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1

A MIV-150/Zinc Acetate Gel Inhibits SHIV-RT Infection in Macaque Vaginal Explants  

PubMed Central

To extend our observations that single or repeated application of a gel containing the NNRTI MIV-150 (M) and zinc acetate dihydrate (ZA) in carrageenan (CG) (MZC) inhibits vaginal transmission of simian/human immunodeficiency virus (SHIV)-RT in macaques, we evaluated safety and anti-SHIV-RT activity of MZC and related gel formulations ex vivo in macaque mucosal explants. In addition, safety was further evaluated in human ectocervical explants. The gels did not induce mucosal toxicity. A single ex vivo exposure to diluted MZC (1?30, 1?100) and MC (1?30, the only dilution tested), but not to ZC gel, up to 4 days prior to viral challenge, significantly inhibited SHIV-RT infection in macaque vaginal mucosa. MZC's activity was not affected by seminal plasma. The antiviral activity of unformulated MIV-150 was not enhanced in the presence of ZA, suggesting that the antiviral activity of MZC was mediated predominantly by MIV-150. In vivo administration of MZC and CG significantly inhibited ex vivo SHIV-RT infection (51–62% inhibition relative to baselines) of vaginal (but not cervical) mucosa collected 24 h post last gel exposure, indicating barrier effect of CG. Although the inhibitory effect of MZC (65–74%) did not significantly differ from CG (32–45%), it was within the range of protection (?75%) against vaginal SHIV-RT challenge 24 h after gel dosing. Overall, the data suggest that evaluation of candidate microbicides in macaque explants can inform macaque efficacy and clinical studies design. The data support advancing MZC gel for clinical evaluation. PMID:25259616

Barnable, Patrick; Calenda, Giulia; Ouattara, Louise; Gettie, Agegnehu; Blanchard, James; Jean-Pierre, Ninochka; Kizima, Larisa; Rodriguez, Aixa; Abraham, Ciby; Menon, Radhika; Seidor, Samantha; Cooney, Michael L.; Roberts, Kevin D.; Sperling, Rhoda; Piatak, Michael; Lifson, Jeffrey D.; Fernandez-Romero, Jose A.; Zydowsky, Thomas M.; Robbiani, Melissa; Teleshova, Natalia

2014-01-01

2

R5 Clade C SHIV Strains with Tier 1 or 2 Neutralization Sensitivity: Tools to Dissect Env Evolution and to Develop AIDS Vaccines in Primate Models  

PubMed Central

Background HIV-1 clade C (HIV-C) predominates worldwide, and anti-HIV-C vaccines are urgently needed. Neutralizing antibody (nAb) responses are considered important but have proved difficult to elicit. Although some current immunogens elicit antibodies that neutralize highly neutralization-sensitive (tier 1) HIV strains, most circulating HIVs exhibiting a less sensitive (tier 2) phenotype are not neutralized. Thus, both tier 1 and 2 viruses are needed for vaccine discovery in nonhuman primate models. Methodology/Principal Findings We constructed a tier 1 simian-human immunodeficiency virus, SHIV-1157ipEL, by inserting an “early,” recently transmitted HIV-C env into the SHIV-1157ipd3N4 backbone [1] encoding a “late” form of the same env, which had evolved in a SHIV-infected rhesus monkey (RM) with AIDS. SHIV-1157ipEL was rapidly passaged to yield SHIV-1157ipEL-p, which remained exclusively R5-tropic and had a tier 1 phenotype, in contrast to “late” SHIV-1157ipd3N4 (tier 2). After 5 weekly low-dose intrarectal exposures, SHIV-1157ipEL-p systemically infected 16 out of 17 RM with high peak viral RNA loads and depleted gut CD4+ T cells. SHIV-1157ipEL-p and SHIV-1157ipd3N4 env genes diverge mostly in V1/V2. Molecular modeling revealed a possible mechanism for the increased neutralization resistance of SHIV-1157ipd3N4 Env: V2 loops hindering access to the CD4 binding site, shown experimentally with nAb b12. Similar mutations have been linked to decreased neutralization sensitivity in HIV-C strains isolated from humans over time, indicating parallel HIV-C Env evolution in humans and RM. Conclusions/Significance SHIV-1157ipEL-p, the first tier 1 R5 clade C SHIV, and SHIV-1157ipd3N4, its tier 2 counterpart, represent biologically relevant tools for anti-HIV-C vaccine development in primates. PMID:20657739

Siddappa, Nagadenahalli B.; Watkins, Jennifer D.; Wassermann, Klemens J.; Song, Ruijiang; Wang, Wendy; Kramer, Victor G.; Lakhashe, Samir; Santosuosso, Michael; Poznansky, Mark C.; Novembre, Francis J.; Villinger, Francois; Else, James G.; Montefiori, David C.; Rasmussen, Robert A.; Ruprecht, Ruth M.

2010-01-01

3

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

PubMed Central

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

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

2014-01-01

4

Neutralization-Sensitive R5-Tropic Simian-Human Immunodeficiency Virus SHIV-2873Nip, Which Carries env Isolated from an Infant with a Recent HIV Clade C Infection?  

PubMed Central

Human immunodeficiency virus clade C (HIV-C) accounts for >56% of all HIV infections worldwide. To investigate vaccine safety and efficacy in nonhuman primates, a pathogenic, R5-tropic, neutralization-sensitive simian-human immunodeficiency virus (SHIV) carrying HIV-C env would be desirable. We have constructed SHIV-2873Ni, an R5-tropic SHIV carrying a primary pediatric HIV-C env gene isolated from a 2-month-old Zambian infant, who died within 1 year of birth. SHIV-2873Ni was constructed using SHIV-1157ipd3N4 (R. J. Song, A. L. Chenine, R. A. Rasmussen, C. R. Ruprecht, S. Mirshahidi, R. D. Grisson, W. Xu, J. B. Whitney, L. M. Goins, H. Ong, P. L. Li, E. Shai-Kobiler, T. Wang, C. M. McCann, H. Zhang, C. Wood, C. Kankasa, W. E. Secor, H. M. McClure, E. Strobert, J. G. Else, and R. M. Ruprecht. J. Virol. 80:8729-8738, 2006) as the backbone, since the latter contains additional NF-?B sites in the long terminal repeats to enhance viral replicative capacity. The parental virus, SHIV-2873Ni, was serially passaged through five rhesus monkeys (RMs); SHIV-2873Nip, the resulting passaged virus, was reisolated from the fourth recipient about 1 year postinoculation. SHIV-2873Nip was replication competent in RM peripheral blood mononuclear cells of all random donors tested and was exclusively R5 tropic, and its env gene clustered with HIV-C by phylogenetic analysis; its high sensitivity to neutralization led to classification as a tier 1 virus. Indian-origin RMs were inoculated by different mucosal routes, resulting in high peak viral RNA loads. Signs of virus-induced disease include depletion of gut CD4+ T lymphocytes, loss of memory T cells in blood, and thrombocytopenia that resulted in fatal cerebral hemorrhage. SHIV-2873Nip is a highly replication-competent, mucosally transmissible, pathogenic R5-tropic virus that will be useful to study viral pathogenesis and to assess the efficacy of immunogens targeting HIV-C Env. PMID:19019970

Siddappa, Nagadenahalli B.; Song, Ruijiang; Kramer, Victor G.; Chenine, Agnes-Laurence; Velu, Vijayakumar; Ong, Helena; Rasmussen, Robert A.; Grisson, Ricky D.; Wood, Charles; Zhang, Hong; Kankasa, Chipeppo; Amara, Rama Rao; Else, James G.; Novembre, Francis J.; Montefiori, David C.; Ruprecht, Ruth M.

2009-01-01

5

Enhanced antiretroviral therapy in rhesus macaques improves RT-SHIV viral decay kinetics.  

PubMed

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 >10(4) 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

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; Schinazi, Raymond F

2014-07-01

6

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

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

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

7

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

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

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

8

Partial protection against multiple RT-SHIV162P3 vaginal challenge of rhesus macaques by a silicone elastomer vaginal ring releasing the NNRTI MC1220  

PubMed Central

Objectives The non-nucleoside reverse transcriptase inhibitor MC1220 has potent in vitro activity against HIV type 1 (HIV-1). A liposome gel formulation of MC1220 has previously been reported to partially protect rhesus macaques against vaginal challenge with a simian HIV (SHIV). Here, we describe the pre-clinical development of an MC1220-releasing silicone elastomer vaginal ring (SEVR), including pharmacokinetic (PK) and efficacy studies in macaques. Methods In vitro release studies were conducted on SEVRs loaded with 400 mg of MC1220, using simulated vaginal fluid (SVF, n?=?4) and 1?:?1 isopropanol/water (IPA/H2O, n?=?4) as release media. For PK evaluation, SEVRs were inserted into adult female macaques (n?=?6) for 30 days. Following a 1week washout period, fresh rings were placed in the same animals, which were then challenged vaginally with RT-SHIV162P3 once weekly for 4 weeks. Results SEVRs released 1.66 and 101 mg of MC1220 into SVF and IPA/H2O, respectively, over 30 days, the differential reflecting the low aqueous solubility of the drug. In macaque PK studies, MC1220 was consistently detected in vaginal fluid (peak 845 ng/mL) and plasma (peak 0.91 ng/mL). Kaplan–Meier analysis over 9weeks showed significantly lower infection rates for animals given MC1220-containing SEVRs than placebo rings (hazard ratio 0.20, P?=?0.0037). Conclusions An MC1220-releasing SEVR partially protected macaques from vaginal challenge. Such ring devices are a practical method for providing sustained, coitally independent protection against vaginal exposure to HIV-1. PMID:23109186

Fetherston, Susan M.; Geer, Leslie; Veazey, Ronald S.; Goldman, Laurie; Murphy, Diarmaid J.; Ketas, Thomas J.; Klasse, Per Johan; Blois, Sylvain; La Colla, Paolo; Moore, John P.; Malcolm, R. Karl

2013-01-01

9

Robust suppression of env-SHIV viremia in M. nemestrina by 3-drug ART is independent of timing of initiation during chronic infection  

PubMed Central

Background Nonhuman primates (NHPs) are an important model organism for studies of HIV pathogenesis and pre-clinical evaluation of anti-HIV therapies. The successful translation of NHP-derived data to clinically relevant anti-HIV studies will require better understanding of the viral strains and NHP species used, and their responses to existing antiretroviral therapies (ART). Methods Five pigtailed macaques (M. nemestrina) were productively infected with the SIV/HIV chimeric virus SHIV-1157ipd3N4 following intravenous challenge. After 8 or 27 weeks, ART (PMPA, FTC, Raltegravir) was initiated. Viral load, T-Cell counts, and production of SHIV-specific antibodies were monitored throughout the course of infection and ART. Results ART led to a rapid and sustained decrease in plasma viral load. Suppression of plasma viremia by ART was independent of the timing of initiation during chronic infection. Conclusions We present a new NHP model of HIV infection on antiretroviral therapy, which should prove applicable to multiple clinically relevant anti-HIV approaches. PMID:24025078

Peterson, Christopher W; Younan, Patrick; Polacino, Patricia S; Maurice, Nicholas J; Miller, Hannah W; Prlic, Martin; Jerome, Keith R; Woolfrey, Ann E; Hu, Shiu-Lok; Kiem, Hans-Peter

2013-01-01

10

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

PubMed Central

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

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

2013-01-01

11

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

Microsoft Academic Search

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

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

12

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

PubMed Central

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

2014-01-01

13

Special Challenges of Rearing Infant Macaques Infected with Lentivirus (SIV, HIV, SHIV)  

Microsoft Academic Search

\\u000a The nonhuman primate lentivirus model is perhaps the best animal model of human immunodeficiency virus (HIV) infection. The\\u000a lentiviruses (lentivirinae), a subfamily of retroviruses (family Retroviridae), include, in addition to HIV-1 and HIV-2, simian\\u000a immunodeficiency virus (SIV) and a variety of simian\\/human immunodeficiency viruses (SHIVs). SHIVs are humanly engineered,\\u000a chimeric viruses made by inserting HIV genes into an SIV. Lentivirus-infected

Julie M. Worlein; James C. Ha; Christy Harris; Jennifer Leigh; Kelsey Stratton; Rodney J. R. Ho

14

Generation and mucosal transmissibility of emtricitabine- and tenofovir-resistant SHIV162P3 mutants in macaques  

Microsoft Academic Search

Transmission of drug-resistant HIV has been widely documented. We generated tenofovir (TFV)- and emtricitabine (FTC)-resistant SHIV162P3 mutants that can be used to investigate the transmission efficiency of drug-resistant viruses and their impact on the efficacy of pre-exposure prophylaxis. Both SHIV162p3M184V and SHIV162p3K65R replicated in vitro at high titers. Drug resistance profiles were similar to those seen in HIV. Virus infectivity

Mian-er Cong; Ae S. Youngpairoj; Wutyi Aung; Sunita Sharma; James Mitchell; Charles Dobard; Walid Heneine; J. Gerardo Garcia-Lerma

2011-01-01

15

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

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

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

16

Prevention of Vaginal SHIV Transmission in Macaques by a Coitally-Dependent Truvada Regimen  

PubMed Central

Background Daily pre-exposure prophylaxis (PrEP) with Truvada (a combination of emtricitabine (FTC) and tenofovir (TFV) disoproxil fumarate (TDF)) is a novel HIV prevention strategy recently found to prevent HIV transmission in men who have sex with men and heterosexual couples. We previously showed that a coitally-dependent Truvada regimen protected macaques against rectal SHIV transmission. Here we examined FTC and tenofovir TFV exposure in vaginal tissues after oral dosing and assessed if peri-coital Truvada also protects macaques against vaginal SHIV infection. Methods The pharmacokinetic profile of emtricitabine (FTC) and tenofovir (TFV) was evaluated at first dose. FTC and TFV levels were measured in blood plasma, rectal, and vaginal secretions. Intracellular concentrations of FTC-triphosphate (FTC-TP) and TFV-diphosphate (TFV-DP) were measured in PBMCs, rectal tissues, and vaginal tissues. Efficacy of Truvada in preventing vaginal SHIV infection was assessed using a repeat-exposure vaginal SHIV transmission model consisting of weekly exposures to low doses of SHIV162p3. Six pigtail macaques with normal menstrual cycles received Truvada 24 h before and 2 h after each weekly virus exposure and six received placebo. Infection was monitored by serology and PCR amplification of SHIV RNA and DNA. Results As in humans, the concentration of FTC was higher than the concentration of TFV in vaginal secretions. Also as in humans, TFV levels in vaginal secretions were lower than in rectal secretions. Intracellular TFV-DP concentrations were also lower in vaginal tissues than in rectal tissues. Despite the low vaginal TFV exposure, all six treated macaques were protected from infection after 18 exposures or 4 full menstrual cycles. In contrast, all 6 control animals were infected. Conclusions We modeled a peri-coital regimen with two doses of Truvada and showed that it fully protected macaques from repeated SHIV exposures. Our results open the possibility for simplified PrEP regimens to prevent vaginal HIV transmission in women. PMID:23226529

Radzio, Jessica; Aung, Wutyi; Holder, Angela; Martin, Amy; Sweeney, Elizabeth; Mitchell, James; Bachman, Shanon; Pau, Chou-Pong; Heneine, Walid; Garcia-Lerma, J. Gerardo

2012-01-01

17

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

SciTech Connect

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.

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

18

Mechanisms for Env Glycoprotein Acquisition by Retroviruses  

PubMed Central

Abstract A mandatory step in the formation of an infectious retroviral particle is the acquisition of its envelope glycoprotein (Env). This step invariably occurs by Env positioning itself in the host membrane at the location of viral budding and being incorporated along with the host membrane into the viral particle. In some ways, this step of the viral life cycle would appear to be imprecise. There is no specific sequence in Env or in the retroviral structural protein, Gag, that is inherently required for the production of an infectious Env-containing particle. Additionally, Env-defective proviruses can efficiently produce infectious particles with any of a number of foreign retroviral Env glycoproteins or even glycoproteins from unrelated viral families, a process termed pseudotyping. However, mounting evidence suggests that Env incorporation is neither passive nor random. Rather, several redundant mechanisms appear to contribute to the carefully controlled process of Env acquisition, many of which are apparently used by a wide variety of enveloped viruses. This review presents and discusses the evidence for these different mechanisms contributing to incorporation. PMID:21247353

2011-01-01

19

Protection against simian/human immunodeficiency virus (SHIV) 89.6P in macaques after coimmunization with SHIV antigen and IL-15 plasmid  

PubMed Central

The cell-mediated immune profile induced by a recombinant DNA vaccine was assessed in the simian/HIV (SHIV) and macaque model. The vaccine strategy included coimmunization of a DNA-based vaccine alone or in combination with an optimized plasmid encoding macaque IL-15 (pmacIL-15). We observed strong induction of vaccine-specific IFN-?-producing CD8+ and CD4+ effector T cells in the vaccination groups. Animals were subsequently challenged with 89.6p. The vaccine groups were protected from ongoing infection, and the IL-15 covaccinated group showed a more rapidly controlled infection than the group treated with DNA vaccine alone. Lymphocytes isolated from the group covaccinated with pmacIL-15 had higher cellular proliferative responses than lymphocytes isolated from the macaques that received SHIV DNA alone. Vaccine antigen activation of lymphocytes was also studied for a series of immunological molecules. Although mRNA for IFN-? was up-regulated after antigen stimulation, the inflammatory molecules IL-8 and MMP-9 were down-regulated. These observed immune profiles are potentially reflective of the ability of the different groups to control SHIV replication. This study demonstrates that an optimized IL-15 immune adjuvant delivered with a DNA vaccine can impact the cellular immune profile in nonhuman primates and lead to enhanced suppression of viral replication. PMID:18000037

Boyer, Jean D.; Robinson, Tara M.; Kutzler, Michele A.; Vansant, Gordon; Hokey, David A.; Kumar, Sanjeev; Parkinson, Rose; Wu, Ling; Sidhu, Maninder K.; Pavlakis, George N.; Felber, Barbara K.; Brown, Charles; Silvera, Peter; Lewis, Mark G.; Monforte, Joseph; Waldmann, Thomas A.; Eldridge, John; Weiner, David B.

2007-01-01

20

CLASSIFYING COMPUTER GENERATED CHARTS V. Shiv Naga Prasad, Behjat Siddiquie, Jennifer Golbeck and Larry S. Davis  

E-print Network

CLASSIFYING COMPUTER GENERATED CHARTS V. Shiv Naga Prasad, Behjat Siddiquie, Jennifer Golbeck for classifying images of charts based on the shape and spatial relationships of their prim- itives. Five categories are considered: bar-charts, curve- plots, pie-charts, scatter-plots and surface-plots. We intro

Davis, Larry

21

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

PubMed

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

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

22

Persistence of Virus Reservoirs in ART-Treated SHIV-Infected Rhesus Macaques after Autologous Hematopoietic Stem Cell Transplant.  

PubMed

Despite many advances in AIDS research, a cure for HIV infection remains elusive. Here, we performed autologous hematopoietic stem cell transplantation (HSCT) in three Simian/Human Immunodeficiency Virus (SHIV)-infected, antiretroviral therapy (ART)-treated rhesus macaques (RMs) using HSCs collected prior to infection and compared them to three SHIV-infected, ART-treated, untransplanted control animals to assess the effect of conditioning and autologous HSCT on viral persistence. As expected, ART drastically reduced virus replication, below 100 SHIV-RNA copies per ml of plasma in all animals. After several weeks on ART, experimental RMs received myeloablative total body irradiation (1080 cGy), which resulted in the depletion of 94-99% of circulating CD4+ T-cells, and low to undetectable SHIV-DNA levels in peripheral blood mononuclear cells. Following HSC infusion and successful engraftment, ART was interrupted (40-75 days post-transplant). Despite the observed dramatic reduction of the peripheral blood viral reservoir, rapid rebound of plasma viremia was observed in two out of three transplanted RMs. In the third transplanted animal, plasma SHIV-RNA and SHIV DNA in bulk PBMCs remained undetectable at week two post-ART interruption. No further time-points could be assessed as this animal was euthanized for clinical reasons; however, SHIV-DNA could be detected in this animal at necropsy in sorted circulating CD4+ T-cells, spleen and lymph nodes but not in the gastro-intestinal tract or tonsils. Furthermore, SIV DNA levels post-ART interruption were equivalent in several tissues in transplanted and control animals. While persistence of virus reservoir was observed despite myeloablation and HSCT in the setting of short term ART, this experiment demonstrates that autologous HSCT can be successfully performed in SIV-infected ART-treated RMs offering a new experimental in vivo platform to test innovative interventions aimed at curing HIV infection in humans. PMID:25254512

Mavigner, Maud; Watkins, Benjamin; Lawson, Benton; Lee, S Thera; Chahroudi, Ann; Kean, Leslie; Silvestri, Guido

2014-09-01

23

Persistence of Virus Reservoirs in ART-Treated SHIV-Infected Rhesus Macaques after Autologous Hematopoietic Stem Cell Transplant  

PubMed Central

Despite many advances in AIDS research, a cure for HIV infection remains elusive. Here, we performed autologous hematopoietic stem cell transplantation (HSCT) in three Simian/Human Immunodeficiency Virus (SHIV)-infected, antiretroviral therapy (ART)-treated rhesus macaques (RMs) using HSCs collected prior to infection and compared them to three SHIV-infected, ART-treated, untransplanted control animals to assess the effect of conditioning and autologous HSCT on viral persistence. As expected, ART drastically reduced virus replication, below 100 SHIV-RNA copies per ml of plasma in all animals. After several weeks on ART, experimental RMs received myeloablative total body irradiation (1080 cGy), which resulted in the depletion of 94–99% of circulating CD4+ T-cells, and low to undetectable SHIV-DNA levels in peripheral blood mononuclear cells. Following HSC infusion and successful engraftment, ART was interrupted (40–75 days post-transplant). Despite the observed dramatic reduction of the peripheral blood viral reservoir, rapid rebound of plasma viremia was observed in two out of three transplanted RMs. In the third transplanted animal, plasma SHIV-RNA and SHIV DNA in bulk PBMCs remained undetectable at week two post-ART interruption. No further time-points could be assessed as this animal was euthanized for clinical reasons; however, SHIV-DNA could be detected in this animal at necropsy in sorted circulating CD4+ T-cells, spleen and lymph nodes but not in the gastro-intestinal tract or tonsils. Furthermore, SIV DNA levels post-ART interruption were equivalent in several tissues in transplanted and control animals. While persistence of virus reservoir was observed despite myeloablation and HSCT in the setting of short term ART, this experiment demonstrates that autologous HSCT can be successfully performed in SIV-infected ART-treated RMs offering a new experimental in vivo platform to test innovative interventions aimed at curing HIV infection in humans. PMID:25254512

Lawson, Benton; Lee, S. Thera; Chahroudi, Ann; Kean, Leslie; Silvestri, Guido

2014-01-01

24

NRM 2061/ENV 2005 Critical Thinking Papers  

E-print Network

NRM 2061/ENV 2005 Critical Thinking Papers Nuts and Bolts: Papers should be short (3 pages or 750 no more than 250 words on your summary). Critical thinking and reflection. Critical thinking is the use of cognitive skills or strategies that are purposeful, reasoned, and goal directed. Critical thinking

Brown, Gregory G.

25

Ecosystem Management ENV SCI 740 Spring 2008  

E-print Network

Ecosystem Management ENV SCI 740 ­ Spring 2008 Lecture: T 6:00 ­ 9:00 PM in MAC 224 Instructor. Principles of Terrestrial Ecosystem Ecology. Springer, New York. 436 p. Assigned readings from primary to the field of Ecosystem Ecology. The course consists of three main components: 1) I will provide general

Dornbush, Mathew E.

26

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

E-print Network

of good quality proposals. It will be used if extra budget becomes available. #12;2 1.1.5. ENV.2010 to deforestation and agriculture in the context of a post- 2012 international agreement on climate change

Milano-Bicocca, Università

27

Retroviral Env Glycoprotein Trafficking and Incorporation into Virions  

PubMed Central

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

Murakami, Tsutomu

2012-01-01

28

Prevention of vaginal SHIV transmission in rhesus macaques through inhibition of CCR5.  

PubMed

Topical agents, such as microbicides, that can protect against human immunodeficiency virus (HIV) transmission are urgently needed. Using a chimeric simian/human immunodeficiency virus (SHIV SF162), which is tropic for the chemokine receptor CCR5, we report that topical application of high doses of PSC-RANTES, an amino terminus-modified analog of the chemokine RANTES, provided potent protection against vaginal challenge in rhesus macaques. These experimental findings have potentially important implications for understanding vaginal transmission of HIV and the design of strategies for its prevention. PMID:15486300

Lederman, Michael M; Veazey, Ronald S; Offord, Robin; Mosier, Donald E; Dufour, Jason; Mefford, Megan; Piatak, Michael; Lifson, Jeffrey D; Salkowitz, Janelle R; Rodriguez, Benigno; Blauvelt, Andrew; Hartley, Oliver

2004-10-15

29

Characterization of a Neutralization-Escape Variant of SHIV KU-1, a Virus That Causes Acquired Immune Deficiency Syndrome in Pig-Tailed Macaques  

Microsoft Academic Search

A chimeric simian-human immunodeficiency virus (SHIV-4) containing thetat, rev, vpu,andenvgenes of HIV type 1 (HIV-1) in a genetic background of SIVmac239 was used to develop an animal model in which a primate lentivirus expressing the HIV-1 envelope glycoprotein caused acquired immune deficiency syndrome (AIDS) in macaques. An SHIV-infected pig-tailed macaque that died from AIDS at 24 weeks postinoculation experienced two

Shanil V. Narayan; Sampa Mukherjee; Fenglan Jia; Zhuang Li; Chunyang Wang; Larry Foresman; Coleen McCormick-Davis; Edward B. Stephens; Sanjay V. Joag; Opendra Narayan

1999-01-01

30

Aaron Shepard's RT Page  

NSDL National Science Digital Library

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.

Shepard, Aaron.

1996-01-01

31

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

32

ENV 6105 Page 1 of 6 Fall 2011 Air Pollution  

E-print Network

ENV 6105 Page 1 of 6 Fall 2011 Syllabus Air Pollution ENV 6105.901 (ref# 90504) Fall 2011 Course Description: A study of air pollution. Emphasis is given to principles underlying our understanding of ambient air pollution, its sources, its effects, and mechanisms for its management. Credit Hours and Work

Stuart, Amy L.

33

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

PubMed Central

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

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

34

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

PubMed

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

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; Martin, Malcolm A; Nishimura, Yoshiaki

2014-09-22

35

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

SciTech Connect

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.

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

36

Implication of the env Gene of the Human Endogenous Retrovirus W Family in the Expression of BDNF and DRD3 and Development of Recent-Onset Schizophrenia  

PubMed Central

Objective: Retrovirus has been suggested as one of agents involved in the development of schizophrenia. In the present study, we examined the role of the human endogenous retrovirus W family (HERV-W) env gene in the etiopathogenesis of recent-onset schizophrenia, using molecular and epidemiological approaches. Methods: Nested RT-PCR was used to detect the messenger RNA (mRNA) of the HERV-w env gene in plasmas. Quantitative real-time polymerase chain reaction (PCR) was employed to detect the viral reverse transcriptase activity in human sera. Human U251 glioma cells were used to study the potential role of the HERV-W env gene in the etiopathogenesis of recent-onset schizophrenia. Results: We identified genes with mRNA sequences homologous to HERV-W env gene from plasmas of 42 out of 118 individuals with recent-onset schizophrenia but not from any of 106 normal persons (P < .01, t test). Quantitative real-time PCR showed a significantly increase in the reverse transcriptase activity in the sera of patients (by 35.59%) compared with controls (by 2.83%) (P < .05, t test). Overexpression of HERV-w env in human U251 glioma cells upregulated brain-derived neurotrophic factor (BDNF), an important schizophrenia-associated gene, neurotrophic tyrosine kinase receptor type 2 (NTRK2, also called TrkB), and dopamine receptor D3 and increased the phosphorylation of cyclic adenosine monophosphate response element–binding (CREB) protein. BDNF promoter reporter gene assays showed that the HERV-W env triggers BDNF production in human U251 glioma cells. Using gene knockdown, we found that CREB is required for the expression of BDNF that is regulated by env. Conclusion: Our data revealed that the transcriptional activation of HERV is associated with the development of schizophrenia in some patients and indicated that HERV-W env regulates the expression of schizophrenia-associated genes. This report is the first to elucidate the signaling pathway responsible for the upregulation of HERV-W env–triggered BDNF. Our study provides new evidence for the involvement of HERV-W in the central nervous system, which will benefit the diagnosis and treatment of the devastating schizophrenia and related disorders. PMID:20100784

Huang, WenJie; Li, Shan; Hu, YuanMing; Yu, Honglian; Luo, Feng; Zhang, Qi; Zhu, Fan

2011-01-01

37

AIDS and optic neuritis in a rhesus monkey infected with the R5 clade C SHIV-1157ipd3N4  

PubMed Central

A Chinese rhesus macaque infected with the pathogenic CCR5-tropic clade C simian-human immunodeficiency virus, SHIV-1157ipd3N4, had persistent viremia, depletion of CD4+ T cells to <200 cells/?l, opportunistic infections, coagulopathy and gradual development of bilateral blindness. MRI revealed marked thickening of both optic nerves. Histopathological evaluation showed diffuse cellular infiltration at necropsy, and a focus of infected cells. This is the first report of CNS pathology following chronic infection with an obligate R5 SHIV. PMID:20412378

Garcia, Ana Patricia; Siddappa, Nagadenahalli B.; Li, Qingsheng; Haase, Ashley T.; Paul, Katherine; Stroud, Fawn; Zhang, Xiaodong; Fountain, Jack A.; Villinger, Francois; Novembre, Francis J.; Else, James G; Secor, W. Evan; Ruprecht, Ruth M.

2011-01-01

38

Estimating the impact of vaccination in acute SHIV-SIV infection  

SciTech Connect

Human Immunodeficiency Virus (HIV) infects approxmately 0.5% of the world population, and is a major cause of morbidity and mortality worldwide. A vaccine for HIV is urgently required, and a variety of vaccine modalities have been tested in animal models of infection. A number of these studies have shown protection in monkey models of infection, although the ability of the vaccine to protect appears to vary with the viral strain and animal model used. The recent failure of a large vaccine study in humans suggests that further understanding of the basic dynamics of infection and impact of vaccination are required, in order to understand the variable efficacy of vaccination in different infections. The dynamics of HIV infection have been studied in humans and in a variety of animal models. The standard model of infection has been used to estimate the basic reproductive ratio (R{sub 0}) of the virus, calculated from the growth rate of virus in acute infection. This method has not been useful in studying the effects of vaccination, since, in the vaccines developed so far, early growth rates of virus do not differ between control and vaccinated animals. Here, we use the standard model of viral dynamics to derive the reproductive ratio from the peak viral load and nadir of target cell numbers in acute infection. We apply this method to data from studies of vaccination in Simian Human Immunodeficiency Virus (SHIV) and Simian Immunodeficiency Virus (SIV) infection and demonstrate that vaccination can reduce the reproductive ratio by 2.3 and 2 fold respectively. This method allows the comparison of vaccination efficacy amongst different viral strains and animal models in vivo.

Ribeiro, Ruy [Los Alamos National Laboratory

2008-01-01

39

Trimeric HIV Env provides epitope occlusion mediated by hypervariable loops.  

PubMed

Hypervariable loops of HIV-1 Env protein gp120 are speculated to play roles in the conformational transition of Env to the receptor binding-induced metastable state. Structural analysis of full-length Env-based immunogens, containing the entire V2 loop, displayed tighter association between gp120 subunits, resulting in a smaller trimeric diameter than constructs lacking V2. A prominent basal quaternary location of V2 and V3' that challenges previous reports would facilitate gp41-independent gp120-gp120 interactions and suggests a quaternary mechanism of epitope occlusion facilitated by hypervariable loops. Deletion of V2 resulted in dramatic exposure of basal, membrane-proximal gp41 epitopes, consistent with its predicted basal location. The structural features of HIV-1 Env characterized here provide grounds for a paradigm shift in loop exposure and epitope occlusion, while providing substantive rationale for epitope display required for elicitation of broadly neutralizing antibodies, as well as substantiating previous pertinent literature disregarded in recent reports. PMID:25395053

Moscoso, Carlos G; Xing, Li; Hui, Jinwen; Hu, Jeffrey; Kalkhoran, Mohammad Baikoghli; Yenigun, Onur M; Sun, Yide; Paavolainen, Lassi; Martin, Loïc; Vahlne, Anders; Zambonelli, Carlo; Barnett, Susan W; Srivastava, Indresh K; Cheng, R Holland

2014-01-01

40

Trimeric HIV Env provides epitope occlusion mediated by hypervariable loops  

PubMed Central

Hypervariable loops of HIV-1 Env protein gp120 are speculated to play roles in the conformational transition of Env to the receptor binding-induced metastable state. Structural analysis of full-length Env-based immunogens, containing the entire V2 loop, displayed tighter association between gp120 subunits, resulting in a smaller trimeric diameter than constructs lacking V2. A prominent basal quaternary location of V2 and V3? that challenges previous reports would facilitate gp41-independent gp120-gp120 interactions and suggests a quaternary mechanism of epitope occlusion facilitated by hypervariable loops. Deletion of V2 resulted in dramatic exposure of basal, membrane-proximal gp41 epitopes, consistent with its predicted basal location. The structural features of HIV-1 Env characterized here provide grounds for a paradigm shift in loop exposure and epitope occlusion, while providing substantive rationale for epitope display required for elicitation of broadly neutralizing antibodies, as well as substantiating previous pertinent literature disregarded in recent reports. PMID:25395053

Moscoso, Carlos G.; Xing, Li; Hui, Jinwen; Hu, Jeffrey; Kalkhoran, Mohammad Baikoghli; Yenigun, Onur M.; Sun, Yide; Paavolainen, Lassi; Martin, Loïc; Vahlne, Anders; Zambonelli, Carlo; Barnett, Susan W.; Srivastava, Indresh K.; Cheng, R. Holland

2014-01-01

41

Tropical Conservation and Ecology in Costa Rica ENV SCI 499  

E-print Network

Tropical Conservation and Ecology in Costa Rica ENV SCI 499 Assistant Professor Mathew Dornbush National Park. Located on Costa Rica's Pacific Coast, Carara is characterized by high biological diversity with park staff enhances group discussions by providing a Costa Rican perspective to Costa Rica's natural

Dornbush, Mathew E.

42

ENVS 4000, Spring (Jan-Apr) 2006 Monitoring Ecosystems  

E-print Network

, and other benefits. Ecosystem health has direct and indirect outcomes for human health, economic systems Impact Assessment, Ecological Risk Analysis, Environmental Monitoring and Assessment, and quantitativeENVS 4000, Spring (Jan-Apr) 2006 Monitoring Ecosystems for Environmental Impacts Humans and human

Johnson, Dan L.

43

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

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.

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

44

Phage display identifies two Caprine Arthritis Encephalitis Virus env epitopes.  

PubMed

Using phage display and IgG of a goat infected with Caprine Arthritis Encephalitis Virus (CAEV) we obtained families of 7 mer constrained peptides with consensus motifs LxSDPF/Y and SWN/KHWSY and mapped the epitopes mimicked by them at the Env 6-LISDPY-11 and 67-WNTYHW-72 sites of the mature gp135 amino acid sequence. The first epitope fell into the N-terminal immunogenic aa1-EDYTLISDPYGFS- aa14 site identified previously with a synthetic peptide approach; the second epitope has not been described previously. The first epitope is mostly conserved across CAEV isolates whereas the second newly described epitope is extremely conserved in Small Ruminant Lentiviruses env sequences. As being immunodominant, the epitopes are candidate targets for mimotope-mediated diagnosis and/or neutralization. PMID:21781322

Gazarian, Karlen; Setién, Alvaro Aguilar; Gazarian, Tatiana; Pierle, Sebastian Aguilar

2011-01-01

45

Phage display identifies two Caprine Arthritis Encephalitis Virus env epitopes  

PubMed Central

Using phage display and IgG of a goat infected with Caprine Arthritis Encephalitis Virus (CAEV) we obtained families of 7 mer constrained peptides with consensus motifs LxSDPF/Y and SWN/KHWSY and mapped the epitopes mimicked by them at the Env 6-LISDPY-11 and 67-WNTYHW-72 sites of the mature gp135 amino acid sequence. The first epitope fell into the N-terminal immunogenic aa1-EDYTLISDPYGFS- aa14 site identified previously with a synthetic peptide approach; the second epitope has not been described previously. The first epitope is mostly conserved across CAEV isolates whereas the second newly described epitope is extremely conserved in Small Ruminant Lentiviruses env sequences. As being immunodominant, the epitopes are candidate targets for mimotope-mediated diagnosis and/or neutralization. PMID:21781322

2011-01-01

46

Env-less endogenous retroviruses are genomic superspreaders  

PubMed Central

Endogenous retroviruses (ERVs) differ from typical retroviruses in being inherited through the host germline and therefore are a unique combination of pathogen and selfish genetic element. Some ERV lineages proliferate by infecting germline cells, as do typical retroviruses, whereas others lack the env gene required for virions to enter cells and thus behave like retrotransposons. We wished to know what factors determined the relative abundance of different ERV lineages, so we analyzed ERV loci recovered from 38 mammal genomes by in silico screening. By modeling the relationship between proliferation and replication mechanism in detail within one group, the intracisternal A-type particles (IAPs), and performing simple correlations across all ERV lineages, we show that when ERVs lose the env gene their proliferation within that genome is boosted by a factor of ?30. We also show that ERV abundance follows the Pareto principle or 20/80 rule, with ?20% of lineages containing 80% of the loci. This rule is observed in many biological systems, including infectious disease epidemics, where commonly ?20% of the infected individuals are responsible for 80% of onward infection. We thus borrow simple epidemiological and ecological models and show that retrotransposition and loss of env is the trait that leads endogenous retroviruses to becoming genomic superspreaders that take over a significant proportion of their host's genome. PMID:22529376

Magiorkinis, Gkikas; Gifford, Robert J.; Katzourakis, Aris; De Ranter, Joris; Belshaw, Robert

2012-01-01

47

The Majority of CD4+ T-Cell Depletion during Acute Simian-Human Immunodeficiency Virus SHIV89.6P Infection Occurs in Uninfected Cells  

PubMed Central

ABSTRACT Untreated human immunodeficiency virus (HIV) infection is characterized by depletion of CD4+ T cells, ultimately leading to the impairment of host immune defenses and death. HIV-infected CD4+ T cells die from direct virus-induced apoptosis and CD8 T-cell-mediated elimination, but a broader and more profound depletion occurs in uninfected CD4+ T cells via multiple indirect effects of infection. We fit mathematical models to data from experiments that tested an HIV eradication strategy in which five macaques with a proportion of CD4+ T cells resistant to simian-human immunodeficiency virus (SHIV) entry were challenged with SHIV89.6P, a highly pathogenic dual-tropic chimeric SIV-HIV viral strain that results in rapid loss of both SHIV-susceptible and SHIV-resistant CD4+ T cells. Our results suggest that uninfected (bystander) cell death accounts for the majority of CD4+ T-lymphocyte loss, with at least 60% and 99% of CD4+ T cell death occurring in uninfected cells during acute and established infection, respectively. Mechanisms to limit the profound indirect killing effects associated with HIV infection may be associated with immune preservation and improved long-term survival. IMPORTANCE HIV infection induces a massive depletion of CD4+ T cells, leading to profound immunodeficiency, opportunistic infections, and eventually death. While HIV induces apoptosis (programmed cell death) by directly entering and replicating in CD4+ T cells, uninfected CD4+ T cells also undergo apoptosis due to ongoing toxic inflammation in the region of infection. In this paper, we use mathematical models in conjunction with data from simian-human immunodeficiency virus SHIV89.6P infection in macaques (a model of HIV infection in humans) to estimate the percentage of cell death that occurs in uninfected cells during the initial period of infection. We reveal that the vast majority of cell death occurs in these cells, which are not infected. The “bystander effects” that lead to enormous reductions in the number of uninfected CD4+ T cells may be a target for future interventions that aim to limit the extent of damage caused by HIV. PMID:24390339

Matrajt, Laura; Younan, Patrick M.; Kiem, Hans-Peter

2014-01-01

48

Coreceptor-Dependent Inhibition of the Cell Fusion Activity of Simian Immunodeficiency Virus Env Proteins  

Microsoft Academic Search

The cytoplasmic tail (R peptide) sequence is able to regulate the fusion activity of the murine leukemia virus (MuLV) envelope (Env) protein. We have previously shown that this sequence exerts a profound inhibitory effect on the fusion activity of simian immunodeficiency virus (SIV)-MuLV chimeric Env proteins which contain the extracellular and transmembrane domains of the SIV Env protein. Recent studies

CHINGLAI YANG; QINGYUAN YANG; RICHARD W. COMPANS

2000-01-01

49

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

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

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; Fernandez-Romero, Jose A.; Zydowsky, Thomas M.; Teleshova, Natalia

2012-01-01

50

SimEnvVis: A Climate Data Visualization Wizard  

NASA Astrophysics Data System (ADS)

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.

