was significantly reduced in animals that received the MVA-SIV recombinant vaccines as compared with animals that received nonrecombinant MVA (P = 0.0011 by repeated-measures analysis of variance). The differences in the degree of virus suppression achieved by the three MVA-SIV vaccines were not significant. Most importantly, the reduction in levels of viremia resulted in a significant increase in median (P < 0.05 by Student's t test) and cumulative (P = 0.010 by log rank test) survival. These results suggest that recombinant MVA has considerable potential as a vaccine vector for human AIDS. PMID:10684290

  4. OmpR and EnvZ are pleiotropic regulatory proteins: Positive regulation of the tripeptide permease ( tppB ) of Salmonella typhimurium

    Microsoft Academic Search

    M. M. Gibson; E. M. Ellis; K. A. Graeme-Cook; C. F. Higgins

    1987-01-01

    The tppB locus of Salmonella typhimurium encodes the anaerobically-induced tripeptide permease. We have demonstrated that expression of tppB requires the function of the ompR and envZ gene products, originally identified as positive regulatory proteins required for the osmotic regulation of porin expression. Significantly, tppB expression is not osmotically regulated. We have also identified three additional genes whose expression depends on

  5. Potential Utility of the Real-Time TMPA-RT Precipitation Estimates in Streamflow Prediction

    NASA Technical Reports Server (NTRS)

    Su, Fengge; Gao, Huilin; Huffman, George J.; Lettenmaier, Dennis P.

    2010-01-01

    We investigate the potential utility of the real-time Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis (TMPA-RT) data for streamflow prediction, both through direct comparisons of TMPA-RT estimates with a gridded gauge product, and through evaluation of streamflow simulations over four tributaries of La Plata Basin (LPB) in South America using the two precipitation products. Our assessments indicate that the relative accuracy and the hydrologic performance of TMPA-RT-based streamflow simulations generally improved after February 2005. The improvements in TMPA-RT since 2005 are closely related to upgrades in the TMPA-RT algorithm in early February, 2005 which include use of additional microwave sensors (AMSR-E and AMSU-B) and implementation of different calibration schemes. Our work suggests considerable potential for hydrologic prediction using purely satellite-derived precipitation estimates (no adjustments by in situ gauges) in parts of the globe where in situ observations are sparse.

  6. Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization

    PubMed Central

    Khorchid, Ahmad; Inouye, Masayori; Ikura, Mitsuhiko

    2004-01-01

    Escherichia coli EnvZ is a membrane sensor histidine kinase that plays a pivotal role in cell adaptation to changes in extracellular osmolarity. Although the cytoplasmic histidine kinase domain of EnvZ has been extensively studied, both biochemically and structurally, little is known about the structure of its periplasmic domain, which has been implicated in the mechanism underlying its osmosensing function. In the present study, we report the biochemical and biophysical characterization of the periplasmic region of EnvZ (Ala38–Arg162). This region was found to form a dimer in solution, and to consist of two well-defined domains: an N-terminal ?-helical domain and a C-terminal core domain (Glu83–Arg162) containing both ?-helical and ?-sheet secondary structures. Our pull-down assays and analytical ultracentrifugation analysis revealed that dimerization of the periplasmic region is highly sensitive to the presence of CHAPS, but relatively insensitive to salt concentration, thus suggesting the significance of hydrophobic interactions between the homodimeric subunits. Periplasmic homodimerization is mediated predominantly by the C-terminal core domain, while a regulatory function may be attributed mainly to the N-terminal ?-helical domain, whose mutations have been shown previously to produce a high-osmolarity phenotype. PMID:15357641

  7. Loss of antigenic epitopes as the result of env gene recombination in retrovirus-induced leukemia in immunocompetent mice.

    PubMed

    Tumas, K M; Poszgay, J M; Avidan, N; Ksiazek, S J; Overmoyer, B; Blank, K J; Prystowsky, M B

    1993-02-01

    The murine leukemia virus, E-55+ virus, induces a thymic lymphoma/leukemia in 100% of BALB.K mice infected as adults after a latent period of 4 months or more (Pozsgay et al., Virology 173, 330-334, 1989). Two molecular clones of virus designated E-55+ and E-55- based on their ability to encode the E-55 epitope detected by the monoclonal antibody 55 (mAb 55) were isolated from a leukemic BALB.K mouse inoculated with a biologically cloned E-55+ virus (Chesebro et al., Virology 112, 131-144, 1981). Env gene sequence analysis of E-55+ and E-55- clones showed that the E-55- virus was generated from the E-55+ virus as the result of a recombination between E-55+ virus and the endogenous ecotropic virus, emv-1, carried in the genome of the BALB.K mouse strain. The recombinant E-55- virus is replication competent. This recombination event and the consequential expression of E-55- virus consistently occur in immunocompetent BALB.K mice inoculated with the E-55+ virus and appear to play a role in the loss of epitopes recognized by virus neutralizing antibodies. The loss of these epitopes apparently allows the virus to evade the host immune response. PMID:7678475

  8. No difference in Gag and Env immune-response profiles between vaccinated and non-vaccinated rhesus macaques that control immunodeficiency virus replication.

    PubMed

    Nieuwenhuis, Ivonne; Beenhakker, Niels; Bogers, Willy M J M; Otting, Nel; Bontrop, Ronald E; Dubois, Patrice; Mooij, Petra; Heeney, Jonathan L; Koopman, Gerrit

    2010-12-01

    Recent advances in human immunodeficiency virus (HIV) vaccine design have resulted in induction of strong CD4 T-cell proliferative and polyfunctional cytokine responses, which are also characteristic for long-term non-progressing (LTNP) HIV-infected individuals. However, limited information is available on the persistence of these responses after infection. Results from studies in non-human primates indicate that vaccine-induced immune responses are partially maintained upon viral infection and differ from the responses seen in non-vaccinated animals that typically progress to disease. However, it is unclear how these partially preserved responses compare to immune responses that are acquired naturally by LTNP animals. In this study, immune-response profiles were compared between vaccinated animals that, upon SHIV??.? challenge, became infected but were able to control virus replication, and a group of animals having spontaneous control of this viral infection. Both groups were found to develop very similar immune responses with regard to induction of CD4 and CD8 T-cell polyfunctional cytokine responses, proliferative capacity and cytotoxic capacity, as measured by a standard ??Cr release assay and more direct ex vivo and in vivo CTL assays. Hence, vaccinated animals that become infected, but control infection, appear to establish immune responses that are similar to those elicited by long-term non-progressors. PMID:20826621

  9. Development of RT-components for the M-3 Strawberry Harvesting Robot

    NASA Astrophysics Data System (ADS)

    Yamashita, Tomoki; Tanaka, Motomasa; Yamamoto, Satoshi; Hayashi, Shigehiko; Saito, Sadafumi; Sugano, Shigeki

    We are now developing the strawberry harvest robot called “M-3” prototype robot system under the 4th urgent project of MAFF. In order to develop the control software of the M-3 robot more efficiently, we innovated the RT-middleware “OpenRTM-aist” software platform. In this system, we developed 9 kind of RT-Components (RTC): Robot task sequence player RTC, Proxy RTC for image processing software, DC motor controller RTC, Arm kinematics RTC, and so on. In this paper, we discuss advantages of RT-middleware developing system and problems about operating the RTC-configured robotic system by end-users.

  10. ISSN0249-0803ISRNINRIA/RT--0439--FR+ENG Project-Teams PANAMA and

    E-print Network

    Paris-Sud XI, Université de

    ISSN0249-0803ISRNINRIA/RT--0439--FR+ENG TECHNICAL REPORT N° 0439 July 2013 Project-Teams PANAMA , Frédéric Bimbot § Project-Teams PANAMA and TEXMEX Technical Report n° 0439 -- version 2¶ -- initial version

  11. Transition and Evaluation of RGB Imagery to WFOs and National Centers by NASA SPoRT

    NASA Technical Reports Server (NTRS)

    Fuell, Kevin K.; Molthan, Andrew L.

    2012-01-01

    MODIS Snow/Cloud and True Color RGB imagery has been used by SPoRT partners since 2004 to examine changes in surface features such as snow cover, vegetation, ocean color, fires, smoke plumes, and oil spills.

  12. ISSN0249-0803ISRNINRIA/RT--0418--FR+ENG November 2011

    E-print Network

    Boyer, Edmond

    ISSN0249-0803ISRNINRIA/RT--0418--FR+ENG TECHNICAL REPORT N° 0418 November 2011 Project-Teams MOAIS Danjean Project-Teams MOAIS Technical Report n° 0418 -- November 2011 -- 45 pages Abstract: In this report

  13. Aerobic and Resistance Training Effects on Energy Intake: The STRRIDE AT/RT Study

    PubMed Central

    Bales, Connie W.; Hawk, Victoria H.; Granville, Esther O.; Rose, Sarah B.; Shields, Tamlyn; Bateman, Lori; Willis, Leslie; Piner, Lucy; Slentz, Cris A.; Houmard, Joseph A.; Gallup, Dianne; Samsa, Greg P.; Kraus, William E.

    2012-01-01

    Purpose Our study characterizes food and energy intake responses to long-term aerobic (AT) and resistance training (RT) during a controlled 8-month trial. Methods In the STRRIDE AT/RT trial, overweight/obese sedentary dyslipidemic men and women were randomized to AT (n = 39), RT (n = 38), or a combined treatment (AT/RT; n = 40) without any advice to change their food intakes. Quantitative food intake assessments (QDI) and food frequency questionnaires (FFQ) were collected at baseline (BEF) and after 8 mo. training (END); body mass (BM) and fat free mass (FFM) were also assessed. Results In AT and AT/RT, respectively, meaningful decreases in reported energy intake (REI) (?217 and ?202 kcal; p < 0.001) and in intakes of fat (?14.9 and ?14.9 g; p < 0.001, p = 0.004), protein (?8.3 and ?10.7 g; p = 0.002, p < 0.001), and carbohydrate (?28.1 and ?14.7 g; p = 0.001, p = 0.030) were found by FFQ. REI relative to FFM decreased (p < 0.001 and p=0.002) as did intakes of fat (?0.2 and ?0.3 g; p = 0.003 and p = 0.014) and protein (?0.1 and ?0.2 g; p = 0.005 and p < 0.001) in AT and AT/RT and carbohydrate (?0.5 g; p<0.003) in AT only. For RT, REI by QDI decreased (?3.0 kcal/kg FFM; p=0.046), as did fat intake (?0.2 g; p = 0.033). BM decreased in AT (?1.3 kg, p=0.006) and AT/RT (?1.5 kg, p = 0.001) but was unchanged (0.6 kg, p = 0.176) in RT. Conclusions Previously sedentary subjects completing 8 months of AT or AT/RT reduced their intakes of kcal and macronutrients and BM. In RT, fat intakes and REI (when expressed per FFM) decreased, BM was unchanged, and FFM increased. PMID:22525775

  14. Generation and Evaluation of Clade C Simian-Human Immunodeficiency Virus Challenge Stocks

    PubMed Central

    Chang, Hui-Wen; Tartaglia, Lawrence J.; Whitney, James B.; Lim, So-Yon; Sanisetty, Srisowmya; Lavine, Christy L.; Seaman, Michael S.; Rademeyer, Cecelia; Williamson, Carolyn; Ellingson-Strouss, Katharine; Stamatatos, Leonidas; Kublin, James

    2014-01-01

    ABSTRACT The development of a panel of mucosally transmissible simian-human immunodeficiency virus (SHIV) challenge stocks from multiple virus clades would facilitate preclinical evaluation of candidate HIV-1 vaccines and therapeutics. The majority of SHIV stocks that have been generated to date have been derived from clade B HIV-1 env sequences from viruses isolated during chronic infection and typically required serial animal-to-animal adaptation for establishing mucosal transmissibility and pathogenicity. To capture essential features of mucosal transmission of clade C viruses, we produced a series of SHIVs with early clade C HIV-1 env sequences from acutely HIV-1-infected individuals from South Africa. SHIV-327c and SHIV-327cRM expressed env sequences that were 99.7 to 100% identical to the original HIV-1 isolate and did not require in vivo passaging for mucosal infectivity. These challenge stocks infected rhesus monkeys efficiently by both intrarectal and intravaginal routes, replicated to high levels during acute infection, and established chronic setpoint viremia in 13 of 17 (76%) infected animals. The SHIV-327cRM challenge stock was also titrated for both single, high-dose intrarectal challenges and repetitive, low-dose intrarectal challenges in rhesus monkeys. These SHIV challenge stocks should facilitate the preclinical evaluation of vaccines and other interventions aimed at preventing clade C HIV-1 infection. IMPORTANCE We describe the development of two related clade C SHIV challenge stocks. These challenge stocks should prove useful for preclinical testing of vaccines and other interventions aimed at preventing clade C HIV-1 infection. PMID:25473043

  15. The T Cell Marker RT6 in A Rat Model of Autoimmune Diabetes

    Microsoft Academic Search

    Dale L. Greiner; Samir Malkani; Toshihiro Kanaitsuka; Rita Bortell; John Doukas; Mark Rigby; Barbara Whalen; Linda A. Stevens; Joel Moss; John P. Mordes; Aldo A. Rossini

    \\u000a The RT6 alloantigenic system of the rat was discovered in the 1970s. It was originally designated Pta, AgF, A.R.T.-2, and\\u000a RTLy-2 by the laboratories involved in its characterization. Exchange of reagents demonstrated that these laboratories had\\u000a identified the same system, and the official designation RT6 was assigned in 1982 (1).

  16. Multiplex RT-PCR detection and microarray typing of vesicular disease viruses

    Microsoft Academic Search

    Oliver Lung; Mathew Fisher; Anne Beeston; Kimberley Burton Hughes; Alfonso Clavijo; Melissa Goolia; John Pasick; William Mauro; Dirk Deregt

    2011-01-01

    A vesicular disease multiplex reverse transcription (RT)-PCR with an accompanying microarray assay was developed for simultaneous detection and typing of foot-and-mouth disease virus (FMDV) and vesicular stomatitis virus (VSV), and for the detection of swine vesicular disease virus (SVDV) and vesicular exanthema of swine virus (VESV). The multiplex RT-PCR successfully detected viral RNA from a collection of 49 strains of

  17. Family 10 and 11 xylanase genes from Caldicellulosiruptor sp. strain Rt69B.1

    Microsoft Academic Search

    Daniel D. Morris; Moreland D. Gibbs; Michelle Ford; Justin Thomas; Peter L. Bergquist

    1999-01-01

    Three family 10 xylanase genes (xynA, xynB, and xynC) and a single family 11 xylanase gene (xynD) were identified from the extreme thermophile Caldicellulosiruptor strain Rt69B.1 through the use of consensus PCR in conjunction with sequencing and polyacrylamide gel electrophoresis. These\\u000a genes appear to comprise the complete endoxylanase system of Rt69B.1. The xynA gene was found to be homologous to

  18. Family 10 and 11 xylanase genes from Caldicellulosiruptor sp. strain Rt69B.1.

    PubMed

    Morris, D D; Gibbs, M D; Ford, M; Thomas, J; Bergquist, P L

    1999-05-01

    Three family 10 xylanase genes (xynA, xynB, and xynC) and a single family 11 xylanase gene (xynD) were identified from the extreme thermophile Caldicellulosiruptor strain Rt69B.1 through the use of consensus PCR in conjunction with sequencing and polyacrylamide gel electrophoresis. These genes appear to comprise the complete endoxylanase system of Rt69B.1. The xynA gene was found to be homologous to the xynA gene of the closely related Caldicellulosiruptor strain Rt8B.4, and primers designed previously to amplify the Rt8B.4 xynA gene could amplify homologous full-length xynA gene fragments from Rt69B.1. The complete nucleotide sequences of the Rt69B.1 xynB, xynC, and xynD genes were obtained using genomic walking PCR. The full-length xynB and xynC genes are more than 5 kb in length and encode highly modular enzymes that are the largest xylanases reported to date. XynB has an architecture similar to the family 10 xylanases from Thermoanaerobacterium saccharolyticum (XynA) and Clostridium thermocellum (XynX) and may be cell wall associated, while XynC is a bifunctional enzyme with an architecture similar to the bifunctional beta-glycanases from Caldicellulosiroptor saccharolyticus. The xynD gene encodes a two-domain family 11 xylanase that is identical in architecture to the XynB family 11 xylanase from the unrelated extreme thermophile Dictyoglomus thermophilum strain Rt46B.1. The sequence similarities between the Rt69B.1 xylanases with respect to their evolution are discussed. PMID:10356996

  19. RT-IPC: An IPC Extension for Real-Time Mach

    Microsoft Academic Search

    Takuro Kitayama; Hideyuki Tokuda; Tatsuo Nakajima

    1993-01-01

    Interprocess communication (IPC) provides the fundamental mechanism for the Machmicrokernel to be extensible and flexible. Mach IPC provides efficient communicationmechanisms for many applications. However, it does not provide sufficient functionalityfor real-time applications which have rigid timing constraints among threads. In RealTimeMach (RT-Mach), we have extended Mach IPC to be priority inversion free forreal-time applications.This paper describes the Real-Time IPC (RT-IPC)...

  20. An economic evaluation of rt-PA locking solution in dialysis catheters.

    PubMed

    Manns, Braden J; Scott-Douglas, Nairne; Tonelli, Marcello; Ravani, Pietro; LeBlanc, Martine; Dorval, Marc; Holden, Rachel; Moist, Louise; Lok, Charmaine; Zimmerman, Deborah; Au, Flora; Hemmelgarn, Brenda R

    2014-12-01

    In a recent randomized trial, weekly recombinant tissue plasminogen activator (rt-PA), 1 mg per lumen, once per week, and twice-weekly heparin as a locking solution (rt-PA/heparin) resulted in lower risks of hemodialysis catheter malfunction and catheter-related bacteremia compared with thrice-weekly heparin (heparin alone). We collected detailed costs within this trial to determine how choice of locking solution would affect overall health care costs, including the cost of locking solutions and all other relevant medical costs over the course of the 6-month trial. Nonparametric bootstrap estimates were used to derive 95% confidence intervals (CIs) and mean cost differences between the treatment groups. The cost of the locking solution was higher in patients receiving rt-PA/heparin, but this was partially offset by lower costs for managing complications. Overall, the difference in unadjusted mean cost for managing patients with rt-PA/heparin versus heparin alone was Can$323 (95% CI, -$935 to $1581; P=0.62). When the costs were extrapolated over a 1-year time horizon using decision analysis, assuming ongoing rt-PA effectiveness, the overall costs of the strategies were similar. This finding was sensitive to plausible variation in the frequency and cost of managing patients with catheter-related bacteremia, and whether the benefit of rt-PA on catheter-related bacteremia was maintained in the long term. In summary, we noted no significant difference in the mean overall cost of an rt-PA/heparin strategy as a locking solution for catheters compared with thrice-weekly heparin. Cost savings due to a lower risk of hospitalization for catheter-related bacteremia partially offset the increased cost of rt-PA. PMID:25012176

  1. Evaluation of several RT-PCR primer pairs for the detection of Apple stem pitting virus.

    PubMed

    Komorowska, B; Malinowski, T; Michalczuk, L

    2010-09-01

    Detection of Apple stem pitting virus (ASPV) using RT-PCR based methods was studied in infected apple and pear trees. Three virus-specific primers (ASPF1CP, ASPF2CP, ASPR3CP) were designed to target the most conservative regions of the coat protein gene of 10 virus isolates in Poland and 7 other ASPV sequences available in GenBank. The suitability of the primer pairs ASPF1CP-ASPR3CP and ASPF2CP-ASPR3CP for detection of 19 virus isolates was checked. Both new primer pairs initiated amplification of a specific product from all sources tested. From 1 to 11 isolates were not detected with the primer sets published previously. Detection of the virus in the samples collected in March, using ASPF1CP-ASPR3CP primer pair, was possible up to 512 times dilution. For the samples collected in July, virus was detected in the extracts from infected plants diluted eight times. More than 100-fold increase of sensitivity could be obtained by semi-nested PCR with primers ASPF2CP-ASPR3CP following the first round with ASPF1CP-ASPR3CP. Identification of virus isolates with different number of deletions in the coat protein gene was possible using RT-PCR with newly designed reverse primer ASPDEL in combination with the published primer ASPV7956. Besides, the comparative analysis of silicacapture-RT-PCR (SC-RT-PCR) versus immunocapture-RT-PCR (IC-RT-PCR) assays was carried out. Few ASPV isolates escaped detection by IC-RT-PCR, while all isolates tested were detected using the SC-RT-PCR with the new primers. PMID:20447421

  2. Short-Term Prediction Research and Transition (SPoRT) Center: Transitioning Satellite Data to Operations

    NASA Technical Reports Server (NTRS)

    Zavodsky, Bradley

    2012-01-01

    The Short-term Prediction Research and Transition (SPoRT) Center located at NASA Marshall Space Flight Center has been conducting testbed activities aimed at transitioning satellite products to National Weather Service operational end users for the last 10 years. SPoRT is a NASA/NOAA funded project that has set the bar for transition of products to operational end users through a paradigm of understanding forecast challenges and forecaster needs, displaying products in end users decision support systems, actively assessing the operational impact of these products, and improving products based on forecaster feedback. Aiming for quality partnerships rather than a large quantity of data users, SPoRT has become a community leader in training operational forecasters on the use of up-and-coming satellite data through the use of legacy instruments and proxy data. Traditionally, SPoRT has supplied satellite imagery and products from NASA instruments such as the Moderate-resolution Imaging Spectroradiometer (MODIS) and the Atmospheric Infrared Sounder (AIRS). However, recently, SPoRT has been funded by the GOES-R and Joint Polar Satellite System (JPSS) Proving Grounds to accelerate the transition of selected imagery and products to help improve forecaster awareness of upcoming operational data from the Visible Infrared Imager Radiometer Suite (VIIRS), Cross-track Infrared Sounder (CrIS), Advanced Baseline Imager (ABI), and Geostationary Lightning Mapper (GLM). This presentation provides background on the SPoRT Center, the SPoRT paradigm, and some example products that SPoRT is excited to work with forecasters to evaluate.

  3. Detection of Banana mild mosaic virus and Banana virus X by polyvalent degenerate oligonucleotide RT-PCR (PDO-RT-PCR).

    PubMed

    Teycheney, Pierre-Yves; Acina, Isabelle; Lockhart, Benham E L; Candresse, Thierry

    2007-06-01

    Viruses are important constraints to the movement and propagation of plant germplasm, especially for vegetatively propagated crops such as banana and plantain. Their control relies primarily on the use of virus-free plant material, whose production and certification requires sensitive and reliable detection methods. An existing polyvalent degenerate oligonucleotide RT-PCR (PDO-RT-PCR) assay was adapted to the detection of Banana mild mosaic virus (BanMMV) and Banana virus X, two Flexiviridae infecting Musa spp. PDO inosine-containing primers were found to be well suited to the detection of BanMMV, despite its high molecular diversity, but not to that of the highly conserved BVX, for which species-specific primers were designed. Sampling and sample processing steps were optimized in order to avoid nucleic acid purification prior to the reverse transcription step. A polyclonal anti-BanMMV antiserum was raised and successfully used for the immunocapture (IC) of BanMMV viral particles from leaf extracts, leading to the development of a PDO-IC-RT-nested PCR assay. Although the anti-BanMMV antiserum could to some extent recognize BVX viral particles, direct binding (DB) was shown to be a more efficient method for processing BVX-infected samples and a PDO-DB-RT-nested PCR assay was developed for the detection of BVX from leaf extracts. PMID:17280722

  4. Natural and Enhanced Attenuation of Chlorinated Solvents Using RT3D

    SciTech Connect

    Johnson, Christian D.; Truex, Michael J.; Clement, T P.

    2006-07-25

    RT3D (Reactive Transport in 3-Dimensions) is a reactive transport code that can be applied to model solute fate and transport for many different purposes. This document specifically addresses application of RT3D for modeling related to evaluation and implementation of Monitored Natural Attenuation (MNA). Selection of MNA as a remedy requires an evaluation process to demonstrate that MNA will meet the remediation goals. The U.S. EPA, through the Office of Solid Waste and Emergency Response (OSWER) Directive 9200.4?17P, provides the regulatory context for the evaluation and implementation of MNA. In a complementary fashion, the context for using fate and transport modeling as part of MNA evaluation is described in the EPA?s technical protocol for chlorinated solvent MNA, the Scenarios Evaluation Tool for Chlorinated Solvent MNA, and in this document. The intent of this document is to describe (1) the context for applying RT3D for chlorinated solvent MNA and (2) the attenuation processes represented in RT3D, (3) dechlorination reactions that may occur, and (4) the general approach for using RT3D reaction modules (including a summary of the RT3D reaction modules that are available) to model fate and transport of chlorinated solvents as part of MNA or for combinations of MNA and selected types of active remediation.

  5. Performance of an RT-nested PCR ELISA for detection of Newcastle disease virus.

    PubMed

    Kho, C L; Mohd-Azmi, M L; Arshad, S S; Yusoff, K

    2000-04-01

    A sensitive and specific RT-nested PCR coupled with an ELISA detection system for detecting Newcastle disease virus is described. Two nested pairs of primer which were highly specific to all the three different pathotypes of NDV were designed from the consensus fusion gene sequence. No cross-reactions with other avian infectious agents such as infectious bronchitis virus, infectious bursal disease virus, influenza virus, and fowl pox virus were observed. Based on agarose electrophoresis detection, the RT-nested PCR was about 100 times more sensitive compared to that of a non-nested RT-PCR. To facilitate the detection of the PCR product, an ELISA detection method was then developed to detect the amplified PCR products and it was shown to be ten times more sensitive than gel electrophoresis. The efficacy of the nested PCR-ELISA was also compared with the conventional NDV detection method (HA test) and non-nested RT-PCR by testing against a total of 35 tissue specimens collected from ND-symptomatic chickens. The RT-nested PCR ELISA found NDV positive in 21 (60%) tissue specimens, while only eight (22.9%) and two (5.7%) out of 35 tissue specimens were tested NDV positive by both the non-nested RT-PCR and conventional HA test, respectively. Due to its high sensitivity for the detection of NDV from tissue specimens, this PCR-ELISA based diagnostic test may be useful for screening large number of samples. PMID:10713378

  6. The SPoRT-WRF: Evaluating the Impact of NASA Datasets on Convective Forecasts

    NASA Technical Reports Server (NTRS)

    Zavodsky, Bradley; Kozlowski, Danielle; Case, Jonathan; Molthan, Andrew

    2012-01-01

    Short-term Prediction Research and Transition (SPoRT) seeks to improve short-term, regional weather forecasts using unique NASA products and capabilities SPoRT has developed a unique, real-time configuration of the NASA Unified Weather Research and Forecasting (WRF)WRF (ARW) that integrates all SPoRT modeling research data: (1) 2-km SPoRT Sea Surface Temperature (SST) Composite, (2) 3-km LIS with 1-km Greenness Vegetation Fraction (GVFs) (3) 45-km AIRS retrieved profiles. Transitioned this real-time forecast to NOAA's Hazardous Weather Testbed (HWT) as deterministic model at Experimental Forecast Program (EFP). Feedback from forecasters/participants and internal evaluation of SPoRT-WRF shows a cool, dry bias that appears to suppress convection likely related to methodology for assimilation of AIRS profiles Version 2 of the SPoRT-WRF will premier at the 2012 EFP and include NASA physics, cycling data assimilation methodology, better coverage of precipitation forcing, and new GVFs

  7. strt ts r sr stst rt t s s s r t ssts t rts r ss

    E-print Network

    Boyer, Edmond

    P P strt ts r sr stst rt t s s s r t ssts t rts r ss ttsttrtssttstrts rts s t s s t r sttrs ts rts r rt t st s r t st t s s rt rstrt tqs t rt t t r r t st t s r rt s tst r s t rs s t strt r r s s t r r s t s srt P ts r r rs s r t s s t t t r t st t trt s r r

  8. Cross-reactivity of anti-HIV-1-p17-derivative peptide (P30-52) antibody to Env V3 peptide.

    PubMed

    Ota, A; Tanaka-Taya, K; Ueda, S

    1999-04-01

    Strong antibody responses are often seen in human immunodeficiency virus type 1 (HIV-1) carriers, but it is not known whether these antibodies are effective in the inhibition of disease progression. In this study, we examined antigenic epitopes for anti-HIV-1 p17 antibody (p17 Ab) in an HIV-1 carrier's serum, and found that the residues of amino acid numbers 1 to 12 (P1-12), 12 to 29 (P12-29) and 30 to 52 (P30-52) of p17 were highly recognized in the serum. Our examination of purified antibodies from the patient using the p17-derivative-peptide-immunoaffinity columns showed that the reactivity of anti-p30-52 Ab (p30-52Ab) was high for p30-52 and the naive protein, p17. In addition, this P30-52Ab cross-reacted with the third variable region of the envelope glycoprotein (Env V3). To confirm this cross-reactivity, we immunized mice with P30-52, and established a monoclonal antibody (MAb), 8H10. We found that 8H10 was also reactive to Env V3. It is unclear whether this cross-reactivity of P30-52 Ab can function as the inhibitor of HIV-1, but these results will be of help in clarifying the interaction of Env protein with HIV-1 gag polyprotein and the relationship of the decline of the p17 antibody titer with the disease progression in HIV-1 carriers. PMID:10380014

  9. An adenovirus-simian immunodeficiency virus env vaccine elicits humoral, cellular, and mucosal immune responses in rhesus macaques and decreases viral burden following vaginal challenge.

    PubMed Central

    Buge, S L; Richardson, E; Alipanah, S; Markham, P; Cheng, S; Kalyan, N; Miller, C J; Lubeck, M; Udem, S; Eldridge, J; Robert-Guroff, M

    1997-01-01

    Six female rhesus macaques were immunized orally and intranasally at 0 weeks and intratracheally at 12 weeks with an adenovirus type 5 host range mutant (Ad5hr)-simian immunodeficiency virus SIVsm env recombinant and at 24 and 36 weeks with native SIVmac251 gp120 in Syntex adjuvant. Four macaques received the Ad5hr vector and adjuvant alone; two additional controls were naive. In vivo replication of the Ad5hr wild-type and recombinant vectors occurred with detection of Ad5 DNA in stool samples and/or nasal secretions in all macaques and increases in Ad5 neutralizing antibody in 9 of 10 macaques following Ad administrations. SIV-specific neutralizing antibodies appeared after the second recombinant immunization and rose to titers > 10,000 following the second subunit boost. Immunoglobulin G (IgG) and IgA antibodies able to bind gp120 developed in nasal and rectal secretions, and SIV-specific IgGs were also observed in vaginal secretions and saliva. T-cell proliferative responses to SIV gp140 and T-helper epitopes were sporadically detected in all immunized macaques. Following vaginal challenge with SIVmac251, transient or persistent infection resulted in both immunized and control monkeys. The mean viral burden in persistently infected immunized macaques was significantly decreased in the primary infection period compared to that of control macaques. These results establish in vivo use of the Ad5hr vector, which overcomes the host range restriction of human Ads for rhesus macaques, thereby providing a new model for evaluation of Ad-based vaccines. In addition, they show that a vaccine regimen using the Ad5hr-SIV env recombinant and gp120 subunit induces strong humoral, cellular, and mucosal immunity in rhesus macaques. The reduced viral burden achieved solely with an env-based vaccine supports further development of Ad-based vaccines comprising additional viral components for immune therapy and AIDS vaccine development. PMID:9343211

  10. The SPoRT-WRF: Evaluating the Impact of NASA Datasets on Convective Forecasts

    NASA Technical Reports Server (NTRS)

    Zavodsky, Bradley; Case, Jonathan; Kozlowski, Danielle; Molthan, Andrew

    2012-01-01

    The Short-term Prediction Research and Transition Center (SPoRT) is a collaborative partnership between NASA and operational forecasting entities, including a number of National Weather Service offices. SPoRT transitions real-time NASA products and capabilities to its partners to address specific operational forecast challenges. One challenge that forecasters face is applying convection-allowing numerical models to predict mesoscale convective weather. In order to address this specific forecast challenge, SPoRT produces real-time mesoscale model forecasts using the Weather Research and Forecasting (WRF) model that includes unique NASA products and capabilities. Currently, the SPoRT configuration of the WRF model (SPoRT-WRF) incorporates the 4-km Land Information System (LIS) land surface data, 1-km SPoRT sea surface temperature analysis and 1-km Moderate resolution Imaging Spectroradiometer (MODIS) greenness vegetation fraction (GVF) analysis, and retrieved thermodynamic profiles from the Atmospheric Infrared Sounder (AIRS). The LIS, SST, and GVF data are all integrated into the SPoRT-WRF through adjustments to the initial and boundary conditions, and the AIRS data are assimilated into a 9-hour SPoRT WRF forecast each day at 0900 UTC. This study dissects the overall impact of the NASA datasets and the individual surface and atmospheric component datasets on daily mesoscale forecasts. A case study covering the super tornado outbreak across the Ce ntral and Southeastern United States during 25-27 April 2011 is examined. Three different forecasts are analyzed including the SPoRT-WRF (NASA surface and atmospheric data), the SPoRT WRF without AIRS (NASA surface data only), and the operational National Severe Storms Laboratory (NSSL) WRF (control with no NASA data). The forecasts are compared qualitatively by examining simulated versus observed radar reflectivity. Differences between the simulated reflectivity are further investigated using convective parameters along with model soundings to determine the impacts of the various NASA datasets. Additionally, quantitative evaluation of select meteorological parameters is performed using the Meteorological Evaluation Tools model verification package to compare forecasts to in situ surface and upper air observations.

  11. Structure of 2G12 Fab2 in Complex with Soluble and Fully Glycosylated HIV-1 Env by Negative-Stain Single-Particle Electron Microscopy

    PubMed Central

    Murin, Charles D.; Julien, Jean-Philippe; Sok, Devin; Stanfield, Robyn L.; Khayat, Reza; Cupo, Albert; Moore, John P.; Burton, Dennis R.; Wilson, Ian A.

    2014-01-01

    ABSTRACT The neutralizing anti-HIV-1 antibody 2G12 is of particular interest due to the sterilizing protection it provides from viral challenge in animal models. 2G12 is a unique, domain-exchanged antibody that binds exclusively to conserved N-linked glycans that form the high-mannose patch on the gp120 outer domain centered on a glycan at position N332. Several glycans in and around the 2G12 epitope have been shown to interact with other potent, broadly neutralizing antibodies; therefore, this region constitutes a supersite of vulnerability on gp120. While crystal structures of 2G12 and 2G12 bound to high-mannose glycans have been solved, no structural information that describes the interaction of 2G12 with gp120 or the Env trimer is available. Here, we present a negative-stain single-particle electron microscopy reconstruction of 2G12 Fab2 in complex with a soluble, trimeric Env at ?17-? resolution that reveals the antibody's interaction with its native and fully glycosylated epitope. We also mapped relevant glycans in this epitope by fitting high-resolution crystal structures and by performing neutralization assays of glycan knockouts. In addition, a reconstruction at ?26 ? of the ternary complex formed by 2G12 Fab2, soluble CD4, and Env indicates that 2G12 may block membrane fusion by induced steric hindrance upon primary receptor binding, thereby abrogating Env's interaction with coreceptor(s). These structures provide a basis for understanding 2G12 binding and neutralization, and our low-resolution model and glycan assignments provide a basis for higher-resolution studies to determine the molecular nature of the 2G12 epitope. IMPORTANCE HIV-1 is a human virus that results in the deaths of millions of people around the world each year. While there are several effective therapeutics available to prolong life, a vaccine is the best long-term solution for curbing this global epidemic. Here, we present structural data that reveal the viral binding site of one of the first HIV-1-neutralizing antibodies isolated, 2G12, and provide a rationale for its effectiveness. These structures provide a basis for higher-resolution studies to determine the molecular nature of the 2G12 epitope, which will aid in vaccine design and antibody-based therapies. PMID:24965454

  12. Human endogenous retrovirus K(HML-2) Gag- and Env-specific T-cell responses are infrequently detected in HIV-1-infected subjects using standard peptide matrix-based screening.

    PubMed

    Jones, R Brad; John, Vivek M; Hunter, Diana V; Martin, Eric; Mujib, Shariq; Mihajlovic, Vesna; Burgers, Peter C; Luider, Theo M; Gyenes, Gabor; Sheppard, Neil C; Sengupta, Devi; Tandon, Ravi; Yue, Feng-Yun; Benko, Erika; Kovacs, Colin; Nixon, Douglas F; Ostrowski, Mario A

    2012-02-01

    T-cell responses to human endogenous retrovirus (HERV) K(HML-2) Gag and Env were mapped in HIV-1-infected subjects using 15 mer peptides. Small peptide pools and high concentrations were used to maximize sensitivity. In the 23 subjects studied, only three bona fide HERV-K(HML-2)-specific responses were detected. At these high peptide concentrations, we detected false-positive responses, three of which were mapped to an HIV-1 Gag peptide contaminant. Thus, HERV-K(HML-2) Gag- and Env-specific T-cell responses are infrequently detected by 15 mer peptide mapping. PMID:22205657

  13. Association Between RT-Induced Changes in Lung Tissue Density and Global Lung Function

    SciTech Connect

    Ma Jinli [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Department of Radiation Oncology, Fudan University Cancer Hospital, Shanghai (China); Zhang Junan; Zhou Sumin [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Hubbs, Jessica L. [Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, NC (United States); Foltz, Rodney J. [Department of Pulmonary Medicine, Duke University Medical Center, Durham, NC (United States); Hollis, Donna R. [Department of Biostatistics, Duke University Medical Center, Durham, NC (United States); Light, Kim L. [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Wong, Terence Z. [Department of Radiology, Duke University Medical Center, Durham, NC (United States); Kelsey, Christopher R. [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Marks, Lawrence B. [Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, NC (United States)], E-mail: marks@med.unc.edu

    2009-07-01

    Purpose: To assess the association between radiotherapy (RT)-induced changes in computed tomography (CT)-defined lung tissue density and pulmonary function tests (PFTs). Methods and Materials: Patients undergoing incidental partial lung RT were prospectively assessed for global (PFTs) and regional (CT and single photon emission CT [SPECT]) lung function before and, serially, after RT. The percent reductions in the PFT and the average changes in lung density were compared (Pearson correlations) in the overall group and subgroups stratified according to various clinical factors. Comparisons were also made between the CT- and SPECT-based computations using the Mann-Whitney U test. Results: Between 1991 and 2004, 343 patients were enrolled in this study. Of these, 111 patients had a total of 203 concurrent post-RT evaluations of changes in lung density and PFTs available for the analyses, and 81 patients had a total of 141 concurrent post-RT SPECT images. The average increases in lung density were related to the percent reductions in the PFTs, albeit with modest correlation coefficients (range, 0.20-0.43). The analyses also indicated that the association between lung density and PFT changes is essentially equivalent to the corresponding association with SPECT-defined lung perfusion. Conclusion: We found a weak quantitative association between the degree of increase in lung density as defined by CT and the percent reduction in the PFTs.

  14. A replication-competent, endogenous retrovirus from an aged DBA/2 mouse contains the complete env from Emv-3 and a novel gag partially related to AKT-8.

    PubMed

    Bartman, T; Murasko, D M; Blank, K J

    1995-05-01

    We previously described an endogenous murine retrovirus, rv-DBA/2aged, isolated from an aged DBA/2 mouse. The previous report showed that a recombination which resulted in the replacement of Emv-3 gag sequences with gag sequences homologous to those found in the AKT-8 virus had taken place. This recombination allowed production of a competent virus from the defective Emv-3 locus. However, the extent of replacement of Emv-3 gag was not known. We report here the entire sequence for the gag gene of rv-DBA/2aged as well as the previously unsequenced 3' end of the Emv-3 gag gene. These data demonstrate that while sequences homologous to the entire gag gene fragment found in AKT-8 are represented in rv-DBA/2aged, the remainder of rv-DBA/2aged gag is not derived from Emv-3 but is a unique gag sequence. Furthermore, a complete comparison of env sequences shows that the env of rv-DBA/2aged is derived entirely from Emv-3. Additional data suggest that the recombination which led to production of the rv-DBA/2aged virus may be a common event in aging DBA/2 mice. Finally, comparison of the new sequences of Emv-3 with those of the Akv virus (also designated AKR-623 and Emv-11) and Emv-1 shows that this endogenous virus locus is very closely related to the other Emv loci at the nucleotide sequence level. PMID:7707556

  15. Structure-function analysis of the LytM domain of EnvC, an activator of cell wall remodeling at the Escherichia coli division site

    PubMed Central

    Peters, Nick T.; Morlot, Cécile; Yang, Desirée C.; Uehara, Tsuyoshi; Vernet, Thierry; Bernhardt, Thomas G.