Heitzler, Magnus; Nocke, Thomas

2013-04-01

51

The HIV-1 Env Protein: A Coat of Many Colors  

PubMed Central

Human immunodeficiency virus type 1 (HIV-1) is completely dependent upon the Env protein to enter cells. The virus typically replicates in activated CD4+ T cells due to viral entry requirements for the CCR5 coreceptor and for high surface levels of the CD4 receptor. This is the case for the transmitted virus and for most of the virus sampled in the blood. Over the course of infection, the env gene can evolve to encode a protein with altered receptor and coreceptor usage allowing the virus to enter alternative host cells. In about 50% of HIV-1 infections, the viral population undergoes coreceptor switching, usually late in disease, allowing the virus to use CXCR4 to enter a different subset of CD4+ T cells. Neurocognitive disorders occur in about 10% of infections, also usually late in disease, but caused (ultimately) by viral replication in the brain either in CD4+ T cells or macrophage and/or microglia. Expanded host range is significantly intertwined with pathogenesis. Identification and characterization of such HIV-1 variants may be useful for early detection which would allow intervention to reduce viral pathogenesis in these alternative cell types. PMID:22237899

Arrildt, Kathryn Twigg; Joseph, Sarah Beth; Swanstrom, Ronald

2013-01-01

52

NMobTec-EnvEdu: M-Learning System for Environmental Education  

ERIC Educational Resources Information Center

This paper introduced the implementation of a New Mobile Technologies and Environmental Education System (NMobTec-EnvEdu) designed for m-learning environments. The NMobTec-EnvEdu system has been developed to provide environmental education in a collaborative framework to undergraduate students through the Internet using mobile phones. The study…

Cavus, Nadire

2008-01-01

53

Clustering and Mobility of HIV-1 Env at Viral Assembly Sites Predict Its Propensity To Induce Cell-Cell Fusion  

PubMed Central

HIV-1 Env mediates virus attachment to and fusion with target cell membranes, and yet, while Env is still situated at the plasma membrane of the producer cell and before its incorporation into newly formed particles, Env already interacts with the viral receptor CD4 on target cells, thus enabling the formation of transient cell contacts that facilitate the transmission of viral particles. During this first encounter with the receptor, Env must not induce membrane fusion, as this would prevent the producer cell and the target cell from separating upon virus transmission, but how Env's fusion activity is controlled remains unclear. To gain a better understanding of the Env regulation that precedes viral transmission, we examined the nanoscale organization of Env at the surface of producer cells. Utilizing superresolution microscopy (stochastic optical reconstruction microscopy [STORM]) and fluorescence recovery after photobleaching (FRAP), we quantitatively assessed the clustering and dynamics of Env upon its arrival at the plasma membrane. We found that Gag assembly induced the aggregation of small Env clusters into larger domains and that these domains were completely immobile. Truncation of the cytoplasmic tail (CT) of Env abrogated Gag's ability to induce Env clustering and restored Env mobility at assembly sites, both of which correlated with increased Env-induced fusion of infected and uninfected cells. Hence, while Env trapping by Gag secures Env incorporation into viral particles, Env clustering and its sequestration at assembly sites likely also leads to the repression of its fusion function, and thus, by preventing the formation of syncytia, Gag helps to secure efficient transfer of viral particles to target cells. PMID:23637402

Roy, Nathan H.; Chan, Jany; Lambele, Marie

2013-01-01

54

Role of the Cytoplasmic Tail of Ecotropic Moloney Murine Leukemia Virus Env Protein in Fusion Pore Formation  

Microsoft Academic Search

Fusion between cells expressing envelope protein (Env) of Moloney murine leukemia virus and target cells were studied by use of video fluorescence microscopy and electrical capacitance measurements. When the full-length 632-amino-acid residue Env was expressed, fusion did not occur at all for 3T3 cells as target and only somewhat for XC6 cells. Expression of Env 616*—a construct of Env with

GRIGORY B. MELIKYAN; RUBEN M. MARKOSYAN; SOFYA A. BRENER; YANINA ROZENBERG; FREDRIC S. COHEN

2000-01-01

55

CD4 Independence of Simian Immunodeficiency Virus Envs Is Associated with Macrophage Tropism, Neutralization Sensitivity, and Attenuated Pathogenicity  

Microsoft Academic Search

To investigate the basis for envelope (Env) determinants influencing simian immunodeficiency virus (SIV) tropism, we studied a number of Envs that are closely related to that of SIVmac239, a pathogenic, T-tropic virus that is neutralization resistant. The Envs from macrophage-tropic (M-tropic) virus strains SIVmac316, 1A11, 17E-Fr, and 1100 facilitated infection of CCR5-positive, CD4-negative cells. In contrast, the SIVmac239 Env was

Bridget A. Puffer; Stefan Pöhlmann; Aimee L. Edinger; Dan Carlin; Melissa D. Sanchez; Julie Reitter; Debbie D. Watry; Howard S. Fox; Ronald C. Desrosiers; Robert W. Doms

2002-01-01

56

The Role of Innate APOBEC3G and Adaptive AID Immune Responses in HLA-HIV/SIV Immunized SHIV Infected Macaques  

PubMed Central

The AID/APOBEC family (activation induced deaminase/apolipoprotein B mRNA editing cytokine deaminase) in B cells play important roles in adaptive and innate immunity. Whereas APOBEC3G has been studied in CD4+ T cells and myeloid cells its functional potential in B cells has received little attention. AID combines two critical functions of antibodies, class switching and affinity maturation and may serve as a functional surrogate of protection. These functions were studied following systemic immunization of rhesus macaques with recombinant HLA constructs, linked with HIV and SIV antigens and HSP70 to dextran. The results showed significant upregulation of AID in CD20+ B cells, APOBEC 3G in CD27+ memory B cells and CD4+ effector memory T cells. After immunization the upregulated APOBEC 3G and AID were directly correlated in B cells (p<0.0001). Following challenge with SHIV SF162.P4 the viral load was inversely correlated with AID in B cells and APOBEC 3G in B and T cells, suggesting that both deaminases may have protective functions. Investigation of major interactions between DC, T cells and B cells showed significant increase in membrane associated IL-15 in DC and CD40L in CD4+ T cells. IL-15 binds the IL-15 receptor complex in CD4+ T and B cells, which may reactivate the DC, T and B cell interactions. The overall results are consistent with AID inhibiting pre-entry SHIV by eliciting IgG and IgA antibodies, whereas APOBEC 3G may contribute to the post-entry control of SHIV replication and cellular spread. PMID:22514633

Wang, Yufei; Whittall, Trevor; Rahman, Durdana; Bunnik, Evelien M.; Vaughan, Robert; Sch?ller, J?rgen; Bergmeier, Lesley A.; Montefiori, David; Singh, Mahavir; Schuitemaker, Hanneke; Lehner, Thomas

2012-01-01

57

Complementation of diverse HIV1 Env defects through cooperative subunit interactions: a general property of the functional trimer  

Microsoft Academic Search

BACKGROUND: The HIV-1 Env glycoprotein mediates virus entry by catalyzing direct fusion between the virion membrane and the target cell plasma membrane. Env is composed of two subunits: gp120, which binds to CD4 and the coreceptor, and gp41, which is triggered upon coreceptor binding to promote the membrane fusion reaction. Env on the surface of infected cells is a trimer

Karl Salzwedel; Edward A Berger

2009-01-01

58

Phenotypes and distribution of mucosal memory B-cell populations in the SIV/SHIV rhesus macaque model.  

PubMed

As vaccine-elicited antibodies have now been associated with HIV protective efficacy, a thorough understanding of mucosal and systemic B-cell development and maturation is needed. We phenotyped mucosal memory B-cells, investigated isotype expression and homing patterns, and defined plasmablasts and plasma cells at three mucosal sites (duodenum, jejunum and rectum) in rhesus macaques, the commonly used animal model for pre-clinical vaccine studies. Unlike humans, macaque mucosal memory B-cells lacked CD27 expression; only two sub-populations were present: naïve (CD21(+)CD27(-)) and tissue-like (CD21(-)CD27(-)) memory. Similar to humans, IgA was the dominant isotype expressed. The homing markers CXCR4, CCR6, CCR9 and ?4?7 were differentially expressed between naïve and tissue-like memory B-cells. Mucosal plasmablasts were identified as CD19(+)CD20(+/-)HLA-DR(+)Ki-67(+)IRF4(+)CD138(+/-) and mucosal plasma cells as CD19(+)CD20(-)HLA-DR(-)Ki-67(-)IRF4(+)CD138(+). Both populations were CD39(+/-)CD27(-). Plasma cell phenotype was confirmed by spontaneous IgA secretion by ELISpot of positively-selected cells and J-chain expression by real-time PCR. Duodenal, jejunal and rectal samples were similar in B-cell memory phenotype, isotype expression, homing receptors and plasmablast/plasma cell distribution among the three tissues. Thus rectal biopsies adequately monitor B-cell dynamics in the gut mucosa, and provide a critical view of mucosal B-cell events associated with development of vaccine-elicited protective immune responses and SIV/SHIV pathogenesis and disease control. PMID:24814239

Demberg, Thorsten; Mohanram, Venkatramanan; Venzon, David; Robert-Guroff, Marjorie

2014-08-01

59

Coreceptor-dependent inhibition of the cell fusion activity of simian immunodeficiency virus Env proteins.  

PubMed

The cytoplasmic tail (R peptide) sequence is able to regulate the fusion activity of the murine leukemia virus (MuLV) envelope (Env) protein. We have previously shown that this sequence exerts a profound inhibitory effect on the fusion activity of simian immunodeficiency virus (SIV)-MuLV chimeric Env proteins which contain the extracellular and transmembrane domains of the SIV Env protein. Recent studies have shown that SIV can utilize several alternative cellular coreceptors for its fusion and entry into the cell. We have investigated the fusion activity of SIV and SIV-MuLV chimeric Env proteins using cells that express different coreceptors. HeLa cells were transfected with plasmid constructs that carry the SIV or SIV-MuLV chimeric Env protein genes and were overlaid with either CEMx174 cells or Ghost Gpr15 cells, which express the Gpr15 coreceptor for SIV, or Ghost CCR5 cells, which express CCR5, an alternate coreceptor for SIV. The R-peptide sequence in the SIV-MuLV chimeric proteins was found to inhibit the fusion with CEMx174 cells or Ghost Gpr15 cells. However, a significant level of fusion was still observed when HeLa cells expressing the chimeric Env proteins were cocultivated with Ghost CCR5 cells. These results show that the R-peptide sequence exerts differential effects on the fusion activity of SIV Env proteins using target cells that express alternative coreceptors. PMID:10846110

Yang, C; Yang, Q; Compans, R W

2000-07-01

60

Human retroviral env and gag polypeptides: serologic assays to measure infection.  

PubMed

Humoral antiviral responses to human retrovirus infections identify persistently infected individuals and can be used to characterize virus-host interactions. Antibodies to native viral polypeptides have been reliably measured, although quantitation of env antibodies is difficult due to a lack of purified antigens. To quantitate antibodies to env antigens, bacterially expressed cloned env polypeptides from the transmembrane regions of human T lymphotropic virus types I and III were applied to nitrocellulose filters in an immunodot assay. A combination of the sensitivity of the Western blot procedure and the specificity of peptides from defined viral sequences was used to detect 49/49 HTLV-III/LAV-infected individuals previously defined as seropositive by radioimmunoprecipitation sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Of these HTLV-III/LAV envelope seropositive people, 22% lacked antibody to p24 in a radioimmunoassay. In contrast, the sensitivity of antibody detection to HTLV-I env antigens and p24 were comparable. Antibodies to HTLV-I and HTLV-III/LAV env transmembrane peptides were not cross-reactive. Levels of antibody to env antigens of both HTLV-I and HTLV-III/LAV persisted without change for at least 26 mo, suggesting that most infections represent stable virus-host interactions. The use of bacterially expressed env peptides offers a rapid serologic approach for distinguishing human retroviral infections and can be used to define immune responses to specific regions of the viral genome. PMID:3014000

Kanner, S B; Cheng-Mayer, C; Geffin, R B; Parks, W P; Beltz, G A; Arthur, L O; Samuel, K P; Papas, T S

1986-07-15

61

Robot technology (RT) trend and standardization  

Microsoft Academic Search

In the near future, the RT is embedded and distributed in the daily life environment and various equipments to provide not only information services but physical services such as physical assistance in our daily life. For this service integration, the development of the RT components and the middleware service are inevitable. In this paper, the RT (robot technology) application extension

M. Mizukawa

2005-01-01

62

Implementing RtI with Gifted Students  

ERIC Educational Resources Information Center

"Implementing RtI With Gifted Students" shares how RtI can fit within the framework of gifted education programming models. This edited book will serve as a reference guide for those interested in learning more about RtI and how it might be effectively implemented to meet the needs of all gifted students. Chapters contributed by top gifted…

Coleman, Mary Ruth, Ed.; Johnsen, Susan K., Ed.

2012-01-01

63

ENVS 411/511 Fall 2013 CLIMATE CHANGE AND INDIGENOUS PEOPLES  

E-print Network

. This course will introduce students to the impacts of climate change on tribal ENVS 411/511 Fall 2013 CLIMATE CHANGE AND INDIGENOUS PEOPLES Indigenous peoples in the U.S. face disproportionate risks from climate change

64

Functional interaction between Env oncogene from Jaagsiekte sheep retrovirus and tumor suppressor Sprouty2  

PubMed Central

Background Jaagsiekte sheep retrovirus (JSRV) is a type D retrovirus capable of transforming target cells in vitro and in vivo. The Envelope (Env) gene from JSRV and from related retroviruses can induce oncogenic transformation, although the detailed mechanism is yet to be clearly understood. Host cell factors are envisaged to play a critical determining role in the regulation of Env-mediated cell transformation. Results JSRV Env-mediated transformation of a lung adenocarcinoma cell line induced rapid proliferation, anchorage-independent growth and tumor formation, but completely abrogated the migration ability. An analysis of the signaling scenario in the transformed cells suggested the involvement of the ERK pathway regulated by Sprouty2 in cell migration, and the PI3K-Akt and STAT3 pathways in proliferation and anchorage-independence. On the other hand, in a normal lung epithelial cell line, Env-mediated transformation only decreased the migration potential while the other functions remained unaltered. We observed that Env induced the expression of a tumor suppressor, Sprouty2, suggesting a correlation between Env-effect and Sprouty2 expression. Overexpression of Sprouty2 per se not only decreased the migratory potential and tumor formation potential of the target cells but also made them resistant to subsequent Env-mediated transformation. On the other hand, over expression of the functional mutants of Sprouty2 had no inhibitory effect, confirming the role of Sprouty2 as a tumor suppressor. Conclusions Our studies demonstrate that Env and Sprouty2 have a functional relationship, probably through shared signaling network. Sprouty2 functions as a tumor suppressor regulating oncogenic transformation of cells, and it therefore has the potential to be exploited as a therapeutic anti-cancer agent. PMID:20678191

2010-01-01

65

Secretion of a murine retroviral Env associated with resistance to infection  

Microsoft Academic Search

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

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

1997-01-01

66

Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution  

PubMed Central

Intrapatient evolution of human immunodeficiency virus type 1 (HIV-1) is driven by the adaptive immune system resulting in rapid change of HIV-1 proteins. When cytotoxic CD8+ T cells or neutralizing antibodies target a new epitope, the virus often escapes via nonsynonymous mutations that impair recognition. Synonymous mutations do not affect this interplay and are often assumed to be neutral. We test this assumption by tracking synonymous mutations in longitudinal intrapatient data from the C2-V5 part of the env gene. We find that most synonymous variants are lost even though they often reach high frequencies in the viral population, suggesting a cost to the virus. Using published data from SHAPE (selective 2?-hydroxyl acylation analyzed by primer extension) assays, we find that synonymous mutations that disrupt base pairs in RNA stems flanking the variable loops of gp120 are more likely to be lost than other synonymous changes: these RNA hairpins might be important for HIV-1. Computational modeling indicates that, to be consistent with the data, a large fraction of synonymous mutations in this genomic region need to be deleterious with a cost on the order of 0.002 per day. This weak selection against synonymous substitutions does not result in a strong pattern of conservation in cross-sectional data but slows down the rate of evolution considerably. Our findings are consistent with the notion that large-scale patterns of RNA structure are functionally relevant, whereas the precise base pairing pattern is not. PMID:23986591

Zanini, Fabio

2013-01-01

67

RT3D tutorials for GMS users  

Microsoft Academic Search

RT3D (Reactive Transport in 3-Dimensions) is a computer code that solves coupled partial differential equations that describe reactive-flow and transport of multiple mobile and\\/or immobile species in a three dimensional saturated porous media. RT3D was developed from the single-species transport code, MT3D (DoD-1.5, 1997 version). As with MT3D, RT3D also uses the USGS groundwater flow model MODFLOW for computing spatial

T. P. Clement; N. L. Jones

1998-01-01

68

Maturation cleavage of the murine leukemia virus Env precursor separates the transmembrane subunits to prime it for receptor triggering  

PubMed Central

The Env protein of murine leukemia virus matures by two cleavage events. First, cellular furin separates the receptor binding surface (SU) subunit from the fusion-active transmembrane (TM) subunit and then, in the newly assembled particle, the viral protease removes a 16-residue peptide, the R-peptide from the endodomain of the TM. Both cleavage events are required to prime the Env for receptor-triggered activation. Cryoelectron microscopy (cryo-EM) analyses have shown that the mature Env forms an open cage-like structure composed of three SU–TM complexes, where the TM subunits formed separated Env legs. Here we have studied the structure of the R-peptide precursor Env by cryo-EM. TM cleavage in Moloney murine leukemia virus was inhibited by amprenavir, and the Envs were solubilized in Triton X-100 and isolated by sedimentation in a sucrose gradient. We found that the legs of the R-peptide Env were held together by trimeric interactions at the very bottom of the Env. This suggested that the R-peptide ties the TM legs together and that this prevents the activation of the TM for fusion. The model was supported by further cryo-EM studies using an R-peptide Env mutant that was fusion-competent despite an uncleaved R-peptide. The Env legs of this mutant were found to be separated, like in the mature Env. This shows that it is the TM leg separation, normally caused by R-peptide cleavage, that primes the Env for receptor triggering. PMID:22547812

Loving, Robin; Wu, Shang-Rung; Sjoberg, Mathilda; Lindqvist, Birgitta; Garoff, Henrik

2012-01-01

69

PALATAL DYSMORPHOGENESIS: QUANTITATIVE RT-PCR  

EPA Science Inventory

ABSTRACT Palatal Dysmorphogenesis : Quantitative RT-PCR Gary A. Held and Barbara D. Abbott Reverse transcription PCR (RT-PCR) is a very sensitive method for detecting mRNA in tissue samples. However, as it is usually performed it is does not yield quantitativ...

70

"Resistance" to PSC-RANTES revisited: two mutations in human immunodeficiency virus type 1 HIV-1 SF162 or simian-human immunodeficiency virus SHIV SF162-p3 do not confer resistance.  

PubMed

Resistance of human immunodeficiency virus type 1 (HIV-1) to small-molecule CCR5 inhibitors is well demonstrated, but resistance to macromolecular CCR5 inhibitors (e.g., PSC-RANTES) that act by both CCR5 internalization and receptor blockade had not been reported until recently (3). The report of a single simian-human immunodeficiency virus SHIV(SF162-p3) variant with one V3 and one gp41 sequence change in gp160 that conferred both altered replicative fitness and resistance to PSC-RANTES was therefore surprising. We introduced the same two mutations into both the parental HIV-1(SF162) and the macaque-adapted SHIV(SF162-p3) and found minor differences in entry fitness but no changes in sensitivity to inhibition by either PSC-RANTES or the small-molecule allosteric inhibitor TAK-779. We attribute the earlier finding to confounding fitness effects with inhibitor sensitivity. PMID:20335248

Nedellec, Rebecca; Coetzer, Mia; Lederman, Michael M; Offord, Robin E; Hartley, Oliver; Mosier, Donald E

2010-06-01

71

BIOCHEMISTRY: RT Slides Home⦠ 

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. To access its target sites, HIV reverse transcriptase (RT) slides and flips on nucleic acid substrates. Although 20 years of crystallographic and biochemical studies have illuminated the molecular details of the chemistry of DNA synthesis, there have been relatively few insights into how RT finds the end of the nucleic acid substrate where it begins DNA synthesis, how it displaces nucleic acid fragments, or where and how it executes masterful leaps when transferring DNA between templates. On page 1092 of this issue, Liu et al. (2) describe elegant single-molecule fluorescence resonance energy transfer (FRET) experiments that provide a view of RT at work. They show that RT has a remarkable ability to slide on nucleic acid duplexes, rapidly shuttling between the two ends and flipping into the polymerase-competent binding mode when needed.

Stefan G. Sarafianos (University of Missouri;Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology); Eddy Arnold (Rutgers University;Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology)

2008-11-14

72

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

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.

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

73

Systematic Evaluation of Allele-Specific Real Time PCR for the Detection of Minor HIV-1 Variants with pol and env Resistance Mutations  

PubMed Central

SUMMARY Allele-specific PCR (ASPCR) is a highly sensitive, and reproducible method for the study of minor HIV-1 variants harboring resistance mutations and is significantly less labor-intensive and time-consuming than other techniques used for similar purposes. Furthermore, ASPCR has multiple applications in HIV research: it provides earlier and more sensitive detection of evolving resistance mutations, a more accurate assessment of transmitted drug-resistant mutants and a better evaluation of resistance selection after post-exposure or mother-to-child-transmission prophylaxis programs. This article outline the principles of ASPCR and illustrates technical challenges in the design and application of ASPCR protocols by describing ASPCR assays developed for detecting resistance mutations in the protease (PR)- and reverse transcriptase (RT)–coding regions of pol and env. The assays achieved sensitivities of <1% for the D30N mutation in HIV-1 PR, M184V and I mutations in RT, and V38A in gp41. This method can be easily adapted to the quantitative detection of other mutations in HIV-1 or other viruses by introducing minor modifications to the methods described. In addition, ASPCR can be used to assess the dynamics of mutant populations in the viral quasispecies in response to changing selection pressures, allowing inferences on viral fitness in vivo through mathematical modeling. PMID:17662474

Paredes, Roger; Marconi, Vincent C.; Campbell, Thomas B.; Kuritzkes, Daniel R.

2014-01-01

74

ENVIRONMETRICS Environmetrics 2002; 13: 105119 (DOI: 10.1002/env.514)  

E-print Network

sampling; wildlife monitoring studies 1. INTRODUCTION The focus of much early wildlife statistics work the principles of design for large-scale wildlife monitoring studies that incorporate estimating detectionENVIRONMETRICS Environmetrics 2002; 13: 105±119 (DOI: 10.1002/env.514) Large scale wildlife

Simons, Theodore R.

75

Disease progression and evolution of the HIV-1 env gene in 24 infected infants  

E-print Network

Disease progression and evolution of the HIV-1 env gene in 24 infected infants§ Antonio Carvajal of Pediatrics, Columbia University College of Physicians and Surgeons and Harlem Hospital Center, NY, USA d and HIV-1 evolution in 24 infants classified as rapid or non-rapid progressors, during nearly the entire

Posada, David

76

J.BACON 2014 SUMMER EJ CRN: 46409 ENVS 435: ENVIRONMENTAL JUSTICE  

E-print Network

J.BACON 2014 SUMMER EJ CRN: 46409 ENVS 435: ENVIRONMENTAL JUSTICE INSTRUCTOR: J. BACON julieb on environmental justice, class exercises to develop self-reflection and a creative personal knowledge mapping the lens of environmental justice critically discuss and evaluate various perspectives on environmental

77

ENVS 411/511 Fall 2014 CLIMATE CHANGE AND INDIGENOUS PEOPLES  

E-print Network

ENVS 411/511 Fall 2014 CLIMATE CHANGE AND INDIGENOUS PEOPLES IN THE UNITED STATES Instructor: Kathy risks from climate change. This course will introduce students to the impacts of climate change knowledge in understanding climate change impacts and solutions, and climate justice. Through this course

78

Service Learning Travel Course ENV SCI 499: Tropical Conservation and Ecology in Costa Rica  

E-print Network

Service Learning Travel Course ENV SCI 499: Tropical Conservation and Ecology in Costa Rica National Park, Costa Rica for the first two weeks in January. Direct student involvement with park staff challenges. Located on Costa Rica's Pacific Coast, Carara National Park manages 4,700 hectares (11,600 acres

Dornbush, Mathew E.

79

ENVS 4000, Spring (Jan-Apr) 2007 Impacts of Climate Change  

E-print Network

ENVS 4000, Spring (Jan-Apr) 2007 Impacts of Climate Change This capstone Environmental Science: science and technology - paleoclimate - climate change theory and modeling; uncertainty and risk - global course, designed for 3rd and 4th year students, includes presentations and discussions related

Johnson, Dan L.

80

Thinking of sticking around this summer? Need to take ENVS 202 for an environmental  

E-print Network

and toxicology, environmental history, and citizen science. In a society which privileges specialized, scientificThinking of sticking around this summer? Need to take ENVS 202 for an environmental studies major or a general education science credit? Interested in the science surrounding current environmental issues

81

Env sequence determinants in CXCR4-using human immunodeficiency virus type-1 subtype C.  

PubMed

HIV-1 subtype C (HIV-1C) CXCR4-using virus is isolated infrequently and is poorly characterized. Understanding HIV-1C env characteristics has implications for the clinical use of antiretrovirals that target viral entry. A total of 209 env clones derived from 10 samples with mixed CCR5-(R5), CXCR4-using (X4) or dual-tropic HIV-1C were phenotyped for coreceptor usage. Intra-patient X4 and R5 variants generally formed distinct monophyletic phylogenetic clusters. X4 compared to R5 envs had significantly greater amino acid variability and insertions, higher net positive charge, fewer glycosylation sites and increased basic amino acid substitutions in the GPGQ crown. Basic amino acid substitution and/or insertion prior to the crown are highly sensitive characteristics for predicting X4 viruses. Chimeric env functional studies suggest that the V3 loop is necessary but often not sufficient to impart CXCR4 utilization. Our studies provide insights into the unique genotypic characteristics of X4 variants in HIV-1C. PMID:22954962

Lin, Nina H; Becerril, Carlos; Giguel, Francoise; Novitsky, Vladimir; Moyo, Sikhulile; Makhema, Joseph; Essex, Myron; Lockman, Shahin; Kuritzkes, Daniel R; Sagar, Manish

2012-11-25

82

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

E-print Network

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

Kececioglu, John

83

PLANNING THEORY SYLLABUS | ENVS 462 | W2013 A Contemplative Seminar in American Planning Thought  

E-print Network

professional males on the historical stage. Where are women? Where are African Americans, Native Americans, Mexican, Japanese, and Chinese Americans? Where are they both as subjects, doing planning, and as objects1 PLANNING THEORY SYLLABUS | ENVS 462 | W2013 A Contemplative Seminar in American Planning Thought

Zaferatos, Nicholas C.

84

Decreased plasticity of coreceptor use by CD4-independent SIV Envs that emerge in vivo  

PubMed Central

Background HIV and SIV generally require CD4 binding prior to coreceptor engagement, but Env can acquire the ability to use CCR5 independently of CD4 under various circumstances. The ability to use CCR5 coupled with low-to-absent CD4 levels is associated with enhanced macrophage infection and increased neutralization sensitivity, but the additional features of these Envs that may affect cell targeting is not known. Results Here we report that CD4-independent SIV variants that emerged in vivo in a CD4+ T cell-depleted rhesus macaque model display markedly decreased plasticity of co-receptor use. While CD4-dependent Envs can use low levels of macaque CCR5 for efficient entry, CD4-independent variants required high levels of CCR5 even in the presence of CD4. CD4-independent Envs were also more sensitive to the CCR5 antagonist Maraviroc. CD4-dependent variants mediated efficient entry using human CCR5, whereas CD4-independent variants had impaired use of human CCR5. Similarly, CD4-independent Envs used the alternative coreceptors GPR15 and CXCR6 less efficiently than CD4-dependent variants. Env amino acids D470N and E84K that confer the CD4-independent phenotype also regulated entry through low CCR5 levels and GPR15, indicating a common structural basis. Treatment of CD4-dependent Envs with soluble CD4 enhanced entry through CCR5 but reduced entry through GPR15, suggesting that induction of CD4-induced conformational changes by non-cell surface-associated CD4 impairs use of this alternative co-receptor. Conclusions CD4 independence is associated with more restricted coreceptor interactions. While the ability to enter target cells through CCR5 independently of CD4 may enable infection of CD4 low-to-negative cells such as macrophages, this phenotype may conversely reduce the potential range of targets such as cells expressing low levels of CCR5, conformational variants of CCR5, or possibly even alternative coreceptors. PMID:24219995

2013-01-01

85

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

SciTech Connect

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.

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

86

Sequential CD4-coreceptor interactions in human immunodeficiency virus type 1 Env function: soluble CD4 activates Env for coreceptor-dependent fusion and reveals blocking activities of antibodies against cryptic conserved epitopes on gp120.  

PubMed

We devised an experimental system to examine sequential events by which the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) interacts with CD4 and coreceptor to induce membrane fusion. Recombinant soluble CD4 (sCD4) activated fusion between effector cells expressing Env and target cells expressing coreceptor (CCR5 or CXCR4) but lacking CD4. sCD4-activated fusion was dose dependent, occurred comparably with two- and four-domain proteins, and demonstrated Env-coreceptor specificities parallel to those reported in conventional fusion and infectivity systems. Fusion activation occurred upon sCD4 preincubation and washing of the Env-expressing effector cells but not the coreceptor-bearing target cells, thereby demonstrating that sCD4 exerts its effects by acting on Env. These findings provide direct functional evidence for a sequential two-step model of Env-receptor interactions, whereby gp120 binds first to CD4 and becomes activated for subsequent functional interaction with coreceptor, leading to membrane fusion. We used the sCD4-activated system to explore neutralization by the anti-gp120 human monoclonal antibodies 17b and 48d. These antibodies reportedly bind conserved CD4-induced epitopes involved in coreceptor interactions but neutralize HIV-1 infection only weakly. We found that 17b and 48d had minimal effects in the standard cell fusion system using target cells expressing both CD4 and coreceptor but potently blocked sCD4-activated fusion with target cells expressing coreceptor alone. Both antibodies strongly inhibited sCD4-activated fusion by Envs from genetically diverse HIV-1 isolates. Thus, the sCD4-activated system reveals conserved Env-blocking epitopes that are masked in native Env and hence not readily detected by conventional systems. PMID:10590121

Salzwedel, K; Smith, E D; Dey, B; Berger, E A

2000-01-01

87

Genetic shift of env V3 loop viral sequences in patients with HIV-associated neurocognitive disorder during antiretroviral therapy.  

PubMed

The development of human immunodeficiency virus type 1 (HIV)-associated neurocognitive disorder (HAND) involves the adaptation of viral sequences coding for the V3 loop of the env protein. The plasma and cerebrospinal fluid (CSF) may contain viral populations from various cellular sources and with differing pathogenicity. Combination antiretroviral therapy (cART) may alter the relative abundance of these viral populations, leading to a genetic shift. We characterized plasma and CNS viral populations prior to and during cART and relate the findings to viral elimination kinetics and the clinical phenotype. Longitudinal plasma and CSF samples of five chronically infected HIV patients, four of whom had HAND, and one seroconverter were analyzed for V3 sequences by RT-PCR and sequence analysis. In the chronically infected patients, pre-cART plasma and CSF viral sequences were different irrespective of viral elimination kinetics and clinical phenotype. cART induced replacement of plasma viral populations in all subjects. CSF viral populations underwent a clear genetic shift in some patients but remained stable in others. This was not dependent on the presence of HAND. The genetic shift of CSF V3 sequences was absent in the two subjects whose CSF viral load initially increased during cART. In one patient, pre- and post-treatment CSF sequences were closely related to the post-treatment plasma sequences, suggesting a common cellular source. We found heterogeneous patterns of genetic compartmentalization and genetic shift over time. Although these did not closely match viral elimination kinetics and clinical phenotype, the results imply different patterns of the dynamics and relative contribution of compartment-specific virus populations in chronic HIV infection. PMID:24101298

Eggers, Christian; Müller, Oliver; Thordsen, Ingo; Schreiber, Michael; Methner, Axel

2013-12-01

88

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

PubMed Central

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

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

2012-01-01

89

Turning of the receptor-binding domains opens up the murine leukaemia virus Env for membrane fusion  

PubMed Central

The activity of the membrane fusion protein Env of Moloney mouse leukaemia virus is controlled by isomerization of the disulphide that couples its transmembrane (TM) and surface (SU) subunits. We have arrested Env activation at a stage prior to isomerization by alkylating the active thiol in SU and compared the structure of isomerization-arrested Env with that of native Env. Env trimers of respective form were isolated from solubilized particles by sedimentation and their structures were reconstructed from electron microscopic images of both vitrified and negatively stained samples. We found that the protomeric unit of both trimers formed three protrusions, a top, middle and a lower one. The atomic structure of the receptor-binding domain of SU fitted into the upper protrusion. This was formed similar to a bent finger. Significantly, in native Env the tips of the fingers were directed against each other enclosing a cavity below, whereas they had turned outward in isomerization-arrested Env transforming the cavity into an open well. This might subsequently guide the fusion peptides in extended TM subunits into the target membrane. PMID:18800055

Wu, Shang-Rung; Sjoberg, Mathilda; Wallin, Michael; Lindqvist, Birgitta; Ekstrom, Maria; Hebert, Hans; Koeck, Philip J B; Garoff, Henrik

2008-01-01

90

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

E-print Network

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

Mitchell, Richard

91

env Chimeric Virus Technology for Evaluating Human Immunodeficiency Virus Susceptibility to Entry Inhibitors  

PubMed Central

We describe the development of chimeric virus technology (CVT) for human immunodeficiency virus (HIV) type 1 (HIV-1) env genes gp120, gp41, and gp160 for evaluation of the susceptibilities of HIV to entry inhibitors. This env CVT allows the recombination of env sequences derived from different strains into a proviral wild-type HIV-1 clone (clone NL4.3) from which the corresponding env gene has been deleted. An HIV-1 strain (strain NL4.3) resistant to the fusion inhibitor T20 (strain NL4.3/T20) was selected in vitro in the presence of T20. AMD3100-resistant strain NL3.4 (strain NL4.3/AMD3100) was previously selected by De Vreese et al. (K. De Vreese et al., J. Virol. 70:689-696, 1996). NL4.3/AMD3100 contains several mutations in its gp120 gene (De Vreese et al., J. Virol. 70:689-696, 1996), whereas NL4.3/T20 has mutations in both gp120 and gp41. Phenotypic analysis revealed that NL4.3/AMD3100 lost its susceptibility to dextran sulfate, AMD3100, AMD2763, T134, and T140 but not its susceptibility to T20, whereas NL4.3/T20 lost its susceptibility only to the inhibitory effect of T20. The recombination of gp120 of NL4.3/AMD3100 and gp41 of NL4.3/T20 or recombination of the gp160 genes of both strains into a wild-type background reproduced the phenotypic (cross-)resistance profiles of the corresponding strains selected in vitro. These data imply that mutations in gp120 alone are sufficient to reproduce the resistance profile of NL4.3/AMD3100. The same can be said for gp41 in relation to NL4.3/T20. In conclusion, we demonstrate the use of env CVT as a research tool in the delineation of the region important for the phenotypic (cross-)resistance of HIV strains to entry inhibitors. In addition, we obtained a proof of principle that env CVT can become a helpful diagnostic tool in assessments of the phenotypic resistance of clinical HIV isolates to HIV entry inhibitors. PMID:12435701

Fikkert, Valery; Cherepanov, Peter; Van Laethem, Kristel; Hantson, Anke; Van Remoortel, Barbara; Pannecouque, Christophe; De Clercq, Erik; Debyser, Zeger; Vandamme, Anne-Mieke; Witvrouw, Myriam

2002-01-01

92

MicroRT - Small animal conformal irradiator  

SciTech Connect

A novel small animal conformal radiation therapy system has been designed and prototyped: MicroRT. The microRT system integrates multimodality imaging, radiation treatment planning, and conformal radiation therapy that utilizes a clinical {sup 192}Ir isotope high dose rate source as the radiation source (teletherapy). A multiparameter dose calculation algorithm based on Monte Carlo dose distribution simulations is used to efficiently and accurately calculate doses for treatment planning purposes. A series of precisely machined tungsten collimators mounted onto a cylindrical collimator assembly is used to provide the radiation beam portals. The current design allows a source-to-target distance range of 1-8 cm at four beam angles: 0 deg. (beam oriented down), 90 deg., 180 deg., and 270 deg. The animal is anesthetized and placed in an immobilization device with built-in fiducial markers and scanned using a computed tomography, magnetic resonance, or positron emission tomography scanner prior to irradiation. Treatment plans using up to four beam orientations are created utilizing a custom treatment planning system--microRTP. A three-axis computer-controlled stage that supports and accurately positions the animals is programmed to place the animal relative to the radiation beams according to the microRTP plan. The microRT system positioning accuracy was found to be submillimeter. The radiation source is guided through one of four catheter channels and placed in line with the tungsten collimators to deliver the conformal radiation treatment. The microRT hardware specifications, the accuracy of the treatment planning and positioning systems, and some typical procedures for radiobiological experiments that can be performed with the microRT device are presented.