    2013-01-01

    Proteins with LytM (Peptidase_M23) domains are broadly distributed in bacteria and have been implicated in a variety of important processes, including cell division and cell-shape determination. Most LytM-like proteins that have been structurally and/or biochemically characterized are metallo-endopeptidases that cleave crosslinks in the peptidoglycan (PG) cell wall matrix. Notable exceptions are the Escherichia coli cell division proteins EnvC and NlpD. These LytM factors are not hydrolases themselves, but instead serve as activators that stimulate PG cleavage by target enzymes called amidases to promote cell separation. Here we report the structure of the LytM domain from EnvC, the first structure of a LytM factor implicated in the regulation of PG hydrolysis. As expected, the fold is highly similar to that of other LytM proteins. However, consistent with its role as a regulator, the active site region is degenerate and lacks a catalytic metal ion. Importantly, genetic analysis indicates that residues in and around this degenerate active site are critical for amidase activation in vivo and in vitro. Thus, in the regulatory LytM factors, the apparent substrate binding pocket conserved in active metallo-endopeptidases has been adapted to control PG hydrolysis by another set of enzymes. PMID:23796240

  16. Peptide Triazole Inactivators of HIV-1 Utilize a Conserved Two-Cavity Binding Site at the Junction of the Inner and Outer Domains of Env gp120

    PubMed Central

    Aneja, Rachna; Rashad, Adel A.; Li, Huiyuan; Sundaram, Ramalingam Venkat Kalyana; Duffy, Caitlin; Bailey, Lauren D.; Chaiken, Irwin

    2015-01-01

    We used coordinated mutagenesis, synthetic design, and flexible docking to investigate the structural mechanism of Env gp120 encounter by peptide triazole (PT) inactivators of HIV-1. Prior results demonstrated that the PT class of inhibitors suppresses binding at both CD4 and coreceptor sites on Env and triggers gp120 shedding, leading to cell-independent irreversible virus inactivation. Despite these enticing anti-HIV-1 phenotypes, structural understanding of the PT–gp120 binding mechanism has been incomplete. Here we found that PT engages two inhibitor ring moieties at the junction between the inner and outer domains of the gp120 protein. The results demonstrate how combined occupancy of two gp120 cavities can coordinately suppress both receptor and coreceptor binding and conformationally entrap the protein in a destabilized state. The two-cavity model has common features with small molecule gp120 inhibitor binding sites and provides a guide for further design of peptidomimetic HIV-1 inactivators based on the PT pharmacophore. PMID:25860784

  17. Formaldehyde-Treated, Heat-Inactivated Virions with Increased Human Immunodeficiency Virus Type 1 Env Can Be Used To Induce High-Titer Neutralizing Antibody Responses

    PubMed Central

    Poon, B.; Hsu, J. F.; Gudeman, V.; Chen, I. S. Y.; Grovit-Ferbas, K.

    2005-01-01

    The lack of success of subunit human immunodeficiency virus (HIV) type 1 vaccines to date suggests that multiple components or a complex virion structure may be required. We hypothesized that the failure of current vaccine strategies to induce protective antibodies is linked to the inability of native envelope structures to readily elicit these types of antibodies. We have previously reported on the ability of a formaldehyde-treated, heat-inactivated vaccine to induce modest antibody responses in animal vaccine models. We investigated here whether immunization for HIV with an envelope-modified, formaldehyde-stabilized, heat-inactivated virion vaccine could produce higher-titer and/or broader neutralizing antibody responses. Thus, a clade B vaccine which contains a single point mutation in gp41 (Y706C) that results in increased incorporation of oligomeric Env into virions was constructed. This vaccine was capable of inducing high-titer antibodies that could neutralize heterologous viruses, including those of clades A and C. These results further support the development of HIV vaccines with modifications in native Env structures for the induction of neutralizing antibody responses. PMID:16051814

  18. Eight-drug/radiation therapy program (MOPP/ABDV/RT) for advanced Hodgkin's disease

    SciTech Connect

    Straus, D.J.; Myers, J.; Passe, S.

    1980-07-15

    Eighty-four evaluable patients with advanced Hodgkin's disease (Stages IIB, IIIA age > 35 or mixed cellularity or lymphocyte depletion histology, IIIB, IVA, and IVB) were treated with alternating monthly MOPP and Adriamycin, bleomycin, dacarbazine, and vinblastine (ABDV). Radiation therapy (RT), 2000 rads in two weeks, was given to areas of initial bulky disease in untreated patients. Complete remission (CR) rates were 80% for previously untreated, 65% for prior RT or minimal chemotherapy treated, and 50% for heavily pretreated patients. Among 49 previously untreated patients there were no primary treatment failures. The estimated two-year relapse rate for the CR group was 9%. The therapeutic effectiveness of this program may have been due to either or both of the following elements: (1) two non-cross-resistant drug combinations; (2) low dose adjuvant RT to initial sites of bulky disease. These early results are among the best reported for the treatment of advanced Hodgkin's disease.

  19. In-flight demonstration of a Real-Time Flush Airdata Sensing (RT-FADS) system

    NASA Technical Reports Server (NTRS)

    Whitmore, Stephen A.; Davis, Roy J.; Fife, John Michael

    1995-01-01

    A prototype real-time flush airdata sensing (RT-FADS) system has been developed and flight tested at the NASA Dryden Flight Research Center. This system uses a matrix of pressure orifices on the vehicle nose to estimate airdata parameters in real time using nonlinear regression. The algorithm is robust to sensor failures and noise in the measured pressures. The RT-FADS system has been calibrated using inertial trajectory measurements that were bootstrapped for atmospheric conditions using meteorological data. Mach numbers as high as 1.6 and angles of attack greater than 45 deg have been tested. The system performance has been evaluated by comparing the RT-FADS to the ship system airdata computer measurements to give a quantitative evaluation relative to an accepted measurement standard. Nominal agreements of approximately 0.003 in Mach number and 0.20 deg in angle of attack and angle of sideslip have been achieved.

  20. HIV-1 RT-associated RNase H function inhibitors: Recent advances in drug development.

    PubMed

    Tramontano, E; Di Santo, R

    2010-01-01

    The HIV-1 genomic RNA reverse transcription is an essential step in the virus cycle carried out by the viral-coded reverse transcriptase (RT), which has two associated functions: the RNA- and DNA-dependent DNA polymerase (RDDP and DDDP) function and the ribonuclease H (RNase H) function. The RNase H function catalyzes the selective hydrolysis of the RNA strand of the RNA:DNA heteroduplex replication intermediate. The RT associated activities are both essential for HIV-1 replication and validated targets for drug development, but only the polymerase function has been widely investigated as drug target. In fact, either nucleoside or non-nucleoside RT inhibitors currently used in therapy act on the polymerase associated activity. In this review, we describe the compounds, reported up to today, which inhibit the HIV-1 RNase H function, their chemical structures, the structure-activity relationships and the mechanism of action. PMID:20858167

  1. Integrating VA's NDF-RT drug terminology with PharmGKB: preliminary results.

    PubMed

    Pathak, Jyotishman; Weiss, Laura C; Durski, Matthew J; Zhu, Qian; Freimuth, Robert R; Chute, Christopher G

    2012-01-01

    Biomedical terminology and vocabulary standards play an important role in enabling consistent, comparable, and meaningful sharing of data within and across institutional boundaries, as well as ensuring semantic interoperability. The Veterans Affairs (VA) National Drug File Reference Terminology (NDF-RT) is a federally recommended standardized terminology resource encompassing medications, ingredients, and a hierarchy for high-level drug classes. In this study, we investigate the drug-disease relationships in NDF-RT and determine how PharmGKB can be leveraged to augment NDF-RT, and vice-versa. Our preliminary results indicate that with additional curation and analyses, information contained in both knowledge resources can be mutually integrated. PMID:22174295

  2. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for diagnosis of dengue

    PubMed Central

    Sahni, Ajay Kumar; Grover, Naveen; Sharma, Ajay; Khan, Inam Danish; Kishore, Jugal

    2012-01-01

    Background Dengue is an emerging public health problem causing serious morbidity and mortality in tropical developing countries. Early, sensitive and specific diagnosis is paramount for clinical decision making. Currently available diagnostic tests are limited in scope and utility. This study highlights applicability of RT-LAMP in dengue diagnosis. Methods 100 dengue confirmed cases, 100 dengue negative cases and 79 healthy negative controls from dengue epidemic between Sep 2009 to Jul 2011 were included. Dengue cases were profiled using WHO guidelines 2006, haematological and biochemical parameters evaluated and diagnosed using NS1 antigen, IgM and IgG enzyme immunoassay, RT-PCR and RT-LAMP. Positive cases were serotyped, genotyped and various tests were compared. Results Mean haematocrit, PT, PTT, platelet count, activated lymphocytes, serum fibrinogen, transaminases, bilirubin, lactate dehydrogenase, protein and sodium were significantly elevated in DHF/DSS as compared to DF. NS1 antigen, RT-PCR and RT-LAMP were sensitive during 1–3 days while ?-capture IgM EIA was specific after 5–7 days of initial infection. DEN-1 genotype III was predominant. Conclusion Deranged haematocrit and liver function tests are indicators of the severity of the disease. RT-LAMP is rapid, cost effective, highly sensitive and specific qualitative and quantitative technique which can detect dengue infection in both early and intermediary stages when NS1 antigen titres are not in the detectable range and the IgM antibody titres have just started to rise. Its superiority over existing techniques, amenability for automation and promising utility in low resource healthcare setups and field conditions raise it as the new gold standard for dengue diagnosis. PMID:24600118

  3. Recovery of dengue virus from urine samples by real-time RT-PCR.

    PubMed

    Van den Bossche, D; Cnops, L; Van Esbroeck, M

    2015-07-01

    Recently, reverse transcription polymerase chain reaction (RT-PCR) for dengue virus (DENV) has been reported to test positive in urine samples for a longer time frame than in serum. We evaluated two RNA extraction procedures from urine and investigated the stability of DENV RNA in urine and serum up to 1 year at different storage temperatures. In addition, 24 urine samples collected from patients with a recent infection were tested with DENV real-time RT-PCR and compared to the RT-PCR results on serum. Five patients with an acute DENV infection were followed up for 6 months by RT-PCR on urine. The automated extraction method with the MagNA Pure LC 2.0 device had a higher yield of DENV RNA compared to the manual QIAGEN method, explained by the higher volume used in the former method. DENV RNA in both serum and urine was stable at room temperature up to 1 month and at 4 °C and -20 °C for at least 1 year. The detection rate by RT-PCR on urine was 50 % (4/8) until day 7, 100 % (6/6) between 1 and 3 weeks after symptom onset, and 25 % (2/8) thereafter. Generally, DENV RNA concentrations are higher in serum than in urine up till day 7, switching to lower concentrations in serum thereafter. Peak concentrations in urine are reached around day 10, and RNA becomes undetectable 3 to 4 weeks following disease onset. This diagnostic tool is of added value in clinical settings by extending the period during which DENV infections are diagnosed by RT-PCR. PMID:25794553

  4. Human immunodeficiency virus 1 (HIV-1)-specific reverse transcriptase (RT) inhibitors may suppress the replication of specific drug-resistant (E138K)RT HIV-1 mutants or select for highly resistant (Y181C-->C181I)RT HIV-1 mutants.

    PubMed Central

    Balzarini, J; Karlsson, A; Sardana, V V; Emini, E A; Camarasa, M J; De Clercq, E

    1994-01-01

    Mutant HIV-1 that expresses a Glu138-->Lys substitution in its RT [(E138K)RT] is resistant to the HIV-1-specific RT inhibitor 2',5'-bis-O-(tert-butyldimethylsilyl)-3'-spiro-5"-(4"-amino-1",2"- oxathiole-2",2"-dioxide)pyrimidine (TSAO). However, cell cultures infected with this mutant were completely protected against virus-mediated destruction by micromolar concentrations of the HIV-1-specific RT inhibitors tetrahydroimidazo[4,5,1-jk][1,4]benzodiazepin-2(1H)-one and -thione (TIBO), nevirapine, and bis(heteroaryl)piperazine (BHAP). In contrast, cells infected with a virus mutant that expresses a Tyr181-->Cys substitution in its RT [(Y181C)RT] were not protected by nevirapine and TIBO and were only temporarily protected by BHAP. HIV-1 mutant that emerged under the latter conditions contained a Cys181-->Ile substitution in their RT [(LC181I)RT]. This mutant proved highly resistant to all HIV-1-specific RT inhibitors tested, except for several 1-(2-hydroxyethoxymethyl)-6-(phenylthio)thymine (HEPT) derivatives. When recombinant (C181I)RT was evaluated for susceptibility to the HIV-1-specific RT inhibitors, it was resistant to all inhibitors except the HEPT compounds. Since a (Y181F)RT HIV mutant strain was isolated from cells infected with (Y181C)RT HIV-1 and treated with BHAP, we postulate that the Ile codon was derived from a Cys-->Phe transversion mutation (TGT-->TTT), followed by a Phe-->Ile transversion mutation (TTT-->ATT). PMID:7517553

  5. Simulating Rayleigh-Taylor (RT) instability using PPM hydrodynamics @scale on Roadrunner (u)

    SciTech Connect

    Woodward, Paul R [Los Alamos National Laboratory; Dimonte, Guy [Los Alamos National Laboratory; Rockefeller, Gabriel M [Los Alamos National Laboratory; Fryer, Christopher L [Los Alamos National Laboratory; Dimonte, Guy [Los Alamos National Laboratory; Dai, W [Los Alamos National Laboratory; Kares, R. J. [Los Alamos National Laboratory

    2011-01-05

    The effect of initial conditions on the self-similar growth of the RT instability is investigated using a hydrodynamics code based on the piecewise-parabolic-method (PPM). The PPM code was converted to the hybrid architecture of Roadrunner in order to perform the simulations at extremely high speed and spatial resolution. This paper describes the code conversion to the Cell processor, the scaling studies to 12 CU's on Roadrunner and results on the dependence of the RT growth rate on initial conditions. The relevance of the Roadrunner implementation of this PPM code to other existing and anticipated computer architectures is also discussed.

  6. EXPRESSION ANALYSIS AND PURIFICATION OF HUMAN RECOMBINANT TISSUE TYPE PLASMINOGEN ACTIVATOR (rt-PA) FROM TRANSGENIC TOBACCO PLANTS

    Microsoft Academic Search

    Haidar Saify Nabiabad; Mohammad Mehdi Yaghoobi; Mokhtar Jalali Javaran; Saman Hosseinkhani

    2011-01-01

    Recombinant tissue-type plasminogen activator (rt-PA) has been produced in different hosts. In this research, transgenic tobacco was selected for production of human rt-PA. Transgenic plants were analyzed by polymerase chain reaction (PCR) and reverse-transcription (RT)-PCR. The protein was extracted by Lysine Sepharose chromatography column and was further purified by HiTrap desalting column. The function of eluted protein was analyzed on

  7. RNA oligoprobe capture RT-PCR, a sensitive method for the detection of Grapevine fanleaf virus in Tunisian grapevines

    Microsoft Academic Search

    Sami Fattouch; Sonia M'hirsi; Hajer Acheche; Mohamed marrakchi; Nejib Marzouki

    2001-01-01

    A simple, sensitive and specific RNA capture method is described for the detection of Grapevine fanleaf virus (GFLV) in infected\\u000a grapevines. This method consists of hybridizing GFLV-RNAs to oligoprobes immobilized on nylon membranes, followed by RT-PCR\\u000a amplification of targeted viral sequences. The RNA oligoprobe capture RT-PCR method is 10-fold more sensitive than IC-RT-PCR.\\u000a The efficiency of the RNA oligoprobe capture

  8. Class I and class II restriction pattern polymorphisms associated with independently derived RT1 haplotypes in inbred rats

    Microsoft Academic Search

    Peter J. Wettstein; Susan Faas; David A. Buck

    1985-01-01

    This communication reports the DNA level identification of class I and class II sequences associated with 20 RT1 haplotypes which have been assigned previously to eight RT1 groups. Sixteen to 22 bands in genomic blots hybridized with the mouse pH-2III class I cDNA probe. Only the three RT1khaplotypes associated with identical class I restriction fragment patterns. Differences in restriction bands

  9. Head-to-head comparison of poxvirus NYVAC and ALVAC vectors expressing 1 identical HIV-1 clade C immunogens in prime/boost combination with Env protein 2 in non-human primates

    E-print Network

    García-Arriaza, Juan; Perdiguero, Beatriz; Heeney, Jonathan; Seaman, Michael; Montefiori, David C.; Labranche, Celia; Yates, Nicole L.; Shen, Xiaoying; Tomaras, Georgia D.; Ferrari, Guido; Foulds, Kathryn E.; McDermott, Adrian; Kao, Shing-Fen; Roederer, Mario; Hawkins, Natalie; Self, Steve; Yao, Jiansheng; Farrell, Patrick; Phogat, Sanjay; Tartaglia, Jim; Barnett, Susan W.; Burke, Brian; Cristillo, Anthony; Weiss, Deborah; Lee, Carter; Kibler, Karen; Jacobs, Bert; Asbach, Benedikt; Wagner, Ralf; Ding, Song; Pantaleo, Giuseppe; Esteban, Mariano

    2015-06-03

    We have compared the HIV-1-specific cellular and humoral immune responses elicited in rhesus macaques immunized with two poxvirus vectors (NYVAC and ALVAC) expressing the same HIV-1 antigens from clade C, Env gp140 as a trimeric cell released...

  10. Protection of monkeys vaccinated with vpr- and\\/or nef-defective simian immunodeficiency virus strain mac\\/human immunodeficiency virus type 1 chimeric viruses: a potential candidate live-attenuated human AIDS vaccine

    Microsoft Academic Search

    Tatsuhiko Igarashi; Yasushi Ami; Hiroshi Yamamoto; Riri Shibata; Takeo Kuwata; Ryozaburo Mukai; Katsuaki Shinohara; Toshihiko Komatsu; Akio Adachi; Masanori Hayami

    Two simian immunodeficiency virus strain mac (SIVmac)\\/human immunodeficiency virus type 1(HIV-1) chimeric viruses (SHIVs), designated NM-3 and NM-3n, with env derived from HIV-1 and defective vpr (plus defective nef for NM-3), were inoculated into seven macaques. These macaques were transiently or persistently infected and most of them produced long-lasting neutralizing anti- bodies and Env-specific killer T cells to HIV-1 with

  11. 136 VOLUME 14 NUMBER 2 FEBRUARY 2013 nature immunology A rt i c l e s

    E-print Network

    Arnold, Jonathan

    136 VOLUME 14 NUMBER 2 FEBRUARY 2013 nature immunology A rt i c l e s Microbial and viral of the acute responses to the parasite 1Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA. 2Department of Microbiology & Immunology, University of California, San

  12. VALIDATION OF OPTICAL-FLOW FOR QUANTIFICATION OF MYOCARDIAL DEFORMATIONS ON SIMULATED RT3D ULTRASOUND

    E-print Network

    . This framework was applied to a clinical data set from a heart transplant patient and dynamic measurements agreed was introduced by Duke University [2, 3] and more recently by Philips Medical Systems (Best, The Netherlands consecutive RT3D ultrasound frames of the beating heart under controlled motion fields, including translation

  13. RtI and the Gifted Child: What Every Parent Should Know

    ERIC Educational Resources Information Center

    Postma, Michael; Peters, Daniel; Gilman, Barbara; Kearney, Kathi

    2011-01-01

    Education has seen its share of trends and movements that either help or hinder the optimal development of the gifted child. In 2001, Congress passed No Child Left Behind (NCLB) in a concerted effort to reach children who were not meeting minimal standardized goals of achievement. Response to Intervention (RtI) is yet another approach to ensure…

  14. 2007 AnnuAl RepoRt Certification of the Financial Statements 50

    E-print Network

    Management Act 2006 from proper accounts and records to present fairly the financial transactions49 2007 AnnuAl RepoRt COnTEnTS Certification of the Financial Statements 50 Income Statement 51 Balance Sheet 52 Statement of Changes in Equity 53 Cash Flow Statement 54 notes to the Financial

  15. A RT I C L E S Dynamic evolution of the innate immune system in

    E-print Network

    Keinan, Alon

    A RT I C L E S Dynamic evolution of the innate immune system in Drosophila Timothy B Sackton1 of the innate immune system. We have identified orthologs and paralogs of 245 Drosophila melanogaster immune that immune-system genes, and especially those encoding recognition proteins, evolve under positive darwinian

  16. CONVERSION FROM RT-11 TO MICRO-RSX FOR REAL-TIME DATA COLLECTION AND ANALYSIS

    EPA Science Inventory

    Many scientists with DEC microcomputers use the RT-11 operating system for the acquisition of real-time data in the laboratory. For these researchers, the work required to learn a new operating system and the time needed to reprogram software prevents them from upgrading their la...

  17. FPGA HardCore single processor implementation of RT control applications

    Microsoft Academic Search

    Slim BEN OTHMAN; Meftah GHRISSI; A. K. Ben Salem; Slim BEN SAOUD

    2008-01-01

    In recent years, field programmable gate array (FPGA) have proven themselves capable of handling a wide variety of tasks, from relatively simple electrical system control functions to more complex, algorithmic operations. According to the controller complexity, the FPGA design can be achieved by mixed Software\\/Hardware solutions. However, in many cases, the FPGA-based controller architectures require extensive real time (RT) testing

  18. About the RepoRt While the notion of business fostering peace is becoming

    E-print Network

    Vertes, Akos

    Al RepoRt 315 septembeR 2012 © 2012 by the United States Institute of Peace. All rights reserved. contents Brown at USIP. 2301 Constitution Ave., NW · Washington, DC 20037 · 202.457.1700 · fax 202.429.6063 speci potential of the business sector to foster peace must account for the size of firms, whether they are state

  19. Real-time RT-PCR assay for detection and differentiation of Citrus tristeza virus isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For universal detection of Citrus tristeza virus (CTV) strains by real time RT-PCR, a protocol was developed based on a set of primers and a Cy5-labeled TaqMan probe. This test included primers and a TET-labeled TaqMan probe selected on the mitochondrial nad5 gene for the simultaneous detection of ...

  20. Performance of an RT-nested PCR ELISA for detection of Newcastle disease virus

    Microsoft Academic Search

    C. L Kho; M. L Mohd-Azmi; S. S Arshad; K Yusoff

    2000-01-01

    A sensitive and specific RT-nested PCR coupled with an ELISA detection system for detecting Newcastle disease virus is described. Two nested pairs of primer which were highly specific to all the three different pathotypes of NDV were designed from the consensus fusion gene sequence. No cross-reactions with other avian infectious agents such as infectious bronchitis virus, infectious bursal disease virus,

  1. Real-time atmospheric transmission large-area systems (RT-ATLAS)

    NASA Astrophysics Data System (ADS)

    Bodrero, Dennis M.; Davis, Roger E.; Yale, James G.; Rollins, John M.

    1999-10-01

    The Atmospheric Transmission Large-Area Analysis System (ATLAS) system has been used by the West Desert Test Center (WDTC), Dugway Proving Ground, UT since 1994 to assist in the characterization of aerosol clouds. The ATLAS is a tool for measuring transmittance through aerosol clouds in the far infrared (8 - 14 micrometers ) spectral region. ATLAS is a passive single-ended system employing a thermal imager for data collection and uses the natural background as the reference source. The final ATLAS product is a 2D transmission map of the aerosol cloud as seen by the imager. Historically ATLAS data reduction and map produce has been a lengthy process. This process includes transportation of the infrared video tapes from the field test site to the WDTC Optical Data Laboratory, digitization of infrared tapes, and subsequent image processing of the video frames to produce transmission maps as a function of time. In order to significantly reduce data processing and delivery time, the WDTC and Science and Technology Corporation have developed the Real-Time ATLAS (RT-ATLAS) system. RT-ATLAS is a field- portable system that reduces turn-around time from days to real-time for approximate results and to tens of minutes for final products. This paper describes the physics of the ATLAS technique, the physical RT-ATLAS system, and new enhancements to the ATLAS system. Data examples and analysis are presented and RT-ATLAS strengths and limitations are discussed.

  2. 1999-2008 Index.hu Rt. Minden jog fenntartva. A magyar szerverek tbbsge vdtelen

    E-print Network

    Bencsáth, Boldizsár

    ©1999-2008 Index.hu Rt. Minden jog fenntartva. A magyar szerverek többsége védtelen Index - ugyelet@mail.index..hu, amik a .hu domén alá tartozó címeken található oldalakat szolgálák ki, és azt találták, hogy 68 nem .hu címeket szolgálnak ki, de Magyarországon üzemelnek; az eredmény itt is hasonló volt, 70

  3. Compensation of Deviations from Homology of RT70 Radio Telescope Main Mirror

    Microsoft Academic Search

    S. G. Olskaya; A. V. Bondarev; A. P. Mozgov; V. G. Gimmelman

    2006-01-01

    RT-70 mirror system was designed according to a principle of homological deformations. Deviations of the deformed mirror from the optimal inscribed paraboloid arising in reality remain the main cause of the radio telescope efficiency reduction. According to the results of the conducted calculations, one can conclude that deviations of the deformed mirror from the approximating paraboloid can be compensated with

  4. RT-Based Administrative Models for Community Cyber Security Information Sharing

    E-print Network

    Sandhu, Ravi

    RT-Based Administrative Models for Community Cyber Security Information Sharing Ravi Sandhu, Khalid Zaman Bijon Institute for Cyber Security World-Leading Research with Real Ravi Sandhu, Khalid Zaman Bijon Institute for Cyber Security University of Texas at San Antonio Oct. 15, 2011 International

  5. RT-Based Administrative Models for Community Cyber Security Information Sharing

    E-print Network

    Sandhu, Ravi

    RT-Based Administrative Models for Community Cyber Security Information Sharing Ravi Sandhu, Khalid Zaman Bijon, Xin Jin, and Ram Krishnan Institute for Cyber Security & Department of Computer Science Institute for Cyber Security & Department of Electrical and Computer Engineering University of Texas at San

  6. Training for Generalization and Maintenance in RtI Implementation: Front-Loading for Sustainability

    ERIC Educational Resources Information Center

    Burns, Matthew K.; Egan, Andrea M.; Kunkel, Amy K.; McComas, Jennifer; Peterson, Meredith M.; Rahn, Naomi L.; Wilson, Jennifer

    2013-01-01

    Response to Intervention (RtI) is being implemented as a new initiative in PK-12 schools with increasing frequency. However, the model must be sustained at the school level, which is potentially difficult due to a number of challenges brought about by systems change. This article applied the Stokes and Baer (1977) framework for programming for…

  7. reaction (RT-PCR) to detect Kashmir bee virus (KBV). This technique requires time-

    E-print Network

    Paris-Sud XI, Université de

    reaction (RT-PCR) to detect Kashmir bee virus (KBV). This technique requires time- consuming virus that circumvents these steps. KBV is one of the picorna-like viruses found in honey bees. It was first isolated from a diseased adult bee of the Asian honey bee, Apis cerana [4]. KBV has also been 1. INTRODUCTION

  8. arXiv:math/0401314v2[math.RT]11Feb2004 Partition Algebras

    E-print Network

    Ram, Arun

    arXiv:math/0401314v2[math.RT]11Feb2004 Partition Algebras Tom Halverson Mathematics and Computer Science Macalester College Saint Paul, MN 55105 halverson@macalester.edu Arun Ram Department Science Foundation (DMS-0097977) and the National Security Agency (MDA904-01-1-0032). #12;2 t. halverson

  9. Real-time RT-PCR Assay for Detection and Differentiation of Citrus Tristeza Virus Isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multiplex one step real time RT-PCR assays using TaqMan probes were developed for detection and strain differentiation of Citrus tristeza virus (CTV). For broad spectrum CTV detection, a TaqMan primer and Cy5-labeled probe were designed using CP gene sequences. An internal control was developed us...

  10. Exploring MultiObjective Fitness Functions and Compositions of Different Fitness Functions in rtNEAT

    E-print Network

    Meeden, Lisa A.

    Exploring MultiObjective Fitness Functions and Compositions of Different Fitness Functions in rtNEAT KJ Bredder and Cole Harbeck Abstract In machine learning, the fitness function is an incredibly to identify a set of sub-goal that can be explicitly rewarded as part of the fitness function. However

  11. RocK coNceRt PRomotioN ROCk CONCERT PROMOTION POLICY _____________________________________________

    E-print Network

    Hemmers, Oliver

    16 RocK coNceRt PRomotioN ROCk CONCERT PROMOTION POLICY a rock music concert (as defined by the Clark County Rock Concert Promotion Ordinance) must have will determine the applicant's suitability for use of UNLV's Rock Concert Promotion License Waiver. A license

  12. Cycle slip Detection in the context of rtK GPs positioning of lightweight UAVs

    E-print Network

    Behnke, Sven

    148 Cycle slip Detection in the context of rtK GPs positioning of lightweight UAVs C. Eling1 , E of a simple test it will be shown that the integration of accelerometers in the RTK GPS float solution allows for a reliable detection and repair of cycle slips. Keywords RTK GPS, UAV, direct georeferencing, cycle slip

  13. Detection of Rift Valley fever virus in mosquitoes by RT-PCR

    Microsoft Academic Search

    M. S. Ibrahim; M. J. Turell; F. K. Knauert; R. S. Lofts

    1997-01-01

    A reverse transcriptase-polymerase chain reaction (RT-PCR) assay to detect Rift Valley fever (RVF) virus RNA in experimentally infected mosquitoes was developed. The specificity of the assay was evaluated with three other phleboviruses; sandfly fever Sicilian (Sabin), sandfly fever Naples (Sabin) and Punta Toro (MSP 3) viruses. The relative sensitivity of the assay, determined by using RVF virus RNA extracted from

  14. ISSN0249-0803ISRNINRIA/RT--0417--FR+ENG December 2011

    E-print Network

    Paris-Sud XI, Université de

    ISSN0249-0803ISRNINRIA/RT--0417--FR+ENG TECHNICAL REPORT N° 0417 December 2011 Project-Teams MOAIS Mentec, Vincent Danjean, Thierry Gautier Project-Teams MOAIS Technical Report n° 0417 -- December 2011 paradigm. X-Kaapi was developed in the MOAIS IN- RIA project by Thierry Gautier, Fabien Le Mentec, Vincent

  15. ISSN0249-0803ISRNINRIA/RT--429--FR+ENG November 2011

    E-print Network

    Paris-Sud XI, Université de

    ISSN0249-0803ISRNINRIA/RT--429--FR+ENG TECHNICAL REPORT N° 429 November 2011 Project-Teams MOAIS X , Fabien Lementec , Vincent Faucher Project-Teams MOAIS Technical Report n° 429 -- November 2011 -- 17 in the MOAIS IN- RIA project by Thierry Gautier, Fabien Le Mentec, Vincent Danjean and Christophe Laferrière

  16. Dispersion data for open inverted microstrip on RT-duroid and fused quartz substrates

    NASA Astrophysics Data System (ADS)

    Tomar, R. S.; Rao, K. V. S.; Bhartia, P.

    1988-09-01

    Accurate dispersion data for open inverted microstrip is presented. Two most commonly used substrate materials, namely, RT-duroid (dielectric constant 2.22) and fused quartz (dielectric constant 3.78) are considered. The work is a continuation of the earlier reported data on a similar structure, called suspended microstrip, and will be an useful addition to the millimeter-wave designer's library.

  17. RT Level Power Analysis y Jianwen Zhu, Poonam Agrawal, Daniel D. Gajski

    E-print Network

    California at Irvine, University of

    RT Level Power Analysis y Jianwen Zhu, Poonam Agrawal, Daniel D. Gajski Department of Information purely statistical approach, we present in this paper a power analysis technique which is analytical of datapath components as well as interconnections is discussed. Then we present the power analysis techniques

  18. RTDT : a Static QoS Manager, RT Scheduling, HW/SW Partitioning CAD Tool

    E-print Network

    Paris-Sud XI, Université de

    RTDT : a Static QoS Manager, RT Scheduling, HW/SW Partitioning CAD Tool H.Tmar+ , J-Ph.Diguet , A, National Engineers school of Sfax, Tunisia, Sfax Abstract The Hardware (HW)/Software (SW) partitioning-added innovations [1]. In the domain of SOC, the designers are relying on reuse of reconfigurable HW or SW

  19. Dean's RepoRt AAt Harvard University's Smithsonian Center for Astrophysics,

    E-print Network

    Walsworth, Ronald L.

    Aa Aa FY09 / 24 Dean's RepoRt AAt Harvard University's Smithsonian Center for Astrophysics physics and biomedical imaging." Enter Harvard Catalyst. Also known as the Harvard Clinical and Translational Science Center, this virtual center was created with a five-year, $117.5-million grant to Harvard

  20. LAL/RT 04-03 THE TESLA HIGH POWER COUPLER PROGRAM AT ORSAY

    E-print Network

    Boyer, Edmond

    LAL/RT 04-03 April 2004 1 THE TESLA HIGH POWER COUPLER PROGRAM AT ORSAY T. Garvey, H. Borie, L, Université de Paris-Sud, B.P. 34, 91898 Orsay, France Abstract Within the general TESLA collaboration-Orsay are centred on the development of RF input couplers for the cavities of the TESLA linear collider study

  1. Extracción Simple de Ácidos Nucléicos para la Detección de Viroides de Cítricos Mediante RT-PCR

    Microsoft Academic Search

    Isidro Humberto Almeyda-León; María Magdalena Iracheta-Cárdenas; Fermín Orona-Castro; Craig J. Kahlke; Mario Alberto Rocha-Peña; Nuevo León

    2003-01-01

    A simple nucleic acids extraction method is described for the detection of citrus viroids by reverse transcription and polymerase chain reaction (RT-PCR). The method involves the use of minimal amounts (250 mg) of citrus tissue and the adding of 1% polyvinylpyrrolidone to the extraction buffer. The complete protocol can be accomplished in 8 h with a least 18 samples simultaneously.

  2. AnnuAl RepoRt PeterWall Institute for Advanced Studies

    E-print Network

    Handy, Todd C.

    Development Workshops 28 Colloquia 30 associates forums 31 TrUsTees' evenT 37 finanCial sUMMary 38 faAnnuAl RepoRt PeterWall Institute for Advanced Studies 2004 ­ 2005 #12;"The Peter Wall Institute 1998 #12;Cover, Above, And PAge 36 Photographs courtesy of Michael Healey, Earth & Ocean Sciences

  3. Large PROFINET IO RT networks for factory automation: A case study

    Microsoft Academic Search

    P. Ferrari; A. Flammini; F. Venturini; A. Augelli

    2011-01-01

    The paper presents a case study regarding a real PROFINET IO network for factory automation. The aim of the study is the evaluation of the time related parameter of a real network. A large factory automation plant has been chosen as testbed since PROFINET IO RT Class 1 and 2 (unsynchronized) are mainly used in those applications. The analyzed network

  4. University of Maryland Center for Environmental Science 2012 AnnuAl RepoRt

    E-print Network

    Boynton, Walter R.

    research centers focused on ecosystem science, the University of Maryland Center for Environmental ScienceUniversity of Maryland Center for Environmental Science 2012 AnnuAl RepoRt #12;annUal rEport 2012 by conducting cutting-edge research into today's most pressing environmental problems. We

  5. RAPID COMMUNICATION CW DFB RT diode laser-based sensor for trace-gas detection

    E-print Network

    RAPID COMMUNICATION CW DFB RT diode laser-based sensor for trace-gas detection of ethane using- moelectrically cooled (TEC), distributed feedback diode laser-based spectroscopic trace-gas sensor for ultra tunable diode laser absorption spectroscopy (TDLAS) and wavelength modulation spectroscopy

  6. lNTfRtHr93 24-29 April1993 The Growth of Software Skill

    E-print Network

    Olson, Judith S.

    one by one, rather than investing in the learning of a specialized method, such as styles. And yetlNTfRtHr93 24-29 April1993 The Growth of Software Skill: A Longitudinal Look at Learning. Lewis & Clark College National University of Singapore The University of Michigan Western Kentucky

  7. RESEARCH Open Access Development of a SYBR green I based RT-PCR

    E-print Network

    Paris-Sud XI, Université de

    RESEARCH Open Access Development of a SYBR green I based RT-PCR assay for yellow fever virus2 , Shashi Sharma3 and Paul Reiter1* Abstract Background: Yellow Fever virus (YFV) is an important for detection and quantification of YFV than other currently used methods. Background Yellow fever (YF) is one

  8. DETECTION OF HUMAN ENTERIC VIRUSES IN STREAM WATER WITH RT-PCR AND CELL CULTURE

    EPA Science Inventory

    A multiplex RT-PCR method was used to measure virus occurrence at five stream water sites that span a range of hydroclimatic, water-quality, and land-use characteristics. The performance of the molecular method was evaluated in comparison to traditional cell culture and Escherich...