Stojadinovic, S.; Low, D. A.; Hope, A. J.; Vicic, M.; Deasy, J. O.; Cui, J.; Khullar, D.; Parikh, P. J.; Malinowski, K. T.; Izaguirre, E. W.; Mutic, S.; Grigsby, P. W. [Washington University School of Medicine, Saint Louis, Missouri 63110 (United States)

2007-12-15

93

522014-15 Suggested Course Plan CIvIl (envIRonmenTal)  

E-print Network

: Theory of Structures I CE 408: Risk Analysis in Civil Engr. CE 451: Water Resources Engineering CE 453522014-15 Suggested Course Plan CIvIl (envIRonmenTal) FIRST YEAR FALL: 16-17 units SPRING: 18 units and Thermodynamics phYS 152l: Electricity and Magnetism oTheR sCIenCe (12 unITs) ChEm 105Al: General Chemistry Ch

Zhou, Chongwu

94

Inhibition of Human Immunodeficiency Virus Type 1 Env-Mediated Fusion by DC-SIGN  

Microsoft Academic Search

DC-SIGN, a lectin expressed on dendritic cell and macrophage subsets, binds to human immunodeficiency virus Env glycoproteins, allowing capture of viral particles. Captured virions either infect target cells or are efficiently transmitted to lymphocytes. Cellular mechanisms underlying the effects of DC-SIGN remain poorly understood. Here we have analyzed the effects of DC-SIGN on viral entry and on syncytium formation induced

Cinzia Nobile; Arnaud Moris; Francoise Porrot; Nathalie Sol-Foulon; Olivier Schwartz

2003-01-01

95

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

PubMed

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

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

96

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

PubMed Central

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

Usami, Yoshiko; Gottlinger, Heinrich

2013-01-01

97

HIV-1 Nef responsiveness is determined by Env variable regions involved in trimer association and correlates with neutralization sensitivity.  

PubMed

HIV-1 Nef and the unrelated murine leukemia virus 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

Usami, Yoshiko; Göttlinger, Heinrich

2013-11-14

98

HIV-1 Tat Promotes Integrin-Mediated HIV Transmission to Dendritic Cells by Binding Env Spikes and Competes Neutralization by Anti-HIV Antibodies  

PubMed Central

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

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.; Butto, 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

99

Saccharomyces cerevisiae Env7 Is a Novel Serine/Threonine Kinase 16-Related Protein Kinase and Negatively Regulates Organelle Fusion at the Lysosomal Vacuole  

PubMed Central

Membrane fusion depends on conserved components and is responsible for organelle biogenesis and vesicular trafficking. Yeast vacuoles are dynamic structures analogous to mammalian lysosomes. We report here that yeast Env7 is a novel palmitoylated protein kinase ortholog that negatively regulates vacuolar membrane fusion. Microscopic and biochemical studies confirmed the localization of tagged Env7 at the vacuolar membrane and implicated membrane association via the palmitoylation of its N-terminal Cys13 to -15. In vitro kinase assays established Env7 as a protein kinase. Site-directed mutagenesis of the Env7 alanine-proline-glutamic acid (APE) motif Glu269 to alanine results in an unstable kinase-dead allele that is stabilized and redistributed to the detergent-resistant fraction by interruption of the proteasome system in vivo. Palmitoylation-deficient Env7C13-15S is also kinase dead and mislocalizes to the cytoplasm. Microscopy studies established that env7? is defective in maintaining fragmented vacuoles during hyperosmotic response and in buds. ENV7 function is not redundant with a similar role of vacuolar membrane kinase Yck3, as the two do not share a substrate, and ENV7 is not a suppressor of yck3?. Bayesian phylogenetic analyses strongly support ENV7 as an ortholog of the gene encoding human STK16, a Golgi apparatus protein kinase with undefined function. We propose that Env7 function in fusion/fission dynamics may be conserved within the endomembrane system. PMID:23166297

Manandhar, Surya P.; Ricarte, Florante; Cocca, Stephanie M.

2013-01-01

100

Long-Term Central and Effector SHIV-Specific Memory T Cell Responses Elicited after a Single Immunization with a Novel Lentivector DNA Vaccine  

PubMed Central

Prevention of HIV acquisition and replication requires long lasting and effective immunity. Given the state of HIV vaccine development, innovative vectors and immunization strategies are urgently needed to generate safe and efficacious HIV vaccines. Here, we developed a novel lentivirus-based DNA vector that does not integrate in the host genome and undergoes a single-cycle of replication. Viral proteins are constitutively expressed under the control of Tat-independent LTR promoter from goat lentivirus. We immunized six macaques once only with CAL-SHIV-IN? DNA using combined intramuscular and intradermal injections plus electroporation. Antigen-specific T cell responses were monitored for 47 weeks post-immunization (PI). PBMCs were assessed directly ex vivo or after 6 and 12 days of in vitro culture using antigenic and/or homeostatic proliferation. IFN-? ELISPOT was used to measure immediate cytokine secretion from antigen specific effector cells and from memory precursors with high proliferative capacity (PHPC). The memory phenotype and functions (proliferation, cytokine expression, lytic content) of specific T cells were tested using multiparametric FACS-based assays. All immunized macaques developed lasting peripheral CD8+ and CD4+ T cell responses mainly against Gag and Nef antigens. During the primary expansion phase, immediate effector cells as well as increasing numbers of proliferating cells with limited effector functions were detected which expressed markers of effector (EM) and central (CM) memory phenotypes. These responses contracted but then reemerged later in absence of antigen boost. Strong PHPC responses comprising vaccine-specific CM and EM T cells that readily expanded and acquired immediate effector functions were detected at 40/47 weeks PI. Altogether, our study demonstrated that a single immunization with a replication-limited DNA vaccine elicited persistent vaccine-specific CM and EM CD8+ and CD4+ T cells with immediate and readily inducible effector functions, in the absence of ongoing antigen expression. PMID:25337803

Arrode-Bruses, Geraldine; Moussa, Maha; Baccard-Longere, Monique; Villinger, Francois; Chebloune, Yahia

2014-01-01

101

Phylogenetic and Structural Diversity in the Feline Leukemia Virus Env Gene  

PubMed Central

Feline leukemia virus (FeLV) belongs to the genus Gammaretrovirus, and causes a variety of neoplastic and non-neoplastic diseases in cats. Alteration of viral env sequences is thought to be associated with disease specificity, but the way in which genetic diversity of FeLV contributes to the generation of such variants in nature is poorly understood. We isolated FeLV env genes from naturally infected cats in Japan and analyzed the evolutionary dynamics of these genes. Phylogenetic reconstructions separated our FeLV samples into three distinct genetic clusters, termed Genotypes I, II, and III. Genotype I is a major genetic cluster and can be further classified into Clades 1–7 in Japan. Genotypes were correlated with geographical distribution; Genotypes I and II were distributed within Japan, whilst FeLV samples from outside Japan belonged to Genotype III. These results may be due to geographical isolation of FeLVs in Japan. The observed structural diversity of the FeLV env gene appears to be caused primarily by mutation, deletion, insertion and recombination, and these variants may be generated de novo in individual cats. FeLV interference assay revealed that FeLV genotypes did not correlate with known FeLV receptor subgroups. We have identified the genotypes which we consider to be reliable for evaluating phylogenetic relationships of FeLV, which embrace the high structural diversity observed in our sample. Overall, these findings extend our understanding of Gammaretrovirus evolutionary patterns in the field, and may provide a useful basis for assessing the emergence of novel strains and understanding the molecular mechanisms of FeLV transmission in cats. PMID:23593376

Watanabe, Shinya; Kawamura, Maki; Odahara, Yuka; Anai, Yukari; Ochi, Haruyo; Nakagawa, So; Endo, Yasuyuki; Tsujimoto, Hajime; Nishigaki, Kazuo

2013-01-01

102

Complementation of diverse HIV-1 Env defects through cooperative subunit interactions: a general property of the functional trimer  

PubMed Central

Background The HIV-1 Env glycoprotein mediates virus entry by catalyzing direct fusion between the virion membrane and the target cell plasma membrane. Env is composed of two subunits: gp120, which binds to CD4 and the coreceptor, and gp41, which is triggered upon coreceptor binding to promote the membrane fusion reaction. Env on the surface of infected cells is a trimer consisting of three gp120/gp41 homo-dimeric protomers. An emerging question concerns cooperative interactions between the protomers in the trimer, and possible implications for Env function. Results We extended studies on cooperative subunit interactions within the HIV-1 Env trimer, using analysis of functional complementation between coexpressed inactive variants harboring different functional deficiencies. In assays of Env-mediated cell fusion, complementation was observed between variants with a wide range of defects in both the gp120 and gp41 subunits. The former included gp120 subunits mutated in the CD4 binding site or incapable of coreceptor interaction due either to mismatched specificity or V3 loop mutation. Defective gp41 variants included point mutations at different residues within the fusion peptide or heptad repeat regions, as well as constructs with modifications or deletions of the membrane proximal tryptophan-rich region or the transmembrane domain. Complementation required the defective variants to be coexpressed in the same cell. The observed complementation activities were highly dependent on the assay system. The most robust activities were obtained with a vaccinia virus-based expression and reporter gene activation assay for cell fusion. In an alternative system involving Env expression from integrated provirus, complementation was detected in cell fusion assays, but not in virus particle entry assays. Conclusion Our results indicate that Env function does not require every subunit in the trimer to be competent for all essential activities. Through cross-talk between subunits, the functional determinants on one defective protomer can cooperatively interact to trigger the functional determinants on an adjacent protomer(s) harboring a different defect, leading to fusion. Cooperative subunit interaction is a general feature of the Env trimer, based on complementation activities observed for a highly diverse range of functional defects. PMID:19671162

Salzwedel, Karl; Berger, Edward A

2009-01-01

103

Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation.  

PubMed

The development of the emerging field of 'paleovirology' allows biologists to reconstruct the evolutionary history of fossil endogenous retroviral sequences integrated within the genome of living organisms and has led to the retrieval of conserved, ancient retroviral genes 'exapted' by ancestral hosts to fulfil essential physiological roles, syncytin genes being undoubtedly among the most remarkable examples of such a phenomenon. Indeed, syncytins are 'new' genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell-cell fusion of syncytial cell layers at the fetal-maternal interface. These genes of exogenous origin, acquired 'by chance' and yet still 'necessary' to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene, subsequently replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage. PMID:23938756

Lavialle, Christian; Cornelis, Guillaume; Dupressoir, Anne; Esnault, Cécile; Heidmann, Odile; Vernochet, Cécile; Heidmann, Thierry

2013-09-19

104

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

PubMed Central

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

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

2012-01-01

105

Quantitative RT-PCR detection of hepatitis A virus, rotaviruses and enteroviruses in the Buffalo River and source water dams in the Eastern Cape Province of South Africa.  

PubMed

Human enteric viruses (HEntVs) are a major cause of water-related diseases. The prevalence of hepatitis A virus (HAV), rotaviruses (RoV) and enteroviruses (EnV) in Buffalo River waters was assessed quantitatively over a period of 12 months (August 2010 to July 2011). Seventy-two samples were collected from six sites, including three dams, and concentrated using the adsorption-elution method. Viral RNA was extracted using a commercial kit, and the viruses were quantified by real-time quantitative reverse transcriptase PCR (RT-qPCR). Two or more viruses were detected in 12.5% of the samples. HAV was detected in 43.1% of the samples and in significantly (p < 0.05) varying concentrations of 1.5 × 10(1)–1.9 × 10(5) genome copies/L compared to RoV and EnV, while RoVs were detected in 13.9% of samples, with concentrations ranging from 2.5 × 10(1)–2.1 × 10(3) genome copies/L, and EnV were detected in 9.7% of the samples, with concentrations ranging from 1.3 × 10(1)–8.6 × 10(1) genome copies/L. Only HAV was detected at all the sites, with the Bridle Drift Dam recording significantly higher (p < 0.05) concentrations. The presence of enteric viruses in Buffalo River may constitute public health risks and the incidence of HAV at all the sites could reflect both the epidemiological status of hepatitis A and HAV persistence in the water environments. PMID:23202829

Chigor, Vincent Nnamdigadi; Okoh, Anthony Ifeanyi

2012-11-01

106

Quantitative RT-PCR Detection of Hepatitis A Virus, Rotaviruses and Enteroviruses in the Buffalo River and Source Water Dams in the Eastern Cape Province of South Africa  

PubMed Central

Human enteric viruses (HEntVs) are a major cause of water-related diseases. The prevalence of hepatitis A virus (HAV), rotaviruses (RoV) and enteroviruses (EnV) in Buffalo River waters was assessed quantitatively over a period of 12 months (August 2010 to July 2011). Seventy-two samples were collected from six sites, including three dams, and concentrated using the adsorption-elution method. Viral RNA was extracted using a commercial kit, and the viruses were quantified by real-time quantitative reverse transcriptase PCR (RT-qPCR). Two or more viruses were detected in 12.5% of the samples. HAV was detected in 43.1% of the samples and in significantly (p < 0.05) varying concentrations of 1.5 × 101–1.9 × 105 genome copies/L compared to RoV and EnV, while RoVs were detected in 13.9% of samples, with concentrations ranging from 2.5 × 101–2.1 × 103 genome copies/L, and EnV were detected in 9.7% of the samples, with concentrations ranging from 1.3 × 101–8.6 × 101 genome copies/L. Only HAV was detected at all the sites, with the Bridle Drift Dam recording significantly higher (p < 0.05) concentrations. The presence of enteric viruses in Buffalo River may constitute public health risks and the incidence of HAV at all the sites could reflect both the epidemiological status of hepatitis A and HAV persistence in the water environments. PMID:23202829

Chigor, Vincent Nnamdigadi; Okoh, Anthony Ifeanyi

2012-01-01

107

Dense display of HIV-1 envelope spikes on the lambda phage scaffold does not result in the generation of improved antibody responses to HIV-1 Env  

PubMed Central

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 envelope oligomers. We compared the immune response to lambda phage particles displaying HIV-1 Env to that elicited by soluble oligomeric gp140 in rabbits. Env-binding antibody titers were higher in animals that received oligomeric gp140 as compared to Env decorated phage particles, as were virus neutralizing antibody responses. The Env decorated phage particles were, however, able to efficiently boost a protein-primed humoral response to levels equivalent to those elicited by high-dose adjuvanted Env oligomers. These results show that display of HIV-1 envelope spikes on the bacteriophage lambda capsid does not result in an improved, Env-specific humoral immune response. PMID:21310193

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

2011-01-01

108

Floor System Vibration Control E.M. Hines, Ph.D., P.E., Res. Asst. Professor, Tufts University, Dept. Civ. & Env. Eng.;  

E-print Network

Floor System Vibration Control E.M. Hines, Ph.D., P.E., Res. Asst. Professor, Tufts UniversityMessurier Consultants C.D. Blanchet, P.E., Associate, LeMessurier Consultants M. Sanayei, Ph.D., Professor, Tufts University, Dept. Civ. & Env. Eng. M.D. Dodge, Graduate Res. Asst., Tufts University, Dept. Civ. & Env. Eng

Hines, Eric

109

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

PubMed Central

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

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

1987-01-01

110

ENV/ERS 467/667: Regional and Global Issues in Environmental and Natural Resource Sciences Spring 2004  

E-print Network

ENV/ERS 467/667: Regional and Global Issues in Environmental and Natural Resource Sciences Spring Spring break 23 Mining in Nevada 25 Mining in Nevada Miller 30 Radioactive Waste: Shallow-land burial in order to address environmental and natural resource problems and issues. The course will use specific

Nowak, Robert S.

111

From sensors to semantic web: the SemsorGrid4env project  

NASA Astrophysics Data System (ADS)

Sensor networks are producing large quantities of valuable data around the planet. However advances are needed in the information management of such systems in order to make it easier to find and obtain the data. This is particularly true of software systems or models which need to automatically find appropriate data sources. The SemsorGrid4Env project is a three year European project to develop an integrated information space where new sensor network data sources can be discovered using web technologies and semantic descriptions. Rapid development of decision support systems are being developed within the context of ocean monitoring for flood and fire warnings. These are based around large quantities of sensors around the southern coast of the UK as well as a new sensor network deployment in forests in Spain. This paper will describe the design of the system, data integration issues, mashups and semantic interfaces.

Martinez, K.; Deroure, D.; Page, K.; Sadler, J.; Hutton, C.; Newman, R.; Roe, S.

2009-12-01

112

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

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.

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

113

Mutation of the Dominant Endocytosis Motif in Human Immunodeficiency Virus Type 1 gp41 Can Complement Matrix Mutations without Increasing Env Incorporation  

PubMed Central

The human immunodeficiency virus type 1 transmembrane glycoprotein (TM) is efficiently endocytosed in a clathrin-dependent manner. Internalization is mediated by a tyrosine-containing motif within the cytoplasmic domain, and replacement of the cytoplasmic tyrosine by cysteine or phenylalanine increased expression of mutant glycoprotein on the surface of transfected cells by as much as 2.5-fold. Because interactions between the cytoplasmic domain of Env and the matrix protein (MA) have been suggested to mediate incorporation of Env in virus particles, we examined whether perturbation of endocytosis would alter incorporation. Proviruses were constructed to contain the wild-type or mutant Env in conjunction with point mutations in MA that had previously been shown to block Env incorporation. These constructs were used to evaluate the effect of glycoprotein endocytosis on incorporation into virus particles and to test the necessity for a specific interaction between Env and MA to mediate incorporation. Viruses produced from transfected 293T cells were used to infect various cell lines, including MAGI, H9, and CEMx174. Viruses encoding both a disrupted endocytosis motif signal and mutations within MA were significantly more infectious in MAGI cells than their counterparts encoding a mutant MA and wild-type Env. This complementation of infectivity for the MA incorporation mutant viruses was not due to increased glycoprotein incorporation into particles but instead reflected an enhanced fusogenicity of the mutated Env proteins. Our findings further support the concept that a specific interaction between the long cytoplasmic domain of TM and MA is required for efficient incorporation of Env into assembling virions. Alteration of the endocytosis signal of Env, and the resulting increase in cell surface glycoprotein, has no effect on incorporation despite demonstrable effects on fusion, virus entry, and infectivity. PMID:11884559

West, John T.; Weldon, Sally K.; Wyss, Stephanie; Lin, Xiaoxu; Yu, Qin; Thali, Markus; Hunter, Eric

2002-01-01

114

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

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

2011-01-01

115

Genetic and functional analysis of full-length human immunodeficiency virus type 1 env genes derived from brain and blood of patients with AIDS.  

PubMed

The genetic evolution of human immunodeficiency virus type 1 (HIV-1) in the brain is distinct from that in lymphoid tissues, indicating tissue-specific compartmentalization of the virus. Few primary HIV-1 envelope glycoproteins (Envs) from uncultured brain tissues have been biologically well characterized. In this study, we analyzed 37 full-length env genes from uncultured brain biopsy and blood samples from four patients with AIDS. Phylogenetic analysis of intrapatient sequence sets showed distinct clustering of brain relative to blood env sequences. However, no brain-specific signature sequence was identified. Furthermore, there was no significant difference in the number or positions of N-linked glycosylation sites between brain and blood env sequences. The patterns of coreceptor usage were heterogeneous, with no clear distinction between brain and blood env clones. Nine Envs used CCR5 as a coreceptor, one used CXCR4, and two used both CCR5 and CXCR4 in cell-to-cell fusion assays. Eight Envs could also use CCR3, CCR8, GPR15, STRL33, Apj, and/or GPR1, but these coreceptors did not play a major role in virus entry into microglia. Recognition of epitopes by the 2F5, T30, AG10H9, F105, 17b, and C11 monoclonal antibodies varied among env clones, reflecting genetic and conformational heterogeneity. Envs from two patients contained 28 to 32 N-glycosylation sites in gp120, compared to around 25 in lab strains and well-characterized primary isolates. These results suggest that HIV-1 Envs in brain cannot be distinguished from those in blood on the basis of coreceptor usage or the number or positions of N-glycosylation sites, indicating that other properties underlie neurotropism. The study also demonstrates characteristics of primary HIV-1 Envs from uncultured tissues and implies that Env variants that are glycosylated more extensively than lab strains and well-characterized primary isolates should be considered during development of vaccines and neutralizing antibodies. PMID:14581570

Ohagen, Asa; Devitt, Amy; Kunstman, Kevin J; Gorry, Paul R; Rose, Patrick P; Korber, Bette; Taylor, Joann; Levy, Robert; Murphy, Robert L; Wolinsky, Steven M; Gabuzda, Dana

2003-11-01

116

6, 1270112728, 2006 3-D polarised RT and  

E-print Network

radar data and a stochastic method for generating 3-D ice water content fields. Although the main infrared methods are 12702 #12;ACPD 6, 12701­12728, 2006 3-D polarised RT and mm/sub-mm cirrus observationsACPD 6, 12701­12728, 2006 3-D polarised RT and mm/sub-mm cirrus observations C. P. Davis et al

Boyer, Edmond

117

A rev1-vpu polymorphism unique to HIV-1 subtype A and C strains impairs envelope glycoprotein expression from rev-vpu-env cassettes and reduces virion infectivity in pseudotyping assays  

SciTech Connect

Functional studies of HIV-1 envelope glycoproteins (Envs) commonly include the generation of pseudoviruses, which are produced by co-transfection of rev-vpu-env cassettes with an env-deficient provirus. Here, we describe six Env constructs from transmitted/founder HIV-1 that were defective in the pseudotyping assay, although two produced infectious virions when expressed from their cognate proviruses. All of these constructs exhibited an unusual gene arrangement in which the first exon of rev (rev1) and vpu were in the same reading frame without an intervening stop codon. Disruption of the rev1-vpu fusion gene by frameshift mutation, stop codon, or abrogation of the rev initiation codon restored pseudovirion infectivity. Introduction of the fusion gene into wildtype Env cassettes severely compromised their function. The defect was not due to altered env and rev transcription or a dominant negative effect of the expressed fusion protein, but seemed to be caused by inefficient translation at the env initiation codon. Although the rev1-vpu polymorphism affects Env expression only in vitro, it can cause problems in studies requiring Env complementation, such as analyses of co-receptor usage and neutralization properties, since 3% of subtype A, 20% of subtype C and 5% of CRF01{sub A}/E viruses encode the fusion gene. A solution is to eliminate the rev initiation codon when amplifying rev-vpu-env cassettes since this increases Env expression irrespective of the presence of the polymorphism.

Kraus, Matthias H.; Parrish, Nicholas F.; Shaw, Katharina S.; Decker, Julie M.; Keele, Brandon F.; Salazar-Gonzalez, Jesus F.; Grayson, Truman; McPherson, David T. [Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 (United States); Ping, Li-Hua; Anderson, Jeffrey A.; Swanstrom, Ronald [University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 (United States); Williamson, Carolyn [Institute of Infectious Disease and Molecular Medicine, University of Cape Town (South Africa); Shaw, George M. [Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 (United States); Hahn, Beatrice H., E-mail: bhahn@uab.ed [Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 (United States); Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294 (United States)

2010-02-20

118

Global Panel of HIV-1 Env Reference Strains for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies  

PubMed Central

ABSTRACT Standardized assessments of HIV-1 vaccine-elicited neutralizing antibody responses are complicated by the genetic and antigenic variability of the viral envelope glycoproteins (Envs). To address these issues, suitable reference strains are needed that are representative of the global epidemic. Several panels have been recommended previously, but no clear answers have been available on how many and which strains are best suited for this purpose. We used a statistical model selection method to identify a global panel of reference Env clones from among 219 Env-pseudotyped viruses assayed in TZM-bl cells with sera from 205 HIV-1-infected individuals. The Envs and sera were sampled globally from diverse geographic locations and represented all major genetic subtypes and circulating recombinant forms of the virus. Assays with a panel size of only nine viruses adequately represented the spectrum of HIV-1 serum neutralizing activity seen with the larger panel of 219 viruses. An optimal panel of nine viruses was selected and augmented with three additional viruses for greater genetic and antigenic coverage. The spectrum of HIV-1 serum neutralizing activity seen with the final 12-virus panel closely approximated the activity seen with subtype-matched viruses. Moreover, the final panel was highly sensitive for detection of many of the known broadly neutralizing antibodies. For broader assay applications, all 12 Env clones were converted to infectious molecular clones using a proviral backbone carrying a Renilla luciferase reporter gene (Env.IMC.LucR viruses). This global panel should facilitate highly standardized assessments of vaccine-elicited neutralizing antibodies across multiple HIV-1 vaccine platforms in different parts of the world. IMPORTANCE An effective HIV-1 vaccine will need to overcome the extraordinary genetic variability of the virus, where most variation occurs in the viral envelope glycoproteins that are the sole targets for neutralizing antibodies. Efforts to elicit broadly cross-reactive neutralizing antibodies that will protect against infection by most circulating strains of the virus are guided in part by in vitro assays that determine the ability of vaccine-elicited antibodies to neutralize genetically diverse HIV-1 variants. Until now, little information was available on how many and which strains of the virus are best suited for this purpose. We applied robust statistical methods to evaluate a large neutralization data set and identified a small panel of viruses that are a good representation of the global epidemic. The neutralization properties of this new panel of reference strains should facilitate the development of an effective HIV-1 vaccine. PMID:24352443

deCamp, Allan; Hraber, Peter; Bailer, Robert T.; Seaman, Michael S.; Ochsenbauer, Christina; Kappes, John; Gottardo, Raphael; Edlefsen, Paul; Self, Steve; Tang, Haili; Greene, Kelli; Gao, Hongmei; Daniell, Xiaoju; Sarzotti-Kelsoe, Marcella; Gorny, Miroslaw K.; Zolla-Pazner, Susan; LaBranche, Celia C.; Mascola, John R.; Korber, Bette T.

2014-01-01

119

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

NASA Astrophysics Data System (ADS)

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.

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

2013-04-01

120

55 2014-15 Suggested Course Plan envIRonmenTaltrack: biOtecHnOlOgy  

E-print Network

and Thermodynamics phYS 152l: Electricity and Magnetism ChemIsTRY (16 unITs) ChEm 105Al: General Chemistry ChEm 105Bl GEN ED. IV GEN ED. V GEN ED. VI engIneeRIng (53-54 unITs) CE 106: Design & Planning CE Systems or CE: Intro. to Env. Engr. Microbiology CE 309: Fluid Mechanics CE 408: Risk Analysis in Civil Engr. CE 451

Zhou, Chongwu

121

Preparation of a murine cell line which stably expresses human T lymphotropic virus type I (HTLV-I) env genome products  

Microsoft Academic Search

We prepared the murine myeloma cell line NS-1, which stably expressed the human T lymphotropic virus type I (HTLV-I) env gene. The plasmid BCMGEnv was constructed from the episomal vector BCMGSNeo, which was primarily derived from bovine papilloma virus. Transfected env expression was detected by Northern blotting, as well as by flow cytometry using envelope protein-specific monoclonal antibodies (mAb). Expression

Tatsuroh Joh; Masatoshi Fujita; Yuetsu Tanaka; Hiroshi Shiku

1995-01-01

122

Simian immunodeficiency virus SIVmac chimeric virus whose env gene was derived from SIV-encephalitic brain is macrophage-tropic but not neurovirulent.  

PubMed Central

We inoculated four rhesus macaques with molecularly cloned simian immunodeficiency virus SIVmac239/17E env, a chimeric virus whose env gene was derived from the brain of an SIV-encephalitic macaque. Blood and lymphoid tissues had high frequencies of infected cells. The virus was neuroinvasive, but productive virus replication did not occur in the brain, and animals did not develop encephalitis. PMID:7815523

Joag, S V; Stephens, E B; Galbreath, D; Zhu, G W; Li, Z; Foresman, L; Zhao, L J; Pinson, D M; Narayan, O

1995-01-01

123

Human Immunodeficiency Virus Type 1 Env with an Intersubunit Disulfide Bond Engages Coreceptors but Requires Bond Reduction after Engagement To Induce Fusion  

Microsoft Academic Search

A mutant human immunodeficiency virus (HIV) envelope protein (Env) with an engineered disulfide bond between the gp120 and gp41 subunits (SOS-Env) was expressed on cell surfaces. With the disulfide bond intact, these cells did not fuse to target cells expressing CD4 and CCR5, but the fusion process did advance to an intermediate state: cleaving the disulfide bond with a reducing

L. G. Abrahamyan; R. M. Markosyan; J. P. Moore; F. S. Cohen; G. B. Melikyan

2003-01-01

124

Genetic and Functional Analysis of Full-Length Human Immunodeficiency Virus Type 1 env Genes Derived from Brain and Blood of Patients with AIDS  

Microsoft Academic Search

The genetic evolution of human immunodeficiency virus type 1 (HIV-1) in the brain is distinct from that in lymphoid tissues, indicating tissue-specific compartmentalization of the virus. Few primary HIV-1 envelope glycoproteins (Envs) from uncultured brain tissues have been biologically well characterized. In this study, we analyzed 37 full-length env genes from uncultured brain biopsy and blood samples from four patients

Asa Ohagen; Amy Devitt; Kevin J. Kunstman; Paul R. Gorry; Patrick P. Rose; Bette Korber; Joann Taylor; Robert Levy; Robert L. Murphy; Steven M. Wolinsky; Dana Gabuzda

2003-01-01

125

Comparing the flammability of fabrics in accordance with EN 531 and ENV 50354.  

PubMed

The purpose of protective clothing and other personal protective equipment (PPE) is to provide escape time, to reduce the burn injury level, and to prevent aggravation of the consequences to workers during exposure to an electric arc. In this study the flammability properties of 12 different types of flame-retardant fabrics were compared with the normally used flame spread test method (EN 532:1994) and electric arc test method (ENV 50354:2001). In the arc test at the lower testing current level of 4 kA, the requirement was passed by materials which did not pass the flame spread test. These materials contained a large amount of melting fibres, and therefore tended to shrink or melt. In order to meet the current level of 7 kA, a rather thick and heavy flame-retardant fabric is needed to pass the requirement. Lighter fabrics tended to break open in the tests. The flame retardancy of the under layer fabric is therefore important to ensure the needed protection. PMID:15377405

Mäkinen, Helena; Mustonen, Suvi Sanna

2004-01-01

126

Serological detection of infection with diverse human and simian immunodeficiency viruses using consensus env peptides.  

PubMed

Cross-species transmission has been shown to play an important role in the emergence of human retroviruses. We developed a generic enzyme immunoassay using synthetic peptides from gp41 and C2V3 consensus sequences (human immunodeficiency virus [HIV] type 1 [HIV-1] groups M, O, and N and the homologous region of simian immunodeficiency virus [SIV] strains from chimpanzees [SIVcpz], SIVcpzGAB1 and SIVcpzANT) to detect divergent HIV and SIV. A cocktail of peptides from gp41 and C2V3 (M-O) detected all HIV-1 group M and O sera and showed cross-reactivity with SIVcpz sera. Further, a mixture of C2V3 peptides (GAB1-ANT) failed to detect HIV-1 infections but reacted with all SIVcpz sera, allowing discrimination of SIVcpz from HIV-1 infections. Since most SIVcpz sera cross-reacted with HIV-1 peptides, we next evaluated SIVcpz serum reactivity with rapid tests for HIV-1/2. SIVcpzANT and SIVcpzUS sera reacted with the Sero-strip and Multispot assays. Both tests are sensitive in detecting group M (97 100%, respectively), although Multispot has lower sensitivity for group O detection (67%) than does Sero-strip (100%). The limited volume and time required to perform these assays make them a generic tool for field screening. The env peptide-based assay and rapid tests should allow for the identification of emerging variants of HIV and SIV. PMID:10882678

Masciotra, S; Rudolph, D L; van der Groen, G; Yang, C; Lal, R B

2000-07-01

127

Serological Detection of Infection with Diverse Human and Simian Immunodeficiency Viruses Using Consensus env Peptides  

PubMed Central

Cross-species transmission has been shown to play an important role in the emergence of human retroviruses. We developed a generic enzyme immunoassay using synthetic peptides from gp41 and C2V3 consensus sequences (human immunodeficiency virus [HIV] type 1 [HIV-1] groups M, O, and N and the homologous region of simian immunodeficiency virus [SIV] strains from chimpanzees [SIVcpz], SIVcpzGAB1 and SIVcpzANT) to detect divergent HIV and SIV. A cocktail of peptides from gp41 and C2V3 (M-O) detected all HIV-1 group M and O sera and showed cross-reactivity with SIVcpz sera. Further, a mixture of C2V3 peptides (GAB1-ANT) failed to detect HIV-1 infections but reacted with all SIVcpz sera, allowing discrimination of SIVcpz from HIV-1 infections. Since most SIVcpz sera cross-reacted with HIV-1 peptides, we next evaluated SIVcpz serum reactivity with rapid tests for HIV-1/2. SIVcpzANT and SIVcpzUS sera reacted with the Sero-strip and Multispot assays. Both tests are sensitive in detecting group M (97 100%, respectively), although Multispot has lower sensitivity for group O detection (67%) than does Sero-strip (100%). The limited volume and time required to perform these assays make them a generic tool for field screening. The env peptide-based assay and rapid tests should allow for the identification of emerging variants of HIV and SIV. PMID:10882678

Masciotra, Silvina; Rudolph, Donna L.; van der Groen, Guido; Yang, Chunfu; Lal, Renu B.

2000-01-01

128

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

NASA Technical Reports Server (NTRS)

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.

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

1991-01-01

129

Human immunodeficiency virus-like, nonreplicating, gag-env particles assemble in a recombinant vaccinia virus expression system.  

PubMed Central

We report the assembly of human immunodeficiency virus (HIV)-like particles in African green monkey kidney cells coinfected with two recombinant vaccinia viruses, one carrying the HIV-1 gag and protease genes and the other the env gene. Biochemical analysis of particles sedimented from culture supernatants of doubly infected cells revealed that they were composed of gag proteins, primarily p24, as well as the env proteins gp120 and gp41. Thin-section immunoelectron microscopy showed that these particles were 100 to 120 nm in diameter, were characterized by the presence of cylindrical core structures, and displayed the mature gp120-gp41 complexes on their surfaces. Furthermore, thin-section immunoelectron microscopy analysis of infected cells showed that particle assembly and budding occurred at the plasma membrane. Nucleic acid hybridization suggested that the particles packaged only the gag mRNA but not the env mRNA. Therefore, the system we present is well suited for studies of HIV virion maturation. In addition, the HIV-like particles provide a novel and attractive approach for vaccine development. Images PMID:2186175

Haffar, O; Garrigues, J; Travis, B; Moran, P; Zarling, J; Hu, S L

1990-01-01

130

A Novel Rabbit Monoclonal Antibody Platform To Dissect the Diverse Repertoire of Antibody Epitopes for HIV-1 Env Immunogen Design  

PubMed Central

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

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

2013-01-01

131

rtORB: a real-time CORBA prototype  

Microsoft Academic Search

A real-time CORBA prototype called rtORB is presented. The key components of rtORB are mainly described. A platform dependent layer is introduced to enhance the portability of ORB. The scheduling service proposed in real-time CORBA specification is extended to support dynamic scheduling. An explicit binding model is used to establish predictable communication channel. A delayered real-time POA (portable object adapter)

Peng Jian; Liu Jin-de; Tan Hao; Luo Zhi-gang

2003-01-01

132

Technetium Distribution throughout Purex Process Cycles at RT1 Plant  

Microsoft Academic Search

Data are presented on the Tc content in the major products of the RT-1 plant and also on its distribution throughout the process flowsheet for reprocessing spent fuel from VVER-440 (440-MW watercooled water-moderated power reactor). At RT-1 plant the process flowsheet allows more than 99% recovery of Tc in the joint extraction cycle and then about 98.5% removal of Tc

A. N. Mashkin; K. K. Korchenkin; N. A. Svetlakova

2002-01-01

133

Diagnosis of Oropouche virus infection by RT-nested-PCR.  

PubMed

Using the RT-PCR with primers that anneal to the 5' and the 3' extremities of the genome segments of bunyaviruses and internal primers that anneal to the S segment of Simbu serogroup viruses in a nested PCR it was possible to amplify the Oropouche virus (ORO) genome from the sera of three patients. These results show that this RT-nested-PCR is a useful tool for rapid diagnosis of Oropouche fever infections. PMID:11748670

Moreli, Marcos Lázaro; Aquino, Victor Hugo; Cruz, Ana Cecília R; Figueiredo, Luiz Tadeu M

2002-01-01

134

Measurement of RT amplitudes and wavelengths of laser driven plates  

SciTech Connect

A laser drive plate, that is a dense solid plate drive by a laser heated, lower density plasma, is inherently Raleigh-Taylor (R-T) unstable, We have previously indicated that observed surface perturbation on the plate are probably R-T instabilities, initiated by the mode structure of the driving laser beam. Using a semi- transparent impact target viewed with a polarized Epi-Illuminated Confocal Streak Microscope, has allowed us to measure the amplitude and growth of the instability.

Frank, A.M.; Gillespie, C.H.