  9. An improved RT-PCR assay for rapid and sensitive detection of grass carp reovirus.

    PubMed

    Zhang, Lanlan; Luo, Qing; Fang, Qin; Wang, Yaping

    2010-10-01

    An improved simple, rapid and sensitive method for detecting grass carp reovirus (GCRV) based on RT-PCR was developed by combining an advanced RNA extraction technique and targeting segment 10 as a template. The results indicate that highly efficient RT-PCR amplification of GCRV genome segments can be obtained using column-extracted RNA as a template, which is suitable not only for full-length gene amplification up to a size of 1.5 kb, but also for partial genome detection. Moreover, by targeting the highly divergent segment 10, the sensitivity of RT-PCR detection is improved significantly; as little as 1.0 fg of the 515 bp S10 dsRNA can be detected by one-step RT-PCR amplification. Furthermore, this method exhibits good reproducibility and specificity, and no amplicons were observed when RNA fragments other than those from GCRV were used as templates. The entire detection process can be completed within 4-5h from RNA extraction, much faster than methods reported previously. Overall, the improved detection technique may be applied for rapid diagnosis of GCRV or other dsRNA viruses. PMID:20599564

  10. The ISL RT-06S Speech-to-Text System Christian Fugen1

    E-print Network

    Schultz, Tanja

    The ISL RT-06S Speech-to-Text System Christian F¨ugen1 , Shajith Ikbal1 , Florian Kraft1 , Kenichi at the Interactive Systems Labora- tories (ISL), for the individual head-mounted microphone (IHM), single distant Introduction In this paper, we present the ISL's most recent speech-to-text systems for lec- tures

  11. Stresa, Italy, 25-27 April 2007 0-LEVEL VACUUM PACKAGING RT PROCESS FOR MEMS RESONATORS

    E-print Network

    Paris-Sud XI, Université de

    Stresa, Italy, 25-27 April 2007 0-LEVEL VACUUM PACKAGING RT PROCESS FOR MEMS RESONATORS Nicolas. The process is compatible with most of MEMS resonators and Resonant Suspended-Gate MOSFET [1] fabrication-processed wafers and avoiding any subsequent degradation of the active devices. 1. INTRODUCTION MEMS resonators

  12. RT-SLAM: a generic and real-time visual SLAM implementation

    E-print Network

    Solà, Joan

    RT-SLAM: a generic and real-time visual SLAM implementation Cyril Roussillon1,2,3 , Aurélien. This article presents a new open-source C++ implementa- tion to solve the SLAM problem, which is focused, that allows the combination of numerous sensors and land- mark types, and the integration of various

  13. SM@RT: Applying Architecture-based Runtime Management into Internetware Systems

    E-print Network

    Boyer, Edmond

    (these models are reusable independently for different pairs of the model and system), and one QVT on Eclipse GUI and Android, C2 arc- hitectural models on JOnAS, Rainbow C/S style on PLASTIC and UML models,version1-24Feb2010 Author manuscript, published in "SM@RT: Towards A

  14. LIVE CARS FOR USE IN CATFISH INDUSTRY Donald C. ,r nland, Rob rt L. ..rill,

    E-print Network

    LIVE CARS FOR USE IN CATFISH INDUSTRY Donald C. ,r nland, Rob rt L. ..rill, & Jam's . IIall Live cars - -m sh "fish -holdmg bags "- -hav a vari tyof applications in th produ tion of pond - rai d chann fish to mov into th liv car . Information on holding capaciti and a m thod to accu- rat ly m t l' fish

  15. RepoRt of the Committee foR the 21st CentuRy

    E-print Network

    Connor, Ed

    RepoRt of the Committee foR the 21st CentuRy septembeR, 23 1994 #12;Report of the Committee was to put forward proposals that would strengthen academic quality, enhance organizational effectiveness, and increase financial self-sufficiency. Strategic Study Groups were established to pursue in depth

  16. a rt i c l e s nature medicine VOLUME 17 | NUMBER 8 | AUGUST 2011 983

    E-print Network

    a rt i c l e s nature medicine VOLUME 17 | NUMBER 8 | AUGUST 2011 983 The vertebrate immune system and exaggerated immune responses. Deficiency of Foxp3 in humans results in a multiorgan autoimmune disease called immune- dysregulation polyendocrinopathy enteropathy X-linked syndrome (IPEX)1,2. Similar multiorgan

  17. ISSN0249-0803ISRNINRIA/RT--427--FR+ENG Project-Team MESCAL

    E-print Network

    Paris-Sud XI, Université de

    ISSN0249-0803ISRNINRIA/RT--427--FR+ENG TECHNICAL REPORT N° 427 July 2012 Project-Team MESCAL So applications. The SoC-Trace project aims at developing an open-source trace management infrastructure able. The proposed prototype allows the user to deal with traces of dierent formats, to access them through a common

  18. ISSN0249-0803ISRNINRIA/RT--427--FR+ENG Project-Team MESCAL

    E-print Network

    ISSN0249-0803ISRNINRIA/RT--427--FR+ENG TECHNICAL REPORT N° 427 July 2012 Project-Team MESCAL So an open-source trace management infrastructure able to exploit multi-core embedded-systems execution with traces of dierent formats, to access them through a common interface and nally to save analysis results

  19. Does the sex of acute stroke patients influence the effectiveness of rt-PA?

    PubMed Central

    2014-01-01

    Background Women have been reported to show more frequent recanalization and better recovery after intravenous (IV) recombinant tissue plasminogen activator (rt-PA) treatment for acute stroke compared with men. To investigate this we studied a series of stroke patients receiving IV rt-PA and undergoing acute transcranial doppler (TCD) examination. Methods Acute stroke patients received IV rt-PA and had acute TCD examination within 4 hours of symptom onset at 4 major stroke centers. TCD findings were interpreted using the Thrombolysis in Brain Ischemia (TIBI) flow grading system. The recanalization rates, and poor 3-month outcomes (modified Rankin scale >2) of men and women were compared using the chi-square test. Multiple regression analysis was used to assess sex as a predictor of recanalization and poor 3-month outcome after controlling for age, baseline NIH Stroke Scale (NIHSS), time to treatment, hypertension, and blood glucose. Results 369 patients had TCD examinations before or during IV rt-PA treatment. The 199 (53.9%) men and 170 (46.1%) women had mean ages of 67?±?13 and 70?±?14 years, respectively. The sexes did not differ significantly in baseline stroke severity, time to TCD examination, or time to thrombolysis. Of the men, 68 (34.2%) had complete recanalization, 58 (29.1%) had partial recanalization, and 73 (36.6%) had no recanalization. Of the women, 53 (31.2%) had complete recanalization, 46 (27%) had partial recanalization, and 71 (41.8%) had no recanalization (p?=?0.6). Multiple regression analyses showed no difference between the sexes in recanalization rate, time to recanalization, or clinical outcome at 3 months. Conclusions In our study; sex is not a significant predictor of recanalization rate, time to recanalization or 3-month outcome in stroke patients following IV rt-PA. Trial registration Data from CLOTBUST trial Clinicaltrails.gov Identifier: NCT01240356. PMID:24669960

  20. SPoRT - An End-to-End R2O Activity

    NASA Technical Reports Server (NTRS)

    Jedlovec, Gary J.

    2009-01-01

    Established in 2002 to demonstrate the weather and forecasting application of real-time EOS measurements, the Short-term Prediction Research and Transition (SPoRT) program has grown to be an end-to-end research to operations activity focused on the use of advanced NASA modeling and data assimilation approaches, nowcasting techniques, and unique high-resolution multispectral observational data applications from EOS satellites to improve short-term weather forecasts on a regional and local scale. SPoRT currently partners with several universities and other government agencies for access to real-time data and products, and works collaboratively with them and operational end users at 13 WFOs to develop and test the new products and capabilities in a "test-bed" mode. The test-bed simulates key aspects of the operational environment without putting constraints on the forecaster workload. Products and capabilities which show utility in the test-bed environment are then transitioned experimentally into the operational environment for further evaluation and assessment. SPoRT focuses on a suite of data and products from MODIS, AMSR-E, and AIRS on the NASA Terra and Aqua satellites, and total lightning measurements from ground-based networks. Some of the observations are assimilated into or used with various versions of the WRF model to provide supplemental forecast guidance to operational end users. SPoRT is enhancing partnerships with NOAA / NESDIS for new product development and data access to exploit the remote sensing capabilities of instruments on the NPOESS satellites to address short term weather forecasting problems. The VIIRS and CrIS instruments on the NPP and follow-on NPOESS satellites provide similar observing capabilities to the MODIS and AIRS instruments on Terra and Aqua. SPoRT will be transitioning existing and new capabilities into the AWIIPS II environment to continue the continuity of its activities.

  1. Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

    PubMed Central

    Loudig, Olivier; Milova, Ekaterina; Brandwein-Gensler, Margaret; Massimi, Aldo; Belbin, Thomas J.; Childs, Geoffrey; Singer, Robert H.; Rohan, Thomas; Prystowsky, Michael B.

    2007-01-01

    Gene expression profiling of formalin-fixed and paraffin-embedded (FFPE) specimens, banked from completed clinical trials and routine clinical care, has the potential to yield valuable information implicating and linking genes with clinical parameters. In order to prepare high-quality cDNA from highly fragmented FFPE-RNA, previously precluded from high-throughput analyses, we have designed a novel strategy based on the nucleic acid restoration of incomplete cDNA sequences prior to T7 in vitro transcription (IVT) amplification. We describe this strategy as complementary-template reverse-transcription (CT-RT) because short single-stranded T7-oligo-dT24-VN-DNA sequences, obtained from FFPE-RNA, are used as primers for the RT of complementary RNA templates contained in a sense-RNA library. We validated our assay by determining the correlation between expression profiles of a matched 10-year-old frozen and FFPE breast cancer sample. We show that T7 IVT-amplification of cDNA transcripts restored by CT-RT is a specific and reliable process that allows recovery of transcriptional features undetectable by direct T7 IVT-amplification of FFPE-RNA. Furthermore, CT-RT restored 35–41% of the transcripts from archived breast and cervical specimens when compared to matched frozen tissue; and profiles included tissue-specific transcripts. Our results indicate that CT-RT allows microarray profiling of severely degraded RNA that could not be analyzed by previous methods. PMID:17636051

  2. Specific hybridization probes demonstrate fewer xenotropic than mink cell focus-forming murine leukemia virus env-related sequences in DNAs from inbred laboratory mice

    SciTech Connect

    O'Neill, R.R.; Khan, A.S.; Hoggan, D.; Hartley, J.W.; Martin, M.A.; Repaske, R.

    1986-05-01

    The authors have derived hybridization probes from analogous 100-base-pair segments located within the N-terminal region of gp70 coding sequences which differentiate xenotropic from mink cell focus-forming (MCF)-related murine leukemia virus (MuLV) DNAs. The MCF probe annealed to the integrated proviruses of all six MCF MuLV isolates tested; the xenotropic probe hybridized to the DNAs of all four xenotropic proviral isolates examined. No cross-hybridization was observed, and neither probe reacted with the env segments of amphotropic or ecotropic MuLV DNAs. Southern blot analysis of HindIII- or EcoRI-digested genomic DNAs from a variety of inbred laboratory mice demonstrated the presence of more MCF- than xenotropic MuLV-related segments in every strain tested.

  3. The MuLV 4070A G541R Env mutation decreases the stability and alters the conformation of the TM ectodomain

    SciTech Connect

    Schneider, William M. [UMDNJ-Robert Wood Johnson Medical School, Department of Biochemistry, 675 Hoes Lane Rm. 636, Piscataway, NJ 08854 (United States)], E-mail: schneiwm@umdnj.edu; Zheng, Haiyan [Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854 (United States)], E-mail: haiyanz@cabm.rutgers.edu; Cote, Marie L. [UMDNJ-Robert Wood Johnson Medical School, Department of Biochemistry, 675 Hoes Lane Rm. 636, Piscataway, NJ 08854 (United States)], E-mail: coteml@umdnj.edu; Roth, Monica J. [UMDNJ-Robert Wood Johnson Medical School, Department of Biochemistry, 675 Hoes Lane Rm. 636, Piscataway, NJ 08854 (United States)], E-mail: roth@umdnj.edu

    2008-02-05

    Virus-cell and cell-cell fusion events are affected by various properties of the fusogenic Env protein on the cell surface. The G541R mutation within the TM ectodomain of murine leukemia virus (MuLV) 4070A arose by positive selection in viral passage and results in a reduction of cell-cell fusion events while maintaining viral titer. Size exclusion chromatography shows that the multimerization properties are similar among expressed wild-type and mutant ectodomain peptides. Circular dichroism measurements reveal decreased thermal stability of the G541R mutant as compared to wild type. The G541R mutant also renders the peptide more susceptible to Lys-C protease cleavage. The 42-114 monoclonal antibody does not bind to the G541R mutant peptides, suggesting a structural difference from wild type. These altered physical properties result in productive viral infection of G541R bearing virus with decreased syncytia.

  4. HIV-specific humoral and cellular immunity in rabbits vaccinated with recombinant human immunodeficiency virus-like gag-env particles

    SciTech Connect

    Haffar, O.K.; Smithgall, M.D.; Moran, P.A.; Travis, B.M.; Zarling, J.M.; Hu, S.L. (Department of Virology, Bristol-Myers Squibb Pharmaceutical Research Institute-Seattle, WA (USA))

    1991-08-01

    Recombinant human immunodeficiency virus type-1 (HIV-1)-like gag-env particles produced in mammalian cells were inoculated into two New Zealand white rabbits. In parallel, two control rabbits were inoculated with the homologous HIV-1 virions inactivated by ultraviolet light (uv) and psoralen treatments. The humoral and cellular immune responses to HIV-1 were evaluated for both groups of animals. Recombinant particles elicited humoral immunity that was specific for all the viral structural proteins. The antibodies recognized both denatured and nondenatured proteins. Moreover, the sera neutralized the in vitro infectivity of the homologous virus in CEM cells. Importantly, the recombinant particles also generated a T helper response by priming with the HIV proteins. Similar results were observed with inactivated virus immunization. Therefore, the authors results suggest that the recombinant HIV-like particles elicit functional humoral immunity as well as cellular immunity and represent a novel vaccine candidate for AIDS.

  5. The Heptad Repeat 2 Domain Is a Major Determinant for Enhanced Human Immunodeficiency Virus Type 1 (HIV-1) Fusion and Pathogenicity of a Highly Pathogenic HIV-1 Env?

    PubMed Central

    Sivaraman, Vijay; Zhang, Liguo; Meissner, Eric G.; Jeffrey, Jerry L.; Su, Lishan

    2009-01-01

    Human immunodeficiency virus type 1 (HIV-1)-mediated depletion of CD4+ lymphocytes in an infected individual is the hallmark of progression to AIDS. However, the mechanism for this depletion remains unclear. To identify mechanisms of HIV-1-mediated CD4 T-cell death, two similar viral isolates obtained from a rapid progressor patient with significantly different pathogenic phenotypes were studied. One isolate (R3A) demonstrates enhanced pathogenesis in both in vivo models and relevant ex vivo lymphoid organ model systems compared to another isolate, R3B. The pathogenic determinants were previously mapped to the V5-gp41 envelope region, correlating functionally with enhanced fusion activity and elevated CXCR4 binding affinity. To further elucidate specific differences between R3A and R3B within the V5-gp41 domains that enhance CD4 depletion, R3A-R3B chimeras to study the V5-gp41 region were developed. Our data demonstrate that six residues in the ectodomain of R3A provide the major determinant for both enhanced Env-cell fusion and pathogenicity. Furthermore, three amino acid differences in the heptad repeat 2 (HR-2) domain of R3A determined its fusion activity and significantly elevated its pathogenic activity. The chimeric viruses with enhanced fusion activity, but not elevated CXCR4 affinity, correlated with high pathogenicity in the thymus organ. We conclude that the functional domain of a highly pathogenic HIV-1 Env is determined by mutations in the HR-2 region that contribute to enhanced fusion and CD4 T-cell depletion. PMID:19726524

  6. Middle School Teacher Satisfaction with Response to Intervention (RtI): An Assessment between Inception and Implementation

    ERIC Educational Resources Information Center

    Zahedi, Karynn Jensen

    2010-01-01

    Response to intervention (RtI) is a multi-tiered process of monitoring student responses to remediation that is designed to help struggling learners succeed within the purview of regular education. Under the RtI model, students are referred to special education only after a series of documented interventions have been attempted. This study…

  7. A SYBR GREEN REAL-TIME RT-PCR METHOD TO DETECT AND QUANTITATE NORWALK VIRUS IN STOOLS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was performed with three objectives: a) to develop a real-time reverse transcription-PCR (rt RT-PCR) procedure for a commonly used laboratory strain of Norwalk virus (NV), b) to evaluate the potential of sample dilution and heat release of viral RNA as an alternative to more complex proce...

  8. An n ua l R e po rt M C S LM C S LMunsell Color Science Laboratory

    E-print Network

    Zanibbi, Richard

    1999 An n ua l R e po rt M C S LM C S LMunsell Color Science Laboratory 1999 An n ua l R e po rt #12;i Munsell Color Science Laboratory Overview & History The Munsell Color Science Laboratory (MCSL Science Laboratory: 1) To provide undergraduate and graduate education in color science, 2) To carry

  9. An n ua l R e po rt M C S LM C S LMunsell Color Science Laboratory

    E-print Network

    Zanibbi, Richard

    2000 An n ua l R e po rt M C S LM C S LMunsell Color Science Laboratory 2000 An n ua l R e po rt Laboratory Overview & History The Munsell Color Science Laboratory (MCSL) was established in 1983 after

  10. SPoRT's Participation in the GOES-R Proving Ground Activity

    NASA Technical Reports Server (NTRS)

    Jedlovec, Gary; Fuell, Kevin; Smith, Matthew; Stano, Geoffrey; Molthan, Andrew

    2011-01-01

    The next generation geostationary satellite, GOES-R, will carry two new instruments with unique atmospheric and surface observing capabilities, the Advanced Baseline Imager (ABI) and the Geostationary Lightning Mapper (GLM), to study short-term weather processes. The ABI will bring enhanced multispectral observing capabilities with frequent refresh rates for regional and full disk coverage to geostationary orbit to address many existing and new forecast challenges. The GLM will, for the first time, provide the continuous monitoring of total lightning flashes over a hemispherical region from space. NOAA established the GOES-R Proving Ground activity several years ago to demonstrate the new capabilities of these instruments and to prepare forecasters for their day one use. Proving Ground partners work closely with algorithm developers and the end user community to develop and transition proxy data sets representing GOES-R observing capabilities. This close collaboration helps to maximize refine algorithms leading to the delivery of a product that effectively address a forecast challenge. The NASA Short-term Prediction Research and Transition (SPoRT) program has been a participant in the NOAA GOES-R Proving Ground activity by developing and disseminating selected GOES-R proxy products to collaborating WFOs and National Centers. Established in 2002 to demonstrate the weather and forecasting application of real-time EOS measurements, the SPoRT program has grown to be an end-to-end research to operations activity focused on the use of advanced NASA modeling and data assimilation approaches, nowcasting techniques, and unique high-resolution multispectral data from EOS satellites to improve short-term weather forecasts on a regional and local scale. Participation in the Proving Ground activities extends SPoRT s activities and taps its experience and expertise in diagnostic weather analysis, short-term weather forecasting, and the transition of research and experimental data to operational decision support systems like NAWIPS, AWIPS, AWIPS2, and Google Earth. Recent SPoRT Proving Ground activities supporting the development and use of a pseudo GLM total lightning product and the transition of the AWG s Convective Initiation (CI) product, both of which were available in AWIPS and AWIPS II environments, by forecasters during the Hazardous Weather Testbed (HWT) Spring Experiment. SPoRT is also providing a suite of SEVIRI and MODIS RGB image products, and a high resolution composite SST product to several National Centers for use in there ongoing demonstration activities. Additionally, SPoRT has involved numerous WFOs in the evaluation of a GOES-MODIS hybrid product which brings ABI-like data sets in front of the forecaster for everyday use. An overview of this activity will be presented at the conference.

  11. Pro-Inflammatory Mediators and Apoptosis Correlate to rt-PA Response in a Novel Mouse Model of Thromboembolic Stroke

    PubMed Central

    Ansar, Saema; Chatzikonstantinou, Eva; Thiagarajah, Rushani; Tritschler, Laurent; Fatar, Marc; Hennerici, Michael G.; Meairs, Stephen

    2014-01-01

    Background A recent study suggests that patients with persistent occlusion of the middle cerebral artery (MCA) following treatment with recombinant tissue plasminogen activator (rt-PA) have better outcomes than patients with MCA occlusion not receiving rt-PA. We performed a study to elucidate possible mechanisms of this finding in a new model of thromboembolic stroke closely mimicking human pathophysiology. Methods Thromboembolic stroke was induced by local injection of thrombin directly into the right MCA of C57 black/6J mice. Rt-PA was administered 20 and 40 min after clot formation. The efficiency of rt-PA to induce thrombolysis was measured by laser Doppler. After 24 h, all animals were euthanized and interleukin (IL)-6, tumor necrosis factor-alpha (TNF-?), matrix metalloproteinase (MMP)-9, Caspase-3, hsp 32 and hsp 70 protein levels were investigated by immunofluorescence. Presence of hemorrhage was verified and infarct volume was measured using histology. Results Thrombin injection resulted in clot formation giving rise to cortical brain infarction. Early rt-PA treatment starting at 20 min after the clot formation resulted in 100% recanalization. However, rt-PA-induced thrombolysis dissolved the clot in only 38% of the animals when administered 40 min after clot formation. Protein levels of IL-6, TNF-?, MMP-9, Caspase-3, hsp 32 and hsp 70 were increased after MCAO, whereas treatment with rt-PA attenuated the expressions of inflammatory markers in those animals where the thrombolysis was successful. In addition, the infarct size was significantly reduced with rt-PA treatment compared to non-treated MCAO, regardless of whether MCA thrombolysis was successful. Conclusions The present study demonstrates a clear correlation of the protein expression of inflammatory mediators, apoptosis and stress genes with the recanalization data after rt-PA treatment. In this model rt-PA treatment decreases the infarct size regardless of whether vessel recanalization is successful. PMID:24465746

  12. Highly Specific Detection of Five Exotic Quarantine Plant Viruses using RT-PCR

    PubMed Central

    Choi, Hoseong; Cho, Won Kyong; Yu, Jisuk; Lee, Jong-Seung; Kim, Kook-Hyung

    2013-01-01

    To detect five plant viruses (Beet black scorch virus, Beet necrotic yellow vein virus, Eggplant mottled dwarf virus, Pelargonium zonate spot virus, and Rice yellow mottle virus) for quarantine purposes, we designed 15 RT-PCR primer sets. Primer design was based on the nucleotide sequence of the coat protein gene, which is highly conserved within species. All but one primer set successfully amplified the targets, and gradient PCRs indicated that the optimal temperature for the 14 useful primer sets was 51.9°C. Some primer sets worked well regardless of annealing temperature while others required a very specific annealing temperature. A primer specificity test using plant total RNAs and cDNAs of other plant virus-infected samples demonstrated that the designed primer sets were highly specific and generated reproducible results. The newly developed RT-PCR primer sets would be useful for quarantine inspections aimed at preventing the entry of exotic plant viruses into Korea. PMID:25288934

  13. Multiplex RT-PCR detection of three common viruses infecting orchids.

    PubMed

    Ali, Raymond N; Dann, Alison L; Cross, Peter A; Wilson, Calum R

    2014-11-01

    A multiplex reverse transcription polymerase chain reaction (RT-PCR) assay was developed for simultaneous detection of three orchid viruses: cymbidium mosaic virus (CymMV), odontoglossum ringspot virus (ORSV), and orchid fleck virus (OFV). Primers were used to amplify nucleocapsid protein gene fragments of 845 bp (ORSV), 505 bp (CymMV) and 160 bp (OFV). A 60-bp amplicon of plant glyceraldehyde-3-phophate dehydrogenase mRNA was included as an internal control against false negatives. The assay was validated against 31 collected plants from six orchid genera and compared with results obtained by transmission electron microscopy (TEM). The RT-PCR assay proved more sensitive than TEM for detection of OFV. PMID:24980395

  14. Feasibility of small animal cranial irradiation with the microRT system

    PubMed Central

    Kiehl, Erich L.; Stojadinovic, Strahinja; Malinowski, Kathleen T.; Limbrick, David; Jost, Sarah C.; Garbow, Joel R.; Rubin, Joshua B.; Deasy, Joseph O.; Khullar, Divya; Izaguirre, Enrique W.; Parikh, Parag J.; Low, Daniel A.; Hope, Andrew J.

    2008-01-01

    Purpose: To develop and validate methods for small-animal CNS radiotherapy using the microRT system. Materials and Methods: A custom head immobilizer was designed and built to integrate with a pre-existing microRT animal couch. The Delrin® couch-immobilizer assembly, compatible with multiple imaging modalities (CT, microCT, microMR, microPET, microSPECT, optical), was first imaged via CT in order to verify the safety and reproducibility of the immobilization method. Once verified, the subject animals were CT-scanned while positioned within the couch-immobilizer assembly for treatment planning purposes. The resultant images were then imported into CERR, an in-house-developed research treatment planning system, and registered to the microRTP treatment planning space using rigid registration. The targeted brain was then contoured and conformal radiotherapy plans were constructed for two separate studies: (1) a whole-brain irradiation comprised of two lateral beams at the 90° and 270° microRT treatment positions and (2) a hemispheric (left-brain) irradiation comprised of a single A-P vertex beam at the 0° microRT treatment position. During treatment, subject animals (n=48) were positioned to the CERR-generated treatment coordinates using the three-axis microRT motor positioning system and were irradiated using a clinical Ir-192 high-dose-rate remote after-loading system. The radiation treatment course consisted of 5 Gy fractions, 3 days per week. 90% of the subjects received a total dose of 30 Gy and 10% received a dose of 60 Gy. Results: Image analysis verified the safety and reproducibility of the immobilizer. CT scans generated from repeated reloading and repositioning of the same subject animal in the couch-immobilizer assembly were fused to a baseline CT. The resultant analysis revealed a 0.09 mm average, center-of-mass translocation and negligible volumetric error in the contoured, murine brain. The experimental use of the head immobilizer added ±0.1 mm to microRT spatial uncertainty along each axis. Overall, the total spatial uncertainty for the prescribed treatments was ±0.3 mm in all three axes, a 0.2 mm functional improvement over the original version of microRT. Subject tolerance was good, with minimal observed side effects and a low procedure-induced mortality rate. Throughput was high, with average treatment times of 7.72 and 3.13 min?animal for the whole-brain and hemispheric plans, respectively (dependent on source strength). Conclusions: The method described exhibits conformality more in line with the size differential between human and animal patients than provided by previous prevalent approaches. Using pretreatment imaging and microRT-specific treatment planning, our method can deliver an accurate, conformal dose distribution to the targeted murine brain (or a subregion of the brain) while minimizing excess dose to the surrounding tissue. Thus, preclinical animal studies assessing the radiotherapeutic response of both normal and malignant CNS tissue to complex dose distributions, which closer resemble human-type radiotherapy, are better enabled. The procedural and mechanistic framework for this method logically provides for future adaptation into other murine target organs or regions. PMID:18975718

  15. Physical properties of RT-LPCVD and LPCVD polysilicon thin films: Application to emitter solar cell

    SciTech Connect

    Lemiti, M.; Semmache, B.; Barbier, D.; Laugier, A. [LPM-INSA de Lyon, Villeurbanne (France); Le, Q.N. [Photowatt International, Bourgoin-Jallieu (France)

    1994-12-31

    This investigation was implemented in the framework of a novel all-low thermal budget polysilicon emitter solar cells fabrication technology. A comparative study of structural and electrical properties of thin silicon layer deposited by silane pyrolysis in a classical hot-wall furnace (LPCVD) and a cold-wall RTP reactor (RT-LPCVD) has been made. Deposition conditions and rapid thermal anneals were varied in order to improve the physical properties of RT-LPCVD polysilicon films. The structural properties have been characterized by means of grazing X-ray diffraction and cross-section TEM analysis. Sheet resistivity measurements performed on POCl{sub 3}-doped and subsequently rapid thermal annealed films showed the feasibility of low resistivity films particularly when the polysilicon layers are initially deposited in the amorphous state. Finally, RTCVD polysilicon emitter solar cells with various thicknesses were tested by spectral photo-response analysis.

  16. Recent Upgrades to NASA SPoRT Initialization Datasets for the Environmental Modeling System

    NASA Technical Reports Server (NTRS)

    Case, Jonathan L.; Lafontaine, Frank J.; Molthan, Andrew L.; Zavodsky, Bradley T.; Rozumalski, Robert A.

    2012-01-01

    The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed several products for its NOAA/National Weather Service (NWS) partners that can initialize specific fields for local model runs within the NOAA/NWS Science and Training Resource Center Environmental Modeling System (EMS). The suite of SPoRT products for use in the EMS consists of a Sea Surface Temperature (SST) composite that includes a Lake Surface Temperature (LST) analysis over the Great Lakes, a Great Lakes sea-ice extent within the SST composite, a real-time Green Vegetation Fraction (GVF) composite, and NASA Land Information System (LIS) gridded output. This paper and companion poster describe each dataset and provide recent upgrades made to the SST, Great Lakes LST, GVF composites, and the real-time LIS runs.

  17. Emulating a crowded intracellular environment in vitro dramatically improves RT-PCR performance

    SciTech Connect

    Lareu, Ricky R. [Tissue Modulation Laboratory, Division of Bioengineering, Faculty of Engineering, National University of Singapore, Division Office Block E3A 04-15, 7 Engineering Drive 1, Singapore 117574 (Singapore); NUS Tissue Engineering Program and Department of Orthopedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore (Singapore); Harve, Karthik S. [Tissue Modulation Laboratory, Division of Bioengineering, Faculty of Engineering, National University of Singapore, Division Office Block E3A 04-15, 7 Engineering Drive 1, Singapore 117574 (Singapore); Raghunath, Michael [Tissue Modulation Laboratory, Division of Bioengineering, Faculty of Engineering, National University of Singapore, Division Office Block E3A 04-15, 7 Engineering Drive 1, Singapore 117574 (Singapore); Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (Singapore)], E-mail: bierm@nus.edu.sg

    2007-11-09

    The polymerase chain reaction's (PCR) phenomenal success in advancing fields as diverse as Medicine, Agriculture, Conservation, or Paleontology is based on the ability of using isolated prokaryotic thermostable DNA polymerases in vitro to copy DNA irrespective of origin. This process occurs intracellularly and has evolved to function efficiently under crowded conditions, namely in an environment packed with macromolecules. However, current in vitro practice ignores this important biophysical parameter of life. In order to more closely emulate conditions of intracellular biochemistry in vitro we added inert macromolecules into reverse transcription (RT) and PCR. We show dramatic improvements in all parameters of RT-PCR including 8- to 10-fold greater sensitivity, enhanced polymerase processivity, higher specific amplicon yield, greater primer annealing and specificity, and enhanced DNA polymerase thermal stability. The faster and more efficient reaction kinetics was a consequence of the cumulative molecular and thermodynamic effects of the excluded volume effect created by macromolecular crowding.

  18. Detection of Brevipalpus -transmitted viruses in their mite vectors by RT–PCR

    Microsoft Academic Search

    K. S. KuboV; V. M. Novelli; M. Bastianel; E. C. Locali-Fabris; R. Antonioli-Luizon; M. A. Machado; J. Freitas-Astúa

    2011-01-01

    The diagnosis of plant diseases caused by Brevipalpus-transmitted viruses (BrTVs) has been done through the analyses of symptoms, transmission electron microscopy, and RT–PCR\\u000a of infected plant tissues. Here, we report the detection of Citrus leprosis virus C, Orchid fleck virus, Clerodendrum chlorotic spot virus and Solanum violaefolium ringspot virus in their viruliferous vectors Brevipalpus spp. using specific primer pairs for

  19. Using metallic resin and aluminum alloy molds to manufacture propellers with RP\\/RT technique

    Microsoft Academic Search

    C. Y. Hsu; C. K. Huang; G. J. Tzou

    2008-01-01

    Purpose – This purpose of this study is to investigate an effective method to manufacture propellers. Design\\/methodology\\/approach – The investment casting process and injection molding process have been applied separately to the rapid prototyping\\/rapid tooling (RP\\/RT) to obtain metal (Al-Si alloy) propellers and plastic (Acrylonitrile butadiene styrene – ABS) propellers. The two different manufacturing processes were compared following the same

  20. Miniature RT-PCR systems integrated with a sample pretreatment device for virus detection

    Microsoft Academic Search

    Kang-Yi Lien; Wang-Ying Lin; Chih-Hao Wang; Huan-Yao Lei; Gwo-Bin Lee

    2007-01-01

    This paper presents a new chip-based reverse transcription polymerase chain reaction (RT-PCR) system integrated with a sample pretreatment device for fast DNA amplification and diagnosis of RNA- based viruses. A new two-way serpentine-shape (S- shape) pneumatic micropump and a magnetic bio- separator were developed for purification and enrichment of viruses. The target RNA-based virus would be bound onto the antibody-conjugated

  1. First Experiment on Levitation and Plasma With HTS Magnet in the RT1 Plasma Device

    Microsoft Academic Search

    Taizo Tosaka; Yasumi Ohtani; Michitaka Ono; Toru Kuriyama; Shoichi Mizumaki; Masanao Shibui; Kazunari Nakamoto; Nobuo Tachikawa; Junji Morikawa; Yuichi Ogawa; Zensho Yoshida

    2007-01-01

    The high temperature superconducting (HTS) floating magnet of the ring trap 1 (RT-1) reached the first experiment on levitation and plasma. The magnet using an HTS coil was levitated stably by levitation coil, and plasma was produced around the ring-shaped HTS magnet by electron cyclotron heating with 8.2 GHz microwave. This novel plasma device was constructed at the University of

  2. Multiplex RT-PCR detection and microarray typing of vesicular disease viruses.

    PubMed

    Lung, Oliver; Fisher, Mathew; Beeston, Anne; Hughes, Kimberley Burton; Clavijo, Alfonso; Goolia, Melissa; Pasick, John; Mauro, William; Deregt, Dirk

    2011-08-01

    A vesicular disease multiplex reverse transcription (RT)-PCR with an accompanying microarray assay was developed for simultaneous detection and typing of foot-and-mouth disease virus (FMDV) and vesicular stomatitis virus (VSV), and for the detection of swine vesicular disease virus (SVDV) and vesicular exanthema of swine virus (VESV). The multiplex RT-PCR successfully detected viral RNA from a collection of 49 strains of vesicular viruses, including multiple strains from all seven serotypes of FMDV and both serotypes of VSV. The multiplex RT-PCR was also able to produce amplified products from the RNA genome of all four viruses simultaneously in mixed samples. An indirect (post-PCR labelling) amplicon labelling method and a direct (concurrent labelling with PCR) amplicon labelling method were compared for the purpose of microarray detection and typing. Accurate detection and typing was achieved with all strains tested in the microarray assay which utilized 163 virus- and serotype-specific probes. It was observed that microarray increased detection for some samples compared to using multiplex RT-PCR alone. This was most likely due to signal amplification resulting from fluorescent labelling. The limit of detection of the microarray assay was as low as 4.6TCID(50)/mL for FMDV. No amplification products or microarray reactivity was observed with non-target livestock pathogens tested or with samples collected from healthy cattle, sheep and pigs. All FMDV and VSV serotypes were detected as early as 2 days post-inoculation from oral swabs obtained from cattle infected experimentally. PMID:21620898

  3. A RT-PCR assay for the differential diagnosis of vesicular viral diseases of swine

    Microsoft Academic Search

    José Ignacio Núñez; Esther Blanco; Teresa Hernández; Concepción Gómez-Tejedor; Mar??a Jesus Mart??n; Joaqu??n Dopazo; Francisco Sobrino

    1998-01-01

    A RT-PCR assay based on specific amplification of RNA sequences from each of the etiological agents of three important vesicular diseases that affect swine, foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), and vesicular stomatitis virus (VSV), was developed. Genotype-specific primers that amplified DNA fragments of differential size from SVDV 3D gene or VSV L gene were selected with

  4. Improving QoS for UGS, rtPS, nrtPS, BE in WIMAX networks

    Microsoft Academic Search

    Jalel Ben-Othman; Lynda Mokdad

    2011-01-01

    In this paper we present a new admission control (AC) for IEEE 802.16. The AC aims to accept new connections according to the negotiated service class (UGS, rtPS, nrTPS, and BE). To achieve this goal we propose to use the token bucket concept that provide QoS for real time traffics without degrading the QoS of non real time traffic. To

  5. Extended-rtPS Algorithm for VoIP Services in IEEE 802.16 systems

    Microsoft Academic Search

    Howon Lee; Taesoo Kwon; Dong-Ho Cho

    2006-01-01

    There are several scheduling algorithms for Voice over IP (VoIP) services in IEEE 802.16 systems, such as unsolicited grant service (UGS), real-time polling service (rtPS), UGS with Activity Detection (UGS-AD), and Lee's algorithm using Grant-Me bit of the generic MAC header. However, these algorithms have some problems of a waste of uplink resources, additional access delay, and MAC overhead for

  6. Cycle-accurate macro-models for RT-level power analysis

    Microsoft Academic Search

    Qinru Qiu; Qing Wu; Massoud Pedram; Chih-Shun Ding

    1997-01-01

    In this paper we present a methodology and techniques for generating cycle-accurate macro-models for RT-level power analysis. The proposed macro-model predicts not only the cycle-by-cycle power consumption of a module, but the power profile of the module over time. The proposed methodology consists of three steps: module equation form generation and variable selection, variable reduction, and population stratification. First order

  7. NASA SPoRT Initialization Datasets for Local Model Runs in the Environmental Modeling System

    NASA Technical Reports Server (NTRS)

    Case, Jonathan L.; LaFontaine, Frank J.; Molthan, Andrew L.; Carcione, Brian; Wood, Lance; Maloney, Joseph; Estupinan, Jeral; Medlin, Jeffrey M.; Blottman, Peter; Rozumalski, Robert A.

    2011-01-01

    The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed several products for its National Weather Service (NWS) partners that can be used to initialize local model runs within the Weather Research and Forecasting (WRF) Environmental Modeling System (EMS). These real-time datasets consist of surface-based information updated at least once per day, and produced in a composite or gridded product that is easily incorporated into the WRF EMS. The primary goal for making these NASA datasets available to the WRF EMS community is to provide timely and high-quality information at a spatial resolution comparable to that used in the local model configurations (i.e., convection-allowing scales). The current suite of SPoRT products supported in the WRF EMS include a Sea Surface Temperature (SST) composite, a Great Lakes sea-ice extent, a Greenness Vegetation Fraction (GVF) composite, and Land Information System (LIS) gridded output. The SPoRT SST composite is a blend of primarily the Moderate Resolution Imaging Spectroradiometer (MODIS) infrared and Advanced Microwave Scanning Radiometer for Earth Observing System data for non-precipitation coverage over the oceans at 2-km resolution. The composite includes a special lake surface temperature analysis over the Great Lakes using contributions from the Remote Sensing Systems temperature data. The Great Lakes Environmental Research Laboratory Ice Percentage product is used to create a sea-ice mask in the SPoRT SST composite. The sea-ice mask is produced daily (in-season) at 1.8-km resolution and identifies ice percentage from 0 100% in 10% increments, with values above 90% flagged as ice.

  8. Performance evaluation of an EtherCAT master using Linux and the RT Patch

    Microsoft Academic Search

    Marco Cereia; Ivan Cibrario Bertolotti; Stefano Scanzio

    2010-01-01

    This paper has the twofold goal of investigating the real-time performance of an EtherCAT master entirely built from open-source components (using Linux and the RT Patch at the operating system level) and assess its ability to support concurrent best-effort tasks without compromising the real-time ones, depending on kernel configuration. This is especially important for the successful adoption of the proposed

  9. RT 2 : real-time ray-tracing for underwater range evaluation

    Microsoft Academic Search

    Giuseppe Casalino; Andrea Caiti; Alessio Turetta; Enrico Simetti

    The paper deals with the distributed acoustic localization of teams of autonomous underwater vehicles (AUVs) and proposes\\u000a a novel algorithm, real-time ray-tracing (RT2), for evaluating the distance between any pair of AUVs in the team. The technique, based on a modified formulation of the\\u000a non-linear sound-ray propagation laws, allows efficient handling of the distorted and reflected acoustic ray paths. The

  10. RNA integrity and the effect on the real-time qRT-PCR performance

    Microsoft Academic Search

    Simone Fleige; Michael W. Pfaffl

    2006-01-01

    The assessment of RNA integrity is a critical first step in obtaining meaningful gene expression data. Working with low-quality RNA may strongly compromise the experimental results of downstream applications which are often labour-intensive, time-consuming, and highly expensive. Using intact RNA is a key element for the successful application of modern molecular biological methods, like qRT-PCR or micro-array analysis. To verify

  11. Detection of Citrus tatter leaf virus with reverse transcription—polymerase chain reaction (RT-PCR)

    Microsoft Academic Search

    D. L. Hailstones; K. L. Bryant; P. Broadbent; C. Zhou

    2000-01-01

    Citrus tatter leaf virus (CTLV) has the potential to cause major losses to the Australian citrus industry if an infected clone is propagated, because\\u000a the predominant rootstocks are intolerant of CTLV infection. We have developed a robust and specific semi-nested reverse transcription—polymerase\\u000a chain reaction (RT-PCR) assay which detects CTLV in a range of citrus tissues. The sensitivity of the assay

  12. Diversity of enterovirus sequences detected in oysters by RT-heminested PCR

    Microsoft Academic Search

    Eric Dubois; Ghislaine Merle; Catherine Roquier; Aurélien Trompette; Françoise Le Guyader; Catherine Crucière; Jean-Jacques Chomel

    2004-01-01

    Oysters harvested in western France, from five sites associated with outbreaks of food-borne norovirus gastroenteritis between February 2000 and March 2001, were assayed for enterovirus RNA by reverse transcriptase-heminested polymerase chain reaction (RT-heminested PCR). Forty percent (21\\/52) of shellfish samples (pool of seven oysters) were contaminated by enteroviruses. Infectious coxsackieviruses serotype A21 were isolated from three of these positive samples.

  13. Detection of GB virus C by the RT-PCR LCx® system

    Microsoft Academic Search

    Ron L Marshall; James Cockerill; Paula Friedman; Mark Hayden; Steve Hodges; Cynthia Holas; Cheryl Jennings; Cynthia K Jou; Jon Kratochvil; Thomas Laffler; Nancy Lewis; Christi Scheffel; Dena Traylor; Lucy Wang; Natalie Solomon

    1998-01-01

    The recent publication of representative genomic sequences of GBV-C has permitted the selection of PCR primers for detection of GBV-C in clinical samples by PCR techniques. Traditional amplification methodologies which couple reverse transcription polymerase chain reaction (RT-PCR) and Southern blot detection are slow, cumbersome, and can be technique dependent. This has hampered studies to determine the clinical significance of GBV-C.