1997-10-16

135

CD4+ T Cells Support Production of Simian Immunodeficiency Virus Env Antibodies That Enforce CD4-Dependent Entry and Shape Tropism In Vivo  

PubMed Central

CD4+ T cells rather than macrophages are the principal cells infected by human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) in vivo. Macrophage tropism has been linked to the ability to enter cells through CCR5 in conjunction with limiting CD4 levels, which are much lower on macrophages than on T cells. We recently reported that rhesus macaques (RM) experimentally depleted of CD4+ T cells before SIV infection exhibit extensive macrophage infection as well as high chronic viral loads and rapid progression to AIDS. Here we show that early-time-point and control Envs were strictly CD4 dependent but that, by day 42 postinfection, plasma virus of CD4+ T cell-depleted RM was dominated by Envs that mediate efficient infection using RM CCR5 independently of CD4. Early-time-point and control RM Envs were resistant to neutralization by SIV-positive (SIV+) plasma but became sensitive if preincubated with sCD4. In contrast, CD4-independent Envs were highly sensitive to SIV+ plasma neutralization. However, plasma from SIV-infected CD4+ T cell-depleted animals lacked this CD4-inducible neutralizing activity and failed to neutralize any Envs regardless of sCD4 pre-exposure status. Enhanced sensitivity of CD4-independent Envs from day 42 CD4+ T cell-depleted RM was also seen with monoclonal antibodies that target both known CD4-inducible and other Env epitopes. CD4 independence and neutralization sensitivity were both conferred by Env amino acid changes E84K and D470N that arose independently in multiple animals, with the latter introducing a potential N-linked glycosylation site within a predicted CD4-binding pocket of gp120. Thus, the absence of CD4 T cells results in failure to produce antibodies that neutralize CD4-independent Envs and CD4-pretriggered control Envs. In the absence of this constraint and with a relative paucity of CD4+ target cells, widespread macrophage infection occurs in vivo accompanied by emergence of variants carrying structural changes that enable entry independently of CD4. PMID:23824793

Francella, Nicholas; Gwyn, Sarah E.; Yi, Yanjie; Li, Bing; Xiao, Peng; Elliott, Sarah T. C.; Ortiz, Alexandra M.; Hoxie, James A.; Paiardini, Mirko; Silvestri, Guido; Derdeyn, Cynthia A.

2013-01-01

136

An Automated HIV-1 Env-Pseudotyped Virus Production for Global HIV Vaccine Trials  

PubMed Central

Background Infections with HIV still represent a major human health problem worldwide and a vaccine is the only long-term option to fight efficiently against this virus. Standardized assessments of HIV-specific immune responses in vaccine trials are essential for prioritizing vaccine candidates in preclinical and clinical stages of development. With respect to neutralizing antibodies, assays with HIV-1 Env-pseudotyped viruses are a high priority. To cover the increasing demands of HIV pseudoviruses, a complete cell culture and transfection automation system has been developed. Methodology/Principal Findings The automation system for HIV pseudovirus production comprises a modified Tecan-based Cellerity system. It covers an area of 5×3 meters and includes a robot platform, a cell counting machine, a CO2 incubator for cell cultivation and a media refrigerator. The processes for cell handling, transfection and pseudovirus production have been implemented according to manual standard operating procedures and are controlled and scheduled autonomously by the system. The system is housed in a biosafety level II cabinet that guarantees protection of personnel, environment and the product. HIV pseudovirus stocks in a scale from 140 ml to 1000 ml have been produced on the automated system. Parallel manual production of HIV pseudoviruses and comparisons (bridging assays) confirmed that the automated produced pseudoviruses were of equivalent quality as those produced manually. In addition, the automated method was fully validated according to Good Clinical Laboratory Practice (GCLP) guidelines, including the validation parameters accuracy, precision, robustness and specificity. Conclusions An automated HIV pseudovirus production system has been successfully established. It allows the high quality production of HIV pseudoviruses under GCLP conditions. In its present form, the installed module enables the production of 1000 ml of virus-containing cell culture supernatant per week. Thus, this novel automation facilitates standardized large-scale productions of HIV pseudoviruses for ongoing and upcoming HIV vaccine trials. PMID:23300558

Fuss, Martina; Mazzotta, Angela S.; Sarzotti-Kelsoe, Marcella; Ozaki, Daniel A.; Montefiori, David C.; von Briesen, Hagen; Zimmermann, Heiko; Meyerhans, Andreas

2012-01-01

137

Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies ?  

PubMed Central

The restricted neutralization breadth of vaccine-elicited antibodies is a major limitation of current human immunodeficiency virus-1 (HIV-1) candidate vaccines. In order to permit the efficient identification of vaccines with enhanced capacity for eliciting cross-reactive neutralizing antibodies (NAbs) and to assess the overall breadth and potency of vaccine-elicited NAb reactivity, we assembled a panel of 109 molecularly cloned HIV-1 Env pseudoviruses representing a broad range of genetic and geographic diversity. Viral isolates from all major circulating genetic subtypes were included, as were viruses derived shortly after transmission and during the early and chronic stages of infection. We assembled a panel of genetically diverse HIV-1-positive (HIV-1+) plasma pools to assess the neutralization sensitivities of the entire virus panel. When the viruses were rank ordered according to the average sensitivity to neutralization by the HIV-1+ plasmas, a continuum of average sensitivity was observed. Clustering analysis of the patterns of sensitivity defined four subgroups of viruses: those having very high (tier 1A), above-average (tier 1B), moderate (tier 2), or low (tier 3) sensitivity to antibody-mediated neutralization. We also investigated potential associations between characteristics of the viral isolates (clade, stage of infection, and source of virus) and sensitivity to NAb. In particular, higher levels of NAb activity were observed when the virus and plasma pool were matched in clade. These data provide the first systematic assessment of the overall neutralization sensitivities of a genetically and geographically diverse panel of circulating HIV-1 strains. These reference viruses can facilitate the systematic characterization of NAb responses elicited by candidate vaccine immunogens. PMID:19939925

Seaman, Michael S.; Janes, Holly; Hawkins, Natalie; Grandpre, Lauren E.; Devoy, Colleen; Giri, Ayush; Coffey, Rory T.; Harris, Linda; Wood, Blake; Daniels, Marcus G.; Bhattacharya, Tanmoy; Lapedes, Alan; Polonis, Victoria R.; McCutchan, Francine E.; Gilbert, Peter B.; Self, Steve G.; Korber, Bette T.; Montefiori, David C.; Mascola, John R.

2010-01-01

138

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 Central

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) 89.6Pcy243. In the controls, the challenge dose (10 to 20 50% monkey infectious doses [MID50]) 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 MID50 (P < 0.0001), and contained acute CD4 loss at 15 MID50 (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

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

2010-01-01

139

Enhanced cell surface expression, immunogenicity and genetic stability resulting from a spontaneous truncation of HIV Env expressed by a recombinant MVA  

SciTech Connect

During propagation of modified vaccinia virus Ankara (MVA) encoding HIV 89.6 Env, a few viral foci stained very prominently. Virus cloned from such foci replicated to higher titers than the parent and displayed enhanced genetic stability on passage. Sequence analysis showed a single nucleotide deletion in the 89.6 env gene of the mutant that caused a frame shift and truncation of 115 amino acids from the cytoplasmic domain. The truncated Env was more highly expressed on the cell surface, induced higher antibody responses than the full-length Env, reacted with HIV neutralizing monoclonal antibodies and mediated CD4/co-receptor-dependent fusion. Intramuscular (IM), intradermal (ID) needleless, and intrarectal (IR) catheter inoculations gave comparable serum IgG responses. However, intraoral (IO) needleless injector route gave the highest IgA in lung washings and IR gave the highest IgA and IgG responses in fecal extracts. Induction of CTL responses in the spleens of individual mice as assayed by intracellular cytokine staining was similar with both the full-length and truncated Env constructs. Induction of acute and memory CTL in the spleens of mice immunized with the truncated Env construct by ID, IO, and IR routes was comparable and higher than by the IM route, but only the IR route induced CTL in the gut-associated lymphoid tissue. Thus, truncation of Env enhanced genetic stability as well as serum and mucosal antibody responses, suggesting the desirability of a similar modification in MVA-based candidate HIV vaccines.

Wyatt, Linda S. [Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 (United States)], E-mail: lwyatt@niaid.nih.gov; Belyakov, Igor M. [Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 (United States); Earl, Patricia L. [Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 (United States); Berzofsky, Jay A. [Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 (United States); Moss, Bernard [Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 (United States)

2008-03-15

140

Monitoring of the Symbiotic Variable RT Cru Requested  

NASA Astrophysics Data System (ADS)

The symbiotic variable RT Cru brightened in hard x-rays. Dr. Jeno Sokoloski, Columbia University, requested AAVSO assistance in monitoring RT Cru both now and in the future to see if it is doing anything unusual in the optical. The Swift/BAT hard X-ray light curve shows RT Cru has apparently been gradually brightening over the past few years. Dr. Sokoloski writes: "The hard X-ray emission from RT Cru suggests that the accreting white dwarf is close to the Chandrasekhar limit (e.g., Luna and Sokoloski 2007, "The Nature of the Hard X-Ray-Emitting Symbiotic Star RT Cru") and that it is therefore a candidate supernova Type-Ia progenitor. Also, since it is a massive white dwarf accreting at a reasonably high rate, it is similar to T CrB - so why isn't it a recurrent nova?? Fast photometry (to look for CV-like flickering from the accretion disk) and optical spectroscopy would also be very interesting and could potentially help interpret the current hard X-ray brightening." Dr. Sokoloski requests time series photometry now for a few days, and then weekly or monthly observations for the forseeable future. Visual observations are also welcome. Finder charts with sequence may be created using the AAVSO Variable Star Plotter (http://www.aavso.org/vsp). Observations should be submitted to the AAVSO International Database. See full Alert Notice for more details and magnitudes.

Waagen, Elizabeth O.

2012-01-01

141

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

PubMed Central

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

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

2014-01-01

142

A limited number of simian immunodeficiency virus (SIV) env variants are transmitted to rhesus macaques vaginally inoculated with SIVmac251.  

PubMed

Single-genome amplification (SGA) and sequencing of HIV-1 RNA in plasma of acutely infected humans allows the identification and enumeration of transmitted/founder viruses responsible for productive systemic infection. Use of this strategy as a means for identifying transmitted viruses suggested that intrarectal simian immunodeficiency virus (SIV) inoculation of macaques recapitulates key features of human rectal infection. However, no studies have used the SGA strategy to identify vaginally transmitted virus(es) in macaques or to determine how early SIV diversification in vaginally infected animals compares with HIV-1 in humans. We used SGA to amplify 227 partial env sequences from a SIVmac251 challenge stock and from seven rhesus macaques at the earliest plasma viral RNA-positive time point after low- and high-dose intravaginal inoculation. Sequences were analyzed phylogenetically to determine the relationship of transmitted/founder viruses within and between each animal and the challenge stock. In each animal, discrete low-diversity env sequence lineages were evident, and these coalesced phylogenetically to identical or near-identical env sequences in the challenge stock, thus confirming the validity of the SGA sequencing and modeling strategy for identifying vaginally transmitted SIV. Between 1 and 10 viruses were responsible for systemic infection, similar to humans infected by sexual contact, and the set of viruses transmitted to the seven animals studied represented the full genetic constellation of the challenge stock. These findings recapitulate many of the features of sexual HIV-1 transmission in women. Furthermore, the SIV rhesus macaque model can be used to understand the factors that influence the transmission of single versus multiple SIV variants. PMID:20463069

Stone, Mars; Keele, Brandon F; Ma, Zhong-Min; Bailes, Elizabeth; Dutra, Joseph; Hahn, Beatrice H; Shaw, George M; Miller, Christopher J

2010-07-01

143

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

PubMed Central

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

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

2002-01-01

144

AWIPS II Application Development, a SPoRT Perspective  

NASA Technical Reports Server (NTRS)

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.

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

2014-01-01

145

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

E-print Network

) 1 1074 180 W BROOKS ST 2520 Sports Information/Coaches rm 2600 1 1075 180 W BROOKS ST 3635 Athletic Director/Development 1 1076 180 W BROOKS ST 2525 Athletic Business Office (ABO) / Media Relations 1 1077/13/2009 #12;ZIP+4 by Route ZIP+4 ADDRESS ROOM DEPARTMENT RT 1081 1005 ASP AVE 186 University College 1 1082

Oklahoma, University of

146

RtI and Comprehensive Assessment: Are They Opposed?  

ERIC Educational Resources Information Center

Response to Intervention (RtI) promotes a well-integrated system connecting general, compensatory, gifted, and special education in providing high quality, standards-based instruction and intervention that are matched to students' academic, social-emotional, and behavioral needs. There are three levels to this framework. Tier 1 (or Universal) is…

Franklin-Rohr, Cheryl

2011-01-01

147

Rt Hon David Cameron MP, The House of Commons,  

E-print Network

Rt Hon David Cameron MP, The House of Commons, Westminster, London SW1A 0AA. 30th November, 2007 Dear Mr Cameron, I'm writing, as your constituent, to bring to your attention an impending crisis sincerely, Dr Alan Barr Witney, Oxfordshire UNIVERSITY OF OXFORD DEPARTMENT OF PHYSICS Denys Wilkinson

Crowther, Paul

148

Pneumovirus N RT-qPCR Animal Health Diagnostic Center  

E-print Network

. Stability Pneumoviruses are extremely labile. An effort should be made to begin purification for testing No AnimalsTested References Renshaw, R.W., Zylich, N.C., Laverack, M.A., Glaser, A.L., Dubovi, E.J., 2010Pneumovirus N RT-qPCR Animal Health Diagnostic Center College of Veterinary Medicine, Cornell

Keinan, Alon

149

Revised 1/12 RT WICHITA STATE UNIVERSITY LIBRARY  

E-print Network

Revised 1/12 RT WICHITA STATE UNIVERSITY LIBRARY GTA LOAN REQUEST/POLICY PRESENT THIS FORM _______________________________________________________________________ ***************************************************************************************** Library GTA Policy This form must be signed by your Advisor and returned to the Circulation Department teaching assistants is designed to help GTA's retain library materials for their teaching assignments

150

AnnuAl RepoRt 2009 Web Science  

E-print Network

to both digital libraries and the deep Web, and also the access to all kinds of text-based, semiAnnuAl RepoRt 2009 Web Science ­ Investigating the Future of Information and Communication #12 a few hundred severs, the Web has devel- oped into a worldwide information and communica- tion

Balke, Wolf-Tilo

151

Parallel Picoliter RT-PCR Assays Using Microfluidics  

E-print Network

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

Quake, Stephen R.

152

Intercompartmental recombination of HIV-1 contributes to env intrahost diversity and modulates viral tropism and sensitivity to entry inhibitors.  

PubMed

HIV-1 circulates within an infected host as a genetically heterogeneous viral population. Viral intrahost diversity is shaped by substitutional evolution and recombination. Although many studies have speculated that recombination could have a significant impact on viral phenotype, this has never been definitively demonstrated. We report here phylogenetic and subsequent phenotypic analyses of envelope genes obtained from HIV-1 populations present in different anatomical compartments. Assessment of env compartmentalization from immunologically discrete tissues was assessed utilizing a single genome amplification approach, minimizing in vitro-generated artifacts. Genetic compartmentalization of variants was frequently observed. In addition, multiple incidences of intercompartment recombination, presumably facilitated by low-level migration of virus or infected cells between different anatomic sites and coinfection of susceptible cells by genetically divergent strains, were identified. These analyses demonstrate that intercompartment recombination is a fundamental evolutionary mechanism that helps to shape HIV-1 env intrahost diversity in natural infection. Analysis of the phenotypic consequences of these recombination events showed that genetic compartmentalization often correlates with phenotypic compartmentalization and that intercompartment recombination results in phenotype modulation. This represents definitive proof that recombination can generate novel combinations of phenotypic traits which differ subtly from those of parental strains, an important phenomenon that may have an impact on antiviral therapy and contribute to HIV-1 persistence in vivo. PMID:21471230

Brown, Richard J P; Peters, Paul J; Caron, Catherine; Gonzalez-Perez, Maria Paz; Stones, Leanne; Ankghuambom, Chiambah; Pondei, Kemebradikumo; McClure, C Patrick; Alemnji, George; Taylor, Stephen; Sharp, Paul M; Clapham, Paul R; Ball, Jonathan K

2011-06-01

153

In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.  

PubMed

Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-Å crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modelled 2'-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5' bond. Both an invariant guanosine and a Mg(2+) are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site. PMID:25410397

Ren, Aiming; Košuti?, Marija; Rajashankar, Kanagalaghatta R; Frener, Marina; Santner, Tobias; Westhof, Eric; Micura, Ronald; Patel, Dinshaw J

2014-01-01

154

Selective Up-regulation of Intact, but not Defective env RNAs of Endogenous Modified Polytropic Retrovirus by the Sgp3 Locus of Lupus-prone Mice1  

PubMed Central

Endogenous retroviruses are implicated in the pathogenesis of systemic lupus erythematosus (SLE). Since four different classes of endogenous retroviruses, i.e. ecotropic, xenotropic, polytropic (PT) or modified polytropic (mPT), are expressed in mice, we investigated the possibility that a particular class of endogenous retroviruses is associated with the development of murine SLE. We observed more than 15-fold increased expression of mPT env (envelope) RNA in livers of all four lupus-prone mice, as compared with those of nine non-autoimmune strains of mice. This was not the case for the three other classes of retroviruses. Furthermore, we found that in addition to intact mPT transcripts, many strains of mice expressed two defective mPT env transcripts which carry a deletion in the env sequence of the 3’ portion of the gp70 surface protein and the 5’ portion of the p15E transmembrane protein, respectively. Remarkably, in contrast to non-autoimmune strains of mice, all four lupus-prone mice expressed abundant levels of intact mPT env transcripts, but only low or non-detectable levels of the mutant env transcripts. The Sgp3 (serum gp70 production 3) locus derived from lupus-prone mice was responsible for the selective up-regulation of the intact mPT env RNA. Finally, we observed that single-stranded RNA-specific TLR7 played a critical role in the production of anti-gp70 autoantibodies. These data suggest that lupus-prone mice may possess a unique genetic mechanism responsible for the expression of mPT retroviruses, which could act as a triggering factor through activating TLR7 for the development of autoimmune responses in mice predisposed to SLE. PMID:19494335

Yoshinobu, Kumiko; Baudino, Lucie; Santiago-Raber, Marie-Laure; Morito, Naoki; Dunand-Sauthier, Isabelle; Morley, Bernard J.; Evans, Leonard H.; Izui, Shozo

2009-01-01

155

Subtype-specific conformational differences within the V3 region of subtype B and subtype C human immunodeficiency virus type 1 Env proteins.  

PubMed

The V3 region of the human immunodeficiency virus type 1 gp120 Env protein is a key domain in Env due to its role in interacting with the coreceptors CCR5 and CXCR4. We examined potential subtype-specific V3 region differences by comparing patterns of amino acid variability and probing for subtype-specific structures using 11 anti-V3 monoclonal antibodies (V3 MAbs). Differences between the subtypes in patterns of variability were most evident in the stem and turn regions of V3 (positions 9 to 24), with the two subtypes being very similar in the base region. The characteristics of the binding of V3 MAbs to Env proteins of the subtype B virus JR-FL and the subtype C virus BR025 suggested three patterns, as each group of MAbs recognized a specific conformation- or sequence-based epitope. Viruses pseudotyped with Env from JR-FL and BR025 were resistant to neutralization by the V3 MAbs, although the replacement of the Env V3 region of the SF162 virus with the JR-FL V3 created a pseudotyped virus that was hypersensitive to neutralization. A single mutation in V3 (H13R) made this chimeric Env selectively resistant to one group of V3 MAbs, consistent with the mAb binding properties. We hypothesize that there are intrinsic differences in V3 conformation between subtype B and subtype C that are localized to the stem and turn regions and that these differences have two important biological consequences: first, subtype B and subtype C V3 regions can have subtype-specific epitopes that will inherently limit antibody cross-reactivity, and second, V3 conformational differences may potentiate the frequent evolution of R5- into X4-tropic variants of subtype B but limit subtype C virus from using the same mechanism to evolve X4-tropic variants as efficiently. PMID:18003735

Patel, Milloni B; Hoffman, Noah G; Swanstrom, Ronald

2008-01-01

156

First-in-Human Evaluation of the Safety and Immunogenicity of a Recombinant Adenovirus Serotype 26 HIV-1 Env Vaccine (IPCAVD 001)  

PubMed Central

Background.?We report the first-in-human safety and immunogenicity assessment of a prototype Ad26 vector-based human immunodeficiency virus (HIV) vaccine in humans. Methods.?Sixty Ad26-seronegative, healthy, HIV-uninfected subjects were enrolled in a randomized, double-blinded, placebo-controlled, dose-escalation phase 1 study. Five groups of 12 subjects received 109–1011 vp of the Ad26-EnvA vaccine (N = 10/group) or placebo (N = 2/group) at weeks 0 and 24 or weeks 0, 4, and 24. Safety and immunogenicity were assessed. Results.?Self-limited reactogenicity was observed after the initial immunization at the highest (1011 vp) dose. No product-related SAEs were observed. All subjects who received the Ad26-EnvA vaccine developed Ad26 NAb titers, EnvA-specific enzyme-linked immunosorbent assays (ELISA) titers, and EnvA-specific enzyme-linked immunospot assays (ELISPOT) responses. These responses persisted at week 52. At week 28 in the 109, 1010, 1011 vp 3-dose and the 1010 and 5 × 1010 vp 2-dose groups, geometric mean EnvA ELISA titers were 6113, 12 470, 8545, 3470, and 9655 and mean EnvA ELISPOT responses were 397, 178, 736, 196, and 1311 SFC/106 peripheral blood mononuclear cells, respectively. Conclusion.?This Ad26 vectored vaccine was generally safe and immunogenic at all doses tested. Reactogenicity was minimal with doses of 5 × 1010 vp or less. Ad26 is a promising new vaccine vector for HIV-1. Clinical Trials Registration.?NCT00618605. PMID:23125444

Baden, Lindsey R.; Walsh, Stephen R.; Seaman, Michael S.; Tucker, Robert P.; Krause, Kathleen H.; Patel, Alka; Johnson, Jennifer A.; Kleinjan, Jane; Yanosick, Katherine E.; Perry, James; Zablowsky, Elise; Abbink, Peter; Peter, Lauren; Iampietro, M. Justin; Cheung, Ann; Pau, Maria G.; Weijtens, Mo; Goudsmit, Jaap; Swann, Edith; Wolff, Mark; Loblein, Hayley; Dolin, Raphael; Barouch, Dan H.

2013-01-01

157

Modeling and analysis of competitive RT-PCR.  

PubMed

The present studies demonstrate a theoretical and practical framework for the accurate quantitation of gene expression in RNA extracted from microscopic tissue samples. The approaches are developed around competitive RT-PCR techniques. Assay performance has been examined and validated at both the RT and PCR steps. Our analysis of RT transcription efficiency for a number of native and competitor combinations shows that this property can differ, even for very similar templates. However, this difference is consistent and, once identified and measured, can be removed as an obstacle to accuracy. Using mathematical modeling, we have examined the simulated co-amplification of native and competitor templates in PCR. Useful insights have emerged from such modeling which indicate that differences in initial amplification efficiency and the rate of decay of amplification efficiency during the reaction can rapidly lead to inaccuracy, even while the slope and linearity of log plots of the competitor input and reaction product ratios are close to ideal. Finally, we show here that competitive RT-PCR reactions do not have to remain in the log-linear phase of PCR in order to accomplish accurate and precise quantification. Using appropriate competitors sharing primer binding sites and high internal sequence similarity, identical amplification efficiencies are preserved throughout the reaction. Reaction products, including heteroduplexes formed between native and competitor templates as reactions progress to plateau, can be identified and quantified accurately using the new technique of denaturing HPLC (dHPLC). This analytical technique allows the accuracy of competitive RT-PCR to be preserved beyond the linear phase. The technique has high sensitivity and precision and target abundances as low as 100 copies could be reliably estimated. PMID:9592131

Hayward, A L; Oefner, P J; Sabatini, S; Kainer, D B; Hinojos, C A; Doris, P A

1998-06-01

158

Architecture of the HeaRT Hybrid Rule Engine  

Microsoft Academic Search

\\u000a In this paper a new rule engine called HeaRT (HeKatE Run Time) is proposed. It uses a custom rule representation called XTT2,\\u000a which is based on a formalized rule description and allows a formalized analysis of rule quality. The engine is integrated\\u000a with a complete design environment that provides visual rule design capabilities. The engine supports modularized rule bases\\u000a and

Grzegorz J. Nalepa

2010-01-01

159

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

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

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

160

CERTIFICATE OF FIELD VERIFICATION AND DIAGNOSTIC TESTING CF-4R-ENV-22 Quality Insulation Installation (QII) -Insulation Stage Checklist (Page 1 of 3)  

E-print Network

CERTIFICATE OF FIELD VERIFICATION AND DIAGNOSTIC TESTING CF-4R-ENV-22 Quality Insulation Installation (QII) - Insulation Stage Checklist (Page 1 of 3) Site Address: Enforcement Agency: Permit Number: ____________ 2008 Residential Compliance Forms May 2012 All structural framing areas shall be insulated in a manner

161

Yersinia pestis Requires the 2-Component Regulatory System OmpR-EnvZ to Resist Innate Immunity During the Early and Late Stages of Plague.  

PubMed

Plague is transmitted by fleas or contaminated aerosols. To successfully produce disease, the causal agent (Yersinia pestis) must rapidly sense and respond to rapid variations in its environment. Here, we investigated the role of 2-component regulatory systems (2CSs) in plague because the latter are known to be key players in bacterial adaptation to environmental change. Along with the previously studied PhoP-PhoQ system, OmpR-EnvZ was the only one of Y. pestis' 23 other 2CSs required for production of bubonic, septicemic, and pneumonic plague. In vitro, OmpR-EnvZ was needed to counter serum complement and leukocytes but was not required for the secretion of antiphagocyte exotoxins. In vivo, Y. pestis lacking OmpR-EnvZ did not induce an early immune response in the skin and was fully virulent in neutropenic mice. We conclude that, throughout the course of Y. pestis infection, OmpR-EnvZ is required to counter toxic effectors secreted by polymorphonuclear leukocytes in the tissues. PMID:24813471

Reboul, Angéline; Lemaître, Nadine; Titecat, Marie; Merchez, Maud; Deloison, Gaspard; Ricard, Isabelle; Pradel, Elizabeth; Marceau, Michaël; Sebbane, Florent

2014-11-01

162

ENVS 411: Imagining the Environment of Tomorrow What does the future have in store for Earth--for us? Have we reached  

E-print Network

ENVS 411: Imagining the Environment of Tomorrow What does the future have in store for Earth--for us? Have we reached the end of nature? Do we only have to keep Earth functional long enough to make vision of what the future holds. Environmentalist movements have often been mobilized against time. We

163

An M?-Containing Heterologous RNA, but Not env mRNA, Is Efficiently Packaged into Avian Retroviral Particles  

PubMed Central

Retroviruses preferentially package full-length genomic RNA over spliced viral messages. For most retroviruses, this preference is likely due to the absence of all or part of the packaging signal on subgenomic RNAs. In avian leukosis-sarcoma virus, however, we have shown that the minimal packaging signal, M?, is located upstream of the 5? splice site and therefore is present on both genomic and spliced RNAs. We now show that an M?-containing heterologous RNA is packaged only 2.6-fold less efficiently than genomic Rous sarcoma virus RNA. Thus, few additional packaging sequences and/or structures exist outside of M?. In contrast, we found that env mRNA is not efficiently packaged. These results indicate that either M? is not functional on this RNA or the RNA is somehow segregated from the packaging machinery. Finally, deletion of sequences from the 3? end of M? was found to reduce the packaging efficiency of heterologous RNAs. PMID:10515997

Banks, Jennifer D.; Kealoha, Bonnie O.; Linial, Maxine L.

1999-01-01

164

Instruments of RT2 experiment onboard CORONAS-PHOTON and their test and evaluation II: RT2\\/CZT payload  

Microsoft Academic Search

Cadmium Zinc Telluride (CZT) detectors are high sensitivity and high resolution devices for hard X-ray imaging and spectroscopic\\u000a studies. The new series of CZT detector modules (OMS40G256) manufactured by Orbotech Medical Solutions (OMS), Israel, are\\u000a used in the RT-2\\/CZT payload onboard the CORONAS-PHOTON satellite. The CZT detectors, sensitive in the energy range of 20\\u000a to 150 keV, are used to image

Tilak B. Kotoch; Anuj Nandi; D. Debnath; J. P. Malkar; A. R. Rao; M. K. Hingar; Vaibhav. P. Madhav; S. Sreekumar; Sandip K. Chakrabarti

2011-01-01

165

Detection and identification of Fabavirus species by one-step RT-PCR and multiplex RT-PCR.  

PubMed

The genus Fabavirus of the family Secoviridae comprises a group of poorly characterized viruses. To date, only five species have been described: Broad bean wilt virus 1 (BBWV-1), Broad bean wilt virus 2 (BBWV-2), Lamium mild mosaic virus (LMMV), Gentian mosaic virus (GeMV) and Cucurbit mild mosaic virus (CuMMV). The development is described of two RT-PCR procedures for the detection and identification of Fabavirus species: a one-step RT-PCR using a single pair of conserved primers for the detection of all fabaviruses, and a one-step multiplex RT-PCR using species-specific primers for the simultaneous detection and identification of the above-mentioned species of the genus Fabavirus. These methods were applied successfully to field samples and the results were compared with those obtained by molecular hybridization and ELISA. The combination of the two techniques enables rapid, sensitive and reliable identification of the five known fabavirus species, as well as the possibility of discovering new species of this genus. PMID:24361876

Panno, Stefano; Ferriol, Inmaculada; Rangel, Ezequiel A; Olmos, Antonio; Han, Cheng-Gui; Martinelli, Federico; Rubio, Luis; Davino, Salvatore

2014-03-01

166

A Functional Interaction between gp41 and gp120 Is Observed for Monomeric but Not Oligomeric, Uncleaved HIV-1 Env gp140  

PubMed Central

The envelope glycoprotein (Env) is the sole antigenic feature on the surface of HIV and the target for the humoral immune system. Soluble, uncleaved gp140 Env constructs truncated at the transmembrane domain are being investigated intensively as potential vaccine immunogens by many groups, and understanding their structural properties is essential. We used hydrogen/deuterium-exchange mass spectrometry and small-angle X-ray scattering to probe structural order in a panel of commonly used gp140 constructs and matched gp120 monomers. We observed that oligomeric forms of uncleaved gp140, generally presumed to be trimeric, contain a protease-resistant form of gp41 akin to the postfusion, helical bundle conformation and appear to lack specific interactions between gp120 and gp41. In contrast, the monomeric form of gp140 shows significant stabilization of the gp120 inner domain imparted by the gp41 region, demonstrating excellent agreement with past mutagenesis studies. Moreover, the gp140 monomers respond to CD4 binding in manner that is consistent with the initial stages of Env activation: CD4 binding induces structural ordering throughout gp120 while loosening its association with gp41. The results indicate that uncleaved gp140 oligomers do not represent an authentic prefusion form of Env, whereas gp140 monomers isolated from the same glycoprotein preparations in many ways exhibit function and internal structural order that are consistent with expectations for certain aspects of native Env. gp140 monomers may thus be a useful reagent for advancing structural and functional studies. PMID:23966389

Guttman, Miklos

2013-01-01

167

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

PubMed Central

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

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

2013-01-01

168

Hypofractionation in the era of modulated radiotherapy (RT).  

PubMed

The use of radiation therapy (RT) as a component of breast-conserving therapy (BCT) has been shown to reduce the risk of local-regional recurrence and improve overall survival. As has been the common practice in the United States and Continental Europe, the majority of studies that demonstrated these benefits utilized daily radiation doses ranging from 1.8 to 2.0 Gray (Gy) per day given for approximately 5 weeks. However, due to geographic limitations, patient preferences, and financial considerations, there have been continued attempts to evaluate the efficacy and safety of abbreviated or hypofractionated courses of whole-breast radiation. Two key factors in these attempts have been: 1) advances in radiobiology allowing for a more precise estimation of equivalent dosing, and 2) advances in the delivery of RT ('modulation') that have resulted in substantially improved dose homogeneity in the target volume. Hypofractionated schedules have been compared to conventional radiation courses in several randomized controlled trials, as well as many prospective and retrospective experiences. These studies, now with about 10 years of follow-up, have demonstrated equivalent rates of local-regional recurrence, disease-free survival, and overall survival. The rates of toxicity have generally not been increased with hypofractionated regimens; however, certain toxicities may take decades to manifest. The generalizability of these results is unclear, as the majority of patients in the trials were elderly with early-stage hormone-receptor positive disease. Nevertheless, there is now sufficient evidence to recommend hypofractionated whole breast RT for a substantial percentage of patients. PMID:24074773

Mouw, Kent W; Harris, Jay R

2013-08-01

169

Request for regular monitoring of the symbiotic variable RT Cru  

NASA Astrophysics Data System (ADS)

Dr. Margarita Karovska (Harvard-Smithsonian Center for Astrophysics) and colleagues have requested AAVSO observer assistance in their campaign on the symbiotic variable RT Cru (member of a new class of hard X-ray emitting symbiotic binaries). Weekly or more frequent monitoring (B, V, and visual) beginning now is requested in support of upcoming Chandra observations still to be scheduled. "We plan Chandra observations of RT Cru in the near future that will help us understand the characteristics of the accretion onto the white dwarf in this sub-class of symbiotics. This is an important step for determining the precursor conditions for formation of a fraction of asymmetric Planetary Nebulae, and the potential of symbiotic systems as progenitors of at least a fraction of Type Ia supernovae." Finder charts with sequence may be created using the AAVSO Variable Star Plotter (http://www.aavso.org/vsp). Observations should be submitted to the AAVSO International Database. See full Alert Notice for more details and observations.

Waagen, Elizabeth O.

2014-08-01

170

Hardware-In-the-Loop Simulation of Power Drives with RT-LAB  

Microsoft Academic Search

This paper presents the RT-LAB Electrical Drive Simulator technology along with practical applications. The RT-LAB simulation software enables the parallel simulation of power drives and electric circuits on clusters of PC running QNX or RT-Linux operating systems at sample time below 10 ?s. Using standard Simulink models including SimPowerSystems models, RT-LAB build computation and communication tasks necessary to make parallel

Christian Dufour; S. Abourida; J. Belanger

2005-01-01

171

Meeting the Needs of Gifted Students within an RtI Framework  

ERIC Educational Resources Information Center

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…

Coleman, Mary Ruth; Hughes, Claire E.

2009-01-01

172

Comparison of Relative RT-PCR and Northern Blot Analyses to Measure Expression of  

E-print Network

chain reaction (RT-PCR) is much more sensitive. Ob- taining quantitative RT-PCR results, however, can chain reaction. Relative RT-PCR with a plant-microbe interaction Dean et al.Introduction Gene expression. Although northern blot analysis is effective for quantifying gene expression, re- verse transcription­polymerase

Hsiang, Tom

173

Detection of equine rotavirus by reverse transcription loop-mediated isothermal amplification (RT-LAMP).  

PubMed

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) was applied to detection of equine rotavirus. Because equine rotavirus of the single P genotype, P[12], is predominant in the equine population worldwide, an RT-LAMP primer set was designed to target the genotype P[12] sequence and thus detect equine rotavirus. The detection limit of the RT-LAMP assay was 10(3) copies of viral RNA, whereas that of semi-nested RT-PCR for genotype P[12] was 10(5) copies. The RT-LAMP assay specifically amplified genotype P[12] but did not amplify the other P genotype strains. The RT-LAMP assay did not amplify any pathogens related to equine intestinal disorder other than rotavirus. Using 96 diarrheal stools, the RT-LAMP assay detected equine rotavirus in 58 samples, whereas semi-nested RT-PCR only detected equine rotavirus in 25 samples. The RT-LAMP assay did not detect equine rotavirus with fecal samples collected from nine healthy foals. These results indicate that the RT-LAMP assay is specific for equine rotavirus and more sensitive than semi-nested RT-PCR. Because it is easy to manipulate without the need for a thermal cycler or gel electrophoresis, the RT-LAMP assay should be applicable to diagnosis of equine rotavirus infections in diagnostic laboratories. PMID:20160420

Nemoto, Manabu; Imagawa, Hiroshi; Tsujimura, Koji; Yamanaka, Takashi; Kondo, Takashi; Matsumura, Tomio

2010-06-01

174

Low pH Is Required for Avian Sarcoma and Leukosis Virus Env-Dependent Viral Penetration into the Cytosol and Not for Viral Uncoating  

Microsoft Academic Search

A novel entry mechanism has been proposed for the avian sarcoma and leukosis virus (ASLV), whereby interaction with specific cell surface receptors activates or primes the viral envelope glycoprotein (Env), rendering it sensitive to subsequent low-pH-dependent fusion triggering in acidic intracellular organelles. However, ASLV fusion seems to proceed to a lipid mixing stage at neutral pH, leading to the suggestion

Richard J. O. Barnard; Shakti Narayan; Geethanjali Dornadula; Michael D. Miller; John A. T. Young

2004-01-01

175

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

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

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

2004-01-01

176

Biomass groups: 13 April 2012 H222c Ener&Env 1. Gillian kenagyg@u.washington.edu , kenagyg@u.washington.edu  

E-print Network

Biomass groups: 13 April 2012 H222c Ener&Env 1. Gillian kenagyg@u.washington.edu , kenagyg@u.washington.edu Tarra ttheisen@u.washington.edu Emily halvoe@u.washington.edu Alex adadgar@u.washington.edu Maddy mjyoung@u.washington.edu 2. Leslie lhedwards2@gmail.com , leslie2@u.washington.edu Addy adairpc@u.washington

177

HIV1 Neutralization Profile and Plant-Based Recombinant Expression of Actinohivin, an Env Glycan-Specific Lectin Devoid of T-Cell Mitogenic Activity  

Microsoft Academic Search

The development of a topical microbicide blocking the sexual transmission of HIV-1 is urgently needed to control the global HIV\\/AIDS pandemic. The actinomycete-derived lectin actinohivin (AH) is highly specific to a cluster of high-mannose-type glycans uniquely found on the viral envelope (Env). Here, we evaluated AH's candidacy toward a microbicide in terms of in vitro anti-HIV-1 activity, potential side effects,

Nobuyuki Matoba; Adam S. Husk; Brian W. Barnett; Michelle M. Pickel; Charles J. Arntzen; David C. Montefiori; Atsushi Takahashi; Kazunobu Tanno; Satoshi Omura; Huyen Cao; Jason P. Mooney; Carl V. Hanson; Haruo Tanaka; Cheryl A. Stoddart

2010-01-01

178

Generation of a monkey-tropic human immunodeficiency virus type 1 carrying env from a CCR5-tropic subtype C clinical isolate.  

PubMed

Several derivatives of human immunodeficiency virus type 1 (HIV-1) that evade macaque restriction factors and establish infection in pig-tailed macaques (PtMs) have been described. These monkey-tropic HIV-1s utilize CXCR4 as a co-receptor that differs from CCR5 used by most currently circulating HIV-1 strains. We generated a new monkey-tropic HIV-1 carrying env from a CCR5-tropic subtype C HIV-1 clinical isolate. Using intracellular homologous recombination, we generated an uncloned chimeric virus consisting of at least seven types of recombination breakpoints in the region between vpr and env. The virus increased its replication capacity while maintaining CCR5 tropism after in vitro passage in PtM primary lymphocytes. PtM infection with the adapted virus exhibited high peak viremia levels in plasma while the virus was undetectable at 12-16 weeks. This virus serves as starting point for generating a pathogenic monkey-tropic HIV-1 with CCR5-tropic subtype C env, perhaps through serial passage in macaques. PMID:25010265

Otsuki, Hiroyuki; Yoneda, Mai; Igarashi, Tatsuhiko; Miura, Tomoyuki

2014-07-01

179

Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo.  

PubMed Central

Multiple targets for immune recognition and cellular tropism are localized to the V1 and V2 hypervariable regions in the amino portion of human immunodeficiency virus type 1 (HIV-1) gp120env. We have assessed genetic diversity in env V1 and V2 hypervariable domains in vivo within epidemiologically related strains of HIV-1. Our strategy was to analyze longitudinal samples from two seropositive mothers and multiple children infected by perinatal transmission. Although the V1 and V2 domains are closely linked in the HIV-1 genome, nucleotide sequences in V1 and in V2 evolved independently in maternal-infant viruses in vivo. A high proportion of the nucleotide substitutions would introduce amino acid diversity in V1 and in V2. A significant excess of nonsynonymous over synonymous substitutions was identified in HIV-1 env V1 and V2 peptides in the mothers and in two older children but was not generally apparent in HIV-1 sequences in infants. An excess of nonsynonymous over synonymous substitutions indicated that there is positive selection for independent genetic variation in the V1 and V2 domains in vivo. It is likely that there are host responses to complex determinants in the V1 or V2 hypervariable domain of HIV-1 gp120. PMID:8510212

Lamers, S L; Sleasman, J W; She, J X; Barrie, K A; Pomeroy, S M; Barrett, D J; Goodenow, M M

1993-01-01

180

Comparison of Three-Dimensional (3D) Conformal Proton Radiotherapy (RT), 3D Conformal Photon RT, and Intensity-Modulated RT for Retroperitoneal and Intra-Abdominal Sarcomas  

SciTech Connect

Purpose: To compare three-dimensional conformal proton radiotherapy (3DCPT), intensity-modulated photon radiotherapy (IMRT), and 3D conformal photon radiotherapy (3DCRT) to predict the optimal RT technique for retroperitoneal sarcomas. Methods and Materials: 3DCRT, IMRT, and 3DCPT plans were created for treating eight patients with retroperitoneal or intra-abdominal sarcomas. The clinical target volume (CTV) included the gross tumor plus a 2-cm margin, limited by bone and intact fascial planes. For photon plans, the planning target volume (PTV) included a uniform expansion of 5 mm. For the proton plans, the PTV was nonuniform and beam-specific. The prescription dose was 50.4 Gy/Cobalt gray equivalent CGE. Plans were normalized so that >95% of the CTV received 100% of the dose. Results: The CTV was covered adequately by all techniques. The median conformity index was 0.69 for 3DCPT, 0.75 for IMRT, and 0.51 for 3DCRT. The median inhomogeneity coefficient was 0.062 for 3DCPT, 0.066 for IMRT, and 0.073 for 3DCRT. The bowel median volume receiving 15 Gy (V15) was 16.4% for 3DCPT, 52.2% for IMRT, and 66.1% for 3DCRT. The bowel median V45 was 6.3% for 3DCPT, 4.7% for IMRT, and 15.6% for 3DCRT. The median ipsilateral mean kidney dose was 22.5 CGE for 3DCPT, 34.1 Gy for IMRT, and 37.8 Gy for 3DCRT. The median contralateral mean kidney dose was 0 CGE for 3DCPT, 6.4 Gy for IMRT, and 11 Gy for 3DCRT. The median contralateral kidney V5 was 0% for 3DCPT, 49.9% for IMRT, and 99.7% for 3DCRT. Regardless of technique, the median mean liver dose was <30 Gy, and the median cord V50 was 0%. The median integral dose was 126 J for 3DCPT, 400 J for IMRT, and 432 J for 3DCRT. Conclusions: IMRT and 3DCPT result in plans that are more conformal and homogenous than 3DCRT. Based on Quantitative Analysis of Normal Tissue Effects in Clinic benchmarks, the dosimetric advantage of proton therapy may be less gastrointestinal and genitourinary toxicity.

Swanson, Erika L. [Department of Radiation Oncology, University of Florida, Gainesville, Florida (United States)] [Department of Radiation Oncology, University of Florida, Gainesville, Florida (United States); Indelicato, Daniel J., E-mail: dindelicato@floridaproton.org [Department of Radiation Oncology, University of Florida, Gainesville, Florida (United States); University of Florida Proton Therapy Institute, Jacksonville, Florida (United States); Louis, Debbie; Flampouri, Stella; Li, Zuofeng [University of Florida Proton Therapy Institute, Jacksonville, Florida (United States)] [University of Florida Proton Therapy Institute, Jacksonville, Florida (United States); Morris, Christopher G.; Paryani, Nitesh [Department of Radiation Oncology, University of Florida, Gainesville, Florida (United States)] [Department of Radiation Oncology, University of Florida, Gainesville, Florida (United States); Slopsema, Roelf [University of Florida Proton Therapy Institute, Jacksonville, Florida (United States)] [University of Florida Proton Therapy Institute, Jacksonville, Florida (United States)

2012-08-01

181

RT variability unrelated to heart period and respiration progressively increases during graded head-up tilt.  

PubMed

Open-loop linear parametric models were exploited to describe ventricular repolarization duration (VRD) variability during graded head-up tilt. Surface ECG and thoracic movements were recorded in 15 healthy humans (age: 24-54 yr, median: 28 yr; 6 women and 9 men). Tilt table inclinations ranged from 15 to 90 degrees and were varied in steps of 15 degrees . All subjects underwent recordings at every step in random order. Heart period was assessed as the time difference between two consecutive R-wave peaks (RR) and the respiratory signal (R) as the sampling of the thoracic movement signal at the R-wave peaks. VRD was measured automatically as the temporal difference between the R-wave peak and T-wave apex (RT(a)) or T-wave end (RT(e)). The best model decomposed RT variability as due to RR changes (RR-related RT variability) to direct respiratory-related inputs (R-related RT variability) and to unknown rhythmical sources unrelated to RR changes and R (RR-R-unrelated RT variability). Using this model, RT(e) variability was found to be less predictable than RT(a) variability and composed of a smaller fraction of RR-related RT variability and a larger fraction of RR-R-unrelated RT variability. Predictability progressively decreased with tilt table angles, suggesting increased complexity of RT regulation. RT variance progressively increased with tilt table inclination. This increase was characterized by a gradual rise of the amount of RR-R-unrelated RT variability, whereas the amount of RR-related RT variability remained unchanged. These results suggest that the amount of RT variability, complexity of RT dynamics, and amount of RR-R-unrelated RT variability increase with the magnitude of the sympathetic drive directly related to tilt table inclination. We propose the utilization of the amount of RR-R-unrelated RT variability instead of overall RT variability as an indirect measure of autonomic regulation directed to ventricles. PMID:20154259

Porta, Alberto; Tobaldini, Eleonora; Gnecchi-Ruscone, Tomaso; Montano, Nicola

2010-05-01

182

Nedd4-Mediated Increase in HIV-1 Gag and Env Proteins and Immunity following DNA-Vaccination of BALB/c Mice  

PubMed Central

The late assembly domain of many viruses is critical for budding. Within these domains, encoded in viral structural proteins, are the conserved motifs PTAP, PPxY and YPxL. These sequences are the key determinants for association of viral proteins with intracellular molecules such as Tsg101, Nedd4 and AIP1/ALIX. While roles for Tsg101 and AIP1/ALIX in HIV-1 budding have been well established, less is known about the role of Nedd4. Recent studies, however, have identified a function for Nedd4-like protein in HIV-1 release. In this study, we investigated post-transcriptional changes of Nedd4 following SHIVSF162P3 infection of rhesus macaques, its role on HIV-1 p24 and gp120 levels in vitro and its potential as an immune modulator in HIV vaccination of BALB/c mice. Increased Nedd4 protein levels were noted in both CD4+ and CD8+ T cells following SHIVSF162P3-infection of naïve macaques. Transient co-transfection studies in 293 cells with HXB2 and Nedd4 demonstrated a Nedd4-mediated increase in p24 and gp120 levels. This increase was found to be dependent on the Ca2+/calmodulin-regulated phospholipid binding C2 domain and not ubiquitin ligase activity or HIV LTR activity. Co-transfection of Nedd4 with plasmid DNA expressing Gag or Env was further shown to augment both intracellular and extracellular Gag or Env proteins. To assess the potential of Nedd4 as an immune modulator, BALB/c mice were immunized intramuscularly with plasmid DNA encoding HIV gag, env and Nedd4. Nedd4 co-administration was found to increase serum anti-p24 but not anti-gp120 antibodies. Nedd4 co-injection was found to have no affect on Gag- or Env-specific IFN? but had a trend of increased Gag-specific IL-6, IL-17A and TNF? that was not seen following Env stimulation. Based on our initial findings, Nedd4-mediated changes in HIV protein levels and its potential use in HIV-1 vaccine development warrants further investigation. PMID:24614057

Lewis, Brad; Whitney, Stephen; Hudacik, Lauren; Galmin, Lindsey; Huaman, Maria Cecilia; Cristillo, Anthony D.

2014-01-01

183

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

NASA Astrophysics Data System (ADS)

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.

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

184

Characterization of novel non-nucleoside reverse transcriptase (RT) inhibitor resistance mutations at residues 132 and 135 in the 51 kDa subunit of HIV-1 RT  

PubMed Central

Several rare and novel NNRTI [non-nucleoside reverse transcriptase (RT) inhibitor] resistance mutations were recently detected at codons 132 and 135 in RTs from clinical isolates using the yeast-based chimaeric TyHRT (Ty1/HIV-1 RT) phenotypic assay. Ile132 and Ile135 form part of the ?7–?8 loop of HIV-1 RT (residues 132–140). To elucidate the contribution of these residues in RT structure–function and drug resistance, we constructed twelve recombinant enzymes harbouring mutations at codons 132 and 135–140. Several of the mutant enzymes exhibited reduced DNA polymerase activities. Using the yeast two-hybrid assay for HIV-1 RT dimerization we show that in some instances this decrease in enzyme activity could be attributed to the mutations, in the context of the 51 kDa subunit of HIV-1 RT, disrupting the subunit–subunit interactions of the enzyme. Drug resistance analyses using purified RT, the TyHRT assay and antiviral assays demonstrated that the I132M mutation conferred high-level resistance (>10-fold) to nevirapine and delavirdine and low-level resistance (?2–3-fold) to efavirenz. The I135A and I135M mutations also conferred low level NNRTI resistance (?2-fold). Subunit selective mutagenesis studies again demonstrated that resistance was conferred via the p51 subunit of HIV-1 RT. Taken together, our results highlight a specific role of residues 132 and 135 in NNRTI resistance and a general role for residues in the ?7–?8 loop in the stability of HIV-1 RT. PMID:17286555

Nissley, Dwight V.; Radzio, Jessica; Ambrose, Zandrea; Sheen, Chih-Wei; Hamamouch, Noureddine; Moore, Katie L.; Tachedjian, Gilda; Sluis-Cremer, Nicolas

2007-01-01

185

Effect of Low Frequency Ultrasound on Combined rt-PA and Eptifibatide Thrombolysis in Human Clots  

PubMed Central

Introduction Fibrinolytics such as recombinant tissue plasminogen activator (rt-PA) are used to treat thrombotic disease such as acute myocardial infarction (AMI) and ischemic stroke. Interest in increasing efficacy and reducing side effects has led to the study of adjuncts such as GP IIb-IIIa inhibitors and ultrasound (US) enhanced thrombolysis. Currently, GP IIb-IIIa inhibitor and fibrinolytic treatment are often used in AMI, and are under investigation for stroke treatment. However, little is known of the efficacy of combined GP IIb-IIIa inhibitor, fibrinolytic and ultrasound treatment. We measure the lytic efficacy of rt-PA, eptifibatide (Epf) and 120 kHz ultrasound treatment in an in-vitro human clot model. Materials and Methods Blood was drawn from 15 subjects after IRB approval. Clots were made in 20 ?L pipettes, and placed in a water tank for microscopic visualization during lytic treatment. Clots were exposed to control, rt-PA (rt-PA), eptifibatide (Epf), or rt-PA+eptifibatide (rt-PA+Epf), with or without ultrasound for 30 minutes at 37°C in human plasma. Clot lysis was measured over time, using a microscopic imaging technique. The fractional clot loss (FCL) and initial lytic rate (LR) were used to quantify lytic efficacy. Results and Conclusions LR values for (?US) treated clots were 0.8±0.1(control), 1.8±0.3 (Epf), 1.5±0.2 (rt-PA), and 1.3±0.4 (rt-PA+Epf) (% clot width/minute) respectively. In comparison, the (+US) group exhibited LR values of 1.6±0.2 (control), 4.3±0.4 (Epf), 6.3±0.4 (rt-PA), and 4.6±0.6 (rt-PA+Epf). For (?US) treated clots, FCL was 6.0±0.8 (control), 9.2±2.5 (Epf), 15.6±1.7 (rt-PA), and 28.0±2.2% (rt-PA+Epf) respectively. FCL for (+US) clots was 13.5±2.4 (control), 20.7±6.4 (Epf), 44.4±3.6 (rt-PA) and 30.3±3.6% (rt-PA+Epf) respectively. Although the addition of eptifibatide enhances the in-vitro lytic efficacy of rt-PA in the absence of ultrasound, the efficacy of ultrasound and rt-PA is greater than that of combined ultrasound, rt-PA and eptifibatide exposure. PMID:18619651

Meunier, Jason M.; Holland, Christy K.; Pancioli, Arthur M.; Lindsell, Christopher J.; Shaw, George J.

2009-01-01

186

FINANCIAL INFoRmATIoN ANU ANNUAl RepoRt 2009 67  

E-print Network

Relations EFTSL equivalent Full-time Student load EIF education Investment Fund GmT Giant Magellan telescope 355 55 31 625 921 202 88 17 303 #12;#12;ANU ANNUAl RepoRt 2009 67 AUDIT REPoRT #12;68pARt 3 | FINANCIAl StAteMeNtS #12;ANU ANNUAl RepoRt 2009 69 STATEmENTS BY DIRECToRS #12;70 FINANCIAL STATEmENTS pARt

Botea, Adi

187

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

Microsoft Academic Search

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

Sujit Dey; Miodrag Potkonjak

1997-01-01

188

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

NASA Technical Reports Server (NTRS)

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.

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

1986-01-01

189

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

PubMed Central

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

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

190

Rapid detection of equine influenza virus H3N8 subtype by insulated isothermal RT-PCR (iiRT-PCR) assay using the POCKIT™ Nucleic Acid Analyzer.  

PubMed

Equine influenza (EI) is an acute, highly contagious viral respiratory disease of equids. Currently, equine influenza virus (EIV) subtype H3N8 continues to be the most important respiratory pathogen of horses in many countries around the world. The need to achieve a rapid diagnosis and to implement effective quarantine and movement restrictions is critical in controlling the spread of EIV. In this study, a novel, inexpensive and user-friendly assay based on an insulated isothermal RT-PCR (iiRT-PCR) method on the POCKIT™, a field-deployable device, was described and validated for point-of-need detection of EIV-H3N8 in clinical samples. The newly established iiRT-PCR assay targeting the EIV HA3 gene was evaluated for its sensitivity using in vitro transcribed (IVT) RNA, as well as ten-fold serial dilutions of RNA extracted from the prototype H3N8 strain A/equine/Miami/1/63. Inclusivity and exclusivity panels were tested for specificity evaluation. Published real-time RT-PCR (rRT-PCR) assays targeting the NP and HA3 genes were used as the reference standards for comparison of RNA extracted from field strains and from nasal swab samples collected from experimentally infected horses, respectively. Limit of detection with a 95% probability (LoD95%) was estimated to be 11copies of IVT RNA. Clinical sensitivity analysis using RNA prepared from serial dilutions of a prototype EIV (Miami 1/63/H3N8) showed that the iiRT-PCR assay was about 100-fold more sensitive than the rRT-PCR assay targeting the NP gene of EIV subtype H3N8. The iiRT-PCR assay identified accurately fifteen EIV H3N8 strains and two canine influenza virus (CIV) H3N8 strains, and did not cross-react with H6N2, H7N7, H1N1 subtypes or any other equine respiratory viral pathogens. Finally, 100% agreement was found between the iiRT-PCR assay and the universal influenza virus type A rRT-PCR assay in detecting the EIV A/equine/Kentucky/7/07 strain in 56 nasal swab samples collected from experimentally inoculated horses. Therefore, the EIV H3N8 subtype specific iiRT-PCR assay along with the portable POCKIT™ Nucleic Acid Analyzer provides a highly reliable, sensitive and specific on-site detection system of both equine and canine influenza viruses. PMID:24992669

Balasuriya, Udeni B R; Lee, Pei-Yu Alison; Tiwari, Ashish; Skillman, Ashley; Nam, Bora; Chambers, Thomas M; Tsai, Yun-Long; Ma, Li-Juan; Yang, Pai-Chun; Chang, Hsiao-Fen Grace; Wang, Hwa-Tang Thomas

2014-10-01

191

One-Step RT-PCR protocols improve the rate of dengue diagnosis compared to Two-Step RT-PCR approaches  

Microsoft Academic Search

Dengue is the most important arboviral disease transmitted to humans. In our laboratory, we have been working on the standardization of the polymerase chain reaction (PCR) diagnosis of this disease. In this work, we compared five commercial kits regularly used on reverse-transcription polymerase chain reaction (RT-PCR) protocols: two Two-Step kits (SuperScript II RT\\/Super Mix kit and reverse transcription system\\/Taq DNA

Sérgio Oliveira De Paula; Cristiane de Melo Lima; Maria Paula Torres; Márcia Rodrigues Garbin Pereira; Benedito Antônio Lopes da Fonseca

2004-01-01

192

Divergent Evolution in Reverse Transcriptase (RT) of HIV-1 Group O and M Lineages: Impact on Structure, Fitness, and Sensitivity to Nonnucleoside RT Inhibitors?  

PubMed Central

Natural evolution in primate lentiviral reverse transcriptase (RT) appears to have been constrained by the necessity to maintain function within an asymmetric protein composed of two identical primary amino acid sequences (66 kDa), of which one is cleaved (51 kDa). In this study, a detailed phylogenetic analysis now segregates groups O and M into clusters based on a cysteine or tyrosine residue located at position 181 of RT and linked to other signature residues. Divergent evolution of two group O (C181 or Y181) and the main (Y181 only) HIV-1 lineages did not appreciably impact RT activity or function. Group O RT structural models, based on group M subtype B RT crystal structures, revealed that most evolutionarily linked amino acids appear on a surface-exposed region of one subunit while in a noncatalytic RT pocket of the other subunit. This pocket binds nonnucleoside RT inhibitors (NNRTI); therefore, NNRTI sensitivity was used to probe enzyme differences in these group O and M lineages. In contrast to observations showing acquired drug resistance associated with fitness loss, the C181Y mutation in the C181 group O lineage resulted in a loss of intrinsic NNRTI resistance and was accompanied by fitness loss. Other mutations linked to the NNRTI-resistant C181 lineage also resulted in altered NNRTI sensitivity and a net fitness cost. Based on RT asymmetry and conservation of the intricate reverse transcription process, millions of years of divergent primate lentivirus evolution may be constrained to discrete mutations that appear primarily in the nonfunctional, solvent-accessible NNRTI binding pocket. PMID:20631150

Tebit, Denis M.; Lobritz, Michael; Lalonde, Matthew; Immonen, Taina; Singh, Kamlendra; Sarafianos, Stefanos; Herchenroder, Ottmar; Krausslich, Hans-Georg; Arts, Eric J.

2010-01-01

193

Divergent evolution in reverse transcriptase (RT) of HIV-1 group O and M lineages: impact on structure, fitness, and sensitivity to nonnucleoside RT inhibitors.  

PubMed

Natural evolution in primate lentiviral reverse transcriptase (RT) appears to have been constrained by the necessity to maintain function within an asymmetric protein composed of two identical primary amino acid sequences (66 kDa), of which one is cleaved (51 kDa). In this study, a detailed phylogenetic analysis now segregates groups O and M into clusters based on a cysteine or tyrosine residue located at position 181 of RT and linked to other signature residues. Divergent evolution of two group O (C181 or Y181) and the main (Y181 only) HIV-1 lineages did not appreciably impact RT activity or function. Group O RT structural models, based on group M subtype B RT crystal structures, revealed that most evolutionarily linked amino acids appear on a surface-exposed region of one subunit while in a noncatalytic RT pocket of the other subunit. This pocket binds nonnucleoside RT inhibitors (NNRTI); therefore, NNRTI sensitivity was used to probe enzyme differences in these group O and M lineages. In contrast to observations showing acquired drug resistance associated with fitness loss, the C181Y mutation in the C181 group O lineage resulted in a loss of intrinsic NNRTI resistance and was accompanied by fitness loss. Other mutations linked to the NNRTI-resistant C181 lineage also resulted in altered NNRTI sensitivity and a net fitness cost. Based on RT asymmetry and conservation of the intricate reverse transcription process, millions of years of divergent primate lentivirus evolution may be constrained to discrete mutations that appear primarily in the nonfunctional, solvent-accessible NNRTI binding pocket. PMID:20631150

Tebit, Denis M; Lobritz, Michael; Lalonde, Matthew; Immonen, Taina; Singh, Kamlendra; Sarafianos, Stefanos; Herchenröder, Ottmar; Kräusslich, Hans-Georg; Arts, Eric J

2010-10-01

194

Host range mutant of human immunodeficiency virus type 1: modification of cell tropism by a single point mutation at the neutralization epitope in the env gene.  

PubMed Central

We have isolated a variant of human immunodeficiency virus type 1 (HIV-1) which is highly infectious to fibroblastlike cells (BT cells) derived from human brain as well as CD4-positive T cells. This variant HIV-1, named HIV[GUN-1V], was obtained by infecting BT cells with a prototype HIV-1 isolate, named HIV[GUN-1WT], which is highly infectious to T cells but barely infectious to BT cells. HIV[GUN-1V] infects BT cells productively and this infection appeared to be mediated by CD4. To elucidate the viral gene responsible for the host range difference between the variant and prototype HIV-1s, we cloned and analyzed the provirus genomes of the two viruses. Examination of the infectivities of BT cells by various recombinant viruses and analyses of the nucleotide sequences of HIV[GUN-1V] and HIV[GUN-1WT] showed that a single nucleotide exchange was responsible for their difference in infectivity of BT cells: HIV[GUN-1V] contains a thymine residue instead of the cytosine residue in HIV[GUN-1WT] at position 931 of the env coding sequence. Replacement of cytosine by thymine at this position of the env coding sequence of the HIV[GUN-1WT] genome induced the ability to infect BT cells. The base exchange at this position was expected to change amino acid 311 of the envelope glycoprotein, gp120, from proline to serine, which is located in a variable region containing type-specific immunodominant epitopes. Thus, HIV[GUN-1V] acquired a wider host range than HIV[GUN-1WT] by a single point mutation in the env gene. Images PMID:2002539

Takeuchi, Y; Akutsu, M; Murayama, K; Shimizu, N; Hoshino, H

1991-01-01

195

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations  

PubMed Central

Background Virus-associated cell membrane proteins acquired by HIV-1 during budding may give information on the cellular source of circulating virions. In the present study, by applying immunosorting of the virus and of the cells with antibodies targeting monocyte (CD36) and lymphocyte (CD26) markers, it was possible to directly compare HIV-1 quasispecies archived in circulating monocytes and T lymphocytes with that present in plasma virions originated from the same cell types. Five chronically HIV-1 infected patients who underwent therapy interruption after prolonged HAART were enrolled in the study. The analysis was performed by the powerful technology of ultra-deep pyrosequencing after PCR amplification of part of the env gene, coding for the viral glycoprotein (gp) 120, encompassing the tropism-related V3 loop region. V3 amino acid sequences were used to establish heterogeneity parameters, to build phylogenetic trees and to predict co-receptor usage. Results The heterogeneity of proviral and viral genomes derived from monocytes was higher than that of T-lymphocyte origin. Both monocytes and T lymphocytes might contribute to virus rebounding in the circulation after therapy interruptions, but other virus sources might also be involved. In addition, both proviral and circulating viral sequences from monocytes and T lymphocytes were predictive of a predominant R5 coreceptor usage. However, minor variants, segregating from the most frequent quasispecies variants, were present. In particular, in proviral genomes harboured by monocytes, minority variant clusters with a predicted X4 phenotype were found. Conclusion This study provided the first direct comparison between the HIV-1 quasispecies archived as provirus in circulating monocytes and T lymphocytes with that of plasma virions replicating in the same cell types. Ultra-deep pyrosequencing generated data with some order of magnitude higher than any previously obtained with conventional approaches. Next generation sequencing allowed the analysis of previously inaccessible aspects of HIV-1 quasispecies, such as co-receptor usage of minority variants present in archived proviral sequences and in actually replicating virions, which may have clinical and therapeutic relevance. PMID:19216757

Rozera, Gabriella; Abbate, Isabella; Bruselles, Alessandro; Vlassi, Crhysoula; D'Offizi, Gianpiero; Narciso, Pasquale; Chillemi, Giovanni; Prosperi, Mattia; Ippolito, Giuseppe; Capobianchi, Maria R

2009-01-01

196

A DEVS-based Modeling and Behavioral Fault Simulator for RT-Level Digital Circuits  

E-print Network

A DEVS-based Modeling and Behavioral Fault Simulator for RT-Level Digital Circuits Capocchi Laurent The domain of fault simulation for digital circuits de- scribed at the RT-level is currently under heavy and the simulation of behavioral faults for digital circuits described in the VHDL language, using a dis- crete event

Boyer, Edmond

197

Effects of Contextual Similarity and Target-Repetition Proportion on Negative Priming in RT Distributional Analyses  

ERIC Educational Resources Information Center

Participants' reaction time (RT) data in a prime-probe flanker task (e.g., ABA-CAC) were analyzed in terms of the characteristics of RT distribution to examine possible mechanisms that produce negative priming. When the prime and probe were presented in the same context and the proportion of repetition-target trials (TRP) was 0.33, negative…

Tse, Chi-Shing; Hutchison, Keith A.; Li, Yongna

2011-01-01

198

District-Level Considerations in Supporting and Sustaining RtI Implementation  

ERIC Educational Resources Information Center

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…

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

2012-01-01

199

RT-isoPCR: nested, high multiplex mRNA amplification.  

PubMed

RT-isoPCR provides multiplex amplification of mRNA targets using a first-stage multiplex RT-PCR reaction with subsequent isothermal amplification for individual target loci detection. We demonstrate detection of 24 mRNA targets with high specificity and sensitivity without compromising sample variation or introducing biases between targets. PMID:23964356

Søe, Martin Jensen; Warthoe, Peter

2013-10-21

200

The KARL\\/KARATE System: Automatic Test Pattern Generation Based on RT Level Descriptions  

Microsoft Academic Search

A system is described for automatic test-pattern generation (ATPG) using symbolic representations and heuristics to attack the test problem at RT level, where redesigns to increase the testability are relatively cheap. In contrast to other ATPG tools based on RT-level hardware descriptions, KARATE includes tests for primitive operators and allows the modification and redefinition of fault models. KARATE has been

Gerold Affs; Reiner W. Hartenstein; Andrea Wodtko

1988-01-01

201

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

E-print Network

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

de Souza, Romualdo T.

202

Development of a multiplex RT-PCR-ELISA to identify four distinct species of tospovirus.  

PubMed

In this study, a multiplex RT-PCR-ELISA was developed to detect and differentiate four tospovirus species found in Thailand, namely Capsicum chlorosis virus (CaCV), Melon yellow spot virus (MYSV), Tomato necrotic ringspot virus (TNRV), and Watermelon silver mottle virus (WSMoV). In this system, nucleocapsid (N) gene fragments of four tospoviruses were simultaneously amplified and labeled with digoxigenin (DIG) in a single RT-PCR reaction using a pair of degenerate primers binding to the same conserved regions in all four tospovirus N genes. The DIG-labeled amplicons were distinguished into species by four parallel hybridizations to species-specific biotinylated probes in streptavidin-coated microtiter wells followed by ELISA detection using a peroxidase-conjugated anti-DIG antibody. Results indicated that the multiplex RT-PCR-ELISA assay could specifically identify each of these four tospoviruses without cross-reactivity between species or reactivity to healthy plant negative controls. Assay sensitivity was 10- to 1000-fold higher than conventional RT-PCR. When applied to naturally infected plants, all samples yielded concordant results between RT-PCR-ELISA and the reference RT-PCR. In conclusion, the multiplex RT-PCR-ELISA developed in this study has superior specificity, sensitivity, and high-throughput capacity compared to conventional RT-PCR and is an attractive alternative for the identification of different tospovirus species. PMID:24642237

Charoenvilaisiri, Saengsoon; Seepiban, Channarong; Bhunchoth, Anjana; Warin, Nuchnard; Luxananil, Plearnpis; Gajanandana, Oraprapai

2014-06-01

203

Evolution of Cross-Neutralizing Antibody Specificities to the CD4-BS and the Carbohydrate Cloak of the HIV Env in an HIV-1-Infected Subject  

PubMed Central

Broadly neutralizing antibodies are considered an important part of a successful HIV vaccine. A better understanding of the factors underlying their development during infection and of the epitopes they target is needed to elicit similar antibody responses by vaccination. We and others reported that, on average, it takes 2 to 3 years for cross-reactive neutralizing antibodies to become detectable in the sera of HIV-1-infected subjects and that they target a limited number of epitopes on the HIV Envelope. Here we investigated the emergence and evolution of the earliest cross-reactive neutralizing antibody specificities in one HIV-1-infected individual, AC053. We defined two distinct epitopes on Env that are targeted by the broadly neutralizing antibody responses developed by AC053. The first specificity became evident at 3 years post infection and targeted the CD4-binding site of Env. Antibodies responsible for that specificity neutralized most, but not all, viruses susceptible to neutralization by the plasma antibodies of AC053. The second specificity became apparent approximately a year later. It was due to PG9-like antibodies, which were able to neutralize those viruses not susceptible to the anti-CD4-BS antibodies in AC053. These findings improve our understanding of the co-development of broadly neutralizing antibodies that target more than one epitope during natural HIV-1-infection in selected HIV+ subjects. They support the hypothesis that developing broadly neutralizing antibody responses targeting distinct epitopes by immunization could be feasible. PMID:23152926

Mikell, Iliyana; Stamatatos, Leonidas

2012-01-01

204

Co-regulation of polysaccharide production, motility, and expression of type III secretion genes by EnvZ/OmpR and GrrS/GrrA systems in Erwinia amylovora.  

PubMed

The EnvZ/OmpR and GrrS/GrrA systems, two widely distributed two-component systems in gamma-Proteobacteria, negatively control amylovoran biosynthesis in Erwinia amylovora, and the two systems regulate motility in an opposing manner. In this study, we examined the interplay of EnvZ/OmpR and GrrS/GrrA systems in controlling various virulence traits in E. amylovora. Results showed that amylovoran production was significantly higher when both systems were inactivated, indicating that the two systems act as negative regulators and their combined effect on amylovoran production appears to be enhanced. In contrast, reduced motility was observed when both systems were deleted as compared to that of grrA/grrS mutants and WT strain, indicating that the two systems antagonistically regulate motility in E. amylovora. In addition, glycogen accumulation was much higher in envZ/ompR and two triple mutants than that of grrS/grrA mutants and WT strain, suggesting that EnvZ/OmpR plays a dominant role in regulating glycogen accumulation, whereas levan production was significantly lower in the grrS/grrA and two triple mutants as compared with that of WT and envZ/ompR mutants, indicating that GrrS/GrrA system dominantly controls levan production. Furthermore, both systems negatively regulated expression of three type III secretion (T3SS) genes and their combined negative effect on hrp-T3SS gene expression increased when both systems were deleted. These results demonstrated that EnvZ/OmpR and GrrS/GrrA systems co-regulate various virulence factors in E. amylovora by still unknown mechanisms or through different target genes, sRNAs, or proteins, indicating that a complex regulatory network may be involved, which needs to be further explored. PMID:24218204

Li, Wenting; Ancona, Veronica; Zhao, Youfu

2014-02-01

205

Convergent Evolution of Reverse Transcriptase (RT) Genes of Human Immunodeficiency Virus Type 1 Subtypes E and B following Nucleoside Analogue RT Inhibitor Therapies  

PubMed Central

Changes in the drug susceptibility, gene lineage, and deduced amino acid sequences of the reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) subtype E following 3?-azido-3?-deoxythymidine (AZT) monotherapy or AZT–2?,3?-dideoxyinosine combination therapy were examined with sequential virus isolates from a single family. The changes were compared to those reported for HIV-1 subtype B, revealing striking similarities in selected phenotype and amino acids independent of differences in the RT backbone sequences that constantly distinguish the two subtypes. Particularly, identical amino acid substitutions were present simultaneously at four different positions (D67N, K70R, T215F, and K219Q) for high-level AZT resistance. These data suggest that HIV-1 subtypes E and B evolve convergently at the phenotypic and amino acid levels when the nucleoside analogue RT inhibitors act as selective forces. PMID:10799614

Sato, Hironori; Tomita, Yasuhiro; Shibamura, Kayo; Shiino, Teiichiro; Miyakuni, Tuyoshi; Takebe, Yutaka

2000-01-01

206

Quantification of Bacterial Transcripts during Infection Using Competitive Reverse Transcription-PCR (RT-PCR) and LightCycler RT-PCR  

PubMed Central

Bacteria have evolved sophisticated regulatory circuits to modulate their gene expression in response to disparate environments. In order to monitor bacterial gene expression and regulation in the host, methods for direct transcript analysis from clinical specimens are needed. For most bacterial infections, amplification of the mRNAs of interest is necessary due to the low numbers of cells present and the low levels of specific transcripts. Here we compare two methods of quantitative reverse transcription-PCR (RT-PCR)—competitive RT-PCR using a one-tube system followed by standard gel analysis and the real-time detection of PCR product formation by fluorescence resonance energy transfer technology using the LightCycler unit. We isolated Staphylococcus aureus RNA directly from clinical specimens obtained from cystic fibrosis patients with chronic S. aureus lung infection and from an animal model of foreign-body infection with no further cultivation of the bacteria. Competitive RT-PCR and LightCycler RT-PCR were tested for their ability to quantify the transcription of a constitutively expressed gyrase gene (gyr) and a highly regulated ?-toxin gene (hla) of S. aureus. Reproducible results were obtained with both methods. A sensitivity of 104 (gyr) and 103 (hla) copies, respectively, was reached, which was sufficient for the quantification of transcripts during bacterial infection. Overall, the competitive RT-PCR is a robust technique which does not need special RNA purification. On the negative side, it is labor intensive and time consuming, thus limiting the numbers of samples which can be analyzed at a given time. LightCycler RT-PCR is very susceptible to even traces of inhibitors, but it allows high-throughput processing of samples. PMID:11238208

Goerke, Christiane; Bayer, Manfred G.; Wolz, Christiane

2001-01-01

207

ScriptingRT: A Software Library for Collecting Response Latencies in Online Studies of Cognition  

PubMed Central

ScriptingRT is a new open source tool to collect response latencies in online studies of human cognition. ScriptingRT studies run as Flash applets in enabled browsers. ScriptingRT provides the building blocks of response latency studies, which are then combined with generic Apache Flex programming. Six studies evaluate the performance of ScriptingRT empirically. Studies 1–3 use specialized hardware to measure variance of response time measurement and stimulus presentation timing. Studies 4–6 implement a Stroop paradigm and run it both online and in the laboratory, comparing ScriptingRT to other response latency software. Altogether, the studies show that Flash programs developed in ScriptingRT show a small lag and an increased variance in response latencies. However, this did not significantly influence measured effects: The Stroop effect was reliably replicated in all studies, and the found effects did not depend on the software used. We conclude that ScriptingRT can be used to test response latency effects online. PMID:23805326

Schubert, Thomas W.; Murteira, Carla; Collins, Elizabeth C.; Lopes, Diniz

2013-01-01

208

Temperature Affects Thrombolytic Efficacy Using rt-PA and Eptifibatide, an In Vitro Study  

PubMed Central

The potential for hypothermia as a neuroprotectant during stroke has led to its increase in clinical use. At the same time, combination pharmaceutical therapies for ischemic stroke using recombinant tissue plasminogen activator (rt-PA), and GP IIb-IIIa inhibitors, such as Eptifibatide (Epf?), are under study. However, there is little data on how the reactions triggered by these agents are impacted by temperature. Here, clot lysis during exposure to the combination of rt-PA and Epf is measured in an in vitro human clot model at hypothermic temperatures. The hypothesis is that lytic efficacy of rt-PA and Epf decreases with decreasing temperature. Whole blood clots from 31 volunteers were exposed to rt-PA (0.5??g/mL) and Epf (0.63??g/mL) in human fresh-frozen plasma (rt-PA+Epf?), rt-PA alone in plasma (rt-PA Alone), or to plasma alone (Control), at temperatures from 30°C to 37°C, for 30 minutes. Clot lysis was measured using a microscopic imaging technique; the mean fractional clot loss (FCL) at 30 minutes was used to determine lytic efficacy. Temperature had a significant impact on FCL in clots exposed to rt-PA+Epf, with the FCL being lower at 30°C to 36°C than at 37°C. The FCL remained significantly higher for rt-PA+Epf–treated clots than Controls regardless of temperature, with the exception of measurements made at 30°C when no significant differences in the FCL were observed between groups. The use of hypothermia as a neuroprotectant may negatively impact the therapeutic benefit of thrombolytic agents. PMID:23667777

Chang, Wan-Tsu W.; Bluett, Brent; Wenker, Evan; Lindsell, Christopher J.; Shaw, George J.

2012-01-01

209

Selection of a simian-human immunodeficiency virus strain resistant to a vaginal microbicide in macaques.  