  14. Development of a versatile and stable internal control system for RT-qPCR assays.

    PubMed

    Felder, Eva; Wölfel, Roman

    2014-11-01

    RT-qPCR, an established method for the detection of RNA viruses, requires internal RNA controls for the correct interpretation of PCR results. Robust and versatile RT-PCR controls can be achieved for example by packaging RNA into a virus-derived protein shell. In this study a MS2-based internal control system was developed, that allows stable and universal packing of different RNAs into non-infectious, non-lytic MS2-based viral like particles (VLPs). Two competitive internal controls for a hantavirus assay and a Crimean-Congo Hemorrhagic Fever Virus (CCHFV) assay were cloned for the expression of VLPs. The expression of VLPs containing the RNA of interest could be induced with arabinose in Escherichia coli. The VLPs proved to be temperature resistant and could be frozen and thawed several times without degradation. Distinction of IC RNA from the target RNA was facilitated by a clear shift in the melting temperature or by specific hybridization signals. Furthermore, target and IC PCR amplification could be easily distinguished by their size in gel-electrophoretic analyses. Limits of detection were determined, demonstrating that the application of the IC did not reduce the sensitivity of the target RT-qPCR reactions. The system can be adapted to nearly any required sequence, resulting in a highly flexible method with broad range applications. PMID:25072380

  15. Transition from Classical RM Instability at Embedded Material Interface to Ablative RT Growth

    NASA Astrophysics Data System (ADS)

    Velikovich, A. L.; Schmitt, A. J.; Gardner, J. H.; Metzler, N.; Aglitskiy, Y.

    2004-11-01

    If a laser target is designed with material interface(s) embedded into it, then the imperfections of such interface(s) can contribute to seeding the ablative Rayleigh-Taylor (RT) instability at its accelerated surface. We study the case of a single rippled interface in planar geometry. As the classical Richtmyer-Meshkov (RM) growth starts at the shocked interface, rippled transmitted and reflected shock waves carry the perturbations to the unperturbed rear surface of the target and the ablation front. After the shock breakouts, rarefaction waves from both sides of the target run back to the interface. Rapid deceleration of the interface in a rarefaction wave coming from a lower-density fluid triggers its oscillation that reverses the phase of mass modulation. As a result, the subsequent ablative RT growth starts in the negative direction, in contrast with the regular cases of ablative RT growth initiated by the ripples on either front or rear surface of the target. We present the results of the theory and numerical simulations for hydrodynamic experiments with plastic-foam targets on the Nike KrF laser at NRL.

  16. Application of a master equation for quantitative mRNA analysis using qRT-PCR.

    PubMed

    Liu, Z Lewis; Palmquist, Debra E; Ma, Menggen; Liu, Jiangbo; Alexander, Nancy J

    2009-08-10

    The qRT-PCR has been widely accepted as the assay of choice for mRNA quantification. For conventional practice, housekeeping genes have been applied as internal reference for data normalization and analysis since the technology appeared. However, housekeeping genes vary under different conditions and environmental stimuli and no commonly accepted housekeeping gene references are available. Accurate data acquisition and data reproducibility remain challenging and it is difficult to compare results from different experimental sources. Using yeast and a Fusarium fungus as examples, we demonstrate the independent performance of a sole reference gene, CAB, designated as a constant manual threshold for data acquisition, normalization, and analysis for multiple plate reactions. A robust master equation based on the CAB reference and the set of calibration control genes thereafter was established to estimate mRNA abundance for the same RNA background reactions. A valid range of amplification efficiency between 95% and 100% was observed for the control genes in different RNA background applied on an ABI real time PCR 7500 system. This newly developed robust quality control system provides a reliable means for absolute quantification of mRNA using the qRT-PCR, simplifies the conventional qRT-PCR procedures, and increases data reliability, reproducibility, and throughput of the assay. PMID:19539678

  17. SPoRT Participation in the GOES-R and JPSS Proving Grounds

    NASA Technical Reports Server (NTRS)

    Jedlovec, Gary; Fuell, Kevin; Smith, Matthew

    2013-01-01

    For the last several years, the NASA Short-term Prediction Research and Transition (SPoRT) project at has been working with the various algorithm working groups and science teams to demonstrate the utility of future operational sensors for GOES-R and the suite of instruments for the JPSS observing platforms. For GOES-R, imagery and products have been developed from polar-orbiting sensors such as MODIS and geostationary observations from SEVIRI, simulated imagery, enhanced products derived from existing GOES satellites, and data from ground-based observing systems to generate pseudo or proxy products for the ABI and GLM instruments. The suite of products include GOES-POES basic and RGB hybrid imagery, total lightning flash products, quantitative precipitation estimates, and convective initiation products. SPoRT is using imagery and products from VIIRS, CrIS, ATMS, and OMPS to show the utility of data and products from their operational counterparts on JPSS. The products include VIIRS imagery in swath form, the GOES-POES hybrid, a suite of RGB products including the air mass RGB using water vapor and ozone channels from CrIS, and several DNB products. Over a dozen SPoRT collaborative WFOs and several National Centers are involved in an intensive evaluation of the operational utility of these products.

  18. Aprotinin: an antidote for recombinant tissue-type plasminogen activator (rt-PA) active in vivo.

    PubMed

    Clozel, J P; Banken, L; Roux, S

    1990-08-01

    The goal of the study was to assess if aprotinin, a protease inhibitor, could be used to antagonize in vivo the effects of recombinant tissue-type plasminogen activator (rt-PA). The time course of the lysis of a radioactive jugular vein thrombus was monitored continuously with an external gamma counter in anesthetized rabbits. Recombinant t-PA (0.25 mg) was given intravenously as a bolus injection (10% of the dose), followed by a 4 h infusion (90% of the dose). Rabbits received aprotinin 20 min after the start of the infusion as an intravenous bolus injection at a dose of 60,000 IU/kg (n = 4) or 20,000 IU/kg (n = 4). The rate of lysis in the different groups was compared 2, 60 and 180 min after aprotinin administration. Both doses of aprotinin immediately stopped thrombolysis. Thrombolysis was still blocked at 180 min with the highest dose but not with the lowest dose. Moreover, aprotinin could prevent the increase in bleeding time secondary to the injection of rt-PA. These results suggest that aprotinin might be used in vivo as an antidote for rt-PA. PMID:1695642

  19. Bimodal AIDS Vaccine Approach: Induction of cellular as well as humoral immunity can protect from systemic infection?

    PubMed Central

    Rasmussen, Robert A.; Lakhashe, Samir K.; Ruprecht, Ruth M.

    2015-01-01

    HIV clade C (HIV-C) strains comprise ~56% of all HIV infections worldwide, and AIDS vaccines intended for global use must protect against this subtype. Our vaccine strategy has been to induce balanced antiviral immunity consisting of both neutralizing antibody and cell-mediated immune responses, an approach we tested in primates. As reported earlier, after isolating recently transmitted HIV-C strains from Zambian infants, we used env from one such virus, HIV1084i, to generate a multimeric gp160 immunogen. From another virus, isolated from a different child of the same mother-infant cohort, we cloned env to generate a recombinant simian-human immunodeficiency virus (SHIV), which was adapted to rhesus monkeys to yield SHIV-1157ip. Infant macaques were immunized with recombinant viral proteins, including multimeric HIV-C Env 1084i. To test whether cross-protection could be achieved, we mismatched HIV-C Env immunogens and challenge virus env. All vaccinated and control monkeys were exposed orally to low-dose SHIV-1157ip. Animals with no or only transient infection were rechallenged intrarectally with a high dose of R5 SHIV-1157ipd3N4, a "late”, animal-evolved variant of SHIV-1157ip. Compared to controls, the vaccinees had significantly lower peak viral RNA loads, and one vaccinee remained completely virus-free, even in lymphoid tissues. Data from our novel heterologous mucosal challenge model and our protein-only immunogens imply that significant protection against heterologous viruses circulating in the local community may be achievable with a strategy that seeks to simultaneously induce cellular immunity as well as neutralizing antibody responses. PMID:20510739

  20. Genomic organization and sequence of the rat major histocompatibility complex class Ia gene RT1.A{sup u}

    SciTech Connect

    Walter, L.; Tiemann, C.; Heine, L.; Guenther, E. [Abteilung Immungenetik der Universitaet, Goettingen (Germany)

    1995-03-01

    From a rat cosmid library of LEW.1W genomic DNA (RT1{sup u}) in the pWE15 vector cosmid clone 9b1 was isolated by using rat MHC probe LW2. Clone 9b1 was mapped to the RT1.A region by Southern blotting of DNA of RT1 recombinant congenic rat strains. After stable transfection of cosmid 9b1 into mouse L cells and flow cytometry analysis, a high level of expression (about 100-fold compared with controls) was observed with RT1.A{sup u} class I antigen-specific rat monoclonal antibody NR3/31. Thus cosmid 9b1 contains a complete functional class I gene. Since this gene was derived from the RT1.A region and showed a class Ia-like expression and since its gene product reacted with an RT1.A{sup u} antigen-specific antibody, the clone described here must represent a class Ia RT1.A{sup u} gene. 8 refs., 2 figs.

  1. Universal Single-Probe RT-PCR Assay for Diagnosis of Dengue Virus Infections

    PubMed Central

    Alm, Erik; Lesko, Birgitta; Lindegren, Gunnel; Ahlm, Clas; Söderholm, Sandra; Falk, Kerstin I.; Lagerqvist, Nina

    2014-01-01

    Background Dengue is a mosquito-borne viral disease that has become more prevalent in the last few decades. Most patients are viremic when they present with symptoms, and early diagnosis of dengue is important in preventing severe clinical complications associated with this disease and also represents a key factor in differential diagnosis. Here, we designed and validated a hydrolysis-probe-based one-step real-time RT-PCR assay that targets the genomes of dengue virus serotypes 1–4. Methodology/Principal Findings The primers and probe used in our RT-PCR assay were designed to target the 3? untranslated region of all complete genome sequences of dengue virus available in GenBank (n?=?3,305). Performance of the assay was evaluated using in vitro transcribed RNA, laboratory-adapted virus strains, external control panels, and clinical specimens. The linear dynamic range was found to be 104–1011 GCE/mL, and the detection limit was between 6.0×102 and 1.1×103 GCE/mL depending on target sequence. The assay did not cross-react with human RNA, nor did it produce false-positive results for other human pathogenic flaviviruses or clinically important etiological agents of febrile illnesses. We used clinical serum samples obtained from returning travelers with dengue-compatible symptomatology (n?=?163) to evaluate the diagnostic relevance of our assay, and laboratory diagnosis performed by the RT-PCR assay had 100% positive agreement with diagnosis performed by NS1 antigen detection. In a retrospective evaluation including 60 archived serum samples collected from confirmed dengue cases 1–9 days after disease onset, the RT-PCR assay detected viral RNA up to 9 days after appearance of symptoms. Conclusions/Significance The validation of the RT-PCR assay presented here indicates that this technique can be a reliable diagnostic tool, and hence we suggest that it be introduced as the method of choice during the first 5 days of dengue symptoms. PMID:25522325

  2. The rat T-cell surface protein RT6 is associated with src family tyrosine kinases and generates an activation signal

    Microsoft Academic Search

    Mark R. Rigby; Rita Bortell; Dale L. Greiner; Michael P. Czech; Jes K. Klarlund; John P. Mordes; Aldo A. Rossini

    1996-01-01

    RT6 is a glycosyl-phosphatidylinositol-linked surface molecule present on most mature rat T-cells. RT6+ T-cells can prevent the expression of autoimmune diabetes in the BB rat, but the mechanism is unknown. Because cross-linking of other glycosyl-phosphatidylinositol-linked T-cell proteins is known to activate T-cells, we investigated the signaling properties of RT6. Antibody cross-linking of RT6 enhanced expression of the alpha subunit of

  3. The First Hypervariable Region of the gp120 Env Glycoprotein Defines the Neutralizing Susceptibility of Heterologous Human Immunodeficiency Virus Type 1 Isolates to Neutralizing Antibodies Elicited by the SF162gp140 Immunogen

    Microsoft Academic Search

    Lance K. Ching; Giorgos Vlachogiannis; Katherine A. Bosch; Leonidas Stamatatos

    2008-01-01

    Current vaccine efforts to elicit cross-reactive neutralizing antibodies (NAbs) against human immunodefi- ciency virus (HIV) focus on the engineering of soluble mimetics of the trimeric HIV Env glycoprotein (com- monly termed gp140 immunogens). Such immunogens are thought to be more effective than previously tested monomeric gp120 immunogens at eliciting cross-reactive NAbs. Still, the breadth of neutralizing antibody responses elicited by

  4. Protective efficacy of adenovirus/protein vaccines against SIV challenges in rhesus monkeys.

    PubMed

    Barouch, Dan H; Alter, Galit; Broge, Thomas; Linde, Caitlyn; Ackerman, Margaret E; Brown, Eric P; Borducchi, Erica N; Smith, Kaitlin M; Nkolola, Joseph P; Liu, Jinyan; Shields, Jennifer; Parenteau, Lily; Whitney, James B; Abbink, Peter; Ng'ang'a, David M; Seaman, Michael S; Lavine, Christy L; Perry, James R; Li, Wenjun; Colantonio, Arnaud D; Lewis, Mark G; Chen, Bing; Wenschuh, Holger; Reimer, Ulf; Piatak, Michael; Lifson, Jeffrey D; Handley, Scott A; Virgin, Herbert W; Koutsoukos, Marguerite; Lorin, Clarisse; Voss, Gerald; Weijtens, Mo; Pau, Maria G; Schuitemaker, Hanneke

    2015-07-17

    Preclinical studies of viral vector-based HIV-1 vaccine candidates have previously shown partial protection against neutralization-resistant virus challenges in rhesus monkeys. In this study, we evaluated the protective efficacy of adenovirus serotype 26 (Ad26) vector priming followed by purified envelope (Env) glycoprotein boosting. Rhesus monkeys primed with Ad26 vectors expressing SIVsmE543 Env, Gag, and Pol and boosted with AS01B-adjuvanted SIVmac32H Env gp140 demonstrated complete protection in 50% of vaccinated animals against a series of repeated, heterologous, intrarectal SIVmac251 challenges that infected all controls. Protective efficacy correlated with the functionality of Env-specific antibody responses. Comparable protection was also observed with a similar Ad/Env vaccine against repeated, heterologous, intrarectal SHIV-SF162P3 challenges. These data demonstrate robust protection by Ad/Env vaccines against acquisition of neutralization-resistant virus challenges in rhesus monkeys. PMID:26138104

  5. Detection of HIV type 1 env subtypes A, B, C, and E in Asia using dried blood spots: a new surveillance tool for molecular epidemiology.

    PubMed

    Cassol, S; Weniger, B G; Babu, P G; Salminen, M O; Zheng, X; Htoon, M T; Delaney, A; O'Shaughnessy, M; Ou, C Y

    1996-10-10

    Global surveillance of HIV-1 subtypes for genetic characterization is hampered by the biohazard of processing and the difficulties of shipping whole blood or cells from many developing country regions. We developed a technique for the direct automated sequencing of viral DNA from dried blood spot (DBS) specimens collected on absorbent paper, which can be mailed unrefrigerated in sturdy paper envelopes with low biohazard risk. DBS were collected nonrandomly from HIV-1-infected, mostly asymptomatic, patients in five Asian countries in 1991, and shipped via airmail or hand carried without refrigeration to Bangkok, and then transshipped to North America for processing. After more than 2 years of storage, including 6 months at ambient temperatures, proviral DNA in the DBS was amplified by nested PCR, and a 389-nucleotide segment of the C2-V3 env gene region was sequenced, from which 287 base pairs were aligned and subtyped by phylogenetic analysis with neighbor-joining and other methods. From southern India, there were 25 infections with subtype C and 2 with subtype A. From Myanmar (Burma), we identified the first subtype E infection, as well as six subtype BB, a distinct cluster within subtype B that was first discovered in Thailand and that has now appeared in China, Malaysia, and Japan. From southwest China, one BB was identified, while a "classical" B typical of North American and European strains was found in Indonesia. From Thailand, five DBS of ambiguous serotype were identified as three B, one BB, and one E. A blinded control serotype E specimen was correctly identified, but a serotype BB control was not tested. Most HIV-1 in southern India appears to be env subtype C, with rare A, as others have reported in western and northern India. The subtypes BB and E in Myanmar, and the BB in China, suggest epidemiological linkage with these subtypes in neighboring Thailand. DBS are a practical, economical technique for conducting large-scale molecular epidemiological surveillance to track the global distribution and spread of HIV-1 variants. PMID:8893051

  6. Equine Viperin Restricts Equine Infectious Anemia Virus Replication by Inhibiting the Production and/or Release of Viral Gag, Env, and Receptor via Distortion of the Endoplasmic Reticulum

    PubMed Central

    Tang, Yan-Dong; Na, Lei; Zhu, Chun-Hui; Shen, Nan; Yang, Fei; Fu, Xian-Qiu; Wang, Yu-Hong; Fu, Li-Hua; Wang, Jia-Yi; Lin, Yue-Zhi; Wang, Xue-Feng; Wang, Xiaojun

    2014-01-01

    ABSTRACT Viperin is an endoplasmic reticulum (ER)-associated multifunctional protein that regulates virus replication and possesses broad antiviral activity. In many cases, viperin interferes with the trafficking and budding of viral structural proteins by distorting the membrane transportation system. The lentivirus equine infectious anemia virus (EIAV) has been studied extensively. In this study, we examined the restrictive effect of equine viperin (eViperin) on EIAV replication and investigated the possible molecular basis of this restriction to obtain insights into the effect of this cellular factor on retroviruses. We demonstrated that EIAV infection of primary equine monocyte-derived macrophages (eMDMs) upregulated the expression of eViperin. The overexpression of eViperin significantly inhibited the replication of EIAV in eMDMs, and knockdown of eViperin transcription enhanced the replication of EIAV in eMDMs by approximately 45.8%. Further experiments indicated that eViperin restricts EIAV at multiple steps of viral replication. The overexpression of eViperin inhibited EIAV Gag release. Both the ?-helix domain and radical S-adenosylmethionine (SAM) domain were required for this activity. However, the essential motifs in SAM were different from those reported for the inhibition of HIV-1 Gag by human viperin. Furthermore, eViperin disrupted the synthesis of both EIAV Env and receptor, which consequently inhibited viral production and entry, respectively, and this disruption was dependent on the eViperin ?-helix domain. Using immunofluorescence assays and electron microscopy, we demonstrated that the ?-helix domain is responsible for the distortion of the endoplasmic reticulum (ER). Finally, EIAV did not exhibit counteracting eViperin at the protein level. IMPORTANCE In previous studies, viperin was indicated as restricting virus replications primarily by the inhibition of virus budding. Here, we show that viperin may have multiple antiviral mechanisms, including the reduction of EIAV Gag budding and Env expression, and these activities are dependent on different viperin domains. We especially demonstrate that the overexpression of viperin inhibits EIAV entry by decreasing the level of virus receptor. Therefore, viperin restriction of viruses is determined largely by the dependence of virus on the cellular membrane transportation system. PMID:25122784

  7. The NASA Short-Term Prediction Research and Transition (SPoRT) Center: Opportunities for Collaboration in the Great Lakes Region

    NASA Technical Reports Server (NTRS)

    Molthan, Andrew L.

    2010-01-01

    The presentation slides include: The SPoRT Center, History and Future of SPoRT, Great Lakes Applications, Great Lakes Forecasting Issues, Applications to the WRF-EMS, Precipitation Science, Lake Effect Precipitation, Sensitivity to Microphysics, Exploring New Schemes, Opportunities for Collaboration, and SPoRT Research and Development.

  8. Specific sequences commonly found in the V3 domain of HIV-1 subtype C isolates affect the overall conformation of native Env and induce a neutralization-resistant phenotype independent of V1/V2 masking

    PubMed Central

    Salomon, Aidy; Krachmarov, Chavdar; Lai, Zhong; Honnen, William; Zingman, Barry S.; Sarlo, Julie; Gorny, Miroslaw K.; Zolla-Pazner, Susan; Robinson, James E.; Pinter, Abraham

    2014-01-01

    Primary HIV-1 isolates are relatively resistant to neutralization by antibodies commonly induced after infection or vaccination. This is generally attributed to masking of sensitive epitopes by the V1/V2 domain and/or glycans situated at various positions in Env. Here we identified a novel masking effect mediated by subtype C-specific V3 sequences that contributes to the V1/V2-independent and glycan-independent neutralization resistance of chimeric and primary Envs to antibodies directed against multiple neutralization domains. Positions at several conserved charged and hydrophobic sites in the V3 crown and stem were also shown to affect neutralization phenotype. These results indicated that substitutions typically present in subtype C and related V3 sequences influence the overall conformation of native Env in a way that occludes multiple neutralization targets located both within and outside of the V3 domain, and may reflect an alternative mechanism for neutralization resistance that is particularly active in subtype C and related isolates. PMID:24314667

  9. Insulin treatment prevents diabetes mellitus but not thyroiditis in RT6-depleted diabetes resistant BB\\/Wor rats

    Microsoft Academic Search

    P. A. Gottlieb; E. S. Handler; M. C. Appel; D. L. Greiner; J. P. Mordes; A. A. Rossini

    1991-01-01

    Summary  Prophylactic insulin administration is known to prevent hyperglycaemia in diabetes prone BB rats and non-obese diabetic mice. This study investigated the effect of insulin treatment on the development of overt diabetes, clinically inapparent anti-islet autoreactivity, and thyroiditis in RT6-depleted diabetes resistant BB rats. Fewer than 1% of these animals develop spontaneous diabetes, but if depleted of RT6+ T cells >50%

  10. Statistical models in assessing fold change of gene expression in real-time RT-PCR experiments

    Microsoft Academic Search

    Wenjiang J. Fu; Jianbo Hu; Thomas Spencer; Raymond J. Carroll; Guoyao Wu

    2006-01-01

    Real-time RT-PCR has been frequently used in quantitative research in molecular biology and bioinformatics. It provides remarkably useful technology to assess expression of genes. Although mathematical models for gene amplification process have been studied, statistical models and methods for data analysis in real-time RT-PCR have received little attention. In this paper, we briefly introduce current mathematical models, and study statistical

  11. One-step Multiplex RT-PCR Assay for the Detection of Peste des petits ruminants Virus in Clinical Samples

    Microsoft Academic Search

    V. Balamurugan; A. Sen; P. Saravanan; R. P. Singh; T. J. Rasool; S. K. Bandyopadhyay

    2006-01-01

    A single-tube one-step multiplex RT-PCR was standardized to amplify both 337 bp and 191 bp fragments of N and M genes of peste\\u000a des petits ruminants virus (PPRV), respectively, and only a 337 bp fragment of N gene of Rinderpest virus (RPV). The RT-PCR\\u000a using purified viral RNA was easily adopted for direct detection of PPRV in clinical field samples

  12. Regional nodal recurrence in breast cancer patients treated with conservative surgery and radiation therapy (BCS+RT)

    SciTech Connect

    Pejavar, Sunanda [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT (United States); Wilson, Lynn D. [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT (United States); Haffty, Bruce G. [Department of Radiation Oncology, UMDNJ-Robert Wood Johnson Medical School and Cancer Institute of New Jersey, New Brunswick, NJ (United States)]. E-mail: hafftybg@umdnj.edu

    2006-12-01

    Purpose: To review regional nodal (RN) management and identify predictors of RN relapse in patients treated with breast conserving surgery and radiation therapy (BCS+RT). Methods and Materials: Patients with Stage I and II breast cancer (N = 1920) underwent BCS+RT from 1973 to 2003. Patients undergoing RN were treated with a median dose of 46 Gy. Patients undergoing axillary dissection (AXD, N = 1330) were treated to the breast alone if node-negative (N = 984), and to the breast and supraclavicular fossa if node-positive (N = 346). Patients who did not undergo AXD (N = 590) were treated with RT to the supraclavicular fossa and axilla. Sentinel node biopsy (SNB) was performed on 126 patients. SN-negative patients (N = 110) were treated with tangents only. There were 16 SN-positive patients who did not undergo complete AXD and were treated with RT. Results: As of September 2005, there have been 36 RN relapses for an actuarial nodal control rate (NCR) of 98% at 10 years. There was no difference in NCR between those undergoing AXD (NCR = 97.4%) and those receiving RT without AXD (NCR = 97.9%). In multivariate analysis, young age, non-Caucasian race, and pathologic nodal status correlated with increased risk of nodal relapse. Of the 126 patients undergoing SNB, there was only 1 nodal recurrence. None of the 16 SN-positive patients treated with RT without AXD had nodal failure. Conclusions: In patients undergoing BCS+RT, both regional nodal irradiation and AXD (including SNB) resulted in equally high rates of regional nodal control. Nodal RT may also be an effective treatment for SN-positive patients.

  13. Simulative validations of RT2: A Real-Time Ray-Tracing technique for acoustic-based range evaluation

    Microsoft Academic Search

    Giuseppe Casalino; Alessio Turetta; Enrico Simetti; Andrea Caiti

    2011-01-01

    This paper presents simulations and a sensitivity analysis of a Real-Time Ray-Tracing (RT2) technique for acoustic-based range evaluation. The RT2 is an algorithm that evaluates the range of an acoustic receiver from the emitter, while taking into account the anisotropy of the underwater medium, exploiting the knowledge of the depth information of both the emitter and the receiver, and the

  14. SIMOO-RT-an object-oriented framework for the development of real-time industrial automation systems

    Microsoft Academic Search

    Leandro Buss Becker; Carlos Eduardo Pereira

    2002-01-01

    Presents SIMOO-RT, an object-oriented framework designed to support the whole development cycle of real-time industrial automation systems. It is based on the concept of distributed active objects, which are autonomous execution entities that have their own thread of control, and that interact with each other by means of remote methods invocation. SIMOO-RT covers most of the development phases, from requirements

  15. A Sensitive and Reliable RT-Nested PCR Assay for Detection of Citrus tristeza Virus from Naturally Infected Citrus Plants

    Microsoft Academic Search

    Charith Raj Adkar-Purushothama; P. K. Maheshwar; Teruo Sano; G. R. Janardhana

    2011-01-01

    A specific and sensitive reverse transcriptase-nested polymerase chain reaction assay (RT-nPCR) was developed for the detection\\u000a of Citrus tristeza virus (CTV) from naturally infected citrus samples. Two sets of primer pairs were designed by alignment of nucleotide sequences\\u000a available in GenBank database for different genotypes of CTV. RT-nPCR reaction components and thermal cycling parameters were\\u000a optimized and reaction conditions were

  16. Identification of Reference Genes for Quantitative RT-PCR in Ascending Aortic Aneurysms

    PubMed Central

    Henn, Dominic; Bandner-Risch, Doris; Perttunen, Hilja; Schmied, Wolfram; Porras, Carlos; Ceballos, Francisco; Rodriguez-Losada, Noela; Schäfers, Hans-Joachim

    2013-01-01

    Hypertension and congenital aortic valve malformations are frequent causes of ascending aortic aneurysms. The molecular mechanisms of aneurysm formation under these circumstances are not well understood. Reference genes for gene activity studies in aortic tissue that are not influenced by aortic valve morphology and its hemodynamic consequences, aortic dilatation, hypertension, or antihypertensive medication are not available so far. This study determines genes in ascending aortic tissue that are independent of these parameters. Tissue specimens from dilated and undilated ascending aortas were obtained from 60 patients (age ?70 years) with different morphologies of the aortic valve (tricuspid undilated n?=?24, dilated n?=?11; bicuspid undilated n?=?6, dilated n?=?15; unicuspid dilated n?=?4). Of the studied individuals, 36 had hypertension, and 31 received ACE inhibitors or AT1 receptor antagonists. The specimens were obtained intraoperatively from the wall of the ascending aorta. We analyzed the expression levels of 32 candidate reference genes by quantitative RT-PCR (RT-qPCR). Differential expression levels were assessed by parametric statistics. The expression analysis of these 32 genes by RT-qPCR showed that EIF2B1, ELF1, and PPIA remained constant in their expression levels in the different specimen groups, thus being insensitive to aortic valve morphology, aortic dilatation, hypertension, and medication with ACE inhibitors or AT1 receptor antagonists. Unlike many other commonly used reference genes, the genes EIF2B1, ELF1, and PPIA are neither confounded by aortic comorbidities nor by antihypertensive medication and therefore are most suitable for gene expression analysis of ascending aortic tissue. PMID:23326585

  17. A RT-PCR assay for the differential diagnosis of vesicular viral diseases of swine.

    PubMed

    Núñez, J I; Blanco, E; Hernández, T; Gómez-Tejedor, C; Martín, M J; Dopazo, J; Sobrino, F

    1998-06-01

    A RT-PCR assay based on specific amplification of RNA sequences from each of the etiological agents of three important vesicular diseases that affect swine, foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), and vesicular stomatitis virus (VSV), was developed. Genotype-specific primers that amplified DNA fragments of differential size from SVDV 3D gene or VSV L gene were selected with the aid of a computer program. Experimental testing of the primers predicted as SVDV-specific identified a primer pair, SA2/SS4, that rendered a specific product from SVDV RNAs, but did not amplify RNA from either FMDV or coxsackie B5 virus (CV-B5), a highly related picornavirus. Primers SA2/SS4 were used in combination with primers 3D2/3D1, which amplify a product of different size on FMDV 3D gene (Rodriguez et al., 1992). This combined RT-PCR reaction allowed a sensitive and specific differential detection of FMDV and SVDV RNAs in a single tube, by means of the analysis of the amplified products in agarose gels. The results obtained were similar when RNA extracted from viral stocks or plastic wells coated with either viral supernatants or extracts from lesions of infected animals, were used as starting material in the reactions. Using a similar approach, VSV serotype-specific primers IA/IS and NA/NS were selected for the specific amplification of VSV-Indiana and VSV-New Jersey RNAs, respectively. The combined use of SVDV, FMDV and VSV specific primers in a single reaction resulted in a genotype-specific amplification of each of the viral RNAs. Thus, differential diagnosis of FMDV from SVDV and/or VSV can be carried out in a single RT-PCR reaction, using a rapid and simplified methodology. PMID:9694330

  18. Measurement delay associated with the Guardian® RT continuous glucose monitoring system

    PubMed Central

    Wei, C; Lunn, D J; Acerini, C L; Allen, J M; Larsen, A M; Wilinska, M E; Dunger, D B; Hovorka, R

    2010-01-01

    Aims Using compartment modelling, we assessed the time delay between blood glucose and sensor glucose measured by the Guardian® RT continuous glucose monitoring system in young subjects with Type 1 diabetes (T1D). Methods Twelve children and adolescents with T1D treated by continuous subcutaneous insulin infusion (male/female 7/5; age 13.1 ± 4.2 years; body mass index 21.9 ± 4.3 kg/m2; mean ± sd) were studied over 19 h in a Clinical Research Facility. Guardian® RT was calibrated every 6 h and sensor glucose measured every 5 min. Reference blood glucose was measured every 15 min using a YSI 2300 STAT Plus Analyser. A population compartment model of sensor glucose–blood glucose kinetics was adopted to estimate the time delay, the calibration scale and the calibration shift. Results The population median of the time delay was 15.8 (interquartile range 15.2, 16.5) min, which was corroborated by correlation analysis between blood glucose and 15-min delayed sensor glucose. The delay has a relatively low intersubject variability, with 95% of individuals predicted to have delays between 10.4 and 24.3 min. Population medians (interquartile range) for the scale and shift are 0.800 (0.777, 0.823) (unitless) and 1.66 (1.47, 1.84) mmol/l, respectively. Conclusions In young subjects with T1D, the total time delay associated with the Guardian® RT system was approximately 15 min. This is twice that expected on physiological grounds, suggesting a 5- to 10-min delay because of data processing. Delays above 25 min are rarely to be observed. PMID:20121899

  19. Chemical composition and RT[sub NDT] determinations for Midland weld WF-70

    SciTech Connect

    Nanstad, R.K.; McCabe, D.E.; Swain, R.L.; Miller, M.K. (Oak Ridge National Lab., TN (United States))

    1992-12-01

    The Heavy-Section Steal Irradiation Program Tenth Irradiation Series has the objective to investigate the affects of radiation on the fracture toughness of the low-upper-shelf submerged-arc welds (B W designation WF-70) in the reactor pressure vessel of the canceled Midland Unit 1 nuclear plant. This report discusses determination of variations in chemical composition And reference temperature (RT[sub NDT]) throughout the welds. Specimens were machined from different sections and through thickness locations in both the beltline and nozzle course welds. The nil-ductility transition temperatures ranged from [minus]40 to [minus]60[degrees]C ([minus]40 and [minus]76[degrees]F) while the RT[sub NDT]S, controlled by the Charpy behavior, varied from [minus]20 to 37[degrees]C ([minus]4 to 99[degrees]F). The upper-shelf energies varied from 77 to 108 J (57 to 80 ft-lb). The combined data revealed a mean 41-J (30-ft-lb) temperature of [minus]8[degrees]C (17[degrees]F) with a mean upper-shelf energy of 88 J (65 ft-lb). The copper contents range from 0.21 to 0.34 wt % in the beltline weld and from 0.37 to 0.46 wt % in the nozzle course weld. Atom probe field ion microscope analyses indicated substantial depletion of copper in the matrix but no evidence of copper clustering. Statistical analyses of the Charpy and chemical composition results as well as interpretation of the ASME procedures for RT[sub NDT] determination are discussed.

  20. Ion channels in pediatric CNS Atypical Teratoid/Rhabdoid Tumor (AT/RT) cells: potential targets for novel therapeutic agents.

    PubMed

    Banderali, Umberto; Jayanthan, Aarthi; Hoeksema, Kimberley A; Narendran, Aru; Giles, Wayne R

    2012-03-01

    The central nervous system Atypical Teratoid/Rhabdoid Tumor (CNS AT/RT) is a highly malignant neoplasm that commonly affects infants and young children, and has an extremely poor prognosis. Recently, a small subset of ion channels have been found to be over-expressed in a variety of malignant cells, thus emerging as potential therapeutic targets for difficult to treat tumors. We have studied the electrophysiological properties of AT/RT cell lines with particular attention to cell volume sensitive ion channels (VSC). This class of membrane proteins can play a fundamental role in cellular processes relevant to tumor development. We have found that chloride selective VSCs are particularly active in AT/RT cell lines, compared to non-tumor cells. We evaluated specific inhibitors for activity against chloride selective VSCs and consequently for their ability to inhibit the growth and survival of AT/RT cells in vitro. The results demonstrated that the extent of volume sensitive membrane current inhibition by these agents was correlated with their potency in AT/RT cell growth inhibition in vitro. In addition, we showed that ion channel inhibition enhanced the activity of certain anti-neoplastic agents, suggesting its value in effective drug combination protocols. Results presented provide preliminary in vitro data for possible evaluation of distinct ion channels as plausible therapeutic targets in the treatment of AT/RT. PMID:21971736

  1. Unbiased molecular analysis of T cell receptor expression using template-switch anchored RT-PCR.

    PubMed

    Quigley, Máire F; Almeida, Jorge R; Price, David A; Douek, Daniel C

    2011-08-01

    A detailed knowledge of the principles that guide clonal selection within the memory and effector T cell pools is essential to further our understanding of the factors that influence effective T cell-mediated immunity and has direct implications for the rational design of vaccines and immunotherapies. This unit provides methods for the unbiased quantification and characterization of all expressed T cell receptor (TCR) gene products within any defined T cell population. The approach is based on a template-switch anchored reverse transcription-polymerase chain reaction (RT-PCR) and is optimized for the analysis of antigen-specific T cells isolated directly ex vivo. PMID:21809317

  2. The S2 VLBI Systems: DAS, RT/PT and Correlator

    NASA Technical Reports Server (NTRS)

    Petrachenko, William T.; Bujold, Marc; Cannon, Wayne H.; Carlson, Brent R.; Dewdney, Peter E.; Feil, Georg H.; Newby, Paul; Novikov, Alexander; Popelar, Josef; Wietfeldt, Richard D.

    2000-01-01

    The S2 VLBI system synthesizes wide IF bandwidths by rapidly switching the local oscillator (LO) frequency in a small (1-4) number of baseband converters (BBC's). Data are recorded on video cassettes using an array of 8 VHS transports. Characteristics of the S2 Data Acquisition System (DAS), the S2 Record and Playback Terminals (RT and PT) and the S2 Correlator are summarized. The bandwidth synthesis (BWS) frequency switching sequence used in a series of system validation experiments is presented.

  3. Using the SPoRT POES/GOES Hybrid Product in OCONUS Forecasting

    NASA Technical Reports Server (NTRS)

    Smith, Matt; Fuell, Kevin; Nelson, Jim

    2014-01-01

    The SPoRT (Short-term Prediction and Research Transition) Program at the NASA/Marshall Space Flight Center has been providing unique NASA and NOAA data and techniques to partner Weather Forecast Offices (WFOs) for ten years. Data are provided in the Decision Support System used by WFO forecasters: AWIPS. For the last couple of years, SPoRT has been producing the POES/GOES Hybrid. This suite of products combines the strength ofl5- minute animations of GOES imagery - providing temporal continuity, with the higher resolution, relatively random availability, of polar orbiting (POES) imagery data. The product was first introduced with only MODIS data from NASA's Terra and Aqua satellites, but recently the VIIRS instrument onboard the Suomi-NPP satellite was added, providing better high-resolution coverage. These products represent SPoRT's efforts to prepare for higher resolution, higher frequency GOES-R imagery - as well as helping to move VIIRS (JPSS) data into the mainstream of weather forecasting. SPoRT generates 5 products for this dataset: Visible, Longwave Infrared (11 micrometers), Shortwave IR (3.7 micrometers), Water Vapor (6.7 micrometers), and Fog (Difference of 11 micrometer and 3.7 micrometer channels). The Water Vapor hybrid product has a Red-Blue-Green image from MODIS inlaid, since it provides even more qualitative information than water vapor alone. Animated examples of the products will be shown in this presentation. While the resolution at nadir of GOES imagery is nominally Han (4km for IR channels), the inlaid polar orbiter imagery has a resolution of 250m (lkm for IR channels). This has tremendous application in the continental US. However, in high latitudes, since the usefulness of GOES degrades poleward rapidly, the contrast of GOES and POES data is stark. The consistent temporal nature of GOES, even though at a reduced resolution at high latitudes, provides basic situational awareness, but the introduction of polar data is very helpful in seeing the big picture with clarity - even if only briefly. This presentation will offer real situations where these products helped forecasters make better informed decisions quickly. Plans to augment the product further with the addition of data from several A VHRR instruments will be described.

  4. Challenges in Transitioning Research Data to Operations: The SPoRT Paradigm

    NASA Technical Reports Server (NTRS)

    Jedloved, Gary J.; Smith, Matt; McGrath, Kevin

    2010-01-01

    Established in 2002 to demonstrate the weather and forecasting application of real-time EOS measurements, the NASA Short-term Prediction Research and Transition (SPoRT) program has grown to be an end-to-end research to operations activity focused on the use of advanced NASA modeling and data assimilation approaches, nowcasting techniques, and unique high-resolution multispectral data from EOS satellites to improve short-term weather forecasts on a regional and local scale. With the ever-broadening application of real-time high resolution satellite data from current EOS and planned NPP, JPSS, and GOES-R sensors to weather forecast problems, significant challenges arise in the acquisition, delivery, and integration of the new capabilities into the decision making process of the operational weather community. For polar orbiting sensors such as MODIS, AIRS, VIIRS, and CRiS, the use of direct broadcast ground stations is key to the real-time delivery of the data and derived products in a timely fashion. With the ABI on the geostationary GOES-R satellite, the data volume will likely increase by a factor of 5- 10 from current data streams. However, the high data volume and limited bandwidth of end user facilities presents a formidable obstacle to timely access to the data. This challenge can be addressed through the use of subsetting techniques, innovative web services, and the judicious selection of data formats. Many of these approaches have been implemented by SPoRT for the delivery of real-time products to NWS forecast offices and other weather entities. Once available in decision support systems like AWIPS II, these new data and products must be integrated into existing and new displays that allow for the integration of the data with existing operational products in these systems. SPoRT is leading the way in demonstrating this enhanced capability. This paper will highlight the ways SPoRT is overcoming many of the challenges presented by the enormous data volumes of current and future satellite systems to get unique high quality research data into the operational weather environment.