PubMed

PSC-RANTES binds to CCR5, inhibits human immunodeficiency virus type 1 (HIV-1) entry, and has been shown as a vaginal microbicide to protect rhesus macaques from a simian-human immunodeficiency virus chimera (SHIV(SF162-p3)) infection in a dose-dependent manner. In this study, env gene sequences from SHIV(SF162-p3)-infected rhesus macaques treated with PSC-RANTES were analyzed for possible drug escape variants. Two specific mutations located in the V3 region of gp120 (K315R) and C-helical domain of gp41 (N640D) were identified in a macaque (m584) pretreated with a 100 microM dose of PSC-RANTES. These two env mutations were found throughout infection (through week 77) but were found at only low frequencies in the inoculating SHIV(SF162-p3) stock and in the other SHIV(SF162-p3)-infected macaques. HIV-1 env genes from macaque m584 (env(m584)) and from inoculating SHIV(SF162-p3) (env(p3)) were cloned into an HIV-1 backbone. Increases in 50% inhibitory concentrations to PSC-RANTES with env(m584) were modest (sevenfold) and most pronounced in cells expressing rhesus macaque CCR5 as compared to human CCR5. Nonetheless, virus harboring env(m584), unlike inoculating virus env(p3), could replicate even at the highest tissue culture PSC-RANTES concentrations (100 nM). Dual-virus competitions revealed a dramatic increase in fitness of chimeric virus containing env(m584) (K315R/N640D) over that containing env(p3), but again, only in rhesus CCR5-expressing cells. This study is the first to describe the immediate selection and infection of a drug-resistant SHIV variant in the face of a protective vaginal microbicide, PSC-RANTES. This rhesus CCR5-specific/PSC- RANTES resistance selection is particularly alarming given the relative homogeneity of the SHIV(SF162-p3) stock compared to the potential exposure to a heterogeneous HIV-1 population in human transmission. PMID:19279098

Dudley, Dawn M; Wentzel, Jennifer L; Lalonde, Matthew S; Veazey, Ronald S; Arts, Eric J

2009-05-01

210

Pyruvate minimizes rtPA toxicity from in vitro oxygen-glucose deprivation and reoxygenation  

PubMed Central

Clinical application of recombinant tissue plasminogen activator (rtPA) for stroke is limited by hemorrhagic transformation, which narrows rtPA’s therapeutic window. In addition, mounting evidence indicates that rtPA is potentially neurotoxic if it traverses a compromised blood brain barrier. Here, we demonstrated that pyruvate protects cultured HT22 neuronal and primary microvascular endothelial cells co-cultured with primary astrocytes from oxygen glucose deprivation (OGD)/reoxygenation stress and rtPA cytotoxicity. After 3 or 6 h OGD, cells were reoxygenated with 11 mmol/L glucose±pyruvate (8 mmol/L) and/or rtPA (10 ?g/ml). Measured variables included cellular viability (calcein AM and annexin-V/propidium iodide), reactive oxygen species (ROS; mitosox red and 2?,7?-dichlorofluorescein diacetate), NADPH, NADP+ and ATP contents (spectrophotometry), matrix metalloproteinase-2 (MMP2) activities (gelatin zymography), and cellular contents of MMP2, tissue inhibitor of metalloproteinase-2 (TIMP2), and phosphor-activation of anti-apoptotic p70s6 kinase, Akt and Erk (immunoblot). Pyruvate prevented the loss of HT22 cells after 3 h OGD±rtPA. After 6 h OGD, rtPA sharply lowered cell viability; pyruvate dampened this effect. Three hours OGD and 4 h reoxygenation with rtPA increased ROS formation by about 50%. Pyruvate prevented this ROS formation and doubled cellular NADPH/NADP+ ratio and ATP content. In endothelial cell monolayers, 3 h OGD and 24 h reoxygenation increased FITC-dextran leakage, indicating disruption of intercellular junctions. Although rtPA exacerbated this effect, pyruvate prevented it while sharply lowering MMP2/TIMP2 ratio and increasing phosphorylation of p70s6 kinase, Akt and Erk. Pyruvate protects neuronal cells and microvascular endothelium from hypoxia-reoxygenation and cytotoxic action of rtPA while reducing ROS and activating anti-apoptotic signaling. These results support the proposed use of pyruvate as an adjuvant to dampen the side effects of rtPA treatment, thereby extending rtPA’s therapeutic window. PMID:23891792

Ryou, Myoung-Gwi; Choudhury, Gourav Roy; Winters, Ali; Xie, Luokun; Mallet, Robert T.; Yang, Shao-Hua

2014-01-01

211

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

NASA Astrophysics Data System (ADS)

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.

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

212

RT-PCR and Electrospray Ionization Mass Spectrometry (RT-PCR/ESI-MS) for Identifying Acute Viral Upper Respiratory Tract Infections  

PubMed Central

Diagnosis of respiratory viruses traditionally relies on culture or antigen detection.We aimed to demonstrate capacity of the RT-PCR/ESI-MS platform to identify clinical relevant respiratory viruses in nasopharyngeal aspirate (NPA) samples and compare the diagnostic performance characteristics relative to conventional culture- and antigen-based methods. A RT-PCR/ESI-MS respiratory virus surveillance kit designed to detect respiratory syncytial virus, influenza A and B, parainfluenza types 1-4, adenoviridae types A-F, coronaviridae, human bocavirus, and human metapneumovirus was evaluated using both mock-ups and frozen archived NPA (N=280), 95 of which were positive by clinical virology methods. RT-PCR/ESI-MS detected 74/95 (77.9%) known positive samples and identified an additional 13/185 (7%) from culture negative samples. Viruses that are non-detectable with conventional methods were also identified. Viral load was semi-quantifiable and ranged from 2,400 to >320,000copies/ml. Time to results was 8hrs. RT-PCR/ESI-MS showed promise in rapid detection of respiratory viruses, merits further evaluation for use in clinical settings. PMID:21251562

Chen, Kuan-Fu; Blyn, Lawrence; Rothman, Richard E.; Ramachandran, Padmini; Valsamakis, Alexandra; Ecker, David; Sampath, Rangarajan; Gaydos, Charlotte A.

2010-01-01

213

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

NASA Technical Reports Server (NTRS)

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.

Fuell, Kevin K.; Molthan, Andrew L.

2012-01-01

214

Enabling Hierarchical View of RxNorm with NDF-RT Drug Classes  

PubMed Central

NDF-RT is the proposed source of drug classification information. We set out to construct a hierarchy of NDF-RT drug classes and RxNorm medications and evaluate it on medication records data. NDF-RT and RxNorm are distributed in different file formats, require different tools to manipulate and linking the two into a hierarchy is a non-trivial exercise. Medication data in RxNorm from two institutions was constrained by the hierarchy. Only 37% of records from one and 65% from another institution were accessible. We subsequently enriched the RxNorm mapping in NDF-RT by exploiting relationships between concepts for branded and generic drugs. Coverage improved dramatically to 93% for both institutions. To improve usability of the resulting hierarchy, we grouped clinical drugs by corresponding clinical drug form. PMID:21347044

Palchuk, Matvey B.; Klumpenaar, Michael; Jatkar, Tarang; Zottola, Ralph J.; Adams, William G.; Abend, Aaron H.

2010-01-01

215

NASA/SPoRt: GOES-R Activities in Support of Product Development, Management, and Training  

NASA Technical Reports Server (NTRS)

SPoRT is using current capabilities of MODIS and VIIRS, combined with current GOES (i.e. Hybrid Imagery) to demonstrate mesoscale capabilities of future ABI instrument. SPoRT is transitioning RGBs from EUMETSAT standard "recipes" to demonstrate a method to more efficiently handle the increase channels/frequency of ABI. Challenges for RGB production exist. Internal vs. external production, Bit depth needed, Adding quantitative information, etc. SPoRT forming group to address these issues. SPoRT is leading efforts on the application of total lightning in operations and to educate users of this new capability. Training in many forms is used to support testbed activities and is a key part to the transition process.

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

2012-01-01

216

East elevation of lift bridge, with U.S. Rt. 11 bridge ...  

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

East elevation of lift bridge, with U.S. Rt. 11 bridge in background. - Potomac Edison Company, Chesapeake & Ohio Canal Bridge, Spanning C & O Canal South of U.S. 11, Williamsport, Washington County, MD

217

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

PubMed

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

Komorowska, B; Malinowski, T; Michalczuk, L

2010-09-01

218

Atypical teratoid rhabdoid tumor (AT\\/RT) in adults: review of four cases  

Microsoft Academic Search

Atypical teratoid\\/rhabdoid (AT\\/RT) tumor is a rare, highly malignant tumor of the central nervous system (CNS) most commonly\\u000a found in children less than 5 years of age. Although the vast majority of cases are diagnosed in young children, there have\\u000a been isolated case reports in adults. Since its histological appearance can be confused with other tumors, especially in adults,\\u000a separating AT\\/RT

Addisalem T. Makuria; Elisabeth J. Rushing; Kevin M. McGrail; Dan-Paul Hartmann; Norio Azumi; Metin Ozdemirli

2008-01-01

219

Nucleoprotein gene analysis of fixed and street rabies virus variants using RT-PCR  

Microsoft Academic Search

Summary.  ?A simple and rapid single-step reverse transcriptase-polymerase chain reaction (RT-PCR) was used to investigate the nucleoprotein\\u000a (N) gene of 11 rabies viruses. A conserved set of RT-PCR primers was designed to amplify the most variable region in the N\\u000a gene. N gene regions were amplified from 6 fixed laboratory viruses, 4 street viruses from dogs in Thailand, and a horse

Y. T. Arai; K. Yamada; Y. Kameoka; T. Horimoto; K. Yamamoto; S. Yabe; M. Nakayama; M. Tashiro

1997-01-01

220

Search for new non-nucleoside inhibitors of HIV-1 reverse transcriptase (HIV-1 RT).  

PubMed

The derivatives of dibenzoxazocinone, dibenzoxadiazocine, dibenzoxadiazonine, and benzodiazepine systems were synthesized as potential lead compounds for inhibitors of HIV-1 reverse transcriptase. The suggested structures were derived from analysis of the described spatial and physicochemical requirements for HIV-1 RT inhibitors. All of the evaluated compounds (apart from the oxadiazocine derivatives) showed a week inhibitory activity on recombinant HIV-1 RT from Escherichia coli. PMID:12602800

Brzezi?ska, Elzbieta; Glinka, Ryszard

2002-01-01

221

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

NASA Technical Reports Server (NTRS)

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.

Zavodsky, Bradley

2012-01-01

222

RT-Xen: Towards real-time hypervisor scheduling in Xen  

Microsoft Academic Search

As system integration becomes an increasingly important challenge for complex real-time systems, there has been a signicant demand for supporting real-time systems in virtualized environments. This paper presents RT-Xen, the rst real-time hypervisor scheduling framework for Xen, the most widely used open-source virtual machine monitor (VMM). RT-Xen bridges the gap between real-time scheduling theory and Xen, whose wide-spread adoption makes

Sisu Xi; Justin Wilson; Chenyang Lu; Christopher Gill

2011-01-01

223

Non-scan design-for-testability of RT-level data paths  

Microsoft Academic Search

This paper presents a non-scan design-for-testability technique applicable to register-transfer (RT) level data path circuits, which are usually very hard-to-test due to the presence of complex loop structures. We develop a new testability measure, and utilize the RT-level structure of the data path, for cost-effective re-design of the circuit to make it easily testable, without having to either scan any

Sujit Dey; Miodrag Potkonjak

1994-01-01

224

Monoclonal Antibody 667 Recognizes the Variable Region A Motif of the Ecotropic Retrovirus CasBrE Envelope Glycoprotein and Inhibits Env Binding to the Viral Receptor  

PubMed Central

Monoclonal antibody (MAb) 667 is a neutralizing mouse monoclonal antibody recognizing the envelope glycoprotein (Env) of the ecotropic neurotropic murine retrovirus CasBrE but not that of other murine retroviruses. Since 667 can be used for preclinical studies of antiviral gene therapy as well as for studying the early events of retroviral infection, we have cloned its cDNAs and molecularly characterized it in detail. Spot technique-based experiments showed that 667 recognizes a linear epitope of 12 amino acids located in the variable region A of the receptor binding domain. Alanine scanning experiments showed that six amino acids within the epitope are critical for MAb binding. One of them, D57, is not present in any other murine retroviral Env, which suggests a critical role for this residue in the selectivity of 667. MAb 667 heavy- and light-chain cDNAs were functionally characterized by transient transfection into Cos-7 cells. Enzyme-linked immunosorbent assays and Biacore studies showed that the specificities as well as the antigen-binding thermodynamic and kinetic properties of the recombinant 667 MAb (r667) produced by Cos-7 cells and those of the parental hybridoma-produced MAb (h667) were similar. However, h667 was shown to contain contaminating retroviral and/or retrovirus-like particles which interfere with both viral binding and neutralization experiments. These contaminants could successfully be removed by a stringent purification protocol. Importantly, this purified 667 could completely prevent retrovirus binding to target cells and was as efficient as the r667 MAb produced by transfected Cos-7 cells in neutralization assays. In conclusion, this study shows that the primary mechanism of virus neutralization by MAb 667 is the blocking of the retroviral receptor binding domain of CasBrE Env. In addition, the findings of this study constitute a warning against the direct use of hybridoma cell culture supernatants for studying the initial events of retroviral cell infection as well as for carrying out in vivo neutralization experiments and suggest that either recombinant antibodies or highly purified antibodies are preferable for these purposes. PMID:14512547

Dreja, Hanna; Gros, Laurent; Villard, Sylvie; Bachrach, Estanislao; Oates, Anna; Granier, Claude; Chardes, Thierry; Mani, Jean-Claude; Piechaczyk, Marc; Pelegrin, Mireia

2003-01-01

225

Identification of three feline immunodeficiency virus (FIV) env gene subtypes and comparison of the FIV and human immunodeficiency virus type 1 evolutionary patterns.  

PubMed Central

Feline immunodeficiency virus (FIV) is a lentivirus associated with AIDS-like illnesses in cats. As such, FIV appears to be a feline analog of human immunodeficiency virus (HIV). A hallmark of HIV infection is the large degree of viral genetic diversity that can develop within an infected individual and the even greater and continually increasing level of diversity among virus isolates from different individuals. Our goal in this study was to determine patterns of FIV genetic diversity by focusing on a 684-nucleotide region encompassing variable regions V3, V4, and V5 of the FIV env gene in order to establish parallels and distinctions between FIV and HIV type 1 (HIV-1). Our data demonstrate that, like HIV-1, FIV can be separated into distinct envelope sequence subtypes (three are described here). Similar to that found for HIV-1, the pairwise sequence divergence within an FIV subtype ranged from 2.5 to 15.0%, whereas that between subtypes ranged from 17.8 to 26.2%. However, the high number of synonymous nucleotide changes among FIV V3 to V5 env sequences may also include a significant number of back mutations and suggests that the evolutionary distances among FIV subtypes are underestimated. Although only a few subtype B viruses were available for examination, the pattern of diversity between the FIV A and B subtypes was found to be significantly distinct; subtype B sequences had proportionally fewer mutations that changed amino acids, compared with silent changes, suggesting a more advanced state of adaptation to the host. No similar distinction was evident for HIV-1 subtypes. The diversity of FIV genomes within individual infected cats was found to be as high as 3.7% yet twofold lower than that within HIV-1-infected people over a comparable region of the env gene. Despite these differences, significant parallels between patterns of FIV evolution and HIV-1 evolution exist, indicating that a wide array of potentially divergent virus challenges need to be considered in FIV vaccine and pathogenesis studies. PMID:8139008

Sodora, D L; Shpaer, E G; Kitchell, B E; Dow, S W; Hoover, E A; Mullins, J I

1994-01-01

226

Natural and Enhanced Attenuation of Chlorinated Solvents Using RT3D  

SciTech Connect

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.

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

2006-07-25

227

Detection of enterovirus 71 using reverse transcription loop-mediated isothermal amplification (RT-LAMP).  

PubMed

Reverse transcription loop-mediated isothermal amplification (RT-LAMP), which is a visual assay for nucleic acids, is performed in a single step using one tube at 65 °C for 1.5 h. In this study, RT-LAMP was established as a method for the detection of enterovirus 71 (EV71). The detection limit of the assay was approximately 10 copies, and no cross-reactivity was noted with Coxsackievirus A16, echovirus, human rotavirus (HRV) or norovirus. This assay, which offers greater sensitivity at a lower cost compared with the conventional reverse transcription polymerase chain reaction (RT-PCR), was validated using 252 clinical specimens that had been confirmed by laboratory diagnosis using RT-PCR. Both methods produced the same results with 52 positive samples. The RT-LAMP-based assay does not require specialised equipment, and therefore, it can be performed conveniently during an outbreak or under field conditions. In brief, the RT-LAMP-based assay provided a simple, rapid and efficient method for the detection of EV71 nucleic acid under field conditions. PMID:22155579

Wang, Xiang; Zhu, Jun-ping; Zhang, Qian; Xu, Zi-gang; Zhang, Fang; Zhao, Zhi-hui; Zheng, Wen-zhi; Zheng, Li-shu

2012-02-01

228

Does inhibiting Sur1 complement rt-PA in cerebral ischemia?  

PubMed Central

Hemorrhagic transformation (HT) associated with recombinant tissue plasminogen activator (rt-PA) complicates and limits its use in stroke. Here, we provide a focused review on the involvement of matrix metalloproteinase 9 (MMP-9) in rt-PA–associated HT in cerebral ischemia, and we review emerging evidence that the selective inhibitor of the sulfonylurea receptor 1 (Sur1), glibenclamide (U.S. adopted name, glyburide), may provide protection against rt-PA–associated HT in cerebral ischemia. Glyburide inhibits activation of MMP-9, ameliorates edema formation, swelling, and symptomatic hemorrhagic transformation, and improves preclinical outcomes in several clinically relevant models of stroke, both without and with rt-PA treatment. A retrospective clinical study comparing outcomes in diabetic patients with stroke treated with rt-PA showed that those who were previously on and were maintained on a sulfonylurea fared significantly better than those whose diabetes was managed without sulfonylureas. Inhibition of Sur1 with injectable glyburide holds promise for ameliorating rt-PA–associated HT in stroke. PMID:22994227

Simard, J. Marc; Geng, Zhihua; Silver, Frank L.; Sheth, Kevin N.; Kimberly, W. Taylor; Stern, Barney J.; Colucci, Mario; Gerzanich, Volodymyr

2012-01-01

229

Simultaneous detection and differentiation of three viruses in pear plants by a multiplex RT-PCR.  

PubMed

A multiplex RT-PCR (mRT-PCR) assay was developed for detection and differentiation of the Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV) and Apple chlorotic leaf spot virus (ACLSV), which are viruses frequently occurring in pear trees. Different combinations of mixed primer pairs were tested for their specificity and sensitivity for the simultaneous detection of the three viruses. Three primer pairs were used to amplify their fragments of 247bp, 358bp and 500bp, respectively. The primer pair for ASPV was designed in this work, while the primer pairs for ACLSV and ASGV were from previous reports. The sensitivity and specificity of the mRT-PCR assay for the three viruses were comparable to that of each uniplex RT-PCR. The mRT-PCR was applied successfully for the detection of three viruses in leaves of pear and apple plants, but was unreliable in the detection of ASGV in dormant barks. In conclusion, this mRT-PCR provides a useful tool for the routine and rapid detection and the differentiation of three pear viruses. PMID:24269332

Yao, Bingyu; Wang, Guoping; Ma, Xiaofang; Liu, Wenbin; Tang, Huihui; Zhu, Hui; Hong, Ni

2014-02-01

230

Improved detection of rhinoviruses in nasal and throat swabs by seminested RT-PCR.  

PubMed

A seminested RT-PCR (nRT-PCR) was used to detect picornavirus (PV) RNA in cell cultures inoculated with rhinoviruses (HRVs) and enteroviruses (EVs). PCR tests in which a primary "touchdown" PCR was followed by secondary reactions using PV or HRV specific primers were able to differentiate HRVs of 48 serotypes from EVs. PVnRT-PCR and HRVnRT-PCR were then used to test nasal and throat swabs from adult subjects with naturally acquired respiratory virus infections. The swabs were also analysed for respiratory viruses by cell culture techniques and the rates of PV identification by the two methods were compared. PVnRT-PCR was found to be at least five times more sensitive than cell culture for the detection of PVs in these clinical specimens. Paired acute and convalescent serum samples were tested for complement fixing antibodies to adenovirus, influenza A and B, respiratory syncytial virus, parainfluenza viruses 1, 2, and 3, Myco plasma pneumoniae, and Chlamydia psittaci. An enzyme-linked immunosorbent assay (ELISA) was used to detect rises in antibody level to coronavirus types 229E and OC43. The overall rate of pathogen identification in 159 swabs from adult asthmatics increased from 28% when only cell culture and serology were used to 57% when these methods were supplemented by PVnRT-PCR. PMID:8395557

Ireland, D C; Kent, J; Nicholson, K G

1993-06-01

231

A Arts |CS Community Services | D Disabilities | ED Education | EL Elderly | ENV Environment | F Family H Health | L Literacy | P Poverty, Housing, Hunger | S Science and Technology | Y Youth  

E-print Network

A Arts |CS Community Services | D Disabilities | ED Education | EL Elderly | ENV Environment | F area and assist with reminiscing with patients, reading, or utilizing a special talent such as musical activity outings, which might include cook outs, trips to the park, shopping, walks and fishing. Read

Bogaerts, Steven

232

A Arts |CS Community Services | D Disabilities | ED Education | EL Elderly | ENV Environment | F Family H Health | L Literacy | P Poverty, Housing, Hunger | S Science and Technology | Y Youth  

E-print Network

A Arts |CS Community Services | D Disabilities | ED Education | EL Elderly | ENV Environment | F. Tutor adult students in math, reading and writing. F/ED M: 9am-Noon, 3-7pm W: 8:30am-1pm T & Th: 8:30am area and assist with reminiscing with patients, reading, or utilizing a special talent such as musical

Bogaerts, Steven

233

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

SciTech Connect

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.

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

234

Improved detection of human enteric viruses in foods by RT-PCR.  

PubMed

Human enteric viruses (including hepatitis A virus (HAV) and Norwalk-like viruses (NLVs)) are now recognized as common causes of foodborne disease. While methods to detect these agents in clinical specimens have improved significantly over the last 10 years, applications to food samples have progressed more slowly. In an effort to improve the sensitivity and speed of virus detection from non-shellfish food commodities by reverse transcription-polymerase chain reaction (RT-PCR), we (i) evaluated multiple RNA extraction methods; (ii) compared alternative NLV primer sets; and (iii) developed a one-step RT-PCR method. Hamburger and lettuce samples, processed for virus concentration using a previously reported filtration-extraction-precipitation procedure, were inoculated with HAV or NV. Several RNA extraction methods (guanidinium isothiocyanate, microspin column, QIAshredder Homogenizer, and TRIzol) and primer pairs were compared for overall RNA yield (microg/ml), purity (A(260)/A(280)), and RT-PCR limits of detection. The use of TRIzol with the QIAshredder Homogenizer (TRIzol/Shred) yielded the best RT-PCR detection limits (<1 RT-PCR amplifiable units/reaction for NV), and the NVp110/NVp36 primer set was the most efficient for detecting NV from seeded food samples. A one-step RT-PCR protocol using the TRIzol/Shred extraction method and the NVp110/NVp36 or HAV3/HAV5 primer sets demonstrated improved sensitivity (>10-fold) over the routinely used two-step method. HAV RNA was detected by RT-PCR at initial inoculum levels corresponding to <10 and <100 PFU per 300 microl sample concentrate (corresponding to 6 g food sample) for hamburger and lettuce, respectively. NV RNA was detected by RT-PCR at initial inoculum levels <5 and <50 RT-PCR amplifiable units per 300 microl concentrate (corresponding to 6 g food sample) for hamburger and lettuce, respectively. Residual RT-PCR inhibitors were effectively removed as evidenced by the ability to detect viral RNA in food concentrates without prior dilution. The methods reported here show promise for rapid, sensitive detection of human enteric viruses in foods. PMID:11742653

Sair, Arnie I; D'Souza, Doris H; Moe, Christine L; Jaykus, Lee-Ann

2002-02-01

235

Evolution of human immunodeficiency virus type 1 env sequence variation in patients with diverse rates of disease progression and T-cell function.  

PubMed Central

We examined the relationship between env sequence variation and disease progression in 10 human immunodeficiency virus type 1 (HIV-1)-seropositive subjects selected from a longitudinal cohort receiving zidovudine therapy. Five subjects were chosen for stable clinical status and CD4 counts (slow progressors), and five were selected for rapid clinical deterioration and CD4 count decline (rapid progressors). The slow progressors had significantly lower plasma viral RNA loads and greater lymphoproliferative responses to mitogens than the rapid progressors. DNA sequences representing the C1 through C3 regions of env were amplified from two peripheral blood mononuclear cell DNA samples from each subject separated by an average of 2.5 years. Molecular clones of these amplicons were then sequenced, and DNA sequence and deduced amino acid sequence distances were compared. Inter-time point sequence comparison showed a higher rate of sequence evolution for the rapid progressors in three of five matched pairs of rapid progressors and slow progressors and for the slow progressors in the remaining two subject pairs. However, intra-time point sequence comparisons showed that four of five slow progressors developed a more diverse quasispecies over time and one showed no change. In contrast, four of five rapid progressors showed no change in quasispecies diversity over time and one showed a significant decrease in diversity. The overall C1 through C3 region quasispecies diversity in the slow progressors at baseline was lower than that for the rapid progressors, but this difference was not significant at the follow-up time points. These diversity relationships were obscured if sequence analyses were limited to the 300-bp C2 to V3 region. Thus, HIV-1 quasispecies diversity increased over time in subjects with more functional immune systems. PMID:9032317

McDonald, R A; Mayers, D L; Chung, R C; Wagner, K F; Ratto-Kim, S; Birx, D L; Michael, N L

1997-01-01

236

Preparation of the Virac Radio Telescope RT-32 for E-Vlbi Observations  

NASA Astrophysics Data System (ADS)

A fully steerable parabolic antenna RT-32 with the mirror diameter 32 m owned by the Ventspils International Radio Astronomy Centre (VIRAC) is available for fundamental and applied research in radio astronomy. The RT-32 is supplied with the receiving systems for the frequency range from 327 MHz to 12 GHz. The equipment allows recording of signals in two channels with a bandwidth up to 1 GHz in each. The system has a high stability of the time frame, which is prerequisite for the Very Long Baseline Interferometry (VLBI) observations. In 2012 the RT-32 data receiving systems and the network infrastructure were prepared for the work in the e-VLBI mode. The systems were tested together with the Torun Observatory, and later in the EVN e-VLBI observation session at 5 GHz. Experiments have shown that RT-32 is able to observe at a frequency range of 5 GHz and transfer the data in the e-VLBI mode with the speed up to 1 Gbps. The paper describes the current status of RT-32, the application of its receiving and data acquisition units for the e-VLBI observations and the results of the conducted e-VLBI observational experiments.

Skirmante, K.; Bezrukovs, Vl.; Jekabsons, N.; Shmeld, I.

237

Inconvenient correlation - RT-BOLD relationship for homogeneous and fast reactions.  

PubMed

Reaction time (RT), a widely used measure of human performance in experimental psychology, has recently been included as a regressor of interest in functional magnetic resonance imaging (fMRI) data analysis. Few studies reported RT-related brain regions, but the nature of this activity is not fully understood. We aimed at exploring this topic by implementing a simple saccadic task which evokes fast and homogeneous reactions that require only the basic neural processes. Thus, a spatial cueing paradigm was chosen and implemented in a simultaneous fMRI and eye-tracking experiment. As a result, we found a wide set of brain regions showing trial-by-trial correlations of blood-oxygenation-level-dependent (BOLD) signal with saccadic RT. These regions included medial and lateral frontal lobes, bilateral intraparietal sulci, anterior insular cortices as well as the right thalamus and medial visual cortex. Further analysis was conducted in order to verify quantitatively the impact of a "time on task" effect on task-related hemodynamic responses (HDRs). The results provide evidence that even a small difference in RTs can be linked with significant increase of HDR in task-related areas. Moreover, this increase is not linear, but rather quadratic. Our findings highlight the importance of controlling for RT in fMRI data analysis when contrasting conditions that vary in RT to avoid the misinterpretation of results. PMID:25158673

Domagalik, A; Beldzik, E; Oginska, H; Marek, T; Fafrowicz, M

2014-10-10

238

Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples  

PubMed Central

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a valuable tool for measuring gene expression in biological samples. However, unique challenges are encountered when studies are performed on cells microdissected from tissues derived from animal models or the clinic, including specimen related issues, variability of RNA template quality and quantity, and normalization. qRT-PCR using small amounts of mRNA derived from dissected cell populations requires adaptation of standard methods to allow meaningful comparisons across sample sets. The protocol described here presents the rationale, technical steps, normalization strategy, and data analysis necessary to generate reliable gene expression measurements of transcripts from dissected samples. The entire protocol from tissue microdissection through qRT-PCR analysis requires approximately 16 hours. PMID:19478806

Erickson, Heidi S.; Albert, Paul S.; Gillespie, John W.; Rodriguez-Canales, Jaime; Linehan, W. Marston; Pinto, Peter A.; Chuaqui, Rodrigo F.; Emmert-Buck, Michael R.

2009-01-01

239

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

NASA Technical Reports Server (NTRS)

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.

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

1995-01-01

240

A Combination Microbicide Gel Protects Macaques Against Vaginal Simian Human Immunodeficiency Virus-Reverse Transcriptase Infection, But Only Partially Reduces Herpes Simplex Virus-2 Infection After a Single High-Dose Cochallenge  

PubMed Central

Abstract Herpes simplex virus-2 (HSV-2) infection increases HIV susceptibility. We previously established a rhesus macaque model of vaginal HSV-2 preexposure followed by cochallenge with HSV-2 and simian/human immunodeficiency virus-reverse transcriptase (SHIV-RT). Using this model, we showed that a gel containing the nonnucleoside reverse transcriptase inhibitor (NNRTI) MIV-150 in carrageenan (CG) reduced SHIV-RT infection. To evaluate the efficacy of new generation microbicides against both viruses, we first established dual infection after single vaginal cochallenge with SHIV-RT and HSV-2 in HSV-2-naive macaques. All animals (6/6) became HSV-2 infected, with 4/6 coinfected with SHIV-RT. In a control group cochallenged with SHIV-RT and UV-inactivated HSV-2, 2/4 became SHIV-RT infected, and none had detectable HSV-2. Low-level HSV-2-specific antibody and T cell responses were detected in some HSV-2-infected animals. To test a CG gel containing MIV-150 and zinc acetate (MZC), which provided naive animals full protection from SHIV-RT for at least 8?h, MZC (vs. CG) was applied daily for 14 days followed by cochallenge 8?h later. MZC prevented SHIV-RT infection (0/9 infected, p=0.04?vs. 3/6 in CG controls), but only reduced HSV-2 infection by 20% (6/9 infected vs. 5/6 in CG, p=0.6). In HSV-2-infected animals, none of the gel-treated animals seroconverted, and only the CG controls had measurable HSV-2-specific T cell responses. This study shows the promise of MZC to prevent immunodeficiency virus infection (even in the presence of HSV-2) and reduce HSV-2 infection after exposure to a high-dose inoculum. Additionally, it demonstrates the potential of a macaque coinfection model to evaluate broad-spectrum microbicides. PMID:24117013

Hsu, Mayla; Aravantinou, Meropi; Menon, Radhika; Seidor, Samantha; Goldman, Daniel; Kenney, Jessica; Derby, Nina; Gettie, Agegnehu; Blanchard, James; Piatak, Michael; Lifson, Jeffrey D.; Fernández-Romero, Jose A.; Zydowsky, Thomas M.

2014-01-01

241

Inactivation conditions for human norovirus measured by an in situ capture-qRT-PCR method.  

PubMed

Human norovirus (HuNoV) is a leading cause of foodborne gastroenteritis. Unfortunately, the inactivation parameters for HuNoV in clinical, food and environmental samples have not been established. Due to the inability to cultivate HuNoV in vitro, quantitative real-time RT-PCR (qRT-PCR) is widely-used for detecting HuNoVs. However, qRT-PCR does not indicate viral infectivity. Our method employs histo-blood group antigens (HBGAs) as viral receptors/co-receptors and container-affixed capture agents to concentrate HuNoVs. The captured viruses are denatured and its genome is amplified in the same module by in situ capture qRT-PCR (ISC-qRT-PCR). Greater than three log10 reduction in the receptor-captured viral genomic signal (RCVGS) was observed when HuNoV was treated by heat at 72 °C for 4 min, by chlorine at a final concentration of 16 ppm in less than 1 min, and by UV irradiation at 1J/cm². Treatment of low-titer HuNoV (<10³ copies/sample) with 70% ethanol for 20 s reduced the RCVGS of HuNoV by two log10. However, ethanol had a limited effect on high-titer samples of HuNoV (>10³ copies/sample). The results demonstrate that ISC-qRT-PCR method could be used as an alternative method to measure encapsidated viral RNA and indirectly indicate the inactivation status of HuNoV caused by physical treatment such as heat, and chemical treatment such as chlorine, that damage the ability of the virus to bind to its receptor. PMID:24361836

Wang, Dapeng; Tian, Peng

2014-02-17

242

Making the Right Choice: Optimizing rt-PA and eptifibatide lysis, an in vitro study  

PubMed Central

Introduction Recombinant tissue plasminogen activator (rt-PA) is the only FDA approved lytic therapy for acute ischemic stroke. However, there can be complications such as intra-cerebral hemorrhage. This has led to interest in adjuncts such as GP IIb-IIIa inhibitors. However, there is little data on combined therapies. Here, we measure clot lysis for rt-PA and eptifibatide in an in vitro human clot model, and determine the drug concentrations maximizing lysis. A pharmacokinetic model is used to compare drug concentrations expected in clinical trials with those used here. The hypothesis is that there is a range of rt-PA and eptifibatide concentrations that maximize in vitro clot lysis. Materials and Methods Whole blood clots were made from blood obtained from 28 volunteers, after appropriate institutional approval. Sample clots were exposed to rt-PA and eptifibatide in human fresh-frozen plasma; rt-PA concentrations were 0, 0.5, 1, and 3.15 ?g/ml, and eptifibatide concentrations were 0, 0.63, 1.05, 1.26 and 2.31 ?g/ml. All exposures were for 30 minutes at 37 C. Clot width was measured using a microscopic imaging technique and mean fractional clot loss (FCL) at 30 minutes was used to determine lytic efficacy. On average, 28 clots (range: 6-148) from 6 subjects (3-24) were used in each group. Results and Conclusions FCL for control clots was 14% (95% Confidence Interval: 13-15%). FCL was 58% (55-61%) for clots exposed to both drugs at all concentrations, except those at an rt-PA concentration of 3.15 ?g/ml, and eptifibatide concentrations of 1.26 ?g/ml (Epf) or 2.31 ?g/ml. Here, FCL was 43% (36-51) and 35% (32-38) respectively. FCL is maximized at moderate rt-PA and eptifibatide concentration; these values may approximate the average concentrations used in some rt-PA and eptifibatide treatments. PMID:20813398

Shaw, George J.; Meunier, Jason M.; Lindsell, Christopher J.; Pancioli, Arthur M.; Holland, Christy K.

2010-01-01

243

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

SciTech Connect

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.

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

244

A reanalysis of the light curve of RT Persei with the W-D code  

NASA Astrophysics Data System (ADS)

The UBV photometric observations of RT Per, from Sanwal and Chaubey (1981), were analyzed by the Wilson and Devinney code (1971). The light curves include reflection effects that for the first time has been suggested by Dugan (1911). RT Per has a semi-detached configuration where the lower-mass component is in contact with its respective Roche surface. The higher-mass component very nearly fills its Roche lobe. It has the characteristic of an Algol type system. The absolute dimensions for the primary and secondary of this system were calculated from its spectral types and by combining the photometric solution with inferred component radial velocities (Lu, 1990).

Edalati, M. T.; Zeinali, F.

1996-09-01

245

Covariance of Charged Amino Acids at Positions 322 and 440 of HIV-1 Env Contributes to Coreceptor Specificity of Subtype B Viruses, and Can Be Used to Improve the Performance of V3 Sequence-Based Coreceptor Usage Prediction Algorithms  

PubMed Central

The ability to determine coreceptor usage of patient-derived human immunodeficiency virus type 1 (HIV-1) strains is clinically important, particularly for the administration of the CCR5 antagonist maraviroc. The envelope glycoprotein (Env) determinants of coreceptor specificity lie primarily within the gp120 V3 loop region, although other Env determinants have been shown to influence gp120-coreceptor interactions. Here, we determined whether conserved amino acid alterations outside the V3 loop that contribute to coreceptor usage exist, and whether these alterations improve the performance of V3 sequence-based coreceptor usage prediction algorithms. We demonstrate a significant covariant association between charged amino acids at position 322 in V3 and position 440 in the C4 Env region that contributes to the specificity of HIV-1 subtype B strains for CCR5 or CXCR4. Specifically, positively charged Lys/Arg at position 322 and negatively charged Asp/Glu at position 440 occurred more frequently in CXCR4-using viruses, whereas negatively charged Asp/Glu at position 322 and positively charged Arg at position 440 occurred more frequently in R5 strains. In the context of CD4-bound gp120, structural models suggest that covariation of amino acids at Env positions 322 and 440 has the potential to alter electrostatic interactions that are formed between gp120 and charged amino acids in the CCR5 N-terminus. We further demonstrate that inclusion of a “440 rule” can improve the sensitivity of several V3 sequence-based genotypic algorithms for predicting coreceptor usage of subtype B HIV-1 strains, without compromising specificity, and significantly improves the AUROC of the geno2pheno algorithm when set to its recommended false positive rate of 5.75%. Together, our results provide further mechanistic insights into the intra-molecular interactions within Env that contribute to coreceptor specificity of subtype B HIV-1 strains, and demonstrate that incorporation of Env determinants outside V3 can improve the reliability of coreceptor usage prediction algorithms. PMID:25313689

Cashin, Kieran; Sterjovski, Jasminka; Harvey, Katherine L.; Ramsland, Paul A.; Churchill, Melissa J.; Gorry, Paul R.

2014-01-01

246

Adaptation of Subtype A Human Immunodeficiency Virus Type 1 Envelope to Pig-Tailed Macaque Cells?  

PubMed Central

The relevance of simian/human immunodeficiency virus (SHIV) infection of macaques to HIV-1 infection in humans depends on how closely SHIVs mimic HIV-1 transmission, pathogenesis, and diversity. Circulating HIV-1 strains are predominantly subtypes C and A and overwhelmingly require CCR5 for entry, yet most SHIVs incorporate CXCR4-using subtype B envelopes (Envs). While pathogenic subtype C-based SHIVs have been constructed, the subtype A-based SHIVs (SHIV-As) constructed to date have been unable to replicate in macaque cells. To understand the barriers to SHIV-A replication in macaque cells, HIVAQ23/SIVvif was constructed by engineering a CCR5-tropic subtype A provirus to express SIV vif, which counters the macaque APOBEC3G restriction. HIVAQ23/SIVvif replicated poorly in pig-tailed macaque (Ptm) lymphocytes, but viruses were adapted to Ptm lymphocytes. Two independent mutations in gp120, G312V (V3 loop) and A204E (C2 region), were identified that increased peak virus levels by >100-fold. Introduction of G312V and A204E to multiple subtype A Envs and substitution of G312 and A204 with other residues increased entry into Ptm cells by 10- to 100-fold. G312V and A204E Env variants continued to require CCR5 for entry but were up to 50- and 200-fold more sensitive to neutralization by IgG1b12 and soluble CD4 and had a 5- to 50-fold increase in their ability to utilize Ptm CD4 compared to their wild-type counterparts. These findings identify the inefficient use of Ptm CD4 as an unappreciated restriction to subtype A HIV-1 replication in Ptm cells and reveal amino acid changes to gp120 that can overcome this barrier. PMID:21325401

Humes, Daryl; Overbaugh, Julie

2011-01-01

247

Viral RNA levels and env variants in semen and tissues of mature male rhesus macaques infected with SIV by penile inoculation.  

PubMed

HIV is shed in semen but the anatomic site of virus entry into the genital secretions is unknown. We determined viral RNA (vRNA) levels and the envelope gene sequence in the SIVmac 251 viral populations in the genital tract and semen of 5 adult male rhesus monkeys (Macaca mulatta) that were infected after experimental penile SIV infection. Paired blood and semen samples were collected from 1-9 weeks after infection and the monkeys were necropsied eleven weeks after infection. The axillary lymph nodes, testes, epididymis, prostate, and seminal vesicles were collected and vRNA levels and single-genome analysis of the SIVmac251 env variants was performed. At the time of semen collection, blood vRNA levels were between 3.09 and 7.85 log10 vRNA copies/ml plasma. SIV RNA was found in the axillary lymph nodes of all five monkeys and in 3 of 5 monkeys, all tissues examined were vRNA positive. In these 3 monkeys, vRNA levels (log10 SIVgag copies/ug of total tissue RNA) in the axillary lymph node (6.48 ± 0.50) were significantly higher than in the genital tract tissues: testis (3.67 ± 2.16; p<0.05), epididymis (3.08 ± 1.19; p<0.0001), prostate (3.36 ± 1.30; p<0.01), and seminal vesicle (2.67 ± 1.50; p<0.0001). Comparison of the SIVmac251 env viral populations in blood plasma, systemic lymph node, and genital tract tissues was performed in two of the macaques. Visual inspection of the Neighbor-Joining phylograms revealed that in both animals, all the sequences were generally distributed evenly among all tissue compartments. Importantly, viral populations in the genital tissues were not distinct from those in the systemic tissues. Our findings demonstrate striking similarity in the viral populations in the blood and male genital tract tissues within 3 months of penile SIV transmission. PMID:24146859

Fieni, Francis; Stone, Mars; Ma, Zhong-Min; Dutra, Joseph; Fritts, Linda; Miller, Christopher J

2013-01-01

248

Viral RNA Levels and env Variants in Semen and Tissues of Mature Male Rhesus Macaques Infected with SIV by Penile Inoculation  

PubMed Central

HIV is shed in semen but the anatomic site of virus entry into the genital secretions is unknown. We determined viral RNA (vRNA) levels and the envelope gene sequence in the SIVmac 251 viral populations in the genital tract and semen of 5 adult male rhesus monkeys (Macaca mulatta) that were infected after experimental penile SIV infection. Paired blood and semen samples were collected from 1–9 weeks after infection and the monkeys were necropsied eleven weeks after infection. The axillary lymph nodes, testes, epididymis, prostate, and seminal vesicles were collected and vRNA levels and single-genome analysis of the SIVmac251 env variants was performed. At the time of semen collection, blood vRNA levels were between 3.09 and 7.85 log10 vRNA copies/ml plasma. SIV RNA was found in the axillary lymph nodes of all five monkeys and in 3 of 5 monkeys, all tissues examined were vRNA positive. In these 3 monkeys, vRNA levels (log10 SIVgag copies/ug of total tissue RNA) in the axillary lymph node (6.48±0.50) were significantly higher than in the genital tract tissues: testis (3.67±2.16; p<0.05), epididymis (3.08±1.19; p<0.0001), prostate (3.36±1.30; p<0.01), and seminal vesicle (2.67±1.50; p<0.0001). Comparison of the SIVmac251 env viral populations in blood plasma, systemic lymph node, and genital tract tissues was performed in two of the macaques. Visual inspection of the Neighbor-Joining phylograms revealed that in both animals, all the sequences were generally distributed evenly among all tissue compartments. Importantly, viral populations in the genital tissues were not distinct from those in the systemic tissues. Our findings demonstrate striking similarity in the viral populations in the blood and male genital tract tissues within 3 months of penile SIV transmission. PMID:24146859

Fieni, Francis; Stone, Mars; Ma, Zhong-Min; Dutra, Joseph; Fritts, Linda; Miller, Christopher J.

2013-01-01

249

LITMUS RT : A Status Report # Bj orn B. Brandenburg, Aaron D. Block, John M. Calandrino,  

E-print Network

­ core designs, combined with building interest within the open­source community in supporting real extension of Linux called LITMUS RT (LInux Testbed for MUltiprocessor Scheduling in Real­Time systems) [9, 11, 28], which is being designed to sup­ port real­time workloads on multiprocessor platforms

Anderson, James

250

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

E-print Network

. 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/Exercises with feedback In the final year of secondary school (twelfth grade in the U.S.), U.S. performance was among

de Souza, Romualdo T.

251

Miniature RT-PCR system for diagnosis of RNA-based viruses  

PubMed Central

This paper presents an innovative portable chip-based RT–PCR system for amplification of specific nucleic acid and detection of RNA-based viruses. The miniature RT–PCR chip is fabricated using MEMS (Micro-electro-mechanical-system) techniques, and comprises a micro temperature control module and a PDMS (polydimethylsiloxane)-based microfluidic control module. The heating and sensing elements of temperature control module are both made of platinum and are located within the reaction chambers in order to generate a rapid and uniform thermal cycling. The microfluidic control module is capable of automating testing process with minimum human intervention. In this paper, the proposed miniature RT–PCR system is used to amplify and detect two RNA-based viruses, namely dengue virus type-2 and enterovirus 71 (EV 71). The experimental data confirm the ability of the system to perform a two-step RT–PCR process. The developed miniature system provides a crucial tool for the diagnosis of RNA-based viruses. PMID:16221971

Liao, Chia-Sheng; Lee, Gwo-Bin; Liu, Hsiao-Sheng; Hsieh, Tsung-Min; Luo, Ching-Hsing

2005-01-01

252

676 VOLUME 17 | NUMBER 6 | JUNE 2011 nature medicine a rt i c l e s  

E-print Network

676 VOLUME 17 | NUMBER 6 | JUNE 2011 nature medicine a rt i c l e s Multicellular eukaryotes have and antimicrobial peptides present in phagocytic cells, on body surfaces, secretions and tissue fluids of antibacterial products, such as antibiotics (produced by bacteria and fungi) or animal innate immunity proteins

Gleeson, Joseph G.

253

RT-Based Administrative Models for Community Cyber Security Information Sharing  

E-print Network

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

Sandhu, Ravi

254

RT-Based Administrative Models for Community Cyber Security Information Sharing  

E-print Network

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

Sandhu, Ravi

255

nature medicine VOLUME 20 | NUMBER 3 | MARCH 2014 255 a rt i c l e s  

E-print Network

for the impaired regen- eration observed during aging13. Instead, several reports attribute loss of musclenature medicine VOLUME 20 | NUMBER 3 | MARCH 2014 255 a rt i c l e s During aging, skeletal muscle strength progressively declines (sarcopenia), leading to reduced mobility, muscle function and quality

Cai, Long

256

Climate Change: A Catastrophe in Slow Motion R.T. Pierrehumbert*  

E-print Network

--disasters that are over in an instant and have immediately evident dire consequences. The changes in Earth's climate1 Climate Change: A Catastrophe in Slow Motion R.T. Pierrehumbert* I. INTRODUCTION The word of geological time, human- induced climate change, known more familiarly as "global warming," is a catastrophe

Pierrehumbert, Raymond

257

Department of recreational SportS AnnuAl RepoRt  

E-print Network

6 8 10 12 16 18 20 22 24 Letter from the Director Our Foundation Healthy Living Community StudentReational SpoRtS MiSSion StateMent We inspire healthy living by providing quality recreational and educational these initiatives into a facility design that will heighten our pledge to a healthy campus community. The following

Escher, Christine

258

A RT I C L E S Actin and -actinin orchestrate the assembly and  

E-print Network

A RT I C L E S Actin and -actinin orchestrate the assembly and maturation of nascent adhesions is independent of myosin II but its rate is proportional to the protrusion rate and requires actin polymerization occurs along an -actinin­actin template that elongates centripetally from nascent adhesions. -Actinin

Mogilner, Alex

259

In-Flight Demonstration of a Real-Time Flush Airdata Sensing (RT-FADS) System.  

National Technical Information Service (NTIS)

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 usi...

1995-01-01

260

Chapter 6: Response to Intervention (RtI) and Students with Emotional and Behavioral Disorders  

ERIC Educational Resources Information Center

We review the concept of response to intervention (RtI) as it is being applied to emotional and behavioral disorders (EDB) in the early part of the 21st century, examining how it differs from and incorporates features of other approaches to addressing those problems, including pre-referral interventions, applied behavior analysis, functional…

Kauffman, James M.; Bruce, Andrew; Lloyd, John Wills

2012-01-01

261

The Dean's RepoRT | 20092010 haRvaRD MeDical school  

E-print Network

minds come together, advances in science and medicine seem virtually limitless. The Harvard medicalThe Dean's RepoRT | 2009­2010 haRvaRD MeDical school #12;#12;Aa Aa Despite a challenging financial climate, the Harvard Medical School community came together in 2009 as never before, training remarkable

Goodrich, Lisa V.

262

terc.ucdavis.edu tahoe: state of the Lake RepoRt 2008  

E-print Network

on snowmelt timing, lake water temperature and density stratification. It also shows how muchterc.ucdavis.edu tahoe: state of the Lake RepoRt 2008 2.1 The long-term data set collected on the Lake Tahoe ecosystem by the University of California, Davis, is a valuable tool for understanding eco

Schladow, S. Geoffrey

263

Policy Implications at the State and District Level with RtI for Gifted students  

ERIC Educational Resources Information Center

As a field, gifted education does not endorse any one approach to serving students because of the range of student abilities and resulting concomitant diverse needs. Therefore, service delivery in gifted education is still heavily teacher dependent. Yet, many of the components of Response to Intervention (RtI) are employed in gifted education,…

Brown, Elissa F.; Abernethy, Sherry H.

2009-01-01

264

2013 AnnuAl RepoRtColumbia Columbia university College of Physicians & Surgeons  

E-print Network

2013 AnnuAl RepoRtColumbia Columbia university College of Physicians & Surgeons Medicine Columbia in Neuroscience from MIT's McGovern Insti- tute for Brain Research. Pulitzer Prize winner Siddhartha Mukherjee, MD. The location will be an important new portal for patients to access the network of physicians in the Columbia

Grishok, Alla

265

University of Maryland Center for Environmental Science 2012 AnnuAl RepoRt  

E-print Network

University of Maryland Center for Environmental Science 2012 AnnuAl RepoRt #12;annUal rEport 2012 and environmental science. University of Maryland Center for Environmental Science One of the world's premier research centers focused on ecosystem science, the University of Maryland Center for Environmental Science

Boynton, Walter R.

266

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

E-print Network

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

Arnold, Jonathan

267

Virus detection and identification using random multiplex (RT)PCR with 3'-locked random primers  

Microsoft Academic Search

BACKGROUND: PCR-based detection and identification of viruses assumes a known, relatively stable genome. Unfortunately, high mutation rates may lead to extensive changes in viral nucleic acid sequences making dedicated PCR primer use problematic. Furthermore, in bioterrorism, viral consensus sequences can be genetically modified as a countermeasure to RT-PCR and DNA chip detection. Accordingly, there is a great need for the

Amy L Clem; Jonathan Sims; Sucheta Telang; John W Eaton; Jason Chesney

2007-01-01

268

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

E-print Network

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

Paris-Sud XI, Université de

269

Innovative Methodology Implementation of a Fast 16-Bit Dynamic Clamp Using LabVIEW-RT  

E-print Network

Innovative Methodology Implementation of a Fast 16-Bit Dynamic Clamp Using LabVIEW-RT Paul H. M Submitted 10 June 2003; accepted in final form 22 September 2003 Kullmann, Paul H. M., Diek W. Wheeler) in the cell membrane (Robinson and Kawai 1993; Sharp et al. 1993a,b). Although the value of the dynamic

Horn, John P.

270

S E A T U RT L E S Sea Turtles  

E-print Network

S E A T U RT L E S 1 U N I T 25 Sea Turtles Unit 25 NMFS OFFICE OF PROTECTED RESOURCES Silver CENTER La Jolla California INTRODUCTION Sea turtles are highly migratory and widely dis- tributed ridley, green, leatherback, and hawksbill. In the Pacific Ocean, all these species except the Kemp

271

2014NatureAmerica,Inc.Allrightsreserved. a rt i c l e s  

E-print Network

During aging, skeletal muscle strength progressively declines (sarcopenia), leading to reduced mobility that amelio- rate or reverse the decline in muscle strength in the elderly7,8, which constitutes a costly©2014NatureAmerica,Inc.Allrightsreserved. a rt i c l e s nature medicine advance online publication

Delp, Scott

272

Identification and evaluation of reference genes for qRT-PCR normalization in Ganoderma lucidum.  

PubMed

Quantitative real-time reverse transcription PCR (qRT-PCR) is a rapid, sensitive, and reliable technique for gene expression studies. The accuracy and reliability of qRT-PCR results depend on the stability of the reference genes used for gene normalization. Therefore, a systematic process of reference gene evaluation is needed. Ganoderma lucidum is a famous medicinal mushroom in East Asia. In the current study, 10 potential reference genes were selected from the G. lucidum genomic data. The sequences of these genes were manually curated, and primers were designed following strict criteria. The experiment was conducted using qRT-PCR, and the stability of each candidate gene was assessed using four commonly used statistical programs-geNorm, NormFinder, BestKeeper, and RefFinder. According to our results, PP2A was expressed at the most stable levels under different fermentation conditions, and RPL4 was the most stably expressed gene in different tissues. RPL4, PP2A, and ?-tubulin are the most commonly recommended reference genes for normalizing gene expression in the entire sample set. The current study provides a foundation for the further use of qRT-PCR in G. lucidum gene analysis. PMID:24013612

Xu, Jiang; Xu, ZhiChao; Zhu, YingJie; Luo, HongMei; Qian, Jun; Ji, AiJia; Hu, YuanLei; Sun, Wei; Wang, Bo; Song, JingYuan; Sun, Chao; Chen, ShiLin

2014-01-01

273

arXiv:math.RT/0601343v113Jan2006 Alcove walks, Hecke algebras, spherical functions,  

E-print Network

of this paper form a self contained treatment of the theory of crystals and the path model. It is my hopearXiv:math.RT/0601343v113Jan2006 Alcove walks, Hecke algebras, spherical functions, crystals that this will be useful to the many people who, over the years, have told me that they wished they understood crystals

Ram, Arun

274

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

ERIC Educational Resources Information Center

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…

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

2013-01-01

275

FY 2013 AgencY FinAnciAl RepoRt www.nasa.gov  

E-print Network

FY 2013 AgencY FinAnciAl RepoRt www.nasa.gov National Aeronautics and Space Administration #12;Front Cover: Outside Front Main Image: Artist concept of planets space. (Credit: NASA) Outside Front of extrave- hicular activity (EVA) as work continues on the International Space Station. (Credit: NASA

Waliser, Duane E.

276

Real-time quantitative RT-PCR detection of circulating tumor cells from breast cancer patients.  

PubMed

Circulating tumor cells (CTCs) were recognized as novel tumor biomarker for prognostic and predictive purposes in various cancers. Various detection technologies and devices have been developed to enumerate and characterize CTCs. Most of those approaches are based on the positive enrichment strategy and immunocytological techniques. However, the sensitivity of these approaches proved to be limited in metastatic tumors and the detection of early tumor cell dissemination was problematic. In the present study, we developed a novel CTC detection method by real-time RT-PCR technique in combination of negative enrichment strategy. The developed enrichment approach could recover more than 75% of spiked breast cancer cells from peripheral blood. The detection limit of duplex real-time RT-PCR assay using KRT19 and ERBB2 as targeted genes was consistently one breast tumor cell. Moreover, CTC detection by duplex real-time RT-PCR assay had higher detection sensitivity than that by immunostaining, especially in early breast cancer. In summary, the results of the present study indicated the potential clinical utilities of CTCs identification on breast cancer by duplex real-time RT-PCR in combination with negative enrichment. PMID:25353649

Guo, Maowen; Li, Xiaotian; Zhang, Shaohua; Song, Hua; Zhang, Wenhui; Shang, Xueyi; Zheng, Yuling; Jiang, Hua; Lv, Qingyu; Jiang, Yongqiang; Hao, Huaijie

2015-01-01

277

2012NatureAmerica,Inc.Allrightsreserved. A RT I C L E S  

E-print Network

©2012NatureAmerica,Inc.Allrightsreserved. A RT I C L E S NATURE MEDICINE ADVANCE ONLINE PUBLICATION by the healthy micro- biota1. Indeed, disruption of the healthy microbiota (for example, by antibiotic treatment that disruption of the microbiota by antibiotics predis- poses mice to a lethal sepsis-like disease upon

Vance,. Russell

278

a rt i c l e s nature medicine VOLUME 20 | NUMBER 1 | JANUARY 2014 47  

E-print Network

a rt i c l e s nature medicine VOLUME 20 | NUMBER 1 | JANUARY 2014 47 Despite renewed eradication of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School University of Veterinary Medicine Vienna, Vienna, Austria. 5Institute for Experimental Infection Research

Arnold, Jonathan

279

Selecting control genes for RT-QPCR using public microarray data  

Microsoft Academic Search

BACKGROUND: Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different

Vlad Popovici; Darlene R. Goldstein; Janine Antonov; Rolf Jaggi; Mauro Delorenzi; Pratyaksha Wirapati

2009-01-01

280

ISSN0249-0803ISRNINRIA/RT--0401--FR+ENG Audio, Speech, and Language Processing  

E-print Network

of phoneme variants as a parameter. As no database of infant-directed speech1 containing rich phoneticapport technique ISSN0249-0803ISRNINRIA/RT--0401--FR+ENG Audio, Speech, and Language Processing 39 63 53 30 A note on the generation of allophonic rules Luc Boruta Theme : Audio, Speech

Paris-Sud XI, Université de

281

ISSN0249-0803ISRNINRIA/RT--0401--FR+ENG Audio, Speech, and Language Processing  

E-print Network

to vary the number of phoneme variants as a parameter. As no database of infant-directed speech1apport technique ISSN0249-0803ISRNINRIA/RT--0401--FR+ENG Audio, Speech, and Language Processing on the generation of allophonic rules Luc Boruta Theme : Audio, Speech, and Language Processing Perception

Paris-Sud XI, Université de

282

Synthesis of conformationally locked carbocyclic nucleoside phosphonates to probe the active site of HIV-1 RT  

PubMed Central

The conformationally locked carbocyclic nucleoside phosphonates 2 and 2? and key intermediates for the synthesis of 3 and 3? were prepared from a chiral cyclopentene derivative and epicholorohydrine, respectively. The structure of the nucleoside precursor 6 was confirmed by X-ray crystallography. These carbocyclic nucleoside phosphonates were designed to probe their binding interactions at the active site of HIV-1-RT. PMID:18776534

Saneyoshi, Hisao; Vu, B. Christie; Hughes, Stephen H.; Boyer, Paul L.; Sarafianos, Stefan G.; Marquez, Victor E.

2009-01-01

283

Regional Data Assimilation of AIRS Profiles and Radiances at the SPoRT Center  

NASA Technical Reports Server (NTRS)

This slide presentation reviews the Short Term Prediction Research and Transition (SPoRT) Center's mission to improve short-term weather prediction at the regional and local scale. It includes information on the cold bias in Weather Research and Forcasting (WRF), troposphere recordings from the Atmospheric Infrared Sounder (AIRS), and vertical resolution of analysis grid.

Zavodsky, Brad; Chou, Shih-hung; Jedlovec, Gary

2009-01-01

284

The reproduction number $R_t$ in structured and nonstructured populations  

Microsoft Academic Search

Using daily counts of newly infected individuals, Wallinga and Teunis (WT) introduced a conceptually simple method to estimate the number of secondary cases per primary case (Rt) for a given day. The method requires an estimate of the generation interval probability density function (pdf), which specifies the probabilities for the times between symptom onset in a primary case and symptom

Tom Burr; Gerardo Chowell

2009-01-01

285

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

E-print Network

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 of an inertial/vision SLAM approach, for which several improvements over existing methods have been introduced

Paris-Sud XI, Université de

286

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

E-print Network

RT-SLAM: a generic and real-time visual SLAM implementation Cyril Roussillon1,2,3 , Aur. This article presents a new open-source C++ implementa- tion to solve the SLAM problem, which is focused of an inertial/vision SLAM approach, for which several improvements over existing methods have been introduced

Paris-Sud XI, Université de

287

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

E-print Network

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

Boyer, Edmond

288

The Limitations of Fixed-Priority Interrupt Handling in PREEMPT RT and Alternative Approaches  

E-print Network

}@cs.unc.edu Abstract Threaded interrupt handling is a common technique used in real-time operating systems since thread in such cases. We then survey alternative approaches from academic literature and commercial real-time operating systems to inspire new solutions in PREEMPT RT. 1 Introduction An interrupt is a hardware signal

Anderson, James

289

Minimally Invasive Surgery plus rt-PA for Intracerebral Hemorrhage Evacuation (MISTIE) Decreases Perihematomal Edema  

PubMed Central

Background and Purpose Perihematomal edema (PHE) can worsen outcomes following ICH. Reports suggest that blood degradation products lead to PHE. We hypothesized that hematoma evacuation will reduce PHE volume and that treatment with rt-PA will not exacerbate it. Methods MISTIE II tested safety and efficacy of hematoma evacuation after ICH. We conducted a semi-automated, computerized volumetric analysis on CT to assess impact of hematoma removal on PHE and 2) effects of rt-PA on PHE. Volumetric analyses were performed on Baseline Stability (BLS) and End of Treatment (EOT) scans. Results Seventy-nine surgical and 39 medical patients from MISTIE II were analyzed. Mean hematoma volume at EOT was 19.6±14.5 cc for the surgical cohort and 40.7±13.9 cc for the medical cohort (p<0.001). Edema volume at EOT was lower for the surgical cohort: 27.7±13.3 cc than medical cohort: 41.7±14.6 cc (p<0.001). Graded effect of clot removal on PHE was observed when patients with >65%, 20-65%, and <20% ICH removed were analyzed (p<0.001). Positive correlation between PHE reduction and percent of ICH removed was identified (?=0.658; p<0.001). In the surgical cohort, 69 patients underwent surgical aspiration and rt-PA (S+rt-PA) while 10 underwent surgical aspiration only (SO). Both cohorts achieved similar clot reduction: S+rt-PA, 18.9±14.5 cc; and SO, 24.5±14.0 cc (p=0.26). Edema at EOT in S+rt-PA was 28.1±13.8 cc and 24.4±8.6 cc in SO (p=0.41). Conclusions Hematoma evacuation is associated with significant reduction in PHE. Furthermore, PHE does not appear to be exacerbated by rt-PA, making such neurotoxic effects unlikely when the drug is delivered to intracranial clot. Clinical Trial Registration Information URL: http://clinicaltrials.gov/ct2/show/NCT00224770?term=MISTIE&rank=1 Clinicaltrials.gov ID: NCT00224770 PMID:23391763

Mould, W. Andrew; Carhuapoma, J. Ricardo; Muschelli, John; Lane, Karen; Morgan, Timothy C; McBee, Nichol A; Bistran-Hall, Amanda J; Ullman, Natalie L; Vespa, Paul; Martin, Neil A; Awad, Issam; Zuccarello, Mario; Hanley, Daniel F.

2014-01-01

290

Identification of Reference Genes for qRT-PCR Analysis in Yesso Scallop Patinopecten yessoensis  

PubMed Central

Background Bivalves comprise around 30,000 extant species and have received much attention for their importance in ecosystems, aquaculture and evolutionary studies. Despite the increasing application of real-time quantitative reverse transcription PCR (qRT-PCR) in gene expression studies on bivalve species, little research has been conducted on reference gene selection which is critical for reliable and accurate qRT-PCR analysis. For scallops, systematic evaluation of reference genes that can be used among tissues or embryo/larva stages is lacking, and ?-actin (ACT) is most frequently used as qRT-PCR reference gene without validation. Results In this study, 12 commonly used candidate reference genes were selected from the transcriptome data of Yesso scallop (Patinopecten yessoensis) for suitable qRT-PCR reference genes identification. The expression of these genes in 36 tissue samples and 15 embryo/larva samples under normal physiological conditions was examined by qRT-PCR, and their expression stabilities were evaluated using three statistic algorithms, geNorm, NormFinder, and comparative ?Ct method. Similar results were obtained by the three approaches for the most and the least stably expressed genes. Final comprehensive ranking for the 12 genes combing the results from the three programs showed that, for different tissues, DEAD-box RNA helicase (HELI), ubiquitin (UBQ), and 60S ribosomal protein L16 (RPL16) were the optimal reference genes combination, while for different embryo/larva stages, gene set containing Cytochrome B (CB), Cytochrome C (CC), Histone H3.3 (His3.3), and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were recommended for qRT-PCR normalization. ACT was among the least stable genes for both adult tissues and embryos/larvae. Conclusions This work constitutes the first systematic analysis on reference genes selection for qRT-PCR normalization in scallop under normal conditions. The suitable reference genes we recommended will be useful for the identification of genes related to biological processes in Yesso scallop, and also in the reference gene selection for other scallop or bivalve species. PMID:24069432

Feng, Liying; Yu, Qian; Li, Xue; Ning, Xianhui; Wang, Jing; Zou, Jiajun; Zhang, Lingling; Wang, Shi; Hu, Jingjie; Hu, Xiaoli; Bao, Zhenmin

2013-01-01

291

Hyperacute ischemic stroke without lesions on diffusion-weighted imaging in a patient treated with rtPA thrombolysis  

PubMed Central

Key Clinical Message We report a comatose patient with severe neurological deficits who was without spontaneous language or movement. He had a good response to recombinant tissue plasminogen activator (rtPA) thrombolysis even though there were no detectable lesions on diffusion-weighted imaging (DWI). DWI is very sensitive for diagnosing hyperacute ischemic stroke, and rtPA thrombolysis is the best treatment. However, rtPA thrombolysis in ischemic stroke patients without lesions on DWI has rarely been reported. PMID:25356251

Jing, Zhen; Zhang, Shijun; Tang, Jingjing; Xu, Anding; Ruan, Yiwen; Huang, Li'an

2014-01-01

292

Developmental study of Müller cells in the rat retina using a new monoclonal antibody, RT10F7  

Microsoft Academic Search

We produced the monoclonal antibody RT10F7, characterized its antigenic specificity and expression in the adult and developing retina, in cultured retinal cells and in other parts of the central nervous system. In metabolically-labelled retinal cultures RT10F7 immunoprecipitated a protein of approximately 36?000 mol. wt.In the adult, RT10F7 stained endfeet of Müller cells in the ganglion cell layer, four horizontal bands

E. N Yamasaki; V. E Krupnik; L. L. Y Chun

1998-01-01

293

Diagnosis of Ebola haemorrhagic fever by RT-PCR in an epidemic setting.  

PubMed

This study reports the first field evaluation of a new diagnostic technique for Ebola virus disease with sensitivity and specificity. Ebola virus causes rare but fulminating outbreaks in Equatorial Africa. Rapid differentiation from other infections is critical for timely implementation of public health measures. Patients usually die before developing antibodies, necessitating rapid virus detection. A reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed, implemented and evaluated at Centre International de Recherches Médicales de Franceville (CIRMF) in Gabon, to detect Ebola viral RNA in peripheral blood mononuclear cells (PBMC). Twenty-six laboratory-confirmed patients during and 5 after the acute phase of Ebola haemorrhagic fever, 15 healthy controls and 20 febrile patients not infected with Ebola virus were studied. RT-PCR results were compared with ELISA antigen capture, and Ebola specific IgM and IgG antibody detection. Ebola virus RNA was amplified from 26/26 specimens from the acute phase, 3/5 during recovery, 0/20 febrile patients and 1/15 negative controls. Sensitivity of RT-PCR in identifying acute infection and early convalescence compared with antigen or IgM detection was 100% and 91% respectively, and specificity compared with antigen detection and IgM assay combined was 97%. Antigen capture detected only 83% of those identified by PCR, and IgM only 67%. Ebola virus RNA was detected in all 13 fatalities, only 5 of whom had IgM and none IgG. RT-PCR detected Ebola RNA in PBMC one to three weeks after disappearance of symptoms when antigen was undetectable. RT-PCR was the most sensitive method and able to detect virus from early acute disease throughout early recovery. PMID:10686031

Leroy, E M; Baize, S; Lu, C Y; McCormick, J B; Georges, A J; Georges-Courbot, M C; Lansoud-Soukate, J; Fisher-Hoch, S P

2000-04-01

294

SPoRT - An End-to-End R2O Activity  

NASA Technical Reports Server (NTRS)

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.

Jedlovec, Gary J.

2009-01-01

295

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

PubMed Central

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

2014-01-01

296

HIV-1 Env DNA Vaccine plus Protein Boost Delivered by EP Expands B- and T-Cell Responses and Neutralizing Phenotype In Vivo  

PubMed Central

An effective HIV vaccine will most likely require the induction of strong T-cell responses, broadly neutralizing antibodies (bNAbs), and the elicitation of antibody-dependent cellular cytotoxicity (ADCC). Previously, we demonstrated the induction of strong HIV/SIV cellular immune responses in macaques and humans using synthetic consensus DNA immunogens delivered via adaptive electroporation (EP). However, the ability of this improved DNA approach to prime for relevant antibody responses has not been previously studied. Here, we investigate the immunogenicity of consensus DNA constructs encoding gp140 sequences from HIV-1 subtypes A, B, C and D in a DNA prime-protein boost vaccine regimen. Mice and guinea pigs were primed with single- and multi-clade DNA via EP and boosted with recombinant gp120 protein. Sera were analyzed for gp120 binding and induction of neutralizing antibody activity. Immunization with recombinant Env protein alone induced low-titer binding antibodies with limited neutralization breath. In contrast, the synthetic DNA prime-protein boost protocol induced significantly higher antibody binding titers. Furthermore, sera from DNA prime-protein boost groups were able to neutralize a broader range of viruses in a panel of tier 1 clade B viruses as well as multiple tier 1 clade A and clade C viruses. Further investigation of synthetic DNA prime plus adaptive EP plus protein boost appears warranted. PMID:24391921

Muthumani, Kar; Wise, Megan C.; Broderick, Kate E.; Hutnick, Natalie; Goodman, Jonathan; Flingai, Seleeke; Yan, Jian; Bian, Chaoran B.; Mendoza, Janess; Tingey, Colleen; Wilson, Christine; Wojtak, Krzysztof; Sardesai, Niranjan Y.; Weiner, David B.

2013-01-01

297

The polymorphic nature of HIV type 1 env V4 affects the patterns of potential N-glycosylation sites in proviral DNA at the intrahost level.  

PubMed

We have previously shown that env V4 from HIV-1 plasma RNA is highly heterogeneous within a single patient, due to indel-associated polymorphism. In this study, we have analyzed the variability of V4 in proviral DNA from unfractionated PBMC and sorted T and non-T cell populations within individual patients. Our data show that the degree of sequence variability and length polymorphism in V4 from HIV provirus is even higher than we previously reported in plasma. The data also show that the sequence of V4 depends largely on the experimental approach chosen. We could observe no clear trend for compartmentalization of V4 variants in specific cell types. Of interest is the fact that some variants that had been found to be predominant in plasma were not detected in any of the cell subsets analyzed. Consistently with our observations in plasma, V3 was found to be relatively conserved at both interpatient and intrapatient level. Our data show that V4 polymorphism involving insertions and deletions in addition to point mutations results in changes in the patterns of sequons in HIV-1 proviral DNA as well as in plasma RNA. These rearrangements may result in the coexistence, within the same individual, of a swarm of different V4 regions, each characterized by a different carbohydrate surface shield. Further studies are needed to investigate the mechanism responsible for the variability observed in V4 and its role in HIV pathogenesis. PMID:19239359

Belair, Manon; Dovat, Magali; Foley, Brian; Mayerat, Claude; Pantaleo, Giuseppe; Graziosi, Cecilia

2009-02-01

298

Prevalence of fowl glioma-inducing virus in chickens of zoological gardens in Japan and nucleotide variation in the env gene.  

PubMed

Fowl glioma-inducing virus (FGV), which belongs to subgroup A of avian leukosis virus (ALV), is tumorigenic in the nervous system. In a zoological garden in Japan, approximately 40% of chickens, including Japanese fowls, were infected with FGV. Because this zoological garden plays a role as a major supplier of Japanese fowl for other zoological gardens, FGV infection is suspected to have spread among ornamental chickens. In this study, the prevalence of the disease was examined in a total of 129 chickens in three other zoological gardens by nested polymerase chain reaction (PCR), reverse transcription nested PCR and enzyme-linked immunosorbent assay. Twenty-six to 56 percent of the fowls in each of the examined gardens were positive by nested PCR. The phylogenetic analysis revealed that the 3' untranslated region, including the specific sequence of FGV, of the 14 isolated ALVs showed high sequence identity and a close relationship with FGV. In addition, the env gene of the isolates frequently showed mutations and deletions of nucleotides. These results suggest that FGV is prevalent among ornamental chickens kept in zoological gardens in Japan. PMID:18525168

Hatai, Hitoshi; Ochiai, Kenji; Murakami, Mariko; Imanishi, Syunsuke; Tomioka, Yukiko; Toyoda, Takeshi; Ohashi, Kazuhiko; Umemura, Takashi

2008-05-01

299

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

NASA Technical Reports Server (NTRS)

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.

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

2011-01-01

300

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

NASA Astrophysics Data System (ADS)

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.

Jedlovec, G.; Fuell, K.; Smith, M. R.; Stano, G. T.; Molthan, A.

2011-12-01

301

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

ERIC Educational Resources Information Center

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…

Zahedi, Karynn Jensen

2010-01-01

302

SOIL MIX REMEDIATION TECHNOLOGY (PROJECT SMiRT) In October 2007, Cambridge University launched the largest Technology Strategy  

E-print Network

SOIL MIX REMEDIATION TECHNOLOGY (PROJECT SMiRT) OVERVIEW In October 2007, Cambridge University. Project SMiRT (Soil Mix Remediation Technology) is a £1.24M project led by the contractor Bachy Soletanche launched the largest Technology Strategy Board funded project on Contaminated Land Remediation Technologies

Travis, Adrian

303

Emulating a crowded intracellular environment in vitro dramatically improves RT-PCR performance  

SciTech Connect

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.

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

304

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

PubMed Central

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.

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

2013-01-01

305

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

NASA Technical Reports Server (NTRS)

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.

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

2012-01-01

306

The carbon Cepheid RT Trianguli Australis: additional evidence of triple-? and CNO cycling  

NASA Astrophysics Data System (ADS)

We have used echelle spectra of resolving power 35000 to derive chemical abundances and the 12C/13C ratio in the 1.9-d carbon Cepheid RT TrA and the Cepheid U TrA, employed as a comparison star. We confirm that RT TrA is very metal-rich with [Fe/H]=+0.4. In addition, C and N are substantially in excess, and a small deficiency in O is present. We interpret these anomalies as resulting from the appearance on the stellar surface of material enriched in 12C by the 3-? process, followed by CNO cycling to convert 12C to 13C and 14N. In addition, some 16O has been processed to 14N. The partial processing of 16O to 14N indicates that substantial 17O may be present. Proton capture seems to have enhanced 23Na from the Ne isotopes.

Wallerstein, George; Matt, Sean; Gonzalez, Guillermo

2000-01-01

307

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

PubMed

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

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

2014-11-01

308

Evaluating the Impact of AIRS Observations on Regional Forecasts at the SPoRT Center  

NASA Technical Reports Server (NTRS)

NASA Short-term Prediction Research and Transition (SPoRT) Center collaborates with operational partners of different sizes and operational goals to improve forecasts using targeted projects and data sets. Modeling and DA activities focus on demonstrating utility of NASA data sets and capabilities within operational systems. SPoRT has successfully assimilated the Atmospheric Infrared Sounder (AIRS) radiance and profile data. A collaborative project is underway with the Joint Center for Satellite Data Assimilation (JCSDA) to use AIRS profiles to better understand the impact of AIRS radiances assimilated within Gridpoint Statistical Interpolation (GSI) in hopes of engaging the operational DA community in a reassessment of assimilation methodologies to more effectively assimilate hyperspectral radiances.

Zavodsky, Bradley

2011-01-01

309

A DICOM-RT based ePR radiation therapy information system for managing brain tumor patients  

NASA Astrophysics Data System (ADS)

The need for comprehensive clinical image data and relevant information in image-guided Radiation Therapy (RT) is becoming steadily apparent. Multiple standalone systems utilizing the most technological advancements in imaging, therapeutic radiation, and computerized treatment planning systems acquire key data during the RT treatment course of a patient. One example are patients treated for brain tumors of greater sizes and irregular shapes that utilize state-of-the-art RT technology to deliver pinpoint accurate radiation doses. One such system, the Cyberknife, is a radiation treatment system that utilizes image-guided information to control a multi-jointed, six degrees of freedom, robotic arm to deliver precise and required radiation dose to the tumor site of a cancer patient. The image-guided system is capable of tracking the lesion orientations with respect to the patient"s position throughout the treatment process. This is done by correlating live radiographic images with pre-operative, CT and MR imaging information to determine relative patient and tumor position repeatedly over the course of the treatment. The disparate and complex data generated by the Cyberknife system along with related data is scattered throughout the RT department compromising an efficient clinical workflow since the data crucial for a clinical decision may be time-consuming to retrieve, temporarily missing, or even lost. To address these shortcomings, the ACR-NEMA Standards Committee extended its DICOM (Digital Imaging & Communications in Medicine) Standard from Radiology to RT by ratifying seven DICOM RT objects starting in 1997. However, they are rarely used by the RT community in daily clinical operations. In the past, the research focus of an RT department has primarily been developing new protocols and devices to improve treatment process and outcomes of cancer patients with minimal effort dedicated to integration of imaging and information systems. Our research, tightly-coupling radiology and RT information systems, represents a new frontier for medical informatics research that has never been previously considered. By combining our past experience in medical imaging informatics, DICOM-RT expertise, and system integration, we propose to test our hypothesis using a brain tumor case model that a DICOM-RT electronic patient record (ePR) system can improve clinical workflow efficiency for treatment and management of patients. This RT ePR system integrated with clinical images and RT data can impact the RT department in a similar fashion as PACS has already successfully done for Radiology. As a first step, the specific treatment case of patients with brain tumors specifically patients treated with the Cyberknife system will be the initial proof of concept for the research design, implementation, evaluation, and clinical relevance.