  5. Helical Tomotherapy-Based STAT RT: Dosimetric Evaluation for Clinical Implementation of a Rapid Radiation Palliation Program

    SciTech Connect

    McIntosh, Alyson; Dunlap, Neal; Sheng, Ke; Geezey, Constance; Turner, Benton [Department of Radiation Oncology, University of Virginia, Charlottesville, VA (United States); Blackhall, Leslie; Weiss, Geoffrey [Department of Medicine, University of Virginia, Charlottesville, VA (United States); Lappinen, Eric [Department of Eastern Virginia Medical School, Norfolk, VA (United States); Larner, James M. [Department of Radiation Oncology, University of Virginia, Charlottesville, VA (United States); Read, Paul W., E-mail: pwr3u@virginia.ed [Department of Radiation Oncology, University of Virginia, Charlottesville, VA (United States)

    2010-01-01

    Helical tomotherapy-based STAT radiation therapy (RT) uses an efficient software algorithm for rapid intensity-modulated treatment planning, enabling conformal radiation treatment plans to be generated on megavoltage computed tomography (MVCT) scans for CT simulation, treatment planning, and treatment delivery in one session. We compared helical tomotherapy-based STAT RT dosimetry with standard linac-based 3D conformal plans and standard helical tomotherapy-based intensity-modulated radiation therapy (IMRT) dosimetry for palliative treatments of whole brain, a central obstructive lung mass, multilevel spine disease, and a hip metastasis. Specifically, we compared the conformality, homogeneity, and dose with regional organs at risk (OARs) for each plan as an initial step in the clinical implementation of a STAT RT rapid radiation palliation program. Hypothetical planning target volumes (PTVs) were contoured on an anthropomorphic phantom in the lung, spine, brain, and hip. Treatment plans were created using three planning techniques: 3D conformal on Pinnacle{sup 3}, helical tomotherapy, and helical tomotherapy-based STAT RT. Plan homogeneity, conformality, and dose to OARs were analyzed and compared. STAT RT and tomotherapy improved conformality indices for spine and lung plans (CI spine = 1.21, 1.17; CI lung = 1.20, 1.07, respectively) in comparison with standard palliative anteroposterior/posteroanterior (AP/PA) treatment plans (CI spine = 7.01, CI lung = 7.30), with better sparing of heart, esophagus, and spinal cord. For palliative whole-brain radiotherapy, STAT RT and tomotherapy reduced maximum and mean doses to the orbits and lens (maximum/mean lens dose: STAT RT = 2.94/2.65 Gy, tomotherapy = 3.13/2.80 Gy, Lateral opposed fields = 7.02/3.65 Gy), with an increased dose to the scalp (mean scalp dose: STAT RT = 16.19 Gy, tomotherapy = 15.61 Gy, lateral opposed fields = 14.01 Gy). For bony metastatic hip lesions, conformality with both tomotherapy techniques (CI = 1.01 each) is superior to AP/PA treatments (CI = 1.21), as expected. Helical tomotherapy-based STAT RT treatment planning provides clinically acceptable dosimetry, with conformality and homogeneity that is superior to standard linac-based 3D conformal planning and is only slightly inferior to standard helical tomotherapy IMRT dosimetry. STAT RT facilitates rapid treatment planning and delivery for palliative radiation of patients with metastatic disease, with relative sparing of adjacent OARs compared with standard 3D conformal plans.

  6. Theoretical studies on the molecular basis of HIV-1RT/NNRTIs interactions.

    PubMed

    Decha, Panita; Intharathep, Pathumwadee; Udommaneethanakit, Thanyarat; Sompornpisut, Pornthep; Hannongbua, Supot; Wolschann, Peter; Parasuk, Vudhichai

    2011-02-01

    Molecular dynamics simulations (MD) of the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) complexed with the four non-nucleoside reverse transcriptase inhibitors (NNRTIs): efavirenz (EFV), emivirine (EMV), etravirine (ETV) and nevirapine (NVP), were performed to examine the structures, binding free energies and the importance of water molecules in the binding site. The binding free energy, calculated using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), was found to decrease in the following order: EFV ~ ETV > EMV > NVP. The decrease in stability of the HIV-1 RT/NNRTI complexes is in good agreement with the experimentally derived half maximal inhibitory concentration (IC(50)) values. The interaction energy of the protein-inhibitor complexes was found to be essentially associated with the cluster of seven hydrophobic residues, L100, V106, Y181, Y188, F227, W229 and P236, and two basic residues, K101 and K103. Moreover, these residues are considered to be the most frequently detected mutated amino acids during treatment by various NNRTIs and therefore, those most likely to have been selected in the population for resistance. PMID:20583854

  7. Microdroplet Sandwich Real-Time RT-PCR for Detection of Pandemic and Seasonal Influenza Subtypes

    PubMed Central

    Angione, Stephanie L.; Inde, Zintis; Beck, Christina M.; Artenstein, Andrew W.; Opal, Steven M.; Tripathi, Anubhav

    2013-01-01

    As demonstrated by the recent 2012/2013 flu epidemic, the continual emergence of new viral strains highlights the need for accurate medical diagnostics in multiple community settings. If rapid, robust, and sensitive diagnostics for influenza subtyping were available, it would help identify epidemics, facilitate appropriate antiviral usage, decrease inappropriate antibiotic usage, and eliminate the extra cost of unnecessary laboratory testing and treatment. Here, we describe a droplet sandwich platform that can detect influenza subtypes using real-time reverse-transcription polymerase chain reaction (rtRT-PCR). Using clinical samples collected during the 2010/11 season, we effectively differentiate between H1N1p (swine pandemic), H1N1s (seasonal), and H3N2 with an overall assay sensitivity was 96%, with 100% specificity for each subtype. Additionally, we demonstrate the ability to detect viral loads as low as 104 copies/mL, which is two orders of magnitude lower than viral loads in typical infected patients. This platform performs diagnostics in a miniaturized format without sacrificing any sensitivity, and can thus be easily developed into devices which are ideal for small clinics and pharmacies. PMID:24066051

  8. Dusty shells surrounding the carbon variables S Scuti and RT Capricorni

    NASA Astrophysics Data System (ADS)

    Me?ina, M.; Kerschbaum, F.; Groenewegen, M. A. T.; Ottensamer, R.; Blommaert, J. A. D. L.; Mayer, A.; Decin, L.; Luntzer, A.; Vandenbussche, B.; Posch, Th.; Waelkens, C.

    2014-06-01

    For the Mass-loss of Evolved StarS (MESS) programme, the unprecedented spatial resolution of the PACS photometer on board the Herschel Space Observatory was employed to map the dusty environments of asymptotic giant branch (AGB) and red supergiant (RSG) stars. Among the morphologically heterogeneous sample, a small fraction of targets is enclosed by spherically symmetric detached envelopes. Based on observations in the 70 ?m and 160 ?m wavelength bands, we investigated the surroundings of the two carbon semiregular variables S Sct and RT Cap, which both show evidence for a history of highly variable mass-loss. S Sct exhibits a bright, spherically symmetric detached shell, 138? in diameter and co-spatial with an already known CO structure. Moreover, weak emission is detected at the outskirts, where the morphology seems indicative of a mild shaping by interaction of the wind with the interstellar medium, which is also supported by the stellar space motion. Two shells are found around RT Cap that were not known so far in either dust emission or from molecular line observations. The inner shell with a diameter of 188? shows an almost immaculate spherical symmetry, while the outer ~5' structure is more irregularly shaped. MoD, a modification of the DUSTY radiative transfer code, was used to model the detached shells. Dust temperatures, shell dust masses, and mass-loss rates are derived for both targets. Appendices are available in electronic form at http://www.aanda.org

  9. [Cloning and analysis of reverse transcriptase(RT) of Ty1-copia retrotransposons in Dendrobium officinale].

    PubMed

    Li, Cong; Si, Jin-Ping; Gao, Yan-Hui; Zhu, Yu-Qiu

    2014-01-01

    Using universal primer Ty1-copia retrotransposon RT,43 Ty1-copia like retrotransposon RT with high heterogeneity, stop codon mutation and frameshift mutation were amplified by PCR from genomic DNA of Zhejiang Lin'an (C15) and Yunnan Guangnan (A39) of Dendrobium officinale. The length of these sequences varied from 260 to 266 bp, and was rich in AT and consistency ranged from 47.1% to 97.7%. Different c/s-acting regulatory elements induced by low temperature, heat, light, all kinds of plant growth regulating substances and the starting transcription signals, corresponding to CAAT box, TATA box conserved sequences and some other regulatory elements. When being translated into amino acids, ten sequences presented stop codon mutation, five sequences presented frameshift mutation, and thirty-seven sequences presented conserved sequence "SLYGKQ" mutation. Six categories were identified through phylogenic analysis after alignment analyses of their amino acid sequences, and with other plants (eg. Triticum aestivum, Eleocharis quinqueflora) having high homology, which indicated that horizontal transmission of retrotransposon occurred among the plants in the past. PMID:24761633

  10. Imaging of transverse cracks in austenitic welds with RT-SAFT

    NASA Astrophysics Data System (ADS)

    Höhne, C.; Kolkoori, S. R.; Rahman, M.-U.; Prager, J.

    2014-02-01

    The synthetic aperture focusing technique (SAFT) is an imaging technique commonly used in ultrasonic inspection. In order to apply SAFT to the inspection of austenitic welds, the inhomogeneous anisotropic nature of the weld structure has to be taken into account. A suitable approach to accomplish this, is to couple the SAFT-algorithm with a ray tracing program (RT-SAFT). While SAFT-imaging of cracks in austenitic welds by use of ray tracing has been carried out before, all attempts so far were limited to longitudinal cracks which usually allows a treatment as 2-dimensional problem. In case of transverse cracks, a full 3-dimensional ray tracing is necessary in order to perform a SAFT-reconstruction. In this paper, we give an outline of our attempts to reconstruct images of transverse cracks in austenitic welds, utilizing 3-dimensional ray tracing and a layered structure model derived from an empirical model of grain orientations in welds. We present results of this RT-SAFT on experimental data taken from transverse cracks in different austenitic welds, which show that size and position of the cracks can be estimated with good accuracy, and compare them to images obtained by assuming an isotropic homogeneous medium which corresponds to the application of the classical SAFT-algorithm.

  11. Effect of Inflammatory Mediators on ATP Release of Human Urothelial RT4 Cells

    PubMed Central

    Mansfield, Kylie J.; Hughes, Jessica R.

    2014-01-01

    Inflammation is an important contributor to the aetiology of a number of bladder dysfunctions including interstitial cystitis, painful bladder syndrome, and overactive bladder. The aim of this study was to examine the effects of inflammatory mediators on urothelial ATP release. Human urothelial RT4 cells were exposed to normal buffer or varying concentrations of inflammatory mediators (bradykinin, histamine, and serotonin) in the presence or absence of hypotonic stretch stimuli (1?:?2 dilution of Krebs-Henseleit buffer). Others have demonstrated that bradykinin increased stretch-induced ATP release; however, we observed no change in control or stretch-induced ATP release with bradykinin. Pretreatment of RT4 cells with histamine or serotonin decreased stretch-induced ATP release (P = 0.037, P = 0.040, resp.). Previous studies have demonstrated increased ATP release in response to inflammation utilising whole bladder preparations in contrast to our simple model of cultured urothelial cells. The current study suggests that it is unlikely that there is a direct interaction between the release of inflammatory mediators and increased ATP release, but rather more complex interactions occurring in response to inflammation that lead to increased bladder sensation. PMID:24839598

  12. Construction and Operation of an Internal Coil Device, RT-1, with a High-Temperature Superconductor

    NASA Astrophysics Data System (ADS)

    Ogawa, Yuichi; Yoshida, Zensho; Morikawa, Junji; Saito, Haruhiko; Watanabe, Sho; Yano, Yoshihisa; Mizumaki, Shoichi; Tosaka, Taizo

    An internal coil device called Ring Trap-1 (RT-1) has been constructed to explore an innovative concept for a high-beta plasma based on a new relaxation theory. A high-temperature superconductor (HTS) Bi-2223 tape is employed for the internal coil of RT-1. The coil is cooled to 20 K with helium gas supplied by G-M refrigerators, and charged to a magnetomotive force of 250 kA using an external power supply. For these cooling and charging methods, we have developed several innovative techniques such as a demountable transfer tube system, persistent current switch, detachable electrode, and others. In addition, we have paid much attention to the deterioration of the HTS tape during the fabrication of the internal coil. As a result, we have demonstrated that the decay of the persistent current of the internal coil is ˜1% during 8 h. The internal coil is lifted with a levitation coil located at the upper region of the vacuum vessel. The coil position monitored with laser sensors is feedback controlled through the regulation of the levitation coil current. Stable levitation for a few hours has been demonstrated for various plasma experiments.

  13. RT-PCR and cell culture infectivity assay to detect enteroviruses during drinking water treatment processes.

    PubMed

    Ali, M A; El-Esnawy, N A; Shoaeb, A R; Ibraheim, M; El-Hawaary, S E

    1999-01-01

    In this study, 62 water samples were collected from two water treatment plants (WTPs) in Suez Canal cities (Port Said and Ismaillia) and one plant in Cairo (Giza WTP) in addition to the beginning of the two Nile river branches (Rosetta and Damietta). Viruses were concentrated by adsorption-elution ethod sing 142 mm-diameter nitrocellulose membrane of 0.45 microm pore size and eluted with 3% beef extract at pH 9.5. The concentrated samples were inoculated for 3 successive passages in three cell culture types (Vero, BGM and RD). Enterovirus RNAs in CPE-induced samples were extracted by guanidinium thiocyanate/ phenol/chloroform and heat shock methods and detected by RT-PCR and neutralization test. The results showed that eight samples [14.5% (8/62)] contained enteroviruses most of them were polioviruses [87.5% (7/8)] and coxsackievirus type B2 [12.5% (1/8)]. The three cell cultures were of the same sensitivity to detect the isolated viruses. Also, RT-PCR followed by neutralization assay facilitates and accelerate the results. The guanidinium thiocyanate extraction method was more sensitive than heat shock method. The results turned our attention to review our technology of water treatment and disinfection step in addition to the selection of suitable intake for the drinking water treatment plants. PMID:17219867

  14. RT distributional analysis of cognitive-control-related brain activity in first-episode schizophrenia.

    PubMed

    Fassbender, Catherine; Scangos, Katie; Lesh, Tyler A; Carter, Cameron S

    2014-03-01

    Impairments in cognitive control are a defining feature of schizophrenia. Aspects of cognitive control include proactive control-the maintenance of task rules or goals to bias attention and maintain preparedness-and reactive control-the engagement of attention in reaction to changing cognitive demands. Proactive control is thought to be particularly impaired in schizophrenia. We sought to examine proactive and reactive control in schizophrenia, as measured by reaction time (RT) variability, and especially long RTs, which are thought to represent lapses in proactive control, during the Stroop paradigm. Furthermore, we sought to examine the neural underpinnings of lapses in proactive control and the subsequent engagement of reactive control in those with schizophrenia, as compared to healthy controls, using fMRI. We found that patients with schizophrenia displayed greater RT variability and more extremely long RTs than controls suggesting that proactive control was weaker in the schizophrenia than in the control group. All of the subjects engaged regions of the cognitive control network during long RTs, consistent with an engagement of reactive control following a failure in proactive control on these trials. The schizophrenia group, however, displayed significantly diminished activity in these regions relative to controls. Our results suggest increased failures in proactive control, but also impaired reactive control, in schizophrenia as compared to healthy subjects. PMID:24615691

  15. RT Distributional Analysis of Cognitive Control-Related Brain Activity in First Episode Schizophrenia

    PubMed Central

    Fassbender, Catherine; Scangos, Katie; Lesh, Tyler A.; Carter, Cameron S.

    2014-01-01

    Impairments in cognitive control are a defining feature of schizophrenia. Aspects of cognitive control include proactive control, the maintenance of task rules or goals to bias attention and maintain preparedness, and reactive control, the engagement of attention in reaction to changing cognitive demands. Proactive control is thought to be particularly impaired in schizophrenia. We sought to examine proactive and reactive control in schizophrenia, as measured by reaction time (RT) variability and especially long RTs, thought to represent lapses in proactive control, during the Stroop paradigm. Furthermore we sought to examine the neural underpinnings of lapses in proactive control and the subsequent engagement of reactive control in those with schizophrenia compared to healthy controls, using fMRI. We found that patients with schizophrenia displayed greater RT variability and more especially long RTs than controls, suggesting that proactive control is weaker in the schizophrenia compared with the control group. All participants engaged regions of the cognitive control network during long RTs, consistent with an engagement of reactive control following a failure in proactive control on these trials. The schizophrenia group, however, displayed significantly diminished activity in these regions compared to controls. Our results suggest increased failures in proactive but also impaired reactive control in schizophrenia compared to healthy subjects. PMID:24615691

  16. Evaluation of automated RT-PCR to accelerate the laboratory diagnosis of foot-and-mouth disease virus.

    PubMed

    Reid, Scott M; Grierson, Sylvia S; Ferris, Nigel P; Hutchings, Geoffrey H; Alexandersen, Soren

    2003-02-01

    Automated fluorogenic (5' nuclease probe-based) reverse transcription polymerase chain reaction (RT-PCR) procedures were evaluated for the diagnosis of foot-and-mouth disease (FMD) using suspensions of vesicular epithelium, heparinised or clotted blood, milk and oesophageal-pharyngeal fluid ('probang') samples from the United Kingdom (UK) 2001 epidemic and on sera from animals experimentally infected with the outbreak serotype O FMD virus strain. A MagNA Pure LC was initially programmed to automate the nucleic acid extraction and RT procedures with the PCR amplification carried out manually by fluorogenic assay in a GeneAmp 5700 Sequence Detection System. This allowed 32 samples to be tested by one person in a typical working day or 64 samples by two people within 10-12 h. The PCR amplification was later automated and a protocol developed for one person to complete a single test incorporating 96 RT-PCR results within 2 working days or for two people to do the same thing in around 12 h. The RT-PCR results were directly compared with those obtained by the routine diagnostic tests of ELISA and virus isolation in cell culture. The results on blood, probang and milk samples were in broad agreement between the three procedures but specific RT-PCR protocols for such material have to be fully optimised as perhaps have the positive-negative acceptance criteria. However, the automated RT-PCR achieved definitive diagnostic results (positive or negative) on supernatant fluids from first passage inoculated cell cultures and its sensitivity was greater than ELISA on suspensions of vesicular epithelium (ES) and at least equivalent to that of virus isolation in cell culture. The combined tests of ELISA, virus isolation in cell culture and RT-PCR might, therefore, only be required for confirmation of a first outbreak of FMD in a previously FMD-free country. Should a prolonged outbreak subsequently occur, then either ELISA plus RT-PCR or else RT-PCR alone could be used as the laboratory diagnostic tool(s). Either approach would eliminate the requirement for sample passage in cell culture and considerably advance the issue of laboratory diagnostic test results. PMID:12505626

  17. Evaluating the Impacts of NASA/SPoRT Daily Greenness Vegetation Fraction on Land Surface Model and Numerical Weather Forecasts

    NASA Technical Reports Server (NTRS)

    Bell, Jordan R.; Case, Jonathan L.; Molthan, Andrew L.

    2011-01-01

    The NASA Short-term Prediction Research and Transition (SPoRT) Center develops new products and techniques that can be used in operational meteorology. The majority of these products are derived from NASA polar-orbiting satellite imagery from the Earth Observing System (EOS) platforms. One such product is a Greenness Vegetation Fraction (GVF) dataset, which is produced from Moderate Resolution Imaging Spectroradiometer (MODIS) data aboard the NASA EOS Aqua and Terra satellites. NASA SPoRT began generating daily real-time GVF composites at 1-km resolution over the Continental United States (CONUS) on 1 June 2010. The purpose of this study is to compare the National Centers for Environmental Prediction (NCEP) climatology GVF product (currently used in operational weather models) to the SPoRT-MODIS GVF during June to October 2010. The NASA Land Information System (LIS) was employed to study the impacts of the new SPoRT-MODIS GVF dataset on land surface models apart from a full numerical weather prediction (NWP) model. For the 2010 warm season, the SPoRT GVF in the western portion of the CONUS was generally higher than the NCEP climatology. The eastern CONUS GVF had variations both above and below the climatology during the period of study. These variations in GVF led to direct impacts on the rates of heating and evaporation from the land surface. The second phase of the project is to examine the impacts of the SPoRT GVF dataset on NWP using the Weather Research and Forecasting (WRF) model. Two separate WRF model simulations were made for individual severe weather case days using the NCEP GVF (control) and SPoRT GVF (experimental), with all other model parameters remaining the same. Based on the sensitivity results in these case studies, regions with higher GVF in the SPoRT model runs had higher evapotranspiration and lower direct surface heating, which typically resulted in lower (higher) predicted 2-m temperatures (2-m dewpoint temperatures). The opposite was true for areas with lower GVF in the SPoRT model runs. These differences in the heating and evaporation rates produced subtle yet quantifiable differences in the simulated convective precipitation systems for the selected severe weather case examined.

  18. Transitioning NPOESS Data to Weather Offices: The SPoRT Paradigm with EOS Data

    NASA Technical Reports Server (NTRS)

    Jedlovec, Gary

    2009-01-01

    Real-time satellite information provides one of many data sources used by NWS weather forecast offices (WFOs) to diagnose current weather conditions and to assist in short-term forecast preparation. While GOES satellite data provides relatively coarse spatial resolution coverage of the continental U.S. on a 10-15 minute repeat cycle, polar orbiting imagery has the potential to provide snapshots of weather conditions at high-resolution in many spectral channels. Additionally, polar orbiting sounding data can provide additional information on the thermodynamic structure of the atmosphere in data sparse regions of at asynoptic observation times. The NASA Short-term Prediction Research and Transition (SPoRT) project has demonstrated the utility of polar orbiting MODIS and AIRS data on the Terra and Aqua satellites to improve weather diagnostics and short-term forecasting on the regional and local scales. SPoRT scientists work directly forecasters at selected WFOS in the Southern Region (SR) to help them ingest these unique data streams into their AWIPS system, understand how to use the data (through on-site and distance learn techniques), and demonstrate the utility of these products to address significant forecast problems. This process also prepares forecasters for the use of similar observational capabilities from NPOESS operational sensors. NPOESS environmental data records (EDRs) from the Visible 1 Infrared Imager I Radiometer Suite (VIIRS), the Cross-track Infrared Sounder (CrlS) and Advanced Technology Microwave Sounder (ATMS) instruments and additional value-added products produced by NESDIS will be available in near real-time and made available to WFOs to extend their use of NASA EOS data into the NPOESS era. These new data streams will be integrated into the NWs's new AWIPS II decision support tools. The AWIPS I1 system to be unveiled in WFOs in 2009 will be a JAVA-based decision support system which preserves the functionality of the existing systems and offers unique development opportunities for new data sources and applications in the Service Orientated Architecture ISOA) environment. This paper will highlight some of the SPoRT activities leading to the integration of VllRS and CrIS/ATMS data into the display capabilities of these new systems to support short-term forecasting problems at WFOs.

  19. Development of a novel recombinant encapsidated RNA particle: evaluation as an internal control for diagnostic RT-PCR.

    PubMed

    King, Donald P; Montague, Nick; Ebert, Katja; Reid, Scott M; Dukes, Juliet P; Schädlich, Lysann; Belsham, Graham J; Lomonossoff, George P

    2007-12-01

    This report describes the generation of novel encapsidated RNA particles and their evaluation as in-tube internal controls in diagnostic real-time reverse-transcription PCR (rRT-PCR) assays for the detection of RNA viruses. A cassette containing sequences of 2 diagnostic primer sets for foot-and-mouth disease virus (FMDV) and a set for swine vesicular disease virus (SVDV) was engineered into a full-length cDNA clone containing the RNA-2 segment of Cowpea Mosaic Virus (CPMV). After co-inoculation with a plasmid that expressed CPMV RNA-1, recombinant virus particles were rescued from cowpea plants (Vigna unguiculata). RNA contained in these particles was amplified in diagnostic rRT-PCR assays used for detection of FMDV and SVDV. Amplification of these internal controls was used to confirm that rRT-PCR inhibitors were absent from clinical samples, thereby verifying negative assay results. The recombinant CPMVs did not reduce the analytical sensitivity of the rRT-PCRs when amplification of the insert was performed in the same tube as the diagnostic target. This system provides an attractive solution to the production of internal controls for rRT-PCR assays since CPMV grows to high yields in plants, the particles are thermostable, RNase resistant and simple purification of RNA-2 containing capsids yields a preparation which is non-infectious. PMID:17727966

  20. Seasonal variation in transcript abundance in cork tissue analyzed by real time RT-PCR.

    PubMed

    Soler, Marçal; Serra, Olga; Molinas, Marisa; García-Berthou, Emili; Caritat, Antònia; Figueras, Mercè

    2008-05-01

    The molecular processes underlying cork biosynthesis and differentiation are mostly unknown. Recently, a list of candidate genes for cork biosynthesis and regulation was made available opening new possibilities for molecular studies in cork oak (Quercus suber L.). Based on this list, we analyzed the seasonal variation in mRNA abundance in cork tissue of selected genes by real time reverse-transcriptase polymerase chain reaction (RT-PCR). Relative transcript abundance was evaluated by principal component analysis and genes were clustered in several functional subgroups. Structural genes of suberin pathways such as CYP86A1, GPAT and HCBT, and regulatory genes of the NAM and WRKY families showed highest transcript accumulation in June, a crucial month for cork development. Other cork structural genes, such as FAT and F5H, were significantly correlated with temperature and relative humidity. The stress genes HSP17.4 and ANN were strongly positively correlated to temperature, in accord with their protective role. PMID:18316306

  1. [Establishment of RT- LAMP for rapid detection of foot-and-mouth disease virus].

    PubMed

    Li, Jian; Chen, Qin; Xiong, Wei; Fang, Xue-En

    2009-03-01

    A rapid detection of foot-and-mouth disease virus (FMDV) was established by using reverse transcription loop-mediated isothermal amplification (RT-LAMP) method, meanwhile its specificity and sensitivity were assessed. The results showed that the FMDV RNA could be amplified by incubation at 65degrees C for only 1h using six primers designed based on FMDV polyprotein gene and the amplification products could be detected easily by naked-eye. There is no cross reaction with other virus such as SVDV, SFV and PPV by detecting their RNA samples. The detection limit of this method was found to be 10(-5) dilution of RNA sample which was 100-fold higher than that of PCR and 10-fold higher than real-time PCR. PMID:19678569

  2. Long-term starspot activity of short-period RS Canum Venaticorum stars. II. RT Andromedae

    SciTech Connect

    Zeilik, M.; Cox, D.A.; De Blasi, C.; Rhodes, M.; Budding, E. (New Mexico Univ., Albuquerque (USA) Carter Observatory, Wellington (New Zealand))

    1989-10-01

    The photometric distortion waves in the light curves of the short-period RS CVn system RT And are parameterized by means of a dark, circular starspot model. The light curves are drawn from archival sources and 1987 and 1989 observations. The longitudes, latitudes, and areas of the active regions are inferred and the information content of the archival data is evaluated. It is concluded that one large starspot region on the primary star at high latitude and near quadrature longitudes can account for the major maculation effects since 1920. The temperature difference between the spotted region and the photosphere is 1100 to 1200 K. Good quality light curves result in an eccentricity (e = 0.026) and major axis orientation consistent with those reported by others using different procedures. 36 refs.

  3. Microhard MHX2420 Orbital Performance Evaluation Using RT Logic T400CS

    NASA Technical Reports Server (NTRS)

    TintoreGazulla, Oriol; Lombardi, Mark

    2012-01-01

    RT Logic allows simulation of Ground Station - satellite communications: Static tests have been successful. Dynamic tests have been performed for simple passes. Future dynamic tests are needed to simulate real orbit communications. Satellite attitude changes antenna gain. Atmospheric and rain losses need to be added. STK Plug-in will be the next step to improve the dynamic tests. There is a possibility of running longer simulations. Simulation of different losses available in the STK Plug-in. Microhard optimization: Effect of Microhard settings on the data throughput have been understood. Optimized settings improve data throughput for LEO communications. Longer hop intervals make transfer of larger packets more efficient (more time between hops in frequency). Use of FEC (Reed-Solomon) reduces the number of retransmissions for long-range or noisy communications.

  4. Observation of Classical RM Instability Feeding Ablative RT Growth in Planar Plastic Targets

    NASA Astrophysics Data System (ADS)

    Aglitskiy, Y.; Metzler, N.; Karasik, M.; Serlin, V.; Obenschain, S. P.; Schmitt, A. J.; Velikovich, A. L.; Gardner, J. H.; Varadarajan, J.; Walsh, T.

    2004-11-01

    We observed a classical Richtmyer-Meshkov growth at the shocked embedded foam/plastic interface evolving into an ablative Rayleigh-Taylor growth. Our advanced two-slab targets consisted of a RF foam layer separated by a 2-D sinusoidal interface from a solid plastic layer. The targets were irradiated from the foam side by 4 ns Nike KrF laser pulses at 50 TW/cm2, with and without a 3.5 ns long, 3% foot preceding the main pulse. An observed linear growth of mass modulation amplitude in the positive direction characteristic of the light-to-heavy classical RM instability continued until the amplitude reached a peak value, then its variation changed direction and gradually evolved into the ablative RT growth with a reversed phase. Both the observed timing and amplitude of the peak scaled as predicted when the laser pulse shape was modified by adding a foot.

  5. Multiplex RT-PCR for the Detection of Leukemia-Associated Translocations

    PubMed Central

    Salto-Tellez, Manuel; Shelat, Suresh G.; Benoit, Bernice; Rennert, Hanna; Carroll, Martin; Leonard, Debra G.B.; Nowell, Peter; Bagg, Adam

    2003-01-01

    The aim of this study was to validate the application of a commercially available multiplex reverse transcription polymerase chain reaction (RT-PCR) assay [Hemavision-7 System] for the seven most common leukemia translocations for routine molecular diagnostic hematopathology practice. A total of 98 samples, comprising four groups, were evaluated: Group 1, 16 diagnostic samples molecularly positive by our existing laboratory-developed assays for PML-RAR?/t (15;17) or BCR-ABL/t (9;22); Group 2, 51 diagnostic samples negative by our laboratory-developed assays for PML-RAR?/t (15;17) or BCR-ABL/t (9;22); Group 3, 21 prospectively analyzed diagnostic cases, without prior molecular studies; and Group 4, 10 minimal residual disease (MRD) samples. Analysis of the two previously studied cohorts (Groups 1 and 2) confirmed the diagnostic sensitivity and specificity of the multiplex assay with regard to these two translocations. Additionally, however, in the “negative” Group (Group 2) the assay revealed three unanticipated translocations (CBF?-MYH11, BCR-ABL, and MLL-AF4), two of which were confirmed on cytogenetics. Analysis of the prospective cohort demonstrated that the assay was cost-effective and amenable to standard laboratory practice, with an identically sensitive MRD detection rate to that of our laboratory-developed tests. Virtually all of the results obtained were consistent with the phenotype and karyotype by conventional methods. This study illustrates the utility of a kit-based multiplex RT-PCR assay for the molecular diagnosis and monitoring of leukemias and reinforces the complementary roles of molecular testing and cytogenetics in diagnostic hematopathology. PMID:14573782

  6. Reference gene selection for qRT-PCR in Caragana korshinskii Kom. under different stress conditions.

    PubMed

    Yang, Qi; Yin, Jiajia; Li, Gao; Qi, Liwang; Yang, Feiyun; Wang, Ruigang; Li, Guojing

    2014-01-01

    Caragana korshinskii Kom., which is widely distributed in the northwest China and Mongolia, is an important forage bush belonging to the legume family with high economic and ecological value. Strong tolerance ability to various stresses makes C. korshinskii Kom. a valuable species for plant stress research. In this study, suitable reference genes for quantitative real-time reverse transcription PCR (qRT-PCR) were screened from 11 candidate reference genes, including ACT, GAPDH, EF1?, UBQ, TUA, CAP, TUB, TUB3, SKIP1, SKIP5-1 and SKIP5-2. A total of 129 samples under drought, heat, cold, salt, ABA and high pH treatment were profiled, and software such as geNORM, NormFinder and BestKeeper were used for reference gene evaluation and selection. Different suitable reference genes were selected under different stresses. Across all 129 samples, GAPDH, EF1? and SKIP5-1 were found to be the most stable reference genes, and EF1?+SKIP5-1 is the most stable reference gene combination. Conversely, TUA, TUB and SKIP1 were not suitable for using as reference genes owing to their great expression variation under some stress conditions. The relative expression levels of CkWRKY1 were detected using the stable and unstable reference genes and their applicability was confirmed. These results provide some stable reference genes and reference gene combinations for qRT-PCR under different stresses in C. korshinskii Kom. for future research work, and indicate that CkWRKY1 plays essential roles in response to stresses in C. korshinskii. PMID:24452712

  7. Validity of Physical Activity Intensity Predictions by ActiGraph, Actical, and RT3 Accelerometers

    PubMed Central

    Rothney, Megan P.; Schaefer, Emily V.; Neumann, Megan M.; Choi, Leena; Chen, Kong Y.

    2009-01-01

    Objective: Accelerometers are promising tools for characterizing physical activity (PA) patterns in free-living persons. To date, validation of energy expenditure (EE) predictions from accelerometers has been restricted to short laboratory or simulated free-living protocols. This study seeks to determine the capabilities of eight previously published regression equations for three commercially available accelerometers to predict summary measures of daily EE. Methods and Procedures: Study participants were outfitted with ActiGraph, Actical, and RT3 accelerometers, while measurements were simultaneously made during overnight stays in a room calorimeter, which provided minute-by-minute EE measurements, in a diverse subject population (n = 85). Regression equations for each device were used to predict the minute-by-minute metabolic equivalents (METs) along with the daily PA level (PAL). Results: Two RT3 regressions and one ActiGraph regression were not significantly different from calorimeter measured PAL. When data from the entire visit were divided into four intensity categories—sedentary, light, moderate, and vigorous—significant (P < 0.001) over- and underpredictions were detected in numerous regression equations and intensity categories. Discussion: Most EE prediction equations showed differences of <2% in the moderate and vigorous intensity categories. These differences, though small in magnitude, may limit the ability of these regressions to accurately characterize whether specific PA goals have been met in the field setting. New regression equations should be developed if more accurate prediction of the daily PAL or higher precision in determining the time spent in specific PA intensity categories is desired. PMID:18535553

  8. Reference Gene Validation for RT-qPCR, a Note on Different Available Software Packages

    PubMed Central

    De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

    2015-01-01

    Background An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. Results 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. Conclusions This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use. PMID:25825906

  9. Recent Upgrades to NASA SPoRT Initialization Datasets for the Environmental Modeling System

    NASA Technical Reports Server (NTRS)

    Case, Jonathan L.; LaFontaine, Frank J.; Molthan, Andrew L.; Zavodsky, Bradley T.; Rozumalski, Robert A.

    2012-01-01

    The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed several products for its National Weather Service (NWS) partners that can initialize specific fields for local model runs within the NOAA/NWS Science and Training Resource Center (STRC) Environmental Modeling System (EMS). In last year's NWA abstract on this topic, the suite of SPoRT products supported in the STRC EMS was presented, which includes a Sea Surface Temperature (SST) composite, a Great Lakes sea-ice extent, a Green Vegetation Fraction (GVF) composite, and NASA Land Information System (LIS) gridded output. This abstract and companion presentation describes recent upgrades made to the SST and GVF composites, as well as the real-time LIS runs. The Great Lakes sea-ice product is unchanged from 2011. The SPoRT SST composite product has been expanded geographically and as a result, the resolution has been coarsened from 1 km to 2 km to accommodate the larger domain. The expanded domain covers much of the northern hemisphere from eastern Asia to western Europe (0 N to 80 N latitude and 150 E to 10 E longitude). In addition, the NESDIS POES-GOES product was added to fill in gaps caused by the Moderate Resolution Imaging Spectroradiometer (MODIS) being unable to sense in cloudy regions, replacing the recently-lost Advanced Microwave Scanning Radiometer for EOS with negligible change to product fidelity. The SST product now runs twice per day for Terra and Aqua combined data collections from 0000 to 1200 UTC and from 1200 to 0000 UTC, with valid analysis times at 0600 and 1800 UTC. The twice-daily compositing technique reduces the overall latency of the previous version while still representing the diurnal cycle characteristics. The SST composites are available at approximately four hours after the end of each collection period (i.e. 1600 UTC for the nighttime analysis and 0400 UTC for the daytime analysis). The real-time MODIS GVF composite has only received minor updates in the past year. The domain was expanded slightly to extend further west, north, and east to improve coverage over parts of southern Canada. Minor adjustments were also made to the manner in which GVF is calculated from the distribution of maximum Normalized Difference Vegetation Index from MODIS. The presentation will highlight some examples of the substantial inter-annual change in GVF that occurred from 2010 to 2011 in the U.S. Southern Plains as a result of the summer 2011 drought, and the early vegetation green up across the eastern U.S. due to the very warm conditions in March 2012. Finally, the SPoRT LIS runs the operational Noah land surface model (LSM) in real time over much of the eastern half of the CONUS. The Noah LSM is continually cycled in real time, uncoupled to any model, and driven by operational atmospheric analyses over a long-term, multi-year integration. The LIS-Noah provides the STRC EMS with high-resolution (3 km) LSM initialization data that are in equilibrium with the operational analysis forcing. The Noah LSM within the SPoRT LIS has been upgraded from version 2.7.1 to version 3.2, which has improved look-up table attributes for several land surface quantities. The surface albedo field is now being adjusted based on the input real-time MODIS GVF, thereby improving the net radiation. Also, the LIS-Noah now uses the newer MODIS-based land use classification scheme (i.e. the International Biosphere-Geosphere Programme [IGBP]) that has a better depiction of urban corridors in areas where urban sprawl has occurred. STRC EMS users interested in initializing their LSM fields with high-resolution SPoRT LIS data should set up their model domain with the MODIS-IGBP 20-class land use database and select Noah as the LSM.

  10. A Novel TetR-Regulating Peptide Turns off rtTA-Mediated Activation of Gene Expression

    PubMed Central

    Schmidt, Sebastian; Berens, Christian; Klotzsche, Marcus

    2014-01-01

    Conditional regulation of gene expression is a powerful and indispensable method for analyzing gene function. The “Tet-On” system is a tool widely used for that purpose. Here, the transregulator rtTA mediates expression of a gene of interest after addition of the small molecule effector doxycycline. Although very effective in rapidly turning on gene expression, the system is hampered by the long half-life of doxycycline which makes shutting down gene expression rapidly very difficult to achieve. We isolated an rtTA-binding peptide by in vivo selection that acts as a doxycycline antagonist and leads to rapid and efficient shut down of rtTA-mediated reporter gene expression in a human cell line. This peptide represents the basis for novel effector molecules which complement the “Tet-system” by enabling the investigator to rapidly turn gene expression not just on at will, but now also off. PMID:24810590

  11. A sensitive and reliable RT-nested PCR assay for detection of Citrus tristeza virus from naturally infected citrus plants.

    PubMed

    Adkar-Purushothama, Charith Raj; Maheshwar, P K; Sano, Teruo; Janardhana, G R

    2011-05-01

    A specific and sensitive reverse transcriptase-nested polymerase chain reaction assay (RT-nPCR) was developed for the detection of Citrus tristeza virus (CTV) from naturally infected citrus samples. Two sets of primer pairs were designed by alignment of nucleotide sequences available in GenBank database for different genotypes of CTV. RT-nPCR reaction components and thermal cycling parameters were optimized and reaction conditions were standardized. Sequencing of the PCR products from direct and nested-PCR reactions confirmed the specificity of both primer pairs. Presence of CTV specific amplicons in asymptomatic samples which were collected from diseased orchards indicated the sensitivity of the test. As RT-nPCR technique, developed in the present study, is specific and efficient in detecting CTV, this could be envisioned for diagnostic applications and surveillance. PMID:21298268

  12. Molecular detection of thyroglobulin mRNA transcripts in peripheral blood of patients with thyroid disease by RT-PCR

    PubMed Central

    Bojunga, J; Röddiger, S; Stanisch, M; Kusterer, K; Kurek, R; Renneberg, H; Adams, S; Lindhorst, E; Usadel, K H; Schumm-Draeger, P M

    2000-01-01

    The sensitive detection of circulating tumour cells in patients with differentiated thyroid cancer may precede the detection of relapse by other diagnostic studies – such as serum thyroglobulin – and thus may have important therapeutic and prognostic implications. We performed reverse transcription-polymerase chain reaction (RT-PCR) on blood samples from patients diagnosed with thyroid disease using two different RT-PCR sensitivities. Additionally, tissue specificity of TG mRNA-expression was determined using RNA extracts from 27 different human tissues. The lower limit of detection was 50–100 TG mRNA producing cells/ml blood using a ‘normal’ RT-PCR sensitivity and 10–20 cells/ml blood using a ‘high’ sensitivity. With the normal sensitivity TG mRNA was detected in 9/13 patients with thyroid cancer and metastasis, 63/137 patients with a history of thyroid cancer and no metastasis, 21/85 with non-malignant thyroid disease and 9/50 controls. With the high sensitivity TG mRNA was detected in 11/13 patients with thyroid cancer and metastasis, 111/137 patients with a history of thyroid cancer and no metastasis, 61/85 with non-malignant thyroid disease and 41/50 controls. Interestingly, using the normal RT-PCR sensitivity TG mRNA transcripts are specific for thyroid tissue and detectable in the peripheral blood of controls and patients with thyroid disease, which correlates with a diagnosis of metastasized thyroid cancer. However, with a high RT-PCR sensitivity, TG mRNA expression was found not to be specific for thyroid tissue and was not correlated with a diagnosis of thyroid cancer in patients. As a consequence, to date TG mRNA detected by RT-PCR in the peripheral blood cannot be recommended as a tumour marker superior to TG serum-level. © 2000 Cancer Research Campaign PMID:10817499

  13. The wind of the M-type AGB star RT Virginis probed by VLTI/MIDI

    NASA Astrophysics Data System (ADS)

    Sacuto, S.; Ramstedt, S.; Höfner, S.; Olofsson, H.; Bladh, S.; Eriksson, K.; Aringer, B.; Klotz, D.; Maercker, M.

    2013-03-01

    Aims: We study the circumstellar environment of the M-type AGB star RT Vir using mid-infrared high spatial resolution observations from the ESO-VLTI focal instrument MIDI. The aim of this study is to provide observational constraints on theoretical prediction that the winds of M-type AGB objects can be driven by photon scattering on iron-free silicate grains located in the close environment (about 2 to 3 stellar radii) of the star. Methods: We interpreted spectro-interferometric data, first using wavelength-dependent geometric models. We then used a self-consistent dynamic model atmosphere containing a time-dependent description of grain growth for pure forsterite dust particles to reproduce the photometric, spectrometric, and interferometric measurements of RT Vir. Since the hydrodynamic computation needs stellar parameters as input, a considerable effort was first made to determine these parameters. Results: MIDI differential phases reveal the presence of an asymmetry in the stellar vicinity. Results from the geometrical modeling give us clues to the presence of aluminum and silicate dust in the close circumstellar environment (<5 stellar radii). Comparison between spectro-interferometric data and a self-consistent dust-driven wind model reveals that silicate dust has to be present in the region between 2 to 3 stellar radii to reproduce the 59 and 63 m baseline visibility measurements around 9.8 ?m. This gives additional observational evidence in favor of winds driven by photon scattering on iron-free silicate grains located in the close vicinity of an M-type star. However, other sources of opacity are clearly missing to reproduce the 10-13 ?m visibility measurements for all baselines. Conclusions: This study is a first attempt to understand the wind mechanism of M-type AGB stars by comparing photometric, spectrometric, and interferometric measurements with state-of-the-art, self-consistent dust-driven wind models. The agreement of the dynamic model atmosphere with interferometric measurements in the 8-10 ?m spectral region gives additional observational evidence that the winds of M-type stars can be driven by photon scattering on iron-free silicate grains. Finally, a larger statistical study and progress in advanced self-consistent 3D modeling are still required to solve the remaining problems. Based on observations made with the Very Large Telescope Interferometer at Paranal Observatory under programs 083.D-0234 and 086.D-0737 (Open Time Observations).

  14. USING PORTABLE REAL-TIME POLYMERASE CHAIN REACTION (RT-PCR) ASSAYS TO DETECT SALMONELLA IN RAW MILK

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The purpose of this study was to determine the efficacy of a portable RT-PCR system for detecting Salmonella spp. in raw milk. The bulk milk samples (200) chosen for this study were a subset of a larger study; the subset contained 24 samples that were culture-positive for Salmonella and 176 that we...

  15. arXiv:1011.0928v1[math.RT]3Nov2010 SLICES FOR BIPARABOLICS OF INDEX 11

    E-print Network

    Paris-Sud XI, Université de

    arXiv:1011.0928v1[math.RT]3Nov2010 SLICES FOR BIPARABOLICS OF INDEX 11 Anthony Joseph Donald Frey.millet@univ-st-etienne.fr Key Words: Invariants, Slices, Nil-cones. AMS Classification: 17B35 Abstract Let a be an algebraic Lie

  16. Oceanography Vol. 19, No. 1, Mar. 2006172 T H I S R E P O RT summarizes goals,

    E-print Network

    Leonard, John J.

    Oceanography Vol. 19, No. 1, Mar. 2006172 T H I S R E P O RT summarizes goals, activities Malanotte-Rizzoli is Professor of Physical Oceanography, Massachusetts In- stitute of Technology, Cambridge, MA, USA. Detlef Stammer is Professor of Physical Oceanography, Universität Hamburg, Germany. James

  17. Use of virus suspensions without RNA extraction as RT PCR templates for detection of Newcastle disease virus

    Microsoft Academic Search

    P. N. Wambura

    2006-01-01

    Allantoic fluid (AF) and cell culture supernatant (CCS) obtained from eggs or cells infected with strain I- 2 of Newcastle disease virus were processed by different RNA template preparation methods for direct use in reverse transcriptase-polymerase chain reaction (RT-PCR). The objective was to determine the most effective technique for viral RNA extraction with consideration for efficacy, economy and simplicity. Results

  18. Use of RT-PCR on oral fluid samples to assist the identification of measles cases during an outbreak.

    PubMed Central

    Oliveira, S. A.; Siqueira, M. M.; Camacho, L. A. B.; Castro-Silva, R.; Bruno, B. F.; Cohen, B. J.

    2003-01-01

    This study investigated the occurrence of mild modified measles cases during an outbreak in Niterói, RJ, Brazil by using RT-PCR on oral fluid samples. From August to December 1997 a total of 76 patients with rash were seen at the study sites. Confirmed diagnosis by serology was achieved in 47 cases: measles (39.5%), rubella (13.2%), HHV-6 (3.9%), human parvovirus B19 (3.9%), dengue fever (3%). For 19 of the 29 patients without a conclusive diagnosis paired serum and saliva samples were available for further tests. In four of them, measles virus RNA was detected by RT-PCR in saliva samples in the absence of specific IgM in serum samples. Vaccination histories obtained from three of the RT-PCR positive cases showed that individuals previously immunized can still be infected and contribute to the circulation of measles virus. This study demonstrated the usefulness of RT-PCR on non-invasive clinical samples for the investigation of measles cases. PMID:12613751

  19. Using a Response to Intervention (RtI) Framework with 1st Grade Students: A Model for Occupational Therapy Practitioners

    ERIC Educational Resources Information Center

    McGuire, Beatriz

    2012-01-01

    The most recent reauthorization of the Individual's with Disabilities Education Improvement Act (IDEA, 2004) allows for the expansion of occupational therapy's role in school-based practice to include students who have not been identified for special education through early intervening services such as response to intervention (RtI).…

  20. Validation of reference genes for quantitative gene expression studies in Volvox carteri using real-time RT-PCR.

    PubMed

    Kianianmomeni, Arash; Hallmann, Armin

    2013-12-01

    Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) is a sensitive technique for analysis of gene expression under a wide diversity of biological conditions. However, the identification of suitable reference genes is a critical factor for analysis of gene expression data. To determine potential reference genes for normalization of qRT-PCR data in the green alga Volvox carteri, the transcript levels of ten candidate reference genes were measured by qRT-PCR in three experimental sample pools containing different developmental stages, cell types and stress treatments. The expression stability of the candidate reference genes was then calculated using the algorithms geNorm, NormFinder and BestKeeper. The genes for 18S ribosomal RNA (18S) and eukaryotic translation elongation factor 1?2 (eef1) turned out to have the most stable expression levels among the samples both from different developmental stages and different stress treatments. The genes for the ribosomal protein L23 (rpl23) and the TATA-box binding protein (tbpA) showed equivalent transcript levels in the comparison of different cell types, and therefore, can be used as reference genes for cell-type specific gene expression analysis. Our results indicate that more than one reference gene is required for accurate normalization of qRT-PCRs in V. carteri. The reference genes in our study show a much better performance than the housekeeping genes used as a reference in previous studies. PMID:24057254

  1. 388 nature photonics | VOL 3 | JULY 2009 | www.nature.com/naturephotonics REVIEW aRtIclE | focus

    E-print Network

    Cai, Long

    388 nature photonics | VOL 3 | JULY 2009 | www.nature.com/naturephotonics REVIEW aRtIclE | focus in nanoscopic resolution by exciting SPP at its resonance frequency5,6 . Here we review the mecha. This essentially means that visible light cannot image nanomaterials. Here we review the mechanism for going beyond

  2. Rt Hon Charles Kennedy MP Born in Inverness in 1959, Charles Kennedy was brought up and educated just outside Fort

    E-print Network

    Glasgow, University of

    Rt Hon Charles Kennedy MP Rector Born in Inverness in 1959, Charles Kennedy was brought up. Charles Kennedy was elected the UK Liberal Democrats' Party President, the equivalent of party chairman of the Party in January 2006. In September 2007 Charles Kennedy was unanimously elected President

  3. RT-PCR–RFLP for genetic diversity analysis of Tunisian Grapevine fanleaf virus isolates in their natural host plants

    Microsoft Academic Search

    Sami Fattouch; Hajer Acheche; Sonia M’hirsi; Lotfi Mellouli; Samir Bejar; Mohamed Marrakchi; Najib Marzouki

    2005-01-01

    Genetic diversity was characterized in 20 isolates of Grapevine fanleaf virus (GFLV) recovered from naturally infected grapevine plants (Vitis vinifera) in the North of Tunisia. Viral RNAs were isolated by oligoprobe capture, and a 605bp fragment containing a part of the viral coat protein gene was amplified by RT-PCR. Sequence variation among isolates was characterized by restriction fragment length polymorphism

  4. A collaborative framework for contributing DICOM RT PHI (Protected Health Information) to augment data mining in clinical decision support

    NASA Astrophysics Data System (ADS)

    Deshpande, Ruchi; Thuptimdang, Wanwara; DeMarco, John; Liu, Brent J.

    2014-03-01

    We have built a decision support system that provides recommendations for customizing radiation therapy treatment plans, based on patient models generated from a database of retrospective planning data. This database consists of relevant metadata and information derived from the following DICOM objects - CT images, RT Structure Set, RT Dose and RT Plan. The usefulness and accuracy of such patient models partly depends on the sample size of the learning data set. Our current goal is to increase this sample size by expanding our decision support system into a collaborative framework to include contributions from multiple collaborators. Potential collaborators are often reluctant to upload even anonymized patient files to repositories outside their local organizational network in order to avoid any conflicts with HIPAA Privacy and Security Rules. We have circumvented this problem by developing a tool that can parse DICOM files on the client's side and extract de-identified numeric and text data from DICOM RT headers for uploading to a centralized system. As a result, the DICOM files containing PHI remain local to the client side. This is a novel workflow that results in adding only relevant yet valuable data from DICOM files to the centralized decision support knowledge base in such a way that the DICOM files never leave the contributor's local workstation in a cloud-based environment. Such a workflow serves to encourage clinicians to contribute data for research endeavors by ensuring protection of electronic patient data.

  5. Collaborative Inquiry: A Strategy for Assessing Response to Instruction and Intervention (RtI2) for English Learner Students

    ERIC Educational Resources Information Center

    Vineyard, Lynn

    2010-01-01

    This pilot study describes elementary teachers' use of collaborative inquiry as a strategy for assessing Response to Instruction and Intervention (RtI [superscript 2]) in reading for an English Learner student. The design of the study was based on the sociocultural theory that assessment practices shape teachers' understanding of students and of…

  6. RT-UNNID: A practical solution to real-time network-based intrusion detection using unsupervised neural networks

    Microsoft Academic Search

    Morteza Amini; Rasool Jalili; Hamid Reza Shahriari

    2006-01-01

    With the growing rate of network attacks, intelligent methods for detecting new attacks have attracted increasing interest. The RT-UNNID system, introduced in this paper, is one such system, capable of intelligent real-time intrusion detection using unsupervised neural networks. Unsupervised neural nets can improve their analysis of new data over time without retraining. In previous work, we evaluated Adaptive Resonance Theory

  7. Automatic Systole-Diastole Classification of Mitral Valve Complex from RT-3D Echocardiography based on Multiresolution Processing

    E-print Network

    Wong, Kenneth K.Y.

    Automatic Systole-Diastole Classification of Mitral Valve Complex from RT-3D Echocardiography based, The Chinese University of Hong Kong, Hong Kong ABSTRACT Mitral valve repair is one of the most prevalent operations for various mitral valve conditions. Echocardiography, being famous for its low-cost, non

  8. Detection of EML4-ALK in Lung Adenocarcinoma Using Pleural Effusion with FISH, IHC, and RT-PCR Methods

    PubMed Central

    Zhou, Xiaodie; Song, Yong; Zhou, Xiaojun; Yu, Like; Wang, Jiandong

    2015-01-01

    Anaplastic lymphoma kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) gene rearrangements occur in approximately 5% of non-small-cell lung cancers (NSCLC), leading to the overexpression of anaplastic lymphoma kinase and predicting a response to the targeted inhibitor, crizotinib. Malignant pleural effusion occurs in most patients with advanced lung cancer, especially adenocarcinoma, and tissue samples are not always available from these patients. We attempted to clarify the feasibility of detecting the EML4-ALK fusion gene in pleural effusion cells using different methods. We obtained 66 samples of pleural effusion from NSCLC patients. The pleural effusion fluid was centrifuged, and the cellular components obtained were formalin fixed and paraffin embedded. The EML4-ALK fusion gene status was determined with fluorescent in situ hybridization (FISH), reverse transcription—polymerase chain reaction (RT-PCR), and immunohistochemistry (IHC). EML4-ALK was detected in three of 66 patient samples (4.5%) with RT-PCR. When the RT-PCR data were used as the standard, one false positive and one false negative samples were identified with IHC; and one false negative sample was identified with FISH. These results suggest that a block of pleural effusion cells can be used to detect the EML4-ALK fusion gene. IHC had good sensitivity, but low specificity. FISH had low sensitivity, but high specificity. RT-PCR is a good candidate method for detecting EML4-ALK in blocks of pleural effusion cells from lung cancer patients. PMID:25785456

  9. 710 VOLUME 20 NUMBER 6 JUNE 2013 nature structural & molecular biology a rt i c l e s

    E-print Network

    Bedwell, David M.

    710 VOLUME 20 NUMBER 6 JUNE 2013 nature structural & molecular biology a rt i c l e s During gene of the complex post-transcriptional gene expression networks9. After mRNPs are exported to the cytoplasm,22. Several quality-control mechanisms contribute to ensuring suffi- cient accuracy of gene expression

  10. Supporting Valid Decision Making: Uses and Misuses of Assessment Data within the Context of RtI

    ERIC Educational Resources Information Center

    Ball, Carrie R.; Christ, Theodore J.

    2012-01-01

    Within an RtI problem-solving context, assessment and decision making generally center around the tasks of problem identification, problem analysis, progress monitoring, and program evaluation. We use this framework to discuss the current state of the literature regarding curriculum based measurement, its technical properties, and its utility for…

  11. arXiv:math.RT/0702855v128Feb2007 IMAGINARY HIGHEST-WEIGHT REPRESENTATION THEORY AND

    E-print Network

    Sydney, University of

    }. Equivalent partitions define similar highest-weight theories. All partitions of the root system of a finitearXiv:math.RT/0702855v128Feb2007 IMAGINARY HIGHEST-WEIGHT REPRESENTATION THEORY AND SYMMETRIC FUNCTIONS BENJAMIN J. WILSON Abstract. Affine Lie algebras admit non-classical highest-weight theories

  12. Evidence-based RT-PCR methods for the detection of the 8 most common MLL aberrations in acute leukemias.

    PubMed

    Burmeister, Thomas; Meyer, Claus; Gröger, Daniela; Hofmann, Julia; Marschalek, Rolf

    2015-02-01

    MLL aberrations are detected in around 5-10% of acute myeloid and lymphatic leukemias and an additional 5% of acute myeloid leukemias show a partial internal MLL duplication (PTD). MLL rearrangements are important for therapy stratification, assessment of minimal residual disease and for targeted therapies. However, no truly evidence-based RT-PCR methods for the detection of most of these aberrations have been published yet. Based on the large data collection of MLL genomic breakpoints in acute leukemias comprising more than 1.600 cases at the Diagnostic Center for Acute Leukemias (DCAL) in Frankfurt, Germany that provide an overview over the experimentally observed fusion transcript variants, we developed RT-PCR methods for the reliable detection of the 8 most common MLL aberrations (MLL-AF4, MLL-AF6, MLL-AF9, MLL-AF10, MLL-ENL, MLL-ELL, MLL-EPS15, MLL PTD), together accounting for around 90% of MLL-r cases. The easily implementable RT-PCRs should enable a reliable detection of these MLL fusion transcripts by RT-PCR. PMID:25510485

  13. This paper presents an RT level partitioning approach for sequential circuits described as data path and control part.

    E-print Network

    Zhao, Yuxiao

    by DFT tech­ niques. The control part is also modified to control the circuit in normal mode and test mode. In the normal mode, the cir­ cuit is controlled to perform its function, while in the test modeAbstract This paper presents an RT level partitioning approach for sequential circuits described

  14. A Universal `One-tube' RT-PCR Protocol for Amplifying Isolates of Bovine Viral Diarrhoea Virus

    Microsoft Academic Search

    M. Pfeffer; M. von Freyburg; O.-R. Kaaden; M. Beer

    2000-01-01

    The increase in the knowledge of the genetic variability of BVDV and the identification of some of the genetic determinants of its pathogenicity require robust and practical tools for rapid molecular characterization of the various genotypes of this virus. This study was undertaken to develop a standard protocol for RT-PCR that allows the amplification of various parts of the genome

  15. SAMPLING ANCHOVY LARVAE WITH A PLANKTON PURSE SEINE' GARTH I. MURPHY" AND RORP.RT I. CLUTTER"

    E-print Network

    SAMPLING ANCHOVY LARVAE WITH A PLANKTON PURSE SEINE' GARTH I. MURPHY" AND RORP.RT I. CLUTTER in Kaneohe Bay, Hawaii, together with a 1-m plankton net constructed of the same ma- terial in order to evaluate the sampling efficiency of the towed plankton net on anchovy larvae (Stolephorus purpureus

  16. Characterization of rainbow trout myostatin-2 genes (rtMSTN-2a & -2b): genomic organization, differential expression and pseudogenization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Myostatin is an extremely potent negative regulator of vertebrate skeletal muscle development. A phylogenetic analysis suggests that salmonids should possess four distinct genes, although only MSTN-1 orthologs have been characterized. Described herein are the rainbow trout (rt) MSTN-2a and -2b genes...

  17. Oceanography Vol.21, No.392 W o r k s h o p r e p o rt

    E-print Network

    Buesseler, Ken

    limits the extent of carbon sequestration from the atmo- sphere. The mechanisms controlling both the impact of ongoing climate and ocean circulation changes on this carbon sequestration. To identify gapsOceanography Vol.21, No.392 W o r k s h o p r e p o rt Controls on organic Carbon export

  18. Lung Cancer Lymph Node Micrometastasis Detection Using RT-PCR – Correlation with Vascular Endothelial Growth Factor (VEGF) expression

    PubMed Central

    Nwogu, Chukwumere E.; Yendamuri, Sai; Tan, Wei; Kannisto, Eric; Bogner, Paul; Morrison, Carl; Cheney, Richard; Dexter, Elisabeth; Picone, Anthony; Hennon, Mark; Hutson, Alan; Reid, Mary; Adjei, Alex; Demmy, Todd L.

    2013-01-01

    Objectives Lymph node (LN) staging provides critical information in non-small cell lung cancer (NSCLC) patients. Lymphangiogenesis may be an important contributor to the pathophysiology of lymphatic metastases. We hypothesized that the presence of lymph node micrometastases positively correlates with VEGF-A/C/D and VEGF-receptor-3 (lymphangiogenic factors) expression in lymph nodes. Methods Forty NSCLC patients had pre-operative PET-CT and mediastinoscopy. RT-PCR assays for mRNA expression of epithelial markers (CK-7, CEACAM-5 and PLUNC) were performed in selected fluorodeoxyglucose (FDG)-avid lymph nodes. VEGF-A/C/D and VEGF-receptor-3 expression levels were measured in primary tumors and lymph nodes. Wilcoxon rank sum test was run for the association between the RT-PCR epithelial marker levels and VEGF expression levels in the LNs. Results RT-PCR for CK-7, CEACAM5 or PLUNC indicated lymph node micrometastatic disease in 19 of 35 patients (54%). There was a high correlation between detection of micrometastases and VEGF-A/C/D or VEGF-receptor-3 expression levels in lymph nodes. Median follow-up was 12.6 months. Conclusions RT-PCR analysis of FDG-avid lymph nodes results in up-staging of patients. Micrometastases correlate with the expression of VEGF in lymph nodes in NSCLC patients. This may reflect the role of lymphangiogenesis in promoting metastases. PMID:23414988

  19. arXiv:1312.6930v1[math.RT]25Dec2013 MYSTIC REFLECTION GROUPS

    E-print Network

    Berenstein, Arkady

    arXiv:1312.6930v1[math.RT]25Dec2013 MYSTIC REFLECTION GROUPS YURI BAZLOV AND ARKADY BERENSTEIN To the memory of Andrei Zelevinsky Abstract. This paper aims to systematically study mystic reflection groups to a group G satisfying (a) and (b) above as mystic reflection group. Independently, in [1] we solved

  20. 656 VOLUME 45 | NUMBER 6 | JUNE 2013 Nature GeNetics A rt i c l e s

    E-print Network

    Kaski, Samuel

    656 VOLUME 45 | NUMBER 6 | JUNE 2013 Nature GeNetics A rt i c l e s S. pneumoniae is a human and 23B. Such serology forms the basis of much pneumococcal epidemiology, and the capsule is also-resistant clones identified by the Pneumococcal Molecular Epidemiology Network15 (PMEN) predominately express VT

  1. 406 VOLUME 45 | NUMBER 4 | APRIL 2013 Nature GeNetics A rt i c l e s

    E-print Network

    Reich, David

    overlaps between genomic clones10. Clones are assembled into larger scaffolds on the basis of overlapping406 VOLUME 45 | NUMBER 4 | APRIL 2013 Nature GeNetics A rt i c l e s Physical maps of the human genome, including the sequence of most of its euchromatic portions1,2, are basic resources in human

  2. PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

    PubMed

    Tokheim, Collin; Park, Juw Won; Xing, Yi

    2014-04-01

    The vast majority of multi-exon genes in higher eukaryotes are alternatively spliced and changes in alternative splicing (AS) can impact gene function or cause disease. High-throughput RNA sequencing (RNA-seq) has become a powerful technology for transcriptome-wide analysis of AS, but RT-PCR still remains the gold-standard approach for quantifying and validating exon splicing levels. We have developed PrimerSeq, a user-friendly software for systematic design and visualization of RT-PCR primers using RNA-seq data. PrimerSeq incorporates user-provided transcriptome profiles (i.e., RNA-seq data) in the design process, and is particularly useful for large-scale quantitative analysis of AS events discovered from RNA-seq experiments. PrimerSeq features a graphical user interface (GUI) that displays the RNA-seq data juxtaposed with the expected RT-PCR results. To enable primer design and visualization on user-provided RNA-seq data and transcript annotations, we have developed PrimerSeq as a stand-alone software that runs on local computers. PrimerSeq is freely available for Windows and Mac OS X along with source code at http://primerseq.sourceforge.net/. With the growing popularity of RNA-seq for transcriptome studies, we expect PrimerSeq to help bridge the gap between high-throughput RNA-seq discovery of AS events and molecular analysis of candidate events by RT-PCR. PMID:24747190

  3. Molecular detection of infectious bronchitis and Newcastle disease viruses in broiler chickens with respiratory signs using Duplex RT-PCR

    PubMed Central

    Saba Shirvan, Aylar; Mardani, Karim

    2014-01-01

    Infectious bronchitis (IB) and Newcastle disease (ND) are highly contagious and the most economically important diseases of the poultry affecting respiratory tract and causing economic losses in poultry industry throughout the world. In the present study, the simultaneous detection and differentiation of causative agents of these diseases were investigated using duplex-RT-PCR. RNA was extracted from vaccinal and reference strains of infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) and then cDNA was synthesized. Using two universal primer sets for detection of IBV and NDV, the duplex-RT-PCR was developed. In order to assess the efficiency of the developed duplex RT-PCR, a number of 12 broiler farms with the symptoms of respiratory tract infection was sampled (trachea, lung and kidney were sampled from affected birds suspicious for IBV and NDV infections). After RNA extraction from tissues and cDNA synthesis, the presence of IBV and NDV genome were investigated using duplex-PCR. The results showed that three of twelve examined broiler farms were positive for IBV and two farms were positive for NDV and IBV. The results revealed that the duplex-RT-PCR is a quick and sensitive procedure for simultaneously detecting IBV and NDV in birds with respiratory infections. PMID:25610585

  4. Magnetic properties of RT2Zn20 R = rare earth, T = Fe, Co , Ru, Rh , Os and Ir

    E-print Network

    Canfield, Paul C.

    Magnetic properties of RT2Zn20 R = rare earth, T = Fe, Co , Ru, Rh , Os and Ir by Shuang Jia and Curie law . . . . . . . . . . . . . . . . . . . . . . 10 2.1.3 Weiss Molecular field theory 6. Variation of the magnetic ordering in GdT2Zn20 (T= Fe, Ru, Os, Co, Rh and Ir) and its correlat

  5. The Selection of Low Envelope Glycoprotein Reactivity to Soluble CD4 and Cold during Simian-Human Immunodeficiency Virus Infection of Rhesus Macaques

    PubMed Central

    McGee, Kathleen; Haim, Hillel; Korioth-Schmitz, Birgit; Espy, Nicole; Javanbakht, Hassan; Letvin, Norman

    2014-01-01

    Envelope glycoprotein (Env) reactivity (ER) describes the propensity of human immunodeficiency virus type 1 (HIV-1) Env to change conformation from the metastable unliganded state in response to the binding of ligands (antibodies and soluble CD4 [sCD4]) or incubation in the cold. To investigate Env properties that favor in vivo persistence, we inoculated rhesus macaques with three closely related CCR5-tropic simian-human immunodeficiency viruses (SHIVs) that differ in ER to cold (ERcold) and ER to sCD4 (ERsCD4); these SHIVs were neutralized by antibodies equivalently and thus were similar in ERantibody. All three SHIVs achieved high levels of acute viremia in the monkeys without alteration of their Env sequences, indicating that neither ERcold nor ERsCD4 significantly influences the establishment of infection. Between 14 and 100 days following infection, viruses with high ERcold and ERsCD4 were counterselected. Remarkably, the virus variant with low ERcold and low ERsCD4 did not elicit a neutralizing antibody response against the infecting virus, despite the generation of high levels of anti-Env antibodies in the infected monkeys. All viruses that achieved persistent viremia escaped from any autologous neutralizing antibodies and exhibited low ERcold and low ERsCD4. One set of gp120 changes determined the decrease in ERcold and ERsCD4, and a different set of gp120 changes determined resistance to autologous neutralizing antibodies. Each set of changes contributed to a reduction in Env-mediated entry. During infection of monkeys, any Env replication fitness costs associated with decreases in ERcold and ERsCD4 may be offset by minimizing the elicitation of autologous neutralizing antibodies. PMID:24131720

  6. The selection of low envelope glycoprotein reactivity to soluble CD4 and cold during simian-human immunodeficiency virus infection of rhesus macaques.

    PubMed

    McGee, Kathleen; Haim, Hillel; Korioth-Schmitz, Birgit; Espy, Nicole; Javanbakht, Hassan; Letvin, Norman; Sodroski, Joseph

    2014-01-01

    Envelope glycoprotein (Env) reactivity (ER) describes the propensity of human immunodeficiency virus type 1 (HIV-1) Env to change conformation from the metastable unliganded state in response to the binding of ligands (antibodies and soluble CD4 [sCD4]) or incubation in the cold. To investigate Env properties that favor in vivo persistence, we inoculated rhesus macaques with three closely related CCR5-tropic simian-human immunodeficiency viruses (SHIVs) that differ in ER to cold (ERcold) and ER to sCD4 (ERsCD4); these SHIVs were neutralized by antibodies equivalently and thus were similar in ERantibody. All three SHIVs achieved high levels of acute viremia in the monkeys without alteration of their Env sequences, indicating that neither ERcold nor ERsCD4 significantly influences the establishment of infection. Between 14 and 100 days following infection, viruses with high ERcold and ERsCD4 were counterselected. Remarkably, the virus variant with low ERcold and low ERsCD4 did not elicit a neutralizing antibody response against the infecting virus, despite the generation of high levels of anti-Env antibodies in the infected monkeys. All viruses that achieved persistent viremia escaped from any autologous neutralizing antibodies and exhibited low ERcold and low ERsCD4. One set of gp120 changes determined the decrease in ERcold and ERsCD4, and a different set of gp120 changes determined resistance to autologous neutralizing antibodies. Each set of changes contributed to a reduction in Env-mediated entry. During infection of monkeys, any Env replication fitness costs associated with decreases in ERcold and ERsCD4 may be offset by minimizing the elicitation of autologous neutralizing antibodies. PMID:24131720

  7. Rapid and Sensitive RT-QuIC Detection of Human Creutzfeldt-Jakob Disease Using Cerebrospinal Fluid

    PubMed Central

    Orrú, Christina D.; Groveman, Bradley R.; Hughson, Andrew G.; Zanusso, Gianluigi; Coulthart, Michael B.

    2015-01-01

    ABSTRACT? Fast, definitive diagnosis of Creutzfeldt-Jakob disease (CJD) is important in assessing patient care options and transmission risks. Real-time quaking-induced conversion (RT-QuIC) assays of cerebrospinal fluid (CSF) and nasal-brushing specimens are valuable in distinguishing CJD from non-CJD conditions but have required 2.5 to 5 days. Here, an improved RT-QuIC assay is described which identified positive CSF samples within 4 to 14 h with better analytical sensitivity. Moreover, analysis of 11 CJD patients demonstrated that while 7 were RT-QuIC positive using the previous conditions, 10 were positive using the new assay. In these and further analyses, a total of 46 of 48 CSF samples from sporadic CJD patients were positive, while all 39 non-CJD patients were negative, giving 95.8% diagnostic sensitivity and 100% specificity. This second-generation RT-QuIC assay markedly improved the speed and sensitivity of detecting prion seeds in CSF specimens from CJD patients. This should enhance prospects for rapid and accurate ante mortem CJD diagnosis. Importance? A long-standing problem in dealing with various neurodegenerative protein misfolding diseases is early and accurate diagnosis. This issue is particularly important with human prion diseases, such as CJD, because prions are deadly, transmissible, and unusually resistant to decontamination. The recently developed RT-QuIC test allows for highly sensitive and specific detection of CJD in human cerebrospinal fluid and is being broadly implemented as a key diagnostic tool. However, as currently applied, RT-QuIC takes 2.5 to 5 days and misses 11 to 23% of CJD cases. Now, we have markedly improved RT-QuIC analysis of human CSF such that CJD and non-CJD patients can be discriminated in a matter of hours rather than days with enhanced sensitivity. These improvements should allow for much faster, more accurate, and practical testing for CJD. In broader terms, our study provides a prototype for tests for misfolded protein aggregates that cause many important amyloid diseases, such as Alzheimer’s, Parkinson’s, and tauopathies. PMID:25604790

  8. Comparison of Aerobic Versus Resistance Exercise Training Effects on Metabolic Syndrome (from the Studies of a Targeted Risk Reduction Intervention Through Defined Exercise - STRRIDE-AT/RT)

    PubMed Central

    Bateman, Lori A.; Slentz, Cris A.; Willis, Leslie H.; Shields, A. Tamlyn; Piner, Lucy W.; Bales, Connie W.; Houmard, Joseph A.; Kraus, William E.

    2013-01-01

    Aerobic training (AT) improves the metabolic syndrome (MS) and its component risk factors; however, to our knowledge, no randomized clinical studies have addressed whether resistance training (RT) improves the MS when performed alone or combined with AT. Sedentary, overweight dyslipidemic men and women, aged 18 to 70 years completed a 4-month inactive run-in period and were randomized to 1 of 3 eight-month exercise programs (n = 196). The exercise programs were (1) RT (3 days/week, 3 sets/day of 8 to 12 repetitions of 8 different exercises targeting all major muscle groups); (2) AT (~120 minutes/week at 75% of the maximum oxygen uptake), and (3) AT and RT combined (AT/RT) (exact combination of AT and RT). Of the 196 randomized patients, 144 completed 1 of the 3 exercise programs. The 86 participants with complete data for all 5 MS criteria were used in the present analysis, and a continuous MS z score was calculated. Eight months of RT did not change the MS score. AT improved the MS score (p <0.07) and showed a trend toward significance compared to RT (p <0.10). AT/RT significantly decreased the MS score and was significantly different from RT alone. In conclusion, RT was not effective at improving the MS score; however, AT was effective. Combined AT and RT was similarly effective but not different from AT alone. When weighing the time commitment versus health benefit, the data suggest that AT alone was the most efficient mode of exercise for improving cardiometabolic health. PMID:21741606

  9. Identification of reference genes for qRT-PCR in human lung squamous-cell carcinoma by RNA-Seq.

    PubMed

    Zhan, Cheng; Zhang, Yongxing; Ma, Jun; Wang, Lin; Jiang, Wei; Shi, Yu; Wang, Qun

    2014-04-01

    Although the accuracy of quantitative real-time polymerase chain reaction (qRT-PCR) is highly dependent on the reliable reference genes, many commonly used reference genes are not stably expressed and as such are not suitable for quantification and normalization of qRT-PCR data. The aim of this study was to identify novel reliable reference genes in lung squamous-cell carcinoma. We used RNA sequencing (RNA-Seq) to survey the whole genome expression in 5 lung normal samples and 44 lung squamous-cell carcinoma samples. We evaluated the expression profiles of 15 commonly used reference genes and identified five additional candidate reference genes. To validate the RNA-Seq dataset, we used qRT-PCR to verify the expression levels of these 20 genes in a separate set of 100 pairs of normal lung tissue and lung squamous-cell carcinoma samples, and then analyzed these results using geNorm and NormFinder. With respect to 14 of the 15 common reference genes (B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, and YWHAZ), the expression levels were either too low to be easily detected, or exhibited a high degree of variability either between lung normal and squamous-cell carcinoma samples, or even among samples of the same tissue type. In contrast, 1 of the 15 common reference genes (ACTB) and the 5 additional candidate reference genes (EEF1A1, FAU, RPS9, RPS11, and RPS14) were stably and constitutively expressed at high levels in all the samples tested. ACTB, EEF1A1, FAU, RPS9, RPS11, and RPS14 are ideal reference genes for qRT-PCR analysis of lung squamous-cell carcinoma, while 14 commonly used qRT-PCR reference genes are less appropriate in this context. PMID:24457517

  10. Selection of suitable reference genes for expression analysis in human glioma using RT-qPCR.

    PubMed

    Grube, Susanne; Göttig, Tatjana; Freitag, Diana; Ewald, Christian; Kalff, Rolf; Walter, Jan

    2015-05-01

    In human glioma research, quantitative real-time reverse-transcription PCR is a frequently used tool. Considering the broad variation in the expression of candidate reference genes among tumor stages and normal brain, studies using quantitative RT-PCR require strict definition of adequate endogenous controls. This study aimed at testing a panel of nine reference genes [beta-2-microglobulin, cytochrome c-1 (CYC1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hydroxymethylbilane synthase, hypoxanthine guanine phosphoribosyl transferase 1, ribosomal protein L13a (RPL13A), succinate dehydrogenase, TATA-box binding protein and 14-3-3 protein zeta] to identify and validate the most suitable reference genes for expression studies in human glioma of different grades (World Health Organization grades II-IV). After analysis of the stability values calculated using geNorm, NormFinder, and BestKeeper algorithms, GAPDH, RPL13A, and CYC1 can be indicated as reference genes applicable for accurate normalization of gene expression in glioma compared with normal brain and anaplastic astrocytoma or glioblastoma alone within this experimental setting. Generally, there are no differences in expression levels and variability of candidate genes in glioma tissue compared to normal brain. But stability analyses revealed just a small number of genes suitable for normalization in each of the tumor subgroups and across these groups. Nevertheless, our data show the importance of validation of adequate reference genes prior to every study. PMID:25862007

  11. Pilot Quality Control Program for Audit RT External Beams at Mexican Hospitals

    SciTech Connect

    Alvarez R, J T; Tovar M, V M [Secondary Standard Dosimetry Laboratory SSDL, Ionizing Radiation Metrology Department, ININ Carretera Federal Mexico Toluca S/N, La Marquesa, Ocoyoacac, Estado de Mexico 52 750 (Mexico)

    2008-08-11

    A pilot quality control program for audit 18 radiotherapy RT external beams at 13 Mexican hospitals is described--for eleven {sup 60}Co beams and seven photon beams of 6, 10 and 15 MV from accelerators. This program contains five parts: a) Preparation of the TLD-100 powder: washing, drying and annealing (one hour 400 deg. C plus 24 hrs 80 deg. C). b) Sending two IAEA type capsules to the hospitals for irradiation at the hospital to a nominal D{sub W} = 2 Gy{center_dot}c) Preparation at the SSDL of ten calibration curves CC in the range of 0.5 Gy to 6 Gy in terms of absorbed dose to water D{sub W} for {sup 60}Co with traceability to primary laboratory NRC (Canada), according to a window irradiation: 26/10/2007-7/12/2007. d) Reading all capsules that match their hospital time irradiation and the SSDL window irradiation. f) Evaluation of the Dw imparted by the hospitals.

  12. A multiplex RT-PCR assay for the detection of fish picornaviruses.

    PubMed

    Mor, Sunil K; Phelps, Nicholas B D; Barbknecht, Marisa; Hoffman, Michael A; Goyal, Sagar M

    2015-09-01

    With the emergence of high profile fish diseases in the Great Lakes region, surveillance and regulatory inspections of fish populations have increased. This has resulted in a better understanding of known pathogens and isolation of many new pathogens of fish. In this study, a multiplex RT-PCR assay was developed for the detection of three newly discovered fish picornaviruses: bluegill picornavirus-1 (BGPV-1), fathead minnow picornavirus (FHMPV), and eel picornavirus-1 (EPV-1). This assay was found to be very sensitive with a detection limit of 81.9pg/?l of extracted RNA from a pool of FHMPV and BGPV-1 and was able to detect 501 and 224 gene copies/?l of BGPV-1 and FHMPV, respectively. The assay was highly reproducible and did not cross react with other closely related pathogens. We believe that this new assay provides a rapid and cost effective tool for confirming cell culture isolates and conducting prevalence studies of these newly detected fish picornaviruses. PMID:25962537

  13. Selection of suitable housekeeping genes for expression analysis in glioblastoma using quantitative RT-PCR

    PubMed Central

    Valente, Valeria; Teixeira, Silvia A; Neder, Luciano; Okamoto, Oswaldo K; Oba-Shinjo, Sueli M; Marie, Suely KN; Scrideli, Carlos A; Paçó-Larson, Maria L; Carlotti, Carlos G

    2009-01-01

    Background Considering the broad variation in the expression of housekeeping genes among tissues and experimental situations, studies using quantitative RT-PCR require strict definition of adequate endogenous controls. For glioblastoma, the most common type of tumor in the central nervous system, there was no previous report regarding this issue. Results Here we show that amongst seven frequently used housekeeping genes TBP and HPRT1 are adequate references for glioblastoma gene expression analysis. Evaluation of the expression levels of 12 target genes utilizing different endogenous controls revealed that the normalization method applied might introduce errors in the estimation of relative quantities. Genes presenting expression levels which do not significantly differ between tumor and normal tissues can be considered either increased or decreased if unsuitable reference genes are applied. Most importantly, genes showing significant differences in expression levels between tumor and normal tissues can be missed. We also demonstrated that the Holliday Junction Recognizing Protein, a novel DNA repair protein over expressed in lung cancer, is extremely over-expressed in glioblastoma, with a median change of about 134 fold. Conclusion Altogether, our data show the relevance of previous validation of candidate control genes for each experimental model and indicate TBP plus HPRT1 as suitable references for studies on glioblastoma gene expression. PMID:19257903

  14. LABORATORY EVALUATION: PERFORMANCE OF A 10 RT GAS-ENGINE-DRIVEN HEAT PUMP (GHP)

    SciTech Connect

    Zaltash, Abdolreza [ORNL; Linkous, Randall Lee [ORNL; Geoghegan, Patrick J [ORNL; Vineyard, Edward Allan [ORNL; Wetherington Jr, G Randall [ORNL

    2008-01-01

    Building air-conditioning (cooling) is the single largest use of electricity, driving increases in summer peak electric demand in much of the United States. Increases in peak load on the utility grid lead to high electricity prices, power quality problems, and grid system inefficiencies and even failures. Improved air-conditioning technology thus has the greatest potential impact on the electric grid compared to other technologies that use electricity. Thermally-activated systems, such as natural gas engine-driven heat pumps, can provide overall peak load reduction and electric grid relief for summer peak demand. This study describes the performance of a 10 refrigeration ton (RT) natural gas engine-driven heat pump rooftop unit in a controlled environment over a wide range of operating conditions in heating and cooling modes. Results showed gas COP exceeding the goal of 1.6 at 47 F (8.3 C) rating condition. Gas COP in cooling mode also exceeded the goal of 1.2 at 95 F (35 C) rating condition. Future work will investigate additional applications for gas engine-driven equipment, such as residential space conditioning.

  15. Gastroenteritis outbreaks associated with Norwalk-like viruses and their investigation by nested RT-PCR

    PubMed Central

    O'Neill, Hugh J; McCaughey, Conall; Wyatt, Dorothy E; Mitchell, Frederick; Coyle, Peter V

    2001-01-01

    Background Norwalk-like viruses are the most common cause of gastroenteritis outbreaks and sporadic cases of vomiting and diarrhoea. In healthy individuals infection is often mild and short-lived but in debilitated patients infection can be severe. It is essential that the virus laboratory can offer a sensitive and specific test, delivered in a timely manner. Methods We have developed a nested reverse transcriptase PCR based on published primers against the RNA polymerase gene and after comparison with electronmicroscopy used the assay to investigate 31 outbreaks of gastroenteritis. These were in diverse situations including nursing homes, small district hospitals, large general hospitals, a ferry ship, hotels, restaurants and staff canteens. Results A positive diagnosis was made in 30/31 outbreaks investigated giving an overall outbreak positive detection rate of 97%. At an individual patient level there was a positive diagnostic rate of 11.5% in a large hospital environment to 100% in smaller outbreak situations. The average patient positive rate was 34%. In addition we investigated 532 control faecal specimens from adults. Of these 530 were negative and 2 were repeatedly positive. Conclusions It is essential that insensitive electronmicroscopy is replaced with the more sensitive reverse transcription PCR assays. These tests should be made available "on call" at weekends and public holidays. It is also important that outbreaks of NLV infection are monitored using sensitive RT-PCR assays so that the laboratory information can be used in ascertaining the spread and duration of the outbreak PMID:11511325

  16. Immunogenicity of virus-like particles containing modified human immunodeficiency virus envelope proteins

    PubMed Central

    Quan, Fu-Shi; Sailaja, Gangadhara; Skountzou, Ioanna; Huang, Chunzi; Vzorov, Andrei; Compans, Richard W.; Kang, Sang-Moo

    2007-01-01

    Extensive glycosylation and variable loops of the HIV envelope protein (Env) are reported to shield some neutralizing epitopes. Here, we investigated the immunogenicity of mutated HIV Envs presented in virus-like particles (VLPs). We immunized mice with simian human immunodeficiency virus (SHIV) VLPs containing mutant HIV Env with reduced glycosylation (3G), variable loop-deleted mutations (dV1V2), or combinations of both types of mutations (3G-dV2?1G), and evaluated immune responses. Immune sera from mice that received VLPs with modified HIV Envs (3G or dV1V2) showed higher neutralizing activities against the homologous HIV 89.6 virus as well as heterologous viruses when compared with wild type SHIV VLP-immunized mice. Lymphocytes from immunized mice produced HIV Env-specific cytokines, with the 3G-dV2?1G mutant producing high levels of cytokines. Interestingly, both dendritic cells and B cells were found to interact with VLPs suggesting that VLPs are effective immunogens. Therefore, this study suggests that VLPs containing modified HIV Env have the potential to be developed as candidate vaccines capable of inducing cellular and humoral immune responses including neutralizing activities. PMID:17320250

  17. AcAdemic RefeRee confidentiAl RepoRt ApplicAtion foR postgRAduAte scholARship

    E-print Network

    Frean, Marcus

    AcAdemic RefeRee ­ confidentiAl RepoRt ApplicAtion foR postgRAduAte scholARship Applic must ask at least two referees to supply confidential reports. Thisreportcanbefilledinasasoft no page1of3ApplicAtionfoRpostgRAduAtescholARship:AcAdemicRefeRee­confidentiAlRepoRt #12;Refe

  18. VARIATION OF THE EXPRESSION OF ENDOGENOUS "HOUSEKEEPING" GENES IN B[A]P TREATED MOUSE LUNGS MEASURED BY qRT-PCR

    EPA Science Inventory

    Quantitative RT-PCR is frequently used to analyze gene expression in different experimental systems. In this assay, housekeeping genes are frequently used to normalize for the variability between samples (relative quantification). We have examined the utility of using qRT-PCR and...

  19. Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to

    E-print Network

    Wang, Wei

    , and Peter A. Kollman*, Contribution from the Department of Pharmaceutical Chemistry, Uni. The RT is a heterodimer composed of two subunits, p66 and p51, and two binding sites are important with the enzyme, is located in the p66 palm subdomain. Besides the dNTP site, HIV-1 RT also has an allosteric site

  20. A reliable IC One-step RT-PCR method for the detection of BBrMV to ensure safe exchange of Musa germplasm.

    PubMed

    Iskra-Caruana, Marie-line; Galzi, Serge; Laboureau, Nathalie

    2008-11-01

    An immunocapture (IC) One-step RT-PCR assay was developed to improve the detection of Banana bract mosaic virus (BBrMV) in single and bulked samples of banana plants. In this paper, an atypical strain of BBrMV was described, the BBrMV "Ref" strain, and we showed that detection with available BBrMV tools using ELISA and RT-PCR approaches was not reliable. Primer sets Bract N1/NR and N2/NR specific to BBrMV were designed and used in RT-PCR and IC-RT-PCR assays with two commercial kits that allow the RT and the PCR reactions to take place simultaneously in the same tube. The new assay enabled detection of BBrMV in leaf extract diluted up to 1 x 10(-10) and in bulked samples of 10 plants, and was proposed as a new international standard to index BBrMV. PMID:18675303

  1. Quantification of Hantaan Virus with a SYBR Green ?-Based One-Step qRT-PCR Assay

    PubMed Central

    Zhao, Ke; Zhang, Ye; Du, Hong; Wang, Ping-zhong; Bai, Xue-fan

    2013-01-01

    Hantaan virus (HTNV) is a major zoonotic pathogen that causes hemorrhagic fever with renal syndrome (HFRS) in Asia, especially in China. Shaanxi province, which is located in northwest of China, is one of the areas in China most severely afflicted with HFRS epidemics annually. This study aims to establish a quantitative RT-PCR (qRT-PCR) assay to detect HTNV both in cell culture and clinical serum samples. We established a SYBR Green ?-based one-step qRT-PCR assay that targets the S segment of the HTNV genome for rapid detection and quantification. The HTNV cRNA standards were constructed by in vitro transcription, and the copy numbers of the HTNV cRNA were quantified. Standard curve was generated by determining the mean cycle threshold (Ct) values versus 10-fold serial dilutions of the HTNV cRNA over a range of 1×108 to 1×103 copies/?l. The standard curve had a reaction efficiency of 102.1%, a correlation coefficient (R2) of 0.998, and a slope of -3.273. The coefficient of variation (CV) of the intra- and inter-assays ranged from 0.68% to 3.00% and from 0.86% to 3.21%, respectively. The cycle intervals of the qRT-PCR assay between each dilution ranged from 2.9 to 3.8 cycles, and the lowest detection limit of the qRT-PCR assay was 10 copies/?l. The assay exhibited high specificity that was confirmed by melting curve analysis, and no cross reaction with the Seoul virus (SEOV) and other viruses (HBV, HCV and HIV) was observed. HTNV RNA was also detected in the 27 serum samples of clinical HFRS patients using the assay, and the HTNV RNA viral load ranged from 2.06×101 to 1.95×105 copies/?l. The SYBR Green ?-based one-step qRT-PCR assay is a sensitive, specific, reproducible, and simple method for detecting and quantifying HTNV in cell culture and clinical samples. PMID:24278449

  2. RT-PCR amplification of the complete NF1 coding sequence

    SciTech Connect

    Ming Hong Shen; Meena Upadhyaya [Institute of Medical Genetics, Cardiff (United Kingdom)

    1994-09-01

    Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder. The NF1 gene is a large gene, 350kb in size, with at least 51 exons. It has proved hard to detect mutations in the gene by examining genomic DNA due to the high mutation rate and the large size of the gene. Since the cloning of the gene, only 45 causative mutations have been reported from over 500 unrelated NF1 patients screened. The coding sequence of the NF1 gene is approximately 3% of the genomic sequence; it will therefore be easier to search for unknown mutations by the study of mRNA. We describe a simple RT-PCR-based strategy to amplify the total coding sequence of the NF1 transcript from peripheral blood lymphocyte RNA. This strategy involves an initial cDNA synthesis step utilizing a set of random hexamers, followed by two consecutive rounds of PCR amplifications. The first round of amplification was performed using four NF1-specific nested primer pairs. This amplification allows the construction of overlapping fragments which span a 8694 bp cDNA sequence of the gene. For mutation analysis, the amplified products or their digests were subjected to electrophoresis on Hydrolink gels. Two disease-causing mutations, a 3 bp deletion in exon 17 and a 10 bp deletion in exon 44, originally detected in the genomic DNA from two unrelated NF1 patients, have been confirmed at the RNA level. The combination of this strategy with other established techniques such as SSCP, chemical cleavage of mismatch, protein truncation test (PTT) and quantitative PCR should greatly facilitate mutation and expression analyses in the NF1 gene.

  3. Proteomic analysis and qRT-PCR verification of temperature response to Arthrospira (Spirulina) platensis.

    PubMed

    Huili, Wang; Xiaokai, Zhao; Meili, Lin; Dahlgren, Randy A; Wei, Chen; Jaiopeng, Zhou; Chengyang, Xu; Chunlei, Jin; Yi, Xu; Xuedong, Wang; Li, Ding; Qiyu, Bao

    2013-01-01

    Arthrospira (Spirulina) platensis (ASP) is a representative filamentous, non-N2-fixing cyanobacterium that has great potential to enhance the food supply and possesses several valuable physiological features. ASP tolerates high and low temperatures along with highly alkaline and salty environments, and can strongly resist oxidation and irradiation. Based on genomic sequencing of ASP, we compared the protein expression profiles of this organism under different temperature conditions (15°C, 35°Cand 45°C) using 2-DE and peptide mass fingerprinting techniques. A total of 122 proteins having a significant differential expression response to temperature were retrieved. Of the positively expressed proteins, the homologies of 116 ASP proteins were found in Arthrospira (81 proteins in Arthrospira platensis str. Paraca and 35 in Arthrospira maxima CS-328). The other 6 proteins have high homology with other microorganisms. We classified the 122 differentially expressed positive proteins into 14 functions using the COG database, and characterized their respective KEGG metabolism pathways. The results demonstrated that these differentially expressed proteins are mainly involved in post-translational modification (protein turnover, chaperones), energy metabolism (photosynthesis, respiratory electron transport), translation (ribosomal structure and biogenesis) and carbohydrate transport and metabolism. Others proteins were related to amino acid transport and metabolism, cell envelope biogenesis, coenzyme metabolism and signal transduction mechanisms. Results implied that these proteins can perform predictable roles in rendering ASP resistance against low and high temperatures. Subsequently, we determined the transcription level of 38 genes in vivo in response to temperature and identified them by qRT-PCR. We found that the 26 differentially expressed proteins, representing 68.4% of the total target genes, maintained consistency between transcription and translation levels. The remaining 12 genes showed inconsistent protein expression with transcription level and accounted for 31.6% of the total target genes. PMID:24349519

  4. Proteomic Analysis and qRT-PCR Verification of Temperature Response to Arthrospira (Spirulina) platensis

    PubMed Central

    Huili, Wang; Xiaokai, Zhao; Meili, Lin; Dahlgren, Randy A.; Wei, Chen; Jaiopeng, Zhou; Chengyang, Xu; Chunlei, Jin; Yi, Xu; Xuedong, Wang; Li, Ding; Qiyu, Bao

    2013-01-01

    Arthrospira (Spirulina) platensis (ASP) is a representative filamentous, non-N2-fixing cyanobacterium that has great potential to enhance the food supply and possesses several valuable physiological features. ASP tolerates high and low temperatures along with highly alkaline and salty environments, and can strongly resist oxidation and irradiation. Based on genomic sequencing of ASP, we compared the protein expression profiles of this organism under different temperature conditions (15°C, 35°Cand 45°C) using 2-DE and peptide mass fingerprinting techniques. A total of 122 proteins having a significant differential expression response to temperature were retrieved. Of the positively expressed proteins, the homologies of 116 ASP proteins were found in Arthrospira (81 proteins in Arthrospira platensis str. Paraca and 35 in Arthrospira maxima CS-328). The other 6 proteins have high homology with other microorganisms. We classified the 122 differentially expressed positive proteins into 14 functions using the COG database, and characterized their respective KEGG metabolism pathways. The results demonstrated that these differentially expressed proteins are mainly involved in post-translational modification (protein turnover, chaperones), energy metabolism (photosynthesis, respiratory electron transport), translation (ribosomal structure and biogenesis) and carbohydrate transport and metabolism. Others proteins were related to amino acid transport and metabolism, cell envelope biogenesis, coenzyme metabolism and signal transduction mechanisms. Results implied that these proteins can perform predictable roles in rendering ASP resistance against low and high temperatures. Subsequently, we determined the transcription level of 38 genes in vivo in response to temperature and identified them by qRT-PCR. We found that the 26 differentially expressed proteins, representing 68.4% of the total target genes, maintained consistency between transcription and translation levels. The remaining 12 genes showed inconsistent protein expression with transcription level and accounted for 31.6% of the total target genes. PMID:24349519

  5. Commissioning of a novel microCT/RT system for small animal conformal radiotherapy

    PubMed Central

    Rodriguez, Manuel; Zhou, Hu; Keall, Paul; Graves, Edward

    2010-01-01

    The purpose of this work was to commission a 120 kVp photon beam produced by a micro-computed tomography (microCT) scanner for use in irradiating mice to therapeutic doses. A variable-aperture collimator has been integrated with a microCT scanner to allow the delivery of beams with pseudocircular profiles of arbitrary width between 0.1 and 6.0 cm. The dose rate at the isocenter of the system was measured using ion chamber and gafchromic EBT film as 1.56–2.13 Gy min?1 at the water surface for field diameters between 0.2 and 6.0 cm. The dose rate decreases approximately 10% per every 5 mm depth in water for field diameters between 0.5 and 1.0 cm. The flatness, symmetry and penumbra of the beam are 3.6%, 1.0% and 0.5 mm, respectively. These parameters are sufficient to accurately conform the radiation dose delivered to target organs on mice. The irradiated field size is affected principally by the divergence of the beam. In general, the beam has appropriate dosimetric characteristics to accurately deliver the dose to organs inside the mice’s bodies. Using multiple beams delivered from a variety of angular directions, targets as small as 2 mm may be irradiated while sparing surrounding tissue. This microCT/RT system is a feasible tool to irradiate mice using treatment planning and delivery methods analogous to those applied to humans. PMID:19478377

  6. An extension of the Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data.

    PubMed

    De Neve, Jan; Thas, Olivier; Ottoy, Jean-Pierre; Clement, Lieven

    2013-06-01

    Classical approaches for analyzing reverse transcription quantitative polymerase chain reaction (RT-qPCR) data commonly require normalization before assessing differential expression (DE). Normalization often has a substantial effect on the interpretation and validity of the subsequent analysis steps, but at the same time it causes a reduction in variance and introduces dependence among the normalized outcomes. These effects can be substantial, however, they are typically ignored. Most normalization techniques and methods for DE focus on mean expression and are sensitive to outliers. Moreover, in cancer studies, for example, oncogenes are often only expressed in a subsample of the populations during sampling. This primarily affects the skewness and the tails of the distribution and the mean is therefore not necessarily the best effect size measure within these experimental setups. In our contribution, we propose an extension of the Wilcoxon-Mann-Whitney test which incorporates a robust normalization, and the uncertainty associated with normalization is propagated into the final statistical summaries for DE. Our method relies on semiparametric regression models that focus on the probability P{Y ? Y'}, where Y and Y' denote independent responses for different subject groups. This effect size is robust to outliers, while remaining informative and intuitive when DE affects the shape of the distribution instead of only the mean. We also extend our approach for assessing DE for multiple features simultaneously. Simulation studies show that the test has a good performance, and that it is very competitive with standard methods for this platform. The method is illustrated on two neuroblastoma studies. PMID:23652635

  7. RT3D Reaction Modules for Natural and Enhanced Attenuation of Chloroethanes, Chloroethenes, Chloromethanes, and Daughter Products

    SciTech Connect

    Johnson, Christian D.; Truex, Michael J.

    2006-07-25

    This document describes a suite of MNA/EA reaction modules that were developed for addressing complex chlorinated solvent reactions using RT3D. As an introduction, an overview of these MNA/EA reaction modules is presented, including discussions of similarities between reaction modules, the purpose of key reaction parameters, and important considerations for using the reaction modules. Subsequent sections provide the details of the reaction kinetics (conceptual model and equations), data input requirements, and example (batch reactor) results for each reaction module. This document does not discuss reaction module implementation or validation; such information will accompany the software in the form of release notes or a supplement to the RT3D manual.

  8. Multiplex titration RT-PCR: rapid determination of gene expression patterns for a large number of genes

    NASA Technical Reports Server (NTRS)

    Nebenfuhr, A.; Lomax, T. L.

    1998-01-01

    We have developed an improved method for determination of gene expression levels with RT-PCR. The procedure is rapid and does not require extensive optimization or densitometric analysis. Since the detection of individual transcripts is PCR-based, small amounts of tissue samples are sufficient for the analysis of expression patterns in large gene families. Using this method, we were able to rapidly screen nine members of the Aux/IAA family of auxin-responsive genes and identify those genes which vary in message abundance in a tissue- and light-specific manner. While not offering the accuracy of conventional semi-quantitative or competitive RT-PCR, our method allows quick screening of large numbers of genes in a wide range of RNA samples with just a thermal cycler and standard gel analysis equipment.

  9. Screening of selected plant extracts for in vitro inhibitory activity on HIV-1 reverse transcriptase (HIV-1 RT).

    PubMed

    Mlinaric, A; Kreft, S; Umek, A; Strukelj, B

    2000-01-01

    Methanolic-aqueous extracts of 70 plants were investigated for their ability to inhibit HIV-1 reverse transcriptase activity in vitro. Two thirds of the extracts screened showed more than 50% inhibition. Two extracts inhibited the enzyme completely while four exhibited more than 90% inhibition. Tannins as nonspecific HIV-1 RT inhibitors were detected and removed from the extracts. The IC50 values of the most potent extracts after the removal of tannins for the HIV-1 RT inhibition are as follows: Sambucus racemosa 0.017 mg/ml and Geranium phaeum 0.067 mg/ml. Daunomycine was chosen as a standard substance in the non-radioactive immuno assay used for screening. As a result from the future isolation and characterization of these compounds, new leading structures are expectable. PMID:10683878

  10. WSU foUndation/2006-2007 2006-2007 annUaL REPoRt

    E-print Network

    Collins, Gary S.

    WSU foUndation/2006-2007 2006-2007 annUaL REPoRt #12;2 WSU foUndation/2006-2007 TABLE OF CONTENTS 2 LEttER fRoM tHE PRESidEnt 4 fEatURE StoRiES 10 finanCiaL REPoRt 14 foUndation LEadERSHiP 17 HonoR RoLL of donoRS 8 LaUREatES 22 BEnEfaCtoRS 38 PRESidEnt'S aSSoCiatES 49 LEGaCY aSSoCiatES 52 CoRPoRationS, foUndationS

  11. Duplex Real-Time RT-PCR Assays for the Detection and Typing of Epizootic Haemorrhagic Disease Virus

    PubMed Central

    Viarouge, Cyril; Breard, Emmanuel; Zientara, Stephan; Vitour, Damien; Sailleau, Corinne

    2015-01-01

    Epizootic haemorrhagic disease virus (EHDV) may cause severe clinical episodes in some species of deer and sometimes in cattle. Laboratory diagnosis provides a basis for the design and timely implementation of disease control measures. There are seven distinct EHDV serotypes, VP2 coding segment 2 being the target for serotype specificity. This paper reports the development and validation of eight duplex real-time RT-PCR assays to simultaneously amplify the EHDV target (S9 for the pan-EHDV real-time RT-PCR assay and S2 for the serotyping assays) and endogenous control gene Beta-actin. Analytical and diagnostic sensitivity and specificity, inter- and intra-assay variation and efficiency were evaluated for each assay. All were shown to be highly specific and sensitive. PMID:26161784

  12. Rapid detection and characterisation of infectious bronchitis virus (IBV) from New Zealand using RT-PCR and sequence analysis

    Microsoft Academic Search

    Ramneek; NL Mitchell; RG McFarlane

    2005-01-01

    AIMS: To develop a reverse transcriptase-polymerase chain reaction (RT-PCR) assay to detect infectious bronchitis virus (IBV) from commercially-raised poultry in New Zealand and compare results with those from virus isolation. To characterise the IBV isolates using sequence analysis.METHODS: Pooled tissue samples (trachea, kidney, caecal tonsils and cloacal swabs) from 164 broiler and 53 layer flocks located throughout New Zealand were

  13. GOES-R Proving Ground Activities at the NASA Short-Term Prediction Research and Transition (SPoRT) Center

    NASA Technical Reports Server (NTRS)

    Molthan, Andrew

    2011-01-01

    SPoRT is actively involved in GOES-R Proving Ground activities in a number of ways: (1) Applying the paradigm of product development, user training, and interaction to foster interaction with end users at NOAA forecast offices national centers. (2) Providing unique capabilities in collaboration with other GOES-R Proving Ground partners (a) Hybrid GOES-MODIS imagery (b) Pseudo-GLM via regional lightning mapping arrays (c) Developing new RGB imagery from EUMETSAT guidelines

  14. Determination of photoinitiated polymerization of multifunctional acrylates with acetic acid derivatives of thioxanthone by RT-FTIR

    Microsoft Academic Search

    Feyza Karasu; Meral Aydin; M. Arif Kaya; Demet Karaca Balta; Nergis Arsu

    2009-01-01

    Photopolymerization of multifunctional acrylates with 2-thioxanthone-thioacetic acid (TXSCH2COOH) and 2-(carboxymethoxy) thioxanthone (TXOCH2COOH) as the one-component photoinitiator has been investigated by real-time Fourier transform infrared (RT-FTIR) spectroscopy. The photobleaching of these one-component nature initiators was performed in air. The irradiation time for total bleaching was 240s for TXSCH2COOH and 540s for TXOCH2COOH.

  15. DNA repair genes in human fetal and adult prostatic tissues and cancer cell lines using differential RT-PCR

    Microsoft Academic Search

    Rajvir Dahiya

    1996-01-01

    The present study was designed to investigate the mRNA expression of four DNA repair genes (XPCC, hMSH2, XRCC 1, and ERCC 1) in human fetal and adult prostatic tissues and cancer cell lines using differential reverse transcriptase-polymerase chain reaction (RT-PCR). For this purpose, total RNA from four human prostrate cancer cell lines (LNCaP, PC-3, DU-145, and ND-I) and human fetal

  16. Cyclin E Expression in Operable Breast Cancer Quantified Using Real-Time RT-PCR: A Comparative Study with Immunostaining

    Microsoft Academic Search

    Piotr Potemski; Elzbieta Pluciennik; Andrzej K. Bednarek; Renata Kusinska; Dorota Jesionek-Kupnicka; Grazyna Pasz-Walczak; Cezary Watala; Radzislaw Kordek

    2006-01-01

    Objective: The main purpose of this retrospective study was to compare cyclin E expression levels in operable breast cancer patients determined using real-time RT-PCR and immuno- staining. The prognostic relevance of cyclin E was also investigated. Methods: Specimens of invasive ductal breast cancer tissues obtained from 124 women during radical mastectomy were analyzed. Results: Of the tumor samples, 40.3 and

  17. Selection of Reference Genes for qRT-PCR in High Fat Diet-Induced Hepatic Steatosis Mice Model

    Microsoft Academic Search

    Lingyan XuXinran; Xinran Ma; Bin Cui; Xiaoying Li; Guang Ning; Shu Wang

    2011-01-01

    With the epidemic proportions of obesity worldwide and the concurrent prevalence of hepatic steatosis, there is an urgent\\u000a need for better understanding the intrinsic mechanism of hepatic steatosis, especially the changes of gene expression underlying\\u000a the development of hepatic steatosis and its associated abnormal liver function. Quantitative real-time PCR (qRT-PCR) is a\\u000a sensitive and highly reproducible technique of gene expression

  18. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

    Microsoft Academic Search

    Jo Vandesompele; Katleen De Preter; Filip Pattyn; Bruce Poppe; Nadine Van Roy; Anne De Paepe; Frank Speleman

    2002-01-01

    BACKGROUND: Gene-expression analysis is increasingly important in biological research, with real-time reverse transcription PCR (RT-PCR) becoming the method of choice for high-throughput and accurate expression profiling of selected genes. Given the increased sensitivity, reproducibility and large dynamic range of this methodology, the requirements for a proper internal control gene for normalization have become increasingly stringent. Although housekeeping gene expression has

  19. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems

    Microsoft Academic Search

    S A Bustin

    2002-01-01

    The fluorescence-based real-time reverse transcription PCR (RT-PCR) is widely used for the quantification of steady-state mRNA levels and is a critical tool for basic research, molecular medicine and biotechnology. Assays are easy to perform, capable of high throughput, and can combine high sensitivity with reliable specificity. The technology is evolving rapidly with the introduction of new enzymes, chemistries and instrumentation.

  20. Comparative molecular field analysis (CoMFA) and docking studies of non-nucleoside HIV1 RT inhibitors (NNIs)

    Microsoft Academic Search

    M. L. Barreca; A. Carotti; A. Carrieri; A. Chimirri; A. M. Monforte; M. Pellegrini Calace; A. Rao

    1999-01-01

    A set of TIBO derivatives endowed with reverse transcriptase (RT) inhibitory activity were analyzed by comparative molecular field analysis (CoMFA). Besides conventional steric and electrostatic fields, molecular lipophilicity potential (MLP) was also used as a third field in CoMFA. An informative and statistically significant model (q2=0.70, r2=0.90, s=0.46) was obtained by taking into account the three field types together. The

  1. Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay

    Microsoft Academic Search

    Laurent Perreard; Cheng Fan; John F Quackenbush; Michael Mullins; Nicholas P Gauthier; Edward Nelson; Mary Mone; Heidi Hansen; Saundra S Buys; Karen Rasmussen; Alejandra Ruiz Orrico; Donna Dreher; Rhonda Walters; Joel Parker; Zhiyuan Hu; Xiaping He; Juan P Palazzo; Olufunmilayo I Olopade; Aniko Szabo; Charles M Perou; Philip S Bernard

    2006-01-01

    INTRODUCTION: Predicting the clinical course of breast cancer is often difficult because it is a diverse disease comprised of many biological subtypes. Gene expression profiling by microarray analysis has identified breast cancer signatures that are important for prognosis and treatment. In the current article, we use microarray analysis and a real-time quantitative reverse-transcription (qRT)-PCR assay to risk-stratify breast cancers based

  2. The complete consensus sequence of coxsackievirus B6 and generation of infectious clones by long RT-PCR

    Microsoft Academic Search

    Tami A Martino; Raymond Tellier; Martin Petric; David M Irwin; Ahmad Afshar; Peter P Liu

    1999-01-01

    The full length sequence for the human pathogen coxsackievirus B6 (CVB6, Schmitt strain) has been determined. We used long RT-PCR to generate full length DNA amplicon of CVB6, and then directly sequenced the amplicons. One-step cloning of the full length amplicon enabled us to obtain an infectious clone of CVB6. RNA generated from CVB6 amplicon DNA or CVB6 clones, by

  3. Development of a novel recombinant encapsidated RNA particle: Evaluation as an internal control for diagnostic RT-PCR

    Microsoft Academic Search

    Donald P. King; Nick Montague; Katja Ebert; Scott M. Reid; Juliet P. Dukes; Lysann Schädlich; Graham J. Belsham; George P. Lomonossoff

    2007-01-01

    This report describes the generation of novel encapsidated RNA particles and their evaluation as in-tube internal controls in diagnostic real-time reverse-transcription PCR (rRT-PCR) assays for the detection of RNA viruses. A cassette containing sequences of 2 diagnostic primer sets for foot-and-mouth disease virus (FMDV) and a set for swine vesicular disease virus (SVDV) was engineered into a full-length cDNA clone

  4. Diagnostic real-time RT-PCR for the simultaneous detection of Citrus exocortis viroid and Hop stunt viroid.

    PubMed

    Papayiannis, Lambros C

    2014-02-01

    Citrus exocortis viroid (CEVd) and Hop stunt viroid (HSVd) are two important viroids known to infect several plant species worldwide. In this study, a real-time reverse transcription (RT) TaqMan polymerase chain reaction (PCR) assay was developed and optimized for the simultaneous detection of CEVd and HSVd. The assay's analytical and diagnostic sensitivity and specificity were evaluated using reference isolates. Two different RNA extraction methods and one rapid crude template preparation procedure were compared in terms of extraction purity and efficiency for PCR applications. Extraction method Q included a commercially available kit, whereas method C was a modified chloroform-phase extraction in house protocol. Procedure S involved blotting the sap extract on a positively charged nylon membrane and elution. The multiplex RT-TaqMan PCR assay successfully discriminated the two viroid species from all reference samples and its recorded diagnostic sensitivity (Dse) and specificity (Dsp) was 100%. On the contrary, in conventional RT-PCR tests, the overall Dse and Dsp were lower and estimated at 94 and 95% for CEVd, and 97 and 98% for HSVd, respectively. In a direct comparison, the developed assay presented 1000-fold more analytical sensitivity. Spectrophotometric results showed that RNA extraction methods Q and C, yielded the purest RNA, and gave the lowest mean Ct values. Alternative template preparation method S resulted in Ct values statistically similar to those obtained with methods Q to C when tested by RT-TaqMan PCR. The developed assay, using crude template preparation S, allows the simple, accurate and cost-effective testing of a large number of plant samples, and can be applied in surveys and certification schemes. PMID:24252553

  5. Validation of reference genes for RT-qPCR studies of gene expression in banana fruit under different experimental conditions

    Microsoft Academic Search

    Lei ChenHai-ying; Hai-ying Zhong; Jian-fei Kuang; Jian-guo Li; Wang-jin Lu; Jian-ye Chen

    Reverse transcription quantitative real-time PCR (RT-qPCR) is a sensitive technique for quantifying gene expression, but its\\u000a success depends on the stability of the reference gene(s) used for data normalization. Only a few studies on validation of\\u000a reference genes have been conducted in fruit trees and none in banana yet. In the present work, 20 candidate reference genes\\u000a were selected, and

  6. RT2: A Real-Time Ray-Tracing method for acoustic distance evaluations among cooperating AUVs

    Microsoft Academic Search

    Giuseppe Casalino; Alessio Turetta; Enrico Simetti; Andrea Caiti

    2010-01-01

    The paper deals with the problem of distributed acoustic localization of teams of Autonomous Underwater Vehicles (AUVs) and proposes a novel algorithm, Real-Time Ray-Tracing (RT2), for evaluating the distance between any pair of AUVs in the team. The technique, based on a modified formulation of the non-linear sound-ray propagation laws, allows efficiently handling the distorted and reflected acoustic ray paths,

  7. Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.)

    Microsoft Academic Search

    Julia M Lee; John R Roche; Danny J Donaghy; Anthony Thrush; Puthigae Sathish

    2010-01-01

    BACKGROUND: Perennial ryegrass (Lolium perenne L.) is an important pasture and turf crop. Biotechniques such as gene expression studies are being employed to improve traits in this temperate grass. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is among the best methods available for determining changes in gene expression. Before analysis of target gene expression, it is essential to select an appropriate

  8. Real-time RT-PCR detection of Bovine Viral Diarrhoea virus in whole blood using an external RNA reference

    Microsoft Academic Search

    N. J. Young; C. J. Thomas; M. E. Collins; J. Brownlie

    2006-01-01

    A novel two-step real-time RT-PCR assay using SYBR® Green I was developed for the detection of acute Bovine Viral Diarrhoea virus (BVDV) infection in whole blood from cattle. During infection animals experience a characteristic transient leucopenia and the number of cells per volume of blood changes over time; so quantitation of viral load by reference to a cellular housekeeping gene

  9. Detection of four calla potyviruses by multiplex RT-PCR using nad5 mRNA as an internal control

    Microsoft Academic Search

    Wen-Chi Hu; Chin-Hsing Huang; Shu-Chuan Lee; Chun-I Wu; Ya-Chun Chang

    2010-01-01

    Dasheen mosaic virus (DsMV), Turnip mosaic virus (TuMV), Konjac mosaic virus (KoMV) and Zantedeschia mild mosaic virus (ZaMMV) are important potyviruses previously identified in calla lily plants in Taiwan. In order to save time and cost of\\u000a virus detection, a multiplex RT-PCR assay was developed for these calla potyviruses. Specific primers for each virus were\\u000a designed based on the sequences

  10. HIV-1 Tropism Determination Using a Phenotypic Env Recombinant Viral Assay Highlights Overestimation of CXCR4-Usage by Genotypic Prediction Algorithms for CRRF01_AE and CRF02_AG

    PubMed Central

    Mulinge, Martin; Lemaire, Morgane; Servais, Jean-Yves; Rybicki, Arkadiusz; Struck, Daniel; da Silva, Eveline Santos; Verhofstede, Chris; Lie, Yolanda; Seguin-Devaux, Carole; Schmit, Jean-Claude; Bercoff, Danielle Perez

    2013-01-01

    Background Human Immunodeficiency virus type-1 (HIV) entry into target cells involves binding of the viral envelope (Env) to CD4 and a coreceptor, mainly CCR5 or CXCR4. The only currently licensed HIV entry inhibitor, maraviroc, targets CCR5, and the presence of CXCX4-using strains must be excluded prior to treatment. Co-receptor usage can be assessed by phenotypic assays or through genotypic prediction. Here we compared the performance of a phenotypic Env-Recombinant Viral Assay (RVA) to the two most widely used genotypic prediction algorithms, Geno2Pheno[coreceptor] and webPSSM. Methods Co-receptor tropism of samples from 73 subtype B and 219 non-B infections was measured phenotypically using a luciferase-tagged, NL4-3-based, RVA targeting Env. In parallel, tropism was inferred genotypically from the corresponding V3-loop sequences using Geno2Pheno[coreceptor] (5–20% FPR) and webPSSM-R5X4. For discordant samples, phenotypic outcome was retested using co-receptor antagonists or the validated Trofile® Enhanced-Sensitivity-Tropism-Assay. Results The lower detection limit of the RVA was 2.5% and 5% for X4 and R5 minority variants respectively. A phenotype/genotype result was obtained for 210 samples. Overall, concordance of phenotypic results with Geno2Pheno[coreceptor] was 85.2% and concordance with webPSSM was 79.5%. For subtype B, concordance with Geno2pheno[coreceptor] was 94.4% and concordance with webPSSM was 79.6%. High concordance of genotypic tools with phenotypic outcome was seen for subtype C (90% for both tools). Main discordances involved CRF01_AE and CRF02_AG for both algorithms (CRF01_AE: 35.9% discordances with Geno2Pheno[coreceptor] and 28.2% with webPSSM; CRF02_AG: 20.7% for both algorithms). Genotypic prediction overestimated CXCR4-usage for both CRFs. For webPSSM, 40% discordance was observed for subtype A. Conclusions Phenotypic assays remain the most accurate for most non-B subtypes and new subtype-specific rules should be developed for non-B subtypes, as research studies more and more draw conclusions from genotypically-inferred tropism, and to avoid unnecessarily precluding patients with limited treatment options from receiving maraviroc or other entry inhibitors. PMID:23667426

  11. Comparison of MTT assay, flow cytometry, and RT-PCR in the evaluation of cytotoxicity of five prosthodontic materials.

    PubMed

    Wang, Xue; Xia, Yang; Liu, Laikui; Liu, Mei; Gu, Ning; Guang, Hanbing; Zhang, Feimin

    2010-11-01

    In the present study, the cytotoxic effects of five prosthodontic materials on the L929 cell line were assessed by flow cytometry (FCM), reverse transcription PCR (RT-PCR), and MTT (3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyltetrazoli-umbromide) assay. The cells were treated with eluates resin (RE), pressable ceramics (PC), Co-Cr alloy-porcelain (CC), Ni-Cr alloy-porcelain (NC), and diatomite ceramics (DC). The cytotoxicity of all the materials tested by the MTT assay was grade 1. By FCM analysis, apoptosis rates of DC and PC were low, with no significant difference from the control (p > 0.05). The rest of the groups induced much higher apoptosis rates (p < 0.05), with the highest in the RE group. The necrotic cell levels of RE was also significantly increased (p < 0.05). Bcl-2 and Bax mRNA expression were determined by RT-PCR, and the Bax/Bcl-2 ratio in the DC and PC groups were not significantly different from the control (p > 0.05), whereas CC, NC, and RE groups showed significant differences (p < 0.05). Taken together, the results suggest that FCM and RT-PCR analyses can supplement the traditional MTT assay in evaluating the cytotoxicity of prosthodontic materials for selecting highly biocompatible materials. PMID:20878925

  12. Detection and absolute quantitation of Tomato torrado virus (ToTV) by real time RT-PCR.

    PubMed

    Herrera-Vásquez, José Angel; Rubio, Luis; Alfaro-Fernández, Ana; Debreczeni, Diana Elvira; Font-San-Ambrosio, Isabel; Falk, Bryce W; Ferriol, Inmaculada

    2015-09-01

    Tomato torrado virus (ToTV) causes serious damage to the tomato industry and significant economic losses. A quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) method using primers and a specific TaqMan(®) MGB probe for ToTV was developed for sensitive detection and quantitation of different ToTV isolates. A standard curve using RNA transcripts enabled absolute quantitation, with a dynamic range from 10(4) to 10(10) ToTV RNA copies/ng of total RNA. The specificity of the RT-qPCR was tested with twenty-three ToTV isolates from tomato (Solanum lycopersicum L.), and black nightshade (Solanum nigrum L.) collected in Spain, Australia, Hungary and France, which covered the genetic variation range of this virus. This new RT-qPCR assay enables a reproducible, sensitive and specific detection and quantitation of ToTV, which can be a valuable tool in disease management programs and epidemiological studies. PMID:25956672

  13. Effect of Preservative on Recoverable RT-PCR Amplicon Length from Influenza A Virus in Bird Feces

    PubMed Central

    Evers, David L.; Slemons, Richard D.; Taubenberger, Jeffery K.

    2008-01-01

    SUMMARY Surveillance for avian influenza A viruses in wild bird populations is often limited by requirements for a cold chain from time of specimen collection, by availability of ultra–low temperature specimen storage within a few hours or days, and by laborious classical virologic procedures. Successful storage of specimens in preservatives at ambient temperature and subsequent detection of RNA by reverse transcriptase–polymerase chain reaction (RT-PCR) would assist in helping influenza surveillance efforts become more widespread in remote areas, as well as more timely and inexpensive. Here, we describe bird feces spiked with influenza A virus preserved with guanidine and commercial buffers or alcohols at ambient temperature and analyzed by RT-PCR protocols. Virus-specific RT-PCR products of, at most, 206 bp were recovered for samples preserved with alcohols and up to 521 bp for samples preserved with guanidine or commercial buffers. These results suggest that this approach is feasible in the field and that preserved specimens might be better assayed molecularly when preserved in guanidine or commercial buffers. PMID:18251409

  14. [Application of multiplex nested RT-PCR to detecting 10 fusion genes related with MLL gene in myelodysplastic syndrome].

    PubMed

    Cao, Ting-Ting; Gao, Li; Zhou, Min-Hang; Guo, Yue-Lu; Yan, Zhen; Zhang, Song-Song; Xu, Yuan-Yuan; Ding, Yi; Wang, Li-Li; Yu, Li

    2012-08-01

    This study was aimed to investigate the clinical value of multiplex nested reverse transcription PCR (RT-PCR) in detecting MLL-related fusion genes in myelodysplastic syndrome (MDS). Ten MLL-related genes (dupMLL, MLL-ELL, MLL-ENL, MLL-AF6, MLL-AF9, MLL-AF10, MLL-AF17, MLL-CBP, MLL-AF1P, MLL-AF1Q) in 221 MDS cases were detected by multiplex nested RT-PCR. The results indicated that 20 patients were detected with positive result among 221 patients and the positive rate was 9.05%. The number of the positive cases and positive rates of the above mentioned 10 fusion genes were in order: 7 (3.16%), 2 (0.9%), 1 (0.45%), 1 (0.45%), 2 (0.9%), 2 (0.9%), 1 (0.45%), 2 (0.9%), 1 (0.45%), 1 (10.45%). It is concluded that the multiplex nested RT-PCR has been confirmed to be able to detect 10 fusion genes in MDS patients, which can provide important evidences for assessing diagnosis and treatment, and give related necessary information about minimal residual disease and its prognosis. PMID:22931658

  15. Rapid method for identification of chemopreventive compounds using multiplex RT-PCR for cyclooxygenase mRNA expression.

    PubMed

    Malik, Minnie; Magnuson, Bernadene A

    2004-01-01

    Inhibition of the expression of the cyclooxygenase-2 (COX-2) enzyme has been associated with prevention or reversal of cancer development in several organs. Development of, or screening for, selective cyclooxygenase (COX) inhibitors is an approach for identifying chemopreventive agents. The aim of this project was to develop a rapid semi-quantitative multiplex RT-PCR for analysis of the expression of cyclooxygenase 1 and 2 genes relative to 18S, the housekeeping gene, in a 3-gene multiplex reaction. The optimal conditions for the 3-gene multiplex reaction were determined experimentally. Following RT-PCR, the amplified PCR products are analyzed by capillary electrophoresis-based LabChip and the Agilent 2100 bioanalyzer, which eliminates electrophoresis through ethidium bromide-agarose gels and normalization of band intensities using software programs such as Molecular Analyst. The multiplex RT-PCR assay developed here is a cost effective technique for routine application in laboratories that are screening natural or synthetic compounds for specific inhibitors of cyclooxygenase-2 as potential chemopreventive agents. PMID:15350631

  16. Structural and Population Polymorphism of RT-Like Sequences in Avian Schistosomes Trichobilharzia szidati (Platyhelminthes: Digenea: Schistosomatidae)

    PubMed Central

    Semyenova, S. K.; Chrisanfova, G. G.; Guliaev, A. S.; Yesakova, A. P.; Ryskov, A. P.

    2015-01-01

    Recently we developed the genus-specific markers of the avian schistosomes of the genus Trichobilharzia, the causative agents of human cercarial dermatitis. The 7 novel genome sequences of T. franki, T. regenti, and T. szidati revealed similarity with genome repeat region of African schistosome Schistosoma mansoni. In the present work we analyzed the 37 new T. szidati sequences to study intragenome variability and host specificity for the parasite from three localities of East Europe. DNAs were isolated from cercariae or single sporocysts obtained from 6 lymnaeid snails Lymnaea stagnalis and L. palustris from Belarus and Russia. All sequences formed three diverged groups, one of which consists of the sequences with multiple deletions; other groups involved two paralogous copies with stop codons and frameshift mutations. Strong association between geographical distribution and snail host specificity cannot be established. All studied sequences have homology with the reverse transcriptase domain (RT) of Penelope-like elements (PLE) of S. mansoni and S. japonicum and new members of RT family were identified. We proposed that three diverged groups RT sequences of T. szidati are results of duplication or transposition of PLE during parasite evolution. Implications of the retroelement dynamics in the life history of avian schistosomes are discussed.

  17. Evaluation of a quantitative RT-PCR assay to detect HER2 mRNA overexpression for diagnosis and selection of trastuzumab therapy in breast cancer tissue samples.

    PubMed

    Wang, Hye-Young; Kim, Sunghyun; Park, Sangjung; Kim, Seungil; Jung, Dongju; Park, Kwang Hwa; Lee, Hyeyoung

    2014-12-01

    Breast cancer patients who have a positive result for HER2 overexpression are commonly treated with Herceptin, a HER2-targeted therapy. In the present study, the BrightGen HER2 RT-qDx (Syantra, Calgary, Canada), which is based on a one-tube nested RT-qPCR method that detects HER2 mRNA overexpression, was clinically evaluated in a total of 237 formalin-fixed paraffin-embedded (FFPE) tissue samples from breast cancer patients. Among the 38 HER2 positive samples, which were determined via IHC/FISH methods, 13 samples out of 16 (81.3%) that were IHC2+/FISH+ and 22 samples out of 22 (100%) that were IHC3+ have been decided positive for HER2 expression via the RT-qPCR method. The true positivity and false positivity results for the RT-qPCR were 92% (35/38) and 2% (1/65), respectively. The concordance between RT-qPCR and IHC results and RT-qPCR and IHC/FISH was 87.2% and 92.1%, respectively. Conclusively, the BrightGen HER2 RT-qDx may be a reliable and convenient method that can supplement traditional IHC and FISH methods for efficient use of trastuzumab. PMID:25236569

  18. Combined contrast-enhanced ultrasound and rt-PA treatment is safe and improves impaired microcirculation after reperfusion of middle cerebral artery occlusion.

    PubMed

    Nedelmann, Max; Ritschel, Nouha; Doenges, Simone; Langheinrich, Alexander C; Acker, Till; Reuter, Peter; Yeniguen, Mesut; Pukropski, Jan; Kaps, Manfred; Mueller, Clemens; Bachmann, Georg; Gerriets, Tibo

    2010-10-01

    In monitoring of recanalization and in sonothrombolysis, contrast-enhanced ultrasound (CEUS) is applied in extended time protocols. As extended use may increase the probability of unwanted effects, careful safety evaluation is required. We investigated the safety profile and beneficial effects of CEUS in a reperfusion model. Wistar rats were subjected to filament occlusion of the right middle cerebral artery (MCA). Reperfusion was established after 90?minutes, followed by recombinant tissue-type plasminogen activator (rt-PA) treatment and randomization to additional CEUS (contrast agent: SonoVue; 60?minutes). Blinded outcome evaluation consisted of magnetic resonance imaging (MRI), neurologic assessment, and histology and, in separate experiments, quantitative 3D nano-computed tomography (CT) angiography (900?nm(3) voxel size). Nano-CT revealed severely compromised microcirculation in untreated animals after MCA reperfusion. The rt-PA partially improved hemispheric perfusion. Impairment was completely reversed in animals receiving rt-PA and CEUS. This combination was more effective than treatment with either CEUS without rt-PA or rt-PA and ultrasound or ultrasound alone. In MRI experiments, CEUS and rt-PA treatment resulted in a significantly reduced ischemic lesion volume and edema formation. No unwanted effects were detected on MRI, histology, and intracranial temperature assessment. This study shows that CEUS and rt-PA is safe in the situation of reperfusion and displays beneficial effects on the level of the microvasculature. PMID:20531462

  19. Combined contrast-enhanced ultrasound and rt-PA treatment is safe and improves impaired microcirculation after reperfusion of middle cerebral artery occlusion

    PubMed Central

    Nedelmann, Max; Ritschel, Nouha; Doenges, Simone; Langheinrich, Alexander C; Acker, Till; Reuter, Peter; Yeniguen, Mesut; Pukropski, Jan; Kaps, Manfred; Mueller, Clemens; Bachmann, Georg; Gerriets, Tibo

    2010-01-01

    In monitoring of recanalization and in sonothrombolysis, contrast-enhanced ultrasound (CEUS) is applied in extended time protocols. As extended use may increase the probability of unwanted effects, careful safety evaluation is required. We investigated the safety profile and beneficial effects of CEUS in a reperfusion model. Wistar rats were subjected to filament occlusion of the right middle cerebral artery (MCA). Reperfusion was established after 90?minutes, followed by recombinant tissue-type plasminogen activator (rt-PA) treatment and randomization to additional CEUS (contrast agent: SonoVue; 60?minutes). Blinded outcome evaluation consisted of magnetic resonance imaging (MRI), neurologic assessment, and histology and, in separate experiments, quantitative 3D nano-computed tomography (CT) angiography (900?nm3 voxel size). Nano-CT revealed severely compromised microcirculation in untreated animals after MCA reperfusion. The rt-PA partially improved hemispheric perfusion. Impairment was completely reversed in animals receiving rt-PA and CEUS. This combination was more effective than treatment with either CEUS without rt-PA or rt-PA and ultrasound or ultrasound alone. In MRI experiments, CEUS and rt-PA treatment resulted in a significantly reduced ischemic lesion volume and edema formation. No unwanted effects were detected on MRI, histology, and intracranial temperature assessment. This study shows that CEUS and rt-PA is safe in the situation of reperfusion and displays beneficial effects on the level of the microvasculature. PMID:20531462

  20. Generation of Atoh1-rtTA transgenic mice: a tool for inducible gene expression in hair cells of the inner ear.

    PubMed

    Cox, Brandon C; Dearman, Jennifer A; Brancheck, Joseph; Zindy, Frederique; Roussel, Martine F; Zuo, Jian

    2014-01-01

    Atoh1 is a basic helix-loop-helix transcription factor that controls differentiation of hair cells (HCs) in the inner ear and its enhancer region has been used to create several HC-specific mouse lines. We generated a transgenic tetracycline-inducible mouse line (called Atoh1-rtTA) using the Atoh1 enhancer to drive expression of the reverse tetracycline transactivator (rtTA) protein and human placental alkaline phosphatase. Presence of the transgene was confirmed by alkaline phosphatase staining and rtTA activity was measured using two tetracycline operator (TetO) reporter alleles with doxycycline administered between postnatal days 0-3. This characterization of five founder lines demonstrated that Atoh1-rtTA is expressed in the majority of cochlear and utricular HCs. Although the tetracycline-inducible system is thought to produce transient changes in gene expression, reporter positive HCs were still observed at 6 weeks of age. To confirm that Atoh1-rtTA activity was specific to Atoh1-expressing cells, we also analyzed the cerebellum and found rtTA-driven reporter expression in cerebellar granule neuron precursor cells. The Atoh1-rtTA mouse line provides a powerful tool for the field and can be used in combination with other existing Cre recombinase mouse lines to manipulate expression of multiple genes at different times in the same animal. PMID:25363458

  1. Generation of Atoh1-rtTA transgenic mice: a tool for inducible gene expression in hair cells of the inner ear

    PubMed Central

    Cox, Brandon C.; Dearman, Jennifer A.; Brancheck, Joseph; Zindy, Frederique; Roussel, Martine F.; Zuo, Jian

    2014-01-01

    Atoh1 is a basic helix-loop-helix transcription factor that controls differentiation of hair cells (HCs) in the inner ear and its enhancer region has been used to create several HC-specific mouse lines. We generated a transgenic tetracycline-inducible mouse line (called Atoh1-rtTA) using the Atoh1 enhancer to drive expression of the reverse tetracycline transactivator (rtTA) protein and human placental alkaline phosphatase. Presence of the transgene was confirmed by alkaline phosphatase staining and rtTA activity was measured using two tetracycline operator (TetO) reporter alleles with doxycycline administered between postnatal days 0–3. This characterization of five founder lines demonstrated that Atoh1-rtTA is expressed in the majority of cochlear and utricular HCs. Although the tetracycline-inducible system is thought to produce transient changes in gene expression, reporter positive HCs were still observed at 6 weeks of age. To confirm that Atoh1-rtTA activity was specific to Atoh1-expressing cells, we also analyzed the cerebellum and found rtTA-driven reporter expression in cerebellar granule neuron precursor cells. The Atoh1-rtTA mouse line provides a powerful tool for the field and can be used in combination with other existing Cre recombinase mouse lines to manipulate expression of multiple genes at different times in the same animal. PMID:25363458

  2. Evaluation of a broad range real-time polymerase chain reaction (RT-PCR) assay for the diagnosis of septic synovitis in horses

    PubMed Central

    Elmas, Colette R.; Koenig, Judith B.; Bienzle, Dorothee; Cribb, Nicola C.; Cernicchiaro, Natalia; Coté, Nathalie M.; Weese, J. Scott

    2013-01-01

    Septic synovitis is a potentially debilitating and life-threatening disorder in horses. We hypothesized that a universal bacterial real-time PCR (RT-PCR) assay would have improved sensitivity and decreased turn-around time for detection of bacteria in synovial fluid (SF) samples. Forty-eight SF samples were collected from 36 horses that presented to two referral institutions with suspected septic synovitis. Universal RT-PCR, bacterial culture and SF analysis were performed on all samples, and an interpretation on the sample being septic or not was derived by three board certified specialists from the history, clinical assessment and SF characteristics. RT-PCR results were compared to a composite standard comprised of positive culture and interpretation by all three specialists of samples as “septic”. For 41 of 48 samples (85%), culture and RT-PCR results were concordant. Compared to the composite standard, 83% of samples were correctly classified by RT-PCR (turn-around time of approximately 4 hours). Relative sensitivity and specificity of RT-PCR were 87% and 72% respectively, and 56% and 86% for culture. Hence, universal RT-PCR was a rapid and highly sensitive test, which may accelerate diagnosis and improve outcome for horses with septic synovitis. PMID:24101798

  3. Reference genes for quantitative RT-PCR data in gastric tissues and cell lines

    PubMed Central

    Wisnieski, Fernanda; Calcagno, Danielle Queiroz; Leal, Mariana Ferreira; dos Santos, Leonardo Caires; Gigek, Carolina de Oliveira; Chen, Elizabeth Suchi; Pontes, Thaís Brilhante; Assumpção, Paulo Pimentel; de Assumpção, Mônica Barauna; Demachki, Sâmia; Burbano, Rommel Rodríguez; Smith, Marília de Arruda Cardoso

    2013-01-01

    AIM: To evaluate the suitability of reference genes in gastric tissue samples and cell lines. METHODS: The suitability of genes ACTB, B2M, GAPDH, RPL29, and 18S rRNA was assessed in 21 matched pairs of neoplastic and adjacent non-neoplastic gastric tissues from patients with gastric adenocarcinoma, 27 normal gastric tissues from patients without cancer, and 4 cell lines using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). The ranking of the best single and combination of reference genes was determined by NormFinder, geNorm™, BestKeeper, and DataAssist™. In addition, GenEx software was used to determine the optimal number of reference genes. To validate the results, the mRNA expression of a target gene, DNMT1, was quantified using the different reference gene combinations suggested by the various software packages for normalization. RESULTS: ACTB was the best reference gene for all gastric tissues, cell lines and all gastric tissues plus cell lines. GAPDH + B2M or ACTB + B2M was the best combination of reference genes for all the gastric tissues. On the other hand, ACTB + B2M was the best combination for all the cell lines tested and was also the best combination for analyses involving all the gastric tissues plus cell lines. According to the GenEx software, 2 or 3 genes were the optimal number of references genes for all the gastric tissues. The relative quantification of DNMT1 showed similar patterns when normalized by each combination of reference genes. The level of expression of DNMT1 in neoplastic, adjacent non-neoplastic and normal gastric tissues did not differ when these samples were normalized using GAPDH + B2M (P = 0.32), ACTB + B2M (P = 0.61), or GAPDH + B2M + ACTB (P = 0.44). CONCLUSION: GAPDH + B2M or ACTB + B2M is the best combination of reference gene for all the gastric tissues, and ACTB + B2M is the best combination for the cell lines tested. PMID:24222956

  4. Antibody-mediated protection against mucosal simian-human immunodeficiency virus challenge of macaques immunized with alphavirus replicon particles and boosted with trimeric envelope glycoprotein in MF59 adjuvant.

    PubMed

    Barnett, Susan W; Burke, Brian; Sun, Yide; Kan, Elaine; Legg, Harold; Lian, Ying; Bost, Kristen; Zhou, Fengmin; Goodsell, Amanda; Zur Megede, Jan; Polo, John; Donnelly, John; Ulmer, Jeffrey; Otten, Gillis R; Miller, Christopher J; Vajdy, Michael; Srivastava, Indresh K

    2010-06-01

    We have previously shown that rhesus macaques were partially protected against high-dose intravenous challenge with simian-human immunodeficiency virus SHIV(SF162P4) following sequential immunization with alphavirus replicon particles (VRP) of a chimeric recombinant VEE/SIN alphavirus (derived from Venezuelan equine encephalitis virus [VEE] and the Sindbis virus [SIN]) encoding human immunodeficiency virus type 1 HIV-1(SF162) gp140DeltaV2 envelope (Env) and trimeric Env protein in MF59 adjuvant (R. Xu, I. K. Srivastava, C. E. Greer, I. Zarkikh, Z. Kraft, L. Kuller, J. M. Polo, S. W. Barnett, and L. Stamatatos, AIDS Res. Hum. Retroviruses 22:1022-1030, 2006). The protection did not require T-cell immune responses directed toward simian immunodeficiency virus (SIV) Gag. We extend those findings here to demonstrate antibody-mediated protection against mucosal challenge in macaques using prime-boost regimens incorporating both intramuscular and mucosal routes of delivery. The macaques in the vaccination groups were primed with VRP and then boosted with Env protein in MF59 adjuvant, or they were given VRP intramuscular immunizations alone and then challenged with SHIV(SF162P4) (intrarectal challenge). The results demonstrated that these vaccines were able to effectively protect the macaques to different degrees against subsequent mucosal SHIV challenge, but most noteworthy, all macaques that received the intramuscular VRP prime plus Env protein boost were completely protected. A statistically significant association was observed between the titer of virus neutralizing and binding antibodies as well as the avidity of anti-Env antibodies measured prechallenge and protection from infection. These results highlight the merit of the alphavirus replicon vector prime plus Env protein boost vaccine approach for the induction of protective antibody responses and are of particular relevance to advancing our understanding of the potential correlates of immune protection against HIV infection at a relevant mucosal portal of entry. PMID:20392857

  5. An Effective AIDS Vaccine Based on Live Attenuated Vesicular Stomatitis Virus Recombinants

    Microsoft Academic Search

    Nina F. Rose; Preston A. Marx; Amara Luckay; Douglas F. Nixon; Walter J. Moretto; Sean M. Donahoe; David Montefiori; Anjeanette Roberts; Linda Buonocore; John K. Rose

    2001-01-01

    We developed an AIDS vaccine based on attenuated VSV vectors expressing env and gag genes and tested it in rhesus monkeys. Boosting was accomplished using vectors with glycoproteins from different VSV serotypes. Animals were challenged with a pathogenic AIDS virus (SHIV89.6P). Control monkeys showed a severe loss of CD4+ T cells and high viral loads, and 7\\/8 progressed to AIDS

  6. Development of a One-Step Immunocapture Real-Time RT-PCR Assay for Detection of Tobacco Mosaic Virus in Soil

    PubMed Central

    Yang, Jin-Guang; Wang, Feng-Long; Chen, De-Xin; Shen, Li-Li; Qian, Yu-Mei; Liang, Zhi-Yong; Zhou, Wen-Chang; Yan, Tai-He

    2012-01-01

    Tobacco mosaic virus (TMV) causes significant losses in many economically important crops. Contaminated soils may play roles as reservoirs and sources of transmission for TMV. In this study we report the development of an immunocapture real-time RT-PCR (IC-real-time RT-PCR) assay for direct detection of TMV in soils without RNA isolation. A series of TMV infected leaf sap dilutions of 1:101, 1:102, 1:103, 1:104, 1:105 and 1:106 (w/v, g/mL) were added to one gram of soil. The reactivity of DAS-ELISA and conventional RT-PCR was in the range of 1:102 and 1:103 dilution in TMV-infested soils, respectively. Meanwhile, the detection limit of IC-real-time RT-PCR sensitivity was up to 1:106 dilution. However, in plant sap infected by TMV, both IC-real-time RT-PCR and real-time RT-PCR were up to 1:106 dilution, DAS-ELISA could detect at least 1:103 dilution. IC-real-time RT-PCR method can use either plant sample extracts or cultivated soils, and show higher sensitivity than RT-PCR and DAS-ELISA for detection of TMV in soils. Therefore, the proposed IC-real-time RT-PCR assay provides an alternative for quick and very sensitive detection of TMV in soils, with the advantage of not requiring a concentration or RNA purification steps while still allowing detection of TMV for disease control. PMID:23211755

  7. Detection of BCR-ABL transcripts in chronic myeloid leukemia (CML) using a 'real time' quantitative RT-PCR assay.

    PubMed

    Preudhomme, C; Révillion, F; Merlat, A; Hornez, L; Roumier, C; Duflos-Grardel, N; Jouet, J P; Cosson, A; Peyrat, J P; Fenaux, P

    1999-06-01

    Quantitative competitive RT-PCR techniques have been developed to detect BCR-ABL fusion transcripts in CML but they are hardly reproducible. In this work, we have developed BCR-ABL quantification by real time RT-PCR using the ABI PRISM 7700 (Perkin Elmer), a new technique which allows simple and rapid quantification of a target sequence during the extension phase of PCR amplifications. A fluorogenic probe labeled with both a reporter dye at the 5' end and a quencher-dye at the 3' end hybridizes to the target sequence on the third exon of the ABL gene. The exonuclease activity of the Taq DNA polymerase cleaves the probe and releases the reporter dye, resulting in an increase in the fluorescence signal. The absolute copy number of the target sequence (BCR-ABL) or a control gene (ABL) in an unknown sample can then be calculated using a calibration curve prepared from a set of BCR-ABL RNA standards, and results are expressed as a BCR-ABL/ABL ratio. In our hands, the sensitivity of a serial dilution of total RNA from a positive cell line (K562) in a negative cell line (HL60) was 10(-4). Fifteen CML patients in cytogenetic CR, including 11 allografted patients, two autografted patients and two patients treated by IFN were studied sequentially by this new real time quantitative RT-PCR technique in parallel with conventional qualitative two round nested RT-PCR. The two autografted patients showed high BCR-ABL/ABL ratio in all samples. The two patients treated by IFN showed a progressive decrease in the ratio. In the 11 allografted patients, four were sequentially studied 2 years or more after allo-BMT, and all ratios were below 10(-4). The four patients remained in clinical and cytogenetic CR. The seven other allografted patients were studied immediately after the procedure. Three of them showed a progressive decrease in the BCR-ABL/ABL ratio which reached 10(-4) 7 months after allo-BMT. The three patients remained in hematologic and cytogenetic CR. The remaining four allografted patients had progressive increase of BCR-ABL ratio; three developed cytogenetic relapse 9, 11, 28 months after allo-BMT, and the last patient remained in cytogenetic CR in the bone marrow but developed granulocytic sarcoma. Results of real-time quantitative RT-PCR were in agreement with those of qualitative two round nested PCR. However, evolution changes in the results of real-time quantitative RT-PCR often preceded those of the conventional technique: a decrease of the BCR-ABL/ABL ratio preceded progression from first round to second round positivity and then negativity with the classical technique; conversely, an increase in the ratio preceded evolution with the classical technique. Thus, real-time quantitative RT-PCR may show better correlation with clinical and cytogenetic evolution than conventional qualitative techniques and may help in making early therapeutic decisions in CML, especially after molecular relapse. PMID:10360386

  8. Evaluation of NASA SPoRT's Pseudo-Geostationary Lightning Mapper Products in the 2011 Spring Program

    NASA Technical Reports Server (NTRS)

    Stano, Geoffrey T.; Carcione, Brian; Siewert, Christopher; Kuhlman, Kristin M.

    2012-01-01

    NASA's Short-term Prediction Research and Transition (SPoRT) program is a contributing partner with the GOES-R Proving Ground (PG) preparing forecasters to understand and utilize the unique products that will be available in the GOES-R era. This presentation emphasizes SPoRT s actions to prepare the end user community for the Geostationary Lightning Mapper (GLM). This preparation is a collaborative effort with SPoRT's National Weather Service partners, the National Severe Storms Laboratory (NSSL), and the Hazardous Weather Testbed s Spring Program. SPoRT continues to use its effective paradigm of matching capabilities to forecast problems through collaborations with our end users and working with the developers at NSSL to create effective evaluations and visualizations. Furthermore, SPoRT continues to develop software plug-ins so that these products will be available to forecasters in their own decision support system, AWIPS and eventually AWIPS II. In 2009, the SPoRT program developed the original pseudo geostationary lightning mapper (PGLM) flash extent product to demonstrate what forecasters may see with GLM. The PGLM replaced the previous GLM product and serves as a stepping-stone until the AWG s official GLM proxy is ready. The PGLM algorithm is simple and can be applied to any ground-based total lightning network. For 2011, the PGLM used observations from four ground-based networks (North Alabama, Kennedy Space Center, Oklahoma, and Washington D.C.). While the PGLM is not a true proxy product, it is intended as a tool to train forecasters about total lightning as well as foster discussions on product visualizations and incorporating GLM-resolution data into forecast operations. The PGLM has been used in 2010 and 2011 and is likely to remain the primary lightning training tool for the GOES-R program for the near future. This presentation will emphasize the feedback received during the 2011 Spring Program. This will discuss several topics. Based on feedback from the 2010 Spring Program, SPoRT created two variant PGLM products, which NSSL produced locally and provided in real-time within AWIPS for 2011. The first is the flash initiation density (FID) product, which creates a gridded display showing the number of flashes that originated in each 8 8 km grid box. The second product is the maximum flash density (MFD). This shows the highest PGLM value for each grid point over a specific period of time, ranging from 30 to 120 minutes. In addition to the evaluation of these two new products, the evaluation of the PGLM itself will be covered. The presentation will conclude with forecaster feedback for additional improvements requested for future evaluations, such as within the 2012 Spring Program.

  9. Reduced Toxicity With Intensity Modulated Radiation Therapy (IMRT) for Desmoplastic Small Round Cell Tumor (DSRCT): An Update on the Whole Abdominopelvic Radiation Therapy (WAP-RT) Experience

    SciTech Connect

    Desai, Neil B. [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)] [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Stein, Nicholas F. [Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)] [Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); LaQuaglia, Michael P. [Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)] [Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Alektiar, Kaled M. [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)] [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Kushner, Brian H.; Modak, Shakeel; Magnan, Heather M. [Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)] [Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Goodman, Karyn [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)] [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Wolden, Suzanne L., E-mail: woldens@mskcc.org [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)

    2013-01-01

    Purpose: Desmoplastic small round cell tumor (DSRCT) is a rare malignancy typically involving the peritoneum in young men. Whole abdominopelvic radiation therapy (WAP-RT) using conventional 2-dimensional (2D) radiation therapy (RT) is used to address local recurrence but has been limited by toxicity. Our objectives were to assess the benefit of intensity modulated radiation therapy (IMRT) on toxicity and to update the largest series on radiation for DSRCT. Methods and Materials: The records of 31 patients with DSRCT treated with WAP-RT (22 with 2D-RT and 9 with IMRT) between 1992 and 2011 were retrospectively reviewed. All received multi-agent chemotherapy and maximal surgical debulking followed by 30 Gy of WAP-RT. A further focal boost of 12 to 24 Gy was used in 12 cases. Boost RT and autologous stem cell transplantation were nearly exclusive to patients treated with 2D-RT. Toxicities were assessed with the Common Terminology Criteria for Adverse Events. Dosimetric analysis compared IMRT and simulated 2D-RT dose distributions. Results: Of 31 patients, 30 completed WAP-RT, with a median follow-up after RT of 19 months. Acute toxicity was reduced with IMRT versus 2D-RT: P=.04 for gastrointestinal toxicity of grade 2 or higher (33% vs 77%); P=.02 for grade 4 hematologic toxicity (33% vs 86%); P=.01 for rates of granulocyte colony-stimulating factor; and P=.04 for rates of platelet transfusion. Post treatment red blood cell and platelet transfusion rates were also reduced (P=.01). IMRT improved target homogeneity ([D05-D95]/D05 of 21% vs 46%) and resulted in a 21% mean bone dose reduction. Small bowel obstruction was the most common late toxicity (23% overall). Updated 3-year overall survival and progression-free survival rates were 50% and 24%, respectively. Overall survival was associated with distant metastasis at diagnosis on multivariate analysis. Most failures remained intraperitoneal (88%). Conclusions: IMRT for consolidative WAP-RT in DSRCT improves hematologic toxicity in particular. Although the long-term efficacy of current treatment options remains disappointing, the improved therapeutic index of IMRT may aid in generalizing its use and allowing the addition of novel approaches such as intraperitoneal immunotherapy.

  10. Functional characterization of two scFv-Fc antibodies from an HIV controller selected on soluble HIV-1 Env complexes: a neutralizing V3- and a trimer-specific gp41 antibody.

    PubMed

    Trott, Maria; Wei?, Svenja; Antoni, Sascha; Koch, Joachim; von Briesen, Hagen; Hust, Michael; Dietrich, Ursula

    2014-01-01

    HIV neutralizing antibodies (nAbs) represent an important tool in view of prophylactic and therapeutic applications for HIV-1 infection. Patients chronically infected by HIV-1 represent a valuable source for nAbs. HIV controllers, including long-term non-progressors (LTNP) and elite controllers (EC), represent an interesting subgroup in this regard, as here nAbs can develop over time in a rather healthy immune system and in the absence of any therapeutic selection pressure. In this study, we characterized two particular antibodies that were selected as scFv antibody fragments from a phage immune library generated from an LTNP with HIV neutralizing antibodies in his plasma. The phage library was screened on recombinant soluble gp140 envelope (Env) proteins. Sequencing the selected peptide inserts revealed two major classes of antibody sequences. Binding analysis of the corresponding scFv-Fc derivatives to various trimeric and monomeric Env constructs as well as to peptide arrays showed that one class, represented by monoclonal antibody (mAb) A2, specifically recognizes an epitope localized in the pocket binding domain of the C heptad repeat (CHR) in the ectodomain of gp41, but only in the trimeric context. Thus, this antibody represents an interesting tool for trimer identification. MAb A7, representing the second class, binds to structural elements of the third variable loop V3 and neutralizes tier 1 and tier 2 HIV-1 isolates of different subtypes with matching critical amino acids in the linear epitope sequence. In conclusion, HIV controllers are a valuable source for the selection of functionally interesting antibodies that can be selected on soluble gp140 proteins with properties from the native envelope spike. PMID:24828352

  11. Comparison of the RT3 Research Tracker and Tritrac R3D accelerometers during a backpacking expedition by a single subject.

    PubMed

    DeVoe, Dale

    2004-10-01

    This study compared the RT3 Research Tracker accelerometer and the Tritrac R3D accelerometer in a field setting. A six-day backpacking expedition (122.4 km in length) was completed by a single subject in the Grand Canyon National Park, Arizona. The overall correlation between the counts of vector magnitude activity for the RT3 and R3D was moderate (r =.75, p<.001), with the overall calculated bias [mean difference (RT3 minus R3D) and standard deviation of the differences] across all six days estimated at 235+/-436 vector magnitude activity counts. However, agreement between the instruments is problematic; the RT3 might be 201 activity counts below or 671 activity counts above the R3D in assessing physical activity during backpacking. PMID:15560342

  12. Ten polymorphic DNA loci, including five in the rat MHC (RT1) region, form a single linkage group on rat chromosome 20

    SciTech Connect

    Remmers, E.F.; Du, Y.; Zha, H.; Goldmuntz, E.A.; Wilder, R.L. [National Institutes of Health, Bethesda, MD (United States)

    1995-03-01

    We have described ten markers for polymorphic loci on rat chromosome 20, including five in the rat MHC (RT1) region. These markers formed a single linkage group spanning a recombination distance of 0.40. The markers identified five expressed gene loci - RT1.N1 (thymus leukemia antigen 1), Tnfa (tumor necrosis factor {alpha}), Hspa1 (heat shock protein 70), Ggt1 ({gamma} glutamyl-transferase 1), and Prkacn2 (protein kinase C catalytic subunit binding inhibitor 2), two loci with sequences that are related to expressed genes - RT1.Aw2 (sequence related to a non-RT1A class I {alpha} chain) and Mt21 (sequence related to metallothionein 2), and three anonymous loci - D20Arb548, D20Arb234, and D20Arb249. These polymorphic markers should facilitate mapping studies and genetic monitoring of inbred rat strains. 18 refs., 2 figs., 3 tabs.

  13. A new StaRT-PCR approach to detect and quantify fish Viral Hemorrhagic Septicemia virus (VHSv): enhanced quality control with internal standards.

    PubMed

    Pierce, Lindsey R; Willey, James C; Crawford, Erin L; Palsule, Vrushalee V; Leaman, Douglas W; Faisal, Mohamed; Kim, Robert K; Shepherd, Brian S; Stanoszek, Lauren M; Stepien, Carol A

    2013-04-01

    Viral Hemorrhagic Septicemia virus (VHSv) causes one of the world's most important finfish diseases, killing >80 species across Eurasia and North America. A new and especially virulent strain (IVb) emerged in the North American Great Lakes in 2003, threatening fisheries, baitfish, and aquaculture industries. Weeks-long and costly cell culture is the OIE and USDA-APHIS approved diagnostic. A new Standardized Reverse Transcriptase Polymerase Chain Reaction (StaRT-PCR) assay that uniquely incorporates internal standards to improve accuracy and prevent false negatives was developed and evaluated for its ability to detect and quantify VHSv. Results from StaRT-PCR, SYBR(®) green real time qRT-PCR, and cell culture were compared, as well as the effects of potential PCR inhibitors (EDTA and high RNA). Findings show that StaRT-PCR is sensitive, detecting a single molecule, with 100% accuracy at six molecules, and had no false negatives. In comparison, false negatives ranged from 14 to 47% in SYBR(®) green real time qRT-PCR tests, and 47-70% with cell culture. StaRT-PCR uniquely controlled for EDTA and RNA interference. Range of VHSv quantitation by StaRT-PCR was 1.0×10(0)-1.2×10(5) VHSv/10(6)actb1 molecules in wild caught fishes and 1.0×10(0)-8.4×10(5) molecules in laboratory challenged specimens. In the latter experiments, muskellunge with skin lesions had significantly more viral molecules (mean=1.9×10(4)) than those without (1.1×10(3)) (p<0.04). VHSv infection was detected earlier in injection than in immersion challenged yellow perch (two versus three days), with molecule numbers in both being comparable and relatively consistent over the remaining course of the experiment. Our results show that the StaRT-PCR test accurately and reliably detects and quantifies VHSv. PMID:23375747

  14. Development of one-step real-time RT-PCR assay for detection and quantitation of peste des petits ruminants virus

    Microsoft Academic Search

    Jingyue Bao; Lin Li; Zhiliang Wang; Tom Barrett; Longciren Suo; Wenji Zhao; Yutian Liu; Chunju Liu; Jinming Li

    2008-01-01

    In this study, a rapid and specific TaqMan-based, one-step real-time quantitative reverse transcription PCR (qRT-PCR) has been described for the detection of peste des petits ruminants virus (PPRV). Primers and probe were designed based on the nucleocapsid protein gene sequence. The real-time qRT-PCR assay was able to detect PPRV isolates from very distinct geographical areas (Africa, Middle East and Asia).

  15. Utility of automated real-time RT-PCR for the detection of foot-and-mouth disease virus excreted in milk.

    PubMed

    Reid, Scott M; Parida, Satya; King, Donald P; Hutchings, Geoffrey H; Shaw, Andrew E; Ferris, Nigel P; Zhang, Zhidong; Hillerton, J Eric; Paton, David J

    2006-01-01

    Foot-and-mouth disease virus (FMDV) can be excreted in milk and thereby spread infection to susceptible animals in other holdings. The feasibility of using real-time reverse transcription polymerase chain reaction (rRT-PCR) as a diagnostic tool for detection of FMDV in milk was assessed by studying the excretion of virus from experimentally-infected cattle. Fore- and machine milk samples were collected over a 4-week period from two dairy cows infected with FMDV and from two in-contact cows held in the same pen. The whole, skim, cream and cellular debris components of the milks were tested by automated rRT-PCR and results compared to virus isolation (VI) in cell culture. The onset of clinical signs of FMD in all four cows correlated with viraemia, and the presence of FMDV in other clinical samples. rRT-PCR results matched closely with VI in detecting FMDV in all milk components and generally coincided with, but did not consistently precede, the onset of clinical signs. rRT-PCR detected FMDV in milk up to 23 days post inoculation which was longer than VI. Furthermore, the detection limit of FMDV in milk was greater by rRT-PCR than VI and, in contrast to VI, rRT-PCR detected virus genome following heat treatment that simulated pasteurisation. rRT-PCR was also able to detect FMDV in preservative-treated milk. In conclusion, this study showed that automated rRT-PCR is quicker and more sensitive than VI and can be used to detect FMDV in whole milk as well as milk fractions from infected animals. PMID:16336929

  16. Highly sensitive detection of swine vesicular disease virus based on a single tube RT-PCR system and DIG-ELISA detection

    Microsoft Academic Search

    M Callens; K De Clercq

    1999-01-01

    A highly sensitive detection of swine vesicular disease virus (SVDV) based on a single tube RT-PCR system and digoxigenin (DIG)-PCR-ELISA detection was developed. Using a one tube RT-PCR system, optimisation of the PCR conditions and optimisation of the microwell hybridisation and colourimetric detection of the amplicons resulted in a method that could detect viral RNA in infected tissue culture fluid

  17. The development of a rapid SYBR one step real-time RT-PCR for detection of porcine reproductive and respiratory syndrome virus

    Microsoft Academic Search

    Hong Tian; JingYan Wu; YouJun Shang; Yan Cheng; XiangTao Liu

    2010-01-01

    BACKGROUND: Prompt detection of PRRSV in the field samples is important for effective PRRS control, thereby reducing the potentially serious economic damage which can result from an outbreak. In this study, a rapid SYBR-based, one step real-time RT-PCR quantitative reverse transcription PCR (qRT-PCR) has been developed for the detection of porcine reproductive and respiratory syndrome virus (PRRSV). Primers were designed

  18. Projected Applications of a "Weather in a Box" Computing System at the NASA Short-Term Prediction Research and Transition (SPoRT) Center

    NASA Technical Reports Server (NTRS)

    Jedlovec, Gary J.; Molthan, Andrew; Zavodsky, Bradley T.; Case, Jonathan L.; LaFontaine, Frank J.; Srikishen, Jayanthi

    2010-01-01

    The NASA Short-term Prediction Research and Transition Center (SPoRT)'s new "Weather in a Box" resources will provide weather research and forecast modeling capabilities for real-time application. Model output will provide additional forecast guidance and research into the impacts of new NASA satellite data sets and software capabilities. By combining several research tools and satellite products, SPoRT can generate model guidance that is strongly influenced by unique NASA contributions.

  19. Cloning of the xynB Gene from Dictyoglomus thermophilum Rt46B.1 and Action of the Gene Product on Kraft Pulp

    Microsoft Academic Search

    DANIEL D. MORRIS; MORELAND D. GIBBS; CHARLES W. J. CHIN; MEI-HSIEN KOH; KEN K. Y. WONG; ROBERT W. ALLISON; PETER J. NELSON; PETER L. BERGQUIST; CSIRO Forestry

    1998-01-01

    A two-step PCR protocol was used to identify and sequence a family 11 xylanase gene from Dictyoglomus thermophilum Rt46B.1. Family 11 xylanase consensus fragments (GXCFs) were amplified from Rt46B.1 genomic DNA by using different sets of consensus PCR primers that exhibited broad specificity for conserved motifs within fungal and\\/or bacterial family 11 xylanase genes. On the basis of the sequences

  20. The detection of bovine viral diarrhoea virus in bulk milk samples by the use of a single-tube RT-PCR

    Microsoft Academic Search

    Trevor W Drew; Fenella Yapp; David J Paton

    1999-01-01

    A single step, single-tube reverse transcriptase-polymerase chain reaction (RT-PCR) test was developed to detect the presence of bovine viral diarrhoea virus (BVDV) in somatic cells from bulk milk samples. The test was configured using commercial kit-form RNA extraction and RT-PCR procedures. The test was validated by examining bulk milk samples from ?80 herds with a history of BVDV and comparing