Liu, Brent J.; Law, Maria; Huang, H. K.; Zee, C. S.; Chan, Lawrence

2005-04-01

310

Office of Gift Planning 2013 AnnuAl RepoRt  

E-print Network

Office of Gift Planning 2013 AnnuAl RepoRt AlWAYS Be a pARt of pRInCeton #12;tAB l e of Con ten t to Give Gift Planning Program Overview Charitable Remainder Trusts Charitable Gift Annuities Pooled Income '80, and grandson Matthew W. McCalpin '14 #12;The Office of Gift Planning, within Princeton's Office

311

RT-EP: A Fixed-Priority Real Time Communication Protocol over Standard Ethernet  

Microsoft Academic Search

This paper presents the design and implementation of RT-EP (Real-Time Ethernet Protocol), which is a software-based token-passing Ethernet protocol for multipoint communications in real-time applica- tions, that does not require any modification to existing Ethernet hardware. The protocol allows a fixed priority to be assigned to each message, and consequently well-known schedulability analysis tech- niques can be applied. A precise

José María Martínez; Michael González Harbour

2005-01-01

312

Applicability of RNA standards for evaluating RT-qPCR assays and platforms  

Microsoft Academic Search

The availability of diverse RT-qPCR assay formats and technologies hinder comparability of data between platforms. Reference\\u000a standards to facilitate platform evaluation and comparability are needed. We have explored using universal RNA standards for\\u000a comparing the performance of a novel qPCR platform (Fluidigm® BioMark™) against the widely used ABI 7900HT system. Our results show that such standards may form part of

Alison S Devonshire; Ramnath Elaswarapu; Carole A Foy

2011-01-01

313

NASA SPoRT Initialization Datasets for Local Model Runs in the Environmental Modeling System  

NASA Technical Reports Server (NTRS)

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.

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

314

Miniature RT-PCR systems integrated with a sample pretreatment device for virus detection  

Microsoft Academic Search

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

Kang-Yi Lien; Wang-Ying Lin; Chih-Hao Wang; Huan-Yao Lei; Gwo-Bin Lee

2007-01-01

315

Real-time challenge balance in an RTS game using rtNEAT  

Microsoft Academic Search

This paper explores using the NEAT and rtNEAT neuro-evolution methodologies to generate intelligent opponents in real-time strategy (RTS) games. The main objective is to adapt the challenge generated by the game opponents to match the skill of a player in real-time, ultimately leading to a higher entertainment value perceived by a human player of the game. Results indicate the effectiveness

Jacob Kaae Olesen; Georgios N. Yannakakis; John Hallam

2008-01-01

316

Quantification of mRNA using real-time RT-PCR  

Microsoft Academic Search

The real-time reverse transcription polymerase chain reaction (RT-qPCR) addresses the evident requirement for quantitative data analysis in molecular medicine, biotechnology, microbiology and diagnostics and has become the method of choice for the quantification of mRNA. Although it is often described as a “gold” standard, it is far from being a standard assay. The significant problems caused by variability of RNA

Tania Nolan; Rebecca E Hands; Stephen A Bustin

2006-01-01

317

Real-time RT-PCR methodology for quantification of thiopurine methyltransferase gene expression  

Microsoft Academic Search

ObjectiveThe aim of the present study was to develop a real-time reverse-transcription polymerase chain reaction (RT-PCR) methodology for the quantification of thiopurine methyltransferase (TPMT) gene expression in whole blood and compare it with the TPMT enzyme activity measured in red blood cells.MethodsTPMT gene expression was quantified relative to the housekeeping gene cyclophilin (huCYC) and expressed as a TPMT\\/huCYC ratio. TPMT

Malin Lindqvist; Sven Almer; Curt Peterson; Peter Söderkvist

2003-01-01

318

Multiple gene detection by in situ RT-PCR in isolated plant cells and tissues.  

PubMed

With the number of functional genomic approaches in plant biology increasing daily, the demand for rapid and reliable RNA localization techniques for gene characterization is being felt. We present herein a novel, liquid phase in situ RT-PCR (IS-RT-PCR) protocol using a combination of gene-specific fluorescent primers and spectral confocal microscopy to localize target RNA in epicotyl sections and xylogenic suspension cultures of Zinnia elegans. Potential sources of artefacts from fixation to gene detection were systematically eliminated using both fluorescent primers and nucleotides for 18S rRNA gene detection, resulting in a set of optimal parameters for IS-RT-PCR that may be readily adapted to any target gene. By judiciously choosing fluorescent primers with non-overlapping fluorochromes, we have shown that our technique is readily adapted to multiplex IS-RT-PCR, enabling the simultaneous localization of more than one gene within a complex tissue or heterogeneous cell population. A 6-carboxy-2',4,4',5',7,7'-hexachlorofluorescein (6-HEX)-labelled primer and a tetrachloro-6-carboxy-fluorescein (TET)-labelled primer were designed for two marker genes associated with programmed cell death in tracheary elements (TEs): an endonuclease (Zen1) and a cysteine protease (ZcP4), respectively. An additional Cyan5 (Cy5)-labelled primer was used to monitor 18SrRNA expression. As expected, the 18S signal was constitutively expressed throughout epicotyls sections and living cells in xylogenic in vitro cultures, whereas Zen1 and ZcP4 were co-localized in forming TEs both in planta and in vitro. Analogous to clustering analysis of gene expression using microarrays to elucidate common metabolic pathways and developmental processes, this novel technique is perfectly adapted to gaining a better understanding of gene function via the coordinated expression of genes in specific cell types of complex tissues and cell populations. PMID:15341636

Pesquet, Edouard; Barbier, Odile; Ranocha, Philippe; Jauneau, Alain; Goffner, Deborah

2004-09-01

319

Summary of Proton Test on the Actel RT54SX16 Prototype at Indiana University  

NASA Technical Reports Server (NTRS)

A summary of tests performed at the Indiana University Cyclotron Facility, on the Actel RT54SX16 prototype circuit device is presented. The devices' performances in the test is shown in both a table and a graph and was typical for devices of this class. Another summary of tests performed at the Indiana University Cyclotron Facility, on the Chip Express QYH530 device is presented.The device's performance in the test is shown in a graph and tables.

Katz, Richard

1998-01-01

320

Evaluation of reference genes for gene expression analysis using quantitative RT-PCR in Azospirillum brasilense.  

PubMed

Azospirillum brasilense is a nitrogen fixing bacterium that has been shown to have various beneficial effects on plant growth and yield. Under normal conditions A. brasilense exists in a motile flagellated form, which, under starvation or stress conditions, can undergo differentiation into an encapsulated, cyst-like form. Quantitative RT-PCR can be used to analyse changes in gene expression during this differentiation process. The accuracy of quantification of mRNA levels by qRT-PCR relies on the normalisation of data against stably expressed reference genes. No suitable set of reference genes has yet been described for A. brasilense. Here we evaluated the expression of ten candidate reference genes (16S rRNA, gapB, glyA, gyrA, proC, pykA, recA, recF, rpoD, and tpiA) in wild-type and mutant A. brasilense strains under different culture conditions, including conditions that induce differentiation. Analysis with the software programs BestKeeper, NormFinder and GeNorm indicated that gyrA, glyA and recA are the most stably expressed reference genes in A. brasilense. The results also suggested that the use of two reference genes (gyrA and glyA) is sufficient for effective normalisation of qRT-PCR data. PMID:24841066

McMillan, Mary; Pereg, Lily

2014-01-01

321

SPoRT Participation in the GOES-R and JPSS Proving Grounds  

NASA Technical Reports Server (NTRS)

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.

Jedlovec, Gary; Fuell, Kevin; Smith, Matthew

2013-01-01

322

Quantitative analysis of CD34+ stem cells using RT-PCR on whole cells.  

PubMed

We have employed RT-PCR of whole cells to develop a quantitative method for estimating the number of rare cells expressing a unique mRNA in a large, mixed population of cells. We have demonstrated that RT-PCR can be done on whole cells without the need for extraction of the RNA. This allows for a great saving of time and effort, as well as allowing quantitative analysis to be based on the total number of cells analyzed in a given aliquot and the presence or absence of the specific RT-PCR product. We have employed a limiting dilution series on whole cells, with multiple aliquots at each cell concentration to achieve more statistical power in the analysis of a rare cell type. We have used a nested amplification of the CD34 mRNA to be able to detect a single cell expressing the CD34 mRNA in a larger population of non-CD34-expressing cells. We demonstrate that by using this technique, cells from blood and bone marrow containing the CD34 mRNA can be followed quantitatively during a multistep purification involving immunoadsorption followed by fluorescence-activated cell sorting. We also demonstrate that many cells that express the CD34 protein on their surface no longer contain detectable levels of CD34 mRNA, a phenomenon that appears to be developmentally regulated. PMID:7518719

Molesh, D A; Hall, J M

1994-04-01

323

Identification of Simbu, California and Bunyamwera serogroup bunyaviruses by nested RT-PCR.  

PubMed

We describe a reverse transcription-polymerase chain reaction (RT-PCR) with primers that anneal to the 5' and 3' ends and amplify the Bunyavirus S RNA segments. The RT-PCR was done on the fluids of C6/36 cells infected with each of 21 bunyaviruses. The bunyaviruses studied, with the exception of Catu virus, produced amplicons having 700 to 1300 base pairs and probably contained the whole S RNA segment sequence. A nested PCR performed with these amplicons distinguished California and most Bunyamwera serogroup viruses from other bunyaviruses by use of BBC specific internal primers for the S RNA segment, and distinguished Simbu serogroup viruses from others by use of BS specific internal primers. The nested-PCR amplicons of Guaroa, Maguari, California encephalitis, Bunyamwera, and Oropouche viruses were sequenced. The sequences were aligned with previously known sequences of the S RNA segment of the same viruses, showing a high degree of homology and thus confirming the specific origin of these amplicons. The nested RT-PCR is suitable as a specific screening for most California and Bunyamwera serogroup and Simbu serogroup viruses depending on the use of BBC or BS internal primers. Oropouche virus is an important public health problem in Brazil and the nested PCR with BS primers could be used for the detection of this virus in tissue culture and mouse brain isolates as well as in clinical samples. PMID:11280054

Moreli, M L; Aquino, V H; Figueiredo, L T

2001-01-01

324

Development of a versatile and stable internal control system for RT-qPCR assays.  

PubMed

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

Felder, Eva; Wölfel, Roman

2014-11-01

325

Short communication: retrospective study to time the introduction of HIV type 1 non-B subtypes in Lyon, France, using env genes obtained from primary infection samples.  

PubMed

Using blood samples from primary HIV-1 infection (PHI) patients obtained in Lyon, France, we characterized the newly transmitted HIV-1 variants in this area during the 1992-1996 period. As PHI samples allowed the precise timing of the transmission event, we were able to date the introduction of non-B subtypes or recombinant forms of the virus in Lyon. Genomic DNA from 18 HIV-1-positive patients at primary infection was used to amplify the full-length env gene by nested PCR; after cloning, the gene was sequenced for subsequent phylogenetic analysis. Several non-B subtypes and recombinant forms of HIV-1 were identified among the 18 patients studied (1 subtype F1, 1 CRF01-AE, 2 subtype G and 2 CRF02-AG). We also found a new J/K recombinant form transmitted in 1995 and never described until now. The introduction of CRF02-AG in Lyon, France, occurred prior to 1992 and six transmission events including non-B subtypes were documented in the following 4 years. Heterosexual contacts appeared as the main introduction pathway for non-B subtypes or recombinant forms. Nevertheless, as transmission of these viruses occurred not only during travel to endemic regions, but also in France or Germany, we conclude that non-B strains entered Europe before the studied period. This retrospective study showed that even if subtype B remained prevalent in the spreading HIV-1 infection in Lyon between 1992 and 1996, non-B subtypes and circulating recombinant forms represented a significantly growing part. PMID:15307910

Vachot, Laurence; Ataman-Onal, Yasemin; Terrat, Céline; Durand, Pierre-Yves; Ponceau, Bénédicte; Biron, François; Verrier, Bernard

2004-07-01

326

Rapid detection and high occurrence of porcine rotavirus A, B, and C by RT-qPCR in diagnostic samples.  

PubMed

Rotaviruses are important cause of diarrhea in animals, including humans. Currently, rotavirus species A, B, C, E, and H (RVA-RVC, RVE, and RVH) have been identified in pigs. Traditionally, RVA has been considered the primary cause of diarrhea in pigs, and RVB and RVC had been described sporadically in pigs until recently. Qualitative porcine RVA, RVB, and RVC RT-PCR (RT-qPCR) assays were designed and 7508 porcine diarrheic samples, submitted to University of Minnesota, were tested to estimate the percentage of RVA, RVB, and RVC over a period of approximately 2 years (from 2009 to 2011). The individual RVA and RVC RT-qPCR assays were multiplex into a single RT-qPCR while the RVB RT-qPCR assay remained as an individual RT-qPCR. In total, 83% of the samples were positive for RVA, RVB, or RVC. As expected, RVA was detected at the highest overall percentage (62%). However, 33% and 53% of the samples were positive for RVB and RVC, respectively, indicating that both RVB and RVC are also epidemiologically important in the swine population. RVC was most predominant in young pigs (1-20 days of age), while RVA and RVB were most predominant in ?21 day old pigs. As diagnostic tools, the developed RT-qPCR assays could successfully discriminate among infecting RV species, which could lead to better surveillance and epidemiological studies for ultimately better prevention and control strategies. PMID:25194889

Marthaler, Douglas; Homwong, Nitipong; Rossow, Kurt; Culhane, Marie; Goyal, Sagar; Collins, James; Matthijnssens, Jelle; Ciarlet, Max

2014-12-01

327

A DICOM-RT radiation oncology ePR with decision support utilizing a quantified knowledge base from historical data  

NASA Astrophysics Data System (ADS)

During the last 2 years we have been working on developing a DICOM-RT (Radiation Therapy) ePR (Electronic Patient Record) with decision support that will allow physicists and radiation oncologists during their decision-making process. This ePR allows offline treatment dose calculations and plan evaluation, while at the same time it compares and quantifies treatment planning algorithms using DICOM-RT objects. The ePR framework permits the addition of visualization, processing, and analysis tools, which combined with the core functionality of reporting, importing and exporting of medical studies, creates a very powerful application that can improve the efficiency while planning cancer treatments. Usually a Radiation Oncology department will have disparate and complex data generated by the RT modalities as well as data scattered in RT Information/Management systems, Record & Verify systems, and Treatment Planning Systems (TPS) which can compromise the efficiency of the clinical workflow since the data crucial for a clinical decision may be time-consuming to retrieve, temporarily missing, or even lost. To address these shortcomings, the ACR-NEMA Standards Committee extended its DICOM (Digital Imaging & Communications in Medicine) standard from Radiology to RT by ratifying seven DICOM RT objects starting in 1997 [1,2]. However, they are not broadly used yet by the RT community in daily clinical operations. In the past, the research focus of an RT department has primarily been developing new protocols and devices to improve treatment process and outcomes of cancer patients with minimal effort dedicated to integration of imaging and information systems. Our attempt is to show a proof-of-concept that a DICOM-RT ePR system can be developed as a foundation to perform medical imaging informatics research in developing decision-support tools and knowledge base for future data mining applications.

Documet, Jorge R.; Liu, Brent; Le, Anh; Law, Maria

2008-03-01

328

A DICOM-RT Based ePR radiation therapy information system for decision-support of brain tumor patients  

NASA Astrophysics Data System (ADS)

The need for comprehensive clinical image data and relevant information in image-guided Radiation Therapy (RT) is becoming steadily apparent. Multiple standalone systems utilizing the most technological advancements in imaging, therapeutic radiation, and computerized treatment planning systems acquire key data during the RT treatment course of a patient. One example are patients treated for brain tumors of greater sizes and irregular shapes that utilize state-of-the-art RT technology to deliver pinpoint accurate radiation doses. Various treatment options are available to the patient from Radiation Therapy to Stereotactic Radiosurgery and utilize different RT modalities. The disparate and complex data generated by the RT modalities along with related data scattered throughout the RT department in RT Information/Management systems, Record & Verify systems, and Treatment Planning Systems (TPS) compromise an efficient clinical workflow since the data crucial for a clinical decision may be time-consuming to retrieve, temporarily missing, or even lost. To address these shortcomings, the ACR-NEMA Standards Committee extended its DICOM (Digital Imaging & Communications in Medicine) Standard from Radiology to RT by ratifying seven DICOM RT objects starting in 1997. However, they are rarely used by the RT community in daily clinical operations. In the past, the research focus of an RT department has primarily been developing new protocols and devices to improve treatment process and outcomes of cancer patients with minimal effort dedicated to integration of imaging and information systems. By combining our past experience in medical imaging informatics research, DICOM-RT expertise, and system integration, our research involves using a brain tumor case model to show proof-of-concept that a DICOM-Standard electronic patient record (ePR) system can be developed as a foundation to perform medical imaging informatics research in developing decision-support tools and knowledge base for future data mining applications. As an initial first step, we will develop a methodology to perform medical imaging informatics research on a clinical scenario where brain tumor patients undergo treatment planning for either radiosurgery or radiation therapy. Specifically, we will research the "inverse treatment planning" process that is used for those types of treatments and integrate decision-support knowledge and tools designed to assist in the decision-making process, thus introducing an improved "knowledge-enhanced treatment planning" approach.

Liu, B. J.; Law, M.; Huang, H. K.; Zee, C. S.; Chan, L.

2006-03-01

329

Identification of Reference Genes for Quantitative RT-PCR in Ascending Aortic Aneurysms  

PubMed Central

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

Henn, Dominic; Bandner-Risch, Doris; Perttunen, Hilja; Schmied, Wolfram; Porras, Carlos; Ceballos, Francisco; Rodriguez-Losada, Noela; Schafers, Hans-Joachim

2013-01-01

330

Selecting control genes for RT-QPCR using public microarray data  

PubMed Central

Background Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different samples uses one to several control genes (e.g. housekeeping genes), from which a baseline reference level is constructed. Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones. Results We propose a novel approach for scoring and ranking candidate genes for their suitability as control genes. Our approach relies on publicly available microarray data and allows the combination of multiple data sets originating from different platforms and/or representing different pathologies. The use of microarray data allows the screening of tens of thousands of genes, producing very comprehensive lists of candidates. We also provide two lists of candidate control genes: one which is breast cancer-specific and one with more general applicability. Two genes from the breast cancer list which had not been previously used as control genes are identified and validated by RT-QPCR. Open source R functions are available at Conclusion We proposed a new method for identifying candidate control genes for RT-QPCR which was able to rank thousands of genes according to some predefined suitability criteria and we applied it to the case of breast cancer. We also empirically showed that translating the results from microarray to PCR platform was achievable. PMID:19187545

Popovici, Vlad; Goldstein, Darlene R; Antonov, Janine; Jaggi, Rolf; Delorenzi, Mauro; Wirapati, Pratyaksha

2009-01-01

331

Chemical composition and RT[sub NDT] determinations for Midland weld WF-70  

SciTech Connect

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.

Nanstad, R.K.; McCabe, D.E.; Swain, R.L.; Miller, M.K. (Oak Ridge National Lab., TN (United States))

1992-12-01

332

Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL.  

PubMed

PharmGKB is a leading resource of high quality pharmacogenomics data that provides information about how genetic variations modulate an individual's response to drugs. PharmGKB contains information about genetic variations, pharmacokinetic and pharmacodynamic pathways, and the effect of variations on drug-related phenotypes. These relationships are represented using very general terms, however, and the precise semantic relationships among drugs, and diseases are not often captured. In this paper we develop a protocol to detect and disambiguate general clinical associations between drugs and diseases using more precise annotation terms from other data sources. PharmGKB provides very detailed clinical associations between genetic variants and drug response, including genotype-specific drug dosing guidelines, and this procedure will armGKB. The availability of more detailed data will help investigators to conduct more precise queries, such as finding particular diseases caused or treated by a specific drug. We first mapped drugs extracted from PharmGKB drug-disease relationships to those in the National Drug File Reference Terminology (NDF-RT) and to Structured Product Labels (SPLs). Specifically, we retrieved drug and disease role relationships describing and defining concepts according to their relationships with other concepts from NDF-RT. We also used the NCBO (National Center for Biomedical Ontology) annotator to annotate disease terms from the free text extracted from five SPL sections (indication, contraindication, ADE, precaution, and warning). Finally, we used the detailed drug and disease relationship information from NDF-RT and the SPLs to annotate and disambiguate the more general PharmGKB drug and disease associations. PMID:23727027

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

2013-08-01

333

Quantitative RT-PCR Measurement of Human Cytochrome P-450s: Application to Drug Induction Studies  

Microsoft Academic Search

A quantitative RT-PCR assay has been developed that is able to measure the mRNA content of the major human CYPs (1A1, 1A2, 2A6, 2B6, 2C9, 2C19, 2D6, 2E1, 3A4, and 3A5). The technique is highly specific, reproducible, rapid, and sensitive enough to quantitate low and high abundant mRNAs. The PCR primers were selected to specifically match each CYP mRNA, to

Cristina Rodr??guez-Antona; Ramiro Jover; Maria-José Gómez-Lechón; José V. Castell

2000-01-01

334

The S2 VLBI Systems: DAS, RT/PT and Correlator  

NASA Technical Reports Server (NTRS)

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.

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

335

Challenges in Transitioning Research Data to Operations: The SPoRT Paradigm  

NASA Technical Reports Server (NTRS)

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.

Jedloved, Gary J.; Smith, Matt; McGrath, Kevin

2010-01-01

336

NASA/SPoRT's GOES-R Activities in Support of Product Development, Management, and Training  

NASA Astrophysics Data System (ADS)

The NASA Short-term Prediction Research and Transition (SPoRT) Center supports many activities within the GOES-R Proving Grounds (PG). These include the development of imagery from existing instrumentation as a proxy to future Advanced Baseline Imager (ABI) capabilities on GOES-R. The Moderate Resolution Imaging Spectroradiometer (MODIS) and the Visible/Infrared Imager/Radiometer Suite (VIIRS) instruments are used to provide a glimpse of the multi-spectral capabilities that will become the norm as the number of channels and data rate dramatically increase with GOES-R. The NOAA/NWS has plans to provide operational users with all ABI channels at the highest resolution. Data fusion of individual channels into composite red, green, and blue imagery products will assist the end user with this future wave of information. While increasing the efficiency in the operational use of ABI channels, these composites provide only qualitative information. Within the GOES-R PG, SPoRT and other partners are exploring ways to include quantitative information as part of the composite imagery. However, limitations in local hardware processing and/or data bandwidth for users of the GOES-R data stream are challenges to overcome. This presentation will discuss the creation of these composite images as well as possible solutions to address these processing challenges. In a similar manner the Geostationary Lightning Mapper (GLM) to be launched on GOES-R presents several data management challenges. The GLM is a pioneering instrument to quantify total lightning from a geostationary platform. The expected data frequency from the GLM is to be at a sub-minute interval. Users of such a data set may have little experience in handling such a rapid update of information. To assist users, SPoRT is working with the NWS to develop tools within the user's decision support system to allow tracking and analysis of total lightning from a storm-based perspective. This presentation will discuss the challenges and progress of this tool development work. With new data and products comes the need for user Training. Within the GOES-R PG SPoRT is supporting the demonstration of these future products by providing various training materials to end users. A summary of training provided to operational users will be discussed.

Fuell, K. K.; Jedlovec, G.; Molthan, A.; Stano, G. T.

2012-12-01

337

SPoRT: Transitioning NASA and NOAA Experimental Data to the Operational Weather Community  

NASA Technical Reports Server (NTRS)

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, Suomi NPP, and planned 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 volumes 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.

Jedlovec, Gary J.

2013-01-01

338

Intra-arterial administration of recombinant tissue-type plasminogen activator (rt-PA) causes more intracranial bleeding than does intravenous rt-PA in a transient rat middle cerebral artery occlusion model  

PubMed Central

Background Intra-arterial (IA) administration of rt-PA for ischemic stroke has the potential for greater thrombolytic efficacy, especially for a large thrombus in the M1 or M2 segment of the middle cerebral artery (MCA). Intracranial hemorrhage (ICH) is a concern with IA or intravenous (IV) administration especially as the therapeutic window is extended. However, because IA administration delivers a higher local concentration of agent, the incidence and severity of ICH may be greater than with similar doses IV. We investigated the safety of rt-PA administration by IA compared to IV infusion following 6 hours of MCA occlusion (MCAo) with reflow in the spontaneously hypertensive rat (SHR). Methods Male SHRs were subjected to 6 hours MCAo with 18 hours reflow using a snare ligature model. They were treated with IA saline, IA rt-PA (1, 5, 10, 30 mg/kg), or IV rt-PA (10 and 30 mg/kg) by a 10 to 60 minute infusion beginning approximately 1 minute before reflow. The rats were recovered for 24 hours after MCAo onset at which time Bleeding Score, infarct volume, and Modified Bederson Score were measured. Results Greater hemorrhagic transformation occurred with 10 and 30 mg/kg rt-PA administered IA than IV. The IV 10 mg/kg rt-PA dosage induced significantly less bleeding than did the 1 or 5 mg/kg IA groups. No significant increase in infarct volume was observed after IA or IV treatment. Rats treated with 30 mg/kg rt-PA by either the IA or IV route had greater neurological dysfunction compared to all other groups. Conclusions Administration of rt-PA by the IA route following 6 hours of MCAo results in greater ICH and worse functional recovery than comparable dosages IV. Significantly greater bleeding was observed when the IA dose was a tenth of the IV dose. The increased bleeding did not translate in larger infarct volumes. PMID:21933438

2011-01-01

339

Reduced Estimated Glomerular Filtration Rate Is Associated with Stroke Outcome after Intravenous rt-PA: The Stroke Acute Management with Urgent Risk-Factor Assessment and Improvement (SAMURAI) rt-PA Registry  

Microsoft Academic Search

Background: The aim of this study was to determine whether renal dysfunction affects the outcome of stroke patients treated with recombinant tissue plasminogen activator (rt-PA). Methods: A retrospective, multicenter, observational study was conducted to identify the effects of underlying risk factors on intravenous rt-PA therapy using 0.6 mg\\/kg alteplase in 10 stroke centers in Japan. Consecutive stroke patients with a

Masaki Naganuma; Masatoshi Koga; Yoshiaki Shiokawa; Jyoji Nakagawara; Eisuke Furui; Kazumi Kimura; Hiroshi Yamagami; Yasushi Okada; Yasuhiro Hasegawa; Kazuomi Kario; Satoshi Okuda; Kazutoshi Nishiyama; Kazuo Minematsu; Kazunori Toyoda

2011-01-01

340

Reliable confirmation of antibodies to human immunodeficiency virus type 1 (HIV-1) with an enzyme-linked immunoassay using recombinant antigens derived from the HIV-1 gag, pol, and env genes.  

PubMed Central

An enzyme-linked immunoassay (ELISA) using six recombinant proteins corresponding to large segments of the human immunodeficiency virus type 1 (HIV-1) gag, pol, and env gene products (HIVAGEN; SmithKline Bio-Science Laboratories, Van Nuys, Calif.) was developed to confirm the presence of antibodies to HIV-1 in sera reactive in the whole-cell-derived virion screening ELISAs. Serum samples for testing were obtained from healthy seronegative blood donors and from the different categories of HIV-infected individuals (asymptomatic, acquired immunodeficiency syndrome [AIDS]-related complex, and AIDS). A positive reaction was defined as reactivity against an env and at least one other (either gag or pol) HIV-1 gene product; negative was defined as no reaction with any antigen; and indeterminate was defined as reactivity with gag or pol (or both) or with env alone. None of the 1,180 serum samples from healthy seronegative blood donors gave a positive result, and only 49 of these samples (4%) gave indeterminate results. The recombinant HIV-1 antigen ELISA panel identified seropositive individuals with a high degree of accuracy, as a positive reaction was seen with 99.3% of asymptomatic healthy seropositive individuals, 98.1% of patients with AIDS-related complex, and 90.4% of patients with AIDS. None of the 725 HIV-1-seropositive subjects had a negative test result. Reactivity with the Kp41 antigen, corresponding to an amino-terminal portion of the gp41 envelope glycoprotein, by itself demonstrated 100% sensitivity and specificity in distinguishing seronegative from seropositive sera. A subset of seronegative and seropositive samples were tested both with the recombinant HIV-1 antigen ELISA panel and by Western blot (Du Pont Co.). The recombinant HIV-1 antigen ELISA panel accurately identified more seropositive and seronegative samples and had fewer indeterminate results than did Western blot (interpreted by Du Pont criteria). PMID:2787334

Ng, V L; Chiang, C S; Debouck, C; McGrath, M S; Grove, T H; Mills, J

1989-01-01

341

nature structural & molecular biology VOLUME 19 NUMBER 7 JULY 2012 671 a rt i c l e s  

E-print Network

nature structural & molecular biology VOLUME 19 NUMBER 7 JULY 2012 671 a rt i c l e s Genomic DNA damage: one involving DNA glycosylases, one involving the suicidal O6methylguanineDNA methyltransferases

Dinner, Aaron

342

[The genomic organization and localization on the chromosomes of the HvRT family of DNA repetitive sequences in barley].  

PubMed

HvRT family of repetitive DNA sequences from barley genome appears to have complex hierarchical organization. Tandem repetition of 118-bp monomers constitutes lower level of HvRT-family organization. Amplification units of the higher level consist of several contiguous 118-bp monomers. RFLP between different species and cultivars of barley resulted from the differences in the higher-order repeat structure. Individual chromosomes of barley contain specific HvRT subfamilies. This family also possesses separate domains differing in the restriction enzyme sites density. HvRT family is presented in the genomes of H. vulgare, H. leporinum, H. murinum, H. jubatum, but is absent in the genomes of H. marinum, H. geniculatum and wheat. PMID:2238105

Belostotski?, D A; Kolchinski?, A M; Anan'ev, E V

1990-01-01

343

NASA SPoRT Modeling and Data Assimilation Research and Transition Activities Using WRF, LIS and GSI  

NASA Technical Reports Server (NTRS)

weather research and forecasting ===== The NASA Short-term Prediction Research and Transition (SPoRT) program has numerous modeling and data assimilation (DA) activities in which the WRF model is a key component. SPoRT generates realtime, research satellite products from the MODIS and VIIRS instruments, making the data available to NOAA/NWS partners running the WRF/EMS, including: (1) 2-km northwestern-hemispheric SST composite, (2) daily, MODIS green vegetation fraction (GVF) over CONUS, and (3) NASA Land Information System (LIS) runs of the Noah LSM over the southeastern CONUS. Each of these datasets have been utilized by specific SPoRT partners in local EMS model runs, with select offices evaluating the impacts using a set of automated scripts developed by SPoRT that manage data acquisition and run the NCAR Model Evaluation Tools verification package. SPoRT is engaged in DA research with the Gridpoint Statistical Interpolation (GSI) and Ensemble Kalman Filter in LIS for soil moisture DA. Ongoing DA projects using GSI include comparing the impacts of assimilating Atmospheric Infrared Sounder (AIRS) radiances versus retrieved profiles, and an analysis of extra-tropical cyclones with intense non-convective winds. As part of its Early Adopter activities for the NASA Soil Moisture Active Passive (SMAP) mission, SPoRT is conducting bias correction and soil moisture DA within LIS to improve simulations using the NASA Unified-WRF (NU-WRF) for both the European Space Agency's Soil Moisture Ocean Salinity and upcoming SMAP mission data. SPoRT has also incorporated real-time global GVF data into LIS and WRF from the VIIRS product being developed by NOAA/NESDIS. This poster will highlight the research and transition activities SPoRT conducts using WRF, NU-WRF, EMS, LIS, and GSI.

Case, Jonathan L.; Blankenship, Clay B.; Zavodsky, Bradley T.; Srikishen, Jayanthi; Berndt, Emily B.

2014-01-01

344

Detection of BCR-ABL transcripts in chronic myeloid leukemia (CML) using a ‘real time’ quantitative RT-PCR assay  

Microsoft Academic Search

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

C Preudhomme; F Révillion; A Merlat; L Hornez; C Roumier; N Duflos-Grardel; JP Jouet; A Cosson; JP Peyrat; P Fenaux

1999-01-01

345

Comparison of ELISA and RT-PCR for the detection of beet yellows closterovirus in plants and aphids  

Microsoft Academic Search

A reverse-transcription polymerase chain reaction (RT-PCR) was developed to detect beet yellows closterovirus (BYV) in plants and single aphids using primers spanning the conserved regions of the published sequences of the coat protein gene and open reading frames 7 and 8. Three total RNA extraction procedures were examined and all were found to produce RNA of sufficient quality for RT-PCR,

M. Stevens; R. Hull; H. G. Smith

1997-01-01

346

Effect of inflammatory mediators on ATP release of human urothelial RT4 cells.  

PubMed

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

Mansfield, Kylie J; Hughes, Jessica R

2014-01-01

347

[Cloning and analysis of reverse transcriptase(RT) of Ty1-copia retrotransposons in Dendrobium officinale].  

PubMed

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

Li, Cong; Si, Jin-Ping; Gao, Yan-Hui; Zhu, Yu-Qiu

2014-01-01

348

Pregnancies and menstrual function before and after combined radiation (RT) and chemotherapy (TVPP) for Hodgkin's disease  

SciTech Connect

The menstrual cycle, pregnancies, and offspring were evaluated before and after initial combined radiation (RT) and chemotherapy with thiotepa, vinblastine, vincristine, procarbazine, and prednisone (TVPP), in 34 women between the ages of 18 and 44 (median 26.5 years) treated for Stage II and Stage III Hodgkin's disease. The median range of follow-up is 83.1 months (range 40.5-140). After therapy 94.1% (32/34) continued to menstruate. Two of the four patients over the age of 35 ceased to menstruate. All patients under the age of 35 continued to menstruate (30/30). Age at the time of diagnosis was the only factor affecting change in menses with a significant probability (p = .001) that women greater than 30 years of age will experience some change in menstrual pattern. Seventeen pregnancies occurred in 12 women after therapy; 2 had 4 elective abortions; 10 delivered 12 children with normal physical development; 1 will deliver six months from now. Twelve of thirteen patients who wanted to become pregnant have conceived. The ability to become pregnant and deliver normal children after intensive treatment with combined radiation and chemotherapy (RT/TVPP) was comparable to the patients' pretreatment record.

Lacher, M.J.; Toner, K.

1986-01-01

349

Microdroplet Sandwich Real-Time RT-PCR for Detection of Pandemic and Seasonal Influenza Subtypes  

PubMed Central

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

Angione, Stephanie L.; Inde, Zintis; Beck, Christina M.; Artenstein, Andrew W.; Opal, Steven M.; Tripathi, Anubhav

2013-01-01

350

Development of a SYBR Green real-time RT-PCR assay for the detection of avian encephalomyelitis virus.  

PubMed

Avian encephalomyelitis virus (AEV) causes epidemic diseases in poultry worldwide. A SYBR Green real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay was developed for the rapid detection and quantitation of AEV in this study. A pair of specific primers was designed in the highly conserved VP1 gene of this virus. When comparing this assay with conventional RT-PCR, the rRT-PCR assay was 100 times more sensitive and could detect levels as low as 10 standard DNA copies of the AEV SX strain. The specificity of this technique was evaluated in five other avian pathogens. The AEV RNA was detected as early as three days post-infection in chicken embryos. All 18 clinical chicken brains collected from an AEV outbreak in Northwestern China were detected to be positive (100%) using the rRT-PCR assay. However, only 5 of the 18 samples were positive (28%) using the conventional RT-PCR. The results were confirmed by virus isolation in chicken embryos. This high sensitivity, specificity, and simplicity of the SYBR Green rRT-PCR approach can be a more effective method than the conventional one for AEV diagnosis and surveillance. PMID:24880065

Liu, Qingtian; Yang, Zengqi; Hao, Huafang; Cheng, Shenli; Fan, Wentao; Du, Enqi; Xiao, Sa; Wang, Xinglong; Zhang, Shuxia

2014-09-01

351

A theoretical study of H(2) dissociation on (sq.rt(3) x sq.rt(3))R30 degrees CO/Ru(0001).  

PubMed

We have studied the influence of preadsorbed CO on the dissociative adsorption of H(2) on Ru(0001) with density functional theory calculations. For a coverage of 1/3 ML CO, we investigated different possible reaction paths for hydrogen dissociation using nudged elastic band and adaptive nudged elastic band calculations. One reaction path was studied in detail through an energy decomposition and molecular orbital type of analysis. The minimum barrier for H(2) dissociation is found to be 0.29 eV. At the barrier the H-H bond is hardly stretched. Behind this barrier a molecular chemisorption minimum is present. Next, the molecule overcomes a second barrier, with a second local chemisorption minimum behind it. To finally dissociate to chemisorbed atoms, the molecule has to overcome a third barrier. To move along the reaction path from reactants to products, the hydrogen molecule needs to rotate, and to significantly change its center-of-mass position. The procedure of mapping out reaction paths for H(2) reacting on low-index surfaces of bare metals (computing two-dimensional elbow plots for fixed impact high-symmetry sites and H(2) orientations parallel to the surface) does not work for H(2)+CO/Ru. The first barrier in the path is recovered, but the features of the subsequent stretch to the dissociative chemisorption minimum are not captured, because the molecule is not allowed to change its center-of-mass position or to rotate. The dissociative chemisorption of H(2) on CO/Ru(0001) is endoergic, in contrast to the case of H(2) on bare Ru(0001). The zero-point energy corrected energies of molecularly and dissociatively chemisorbed H(2) are very close, suggesting that it may be possible to detect molecularly chemisorbed H(2) on (sq.rt(3) x sq.rt(3))R30 degrees CO/Ru(0001). The presence of CO on the surface increases the barrier height to dissociation compared with bare Ru(0001). Based on an energy decomposition and molecular orbital analysis we attribute the increase in the barrier height mainly to an occupied-occupied interaction between the bonding H(2) sigma(g) orbital and the (surface-hybridized) CO 1pi orbitals, i.e., to site blocking. There is a small repulsive contribution to the barrier from the interaction between the H(2) molecule and the Ru part of the CO covered Ru surface, but it is smaller than one might expect based on the calculations of H(2) interacting with a clean Ru surface, and on calculations of H(2) interacting with the CO overlayer only. Actually, the analysis suggests that the Ru surface as a subsystem is (slightly) more reactive for the reaction path studied with CO preadsorbed on it than without it. Thus, the results indicate that the influence of CO on H(2) dissociation on Ru is not only a simple site-blocking effect, the electronic structure of the underlying Ru is changed. PMID:20406007

Groot, I M N; Juanes-Marcos, J C; Olsen, R A; Kroes, G J

2010-04-14

352

Helical Tomotherapy-Based STAT RT: Dosimetric Evaluation for Clinical Implementation of a Rapid Radiation Palliation Program  

SciTech Connect

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.

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

353

Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design  

PubMed Central

Understanding human immunodeficiency virus type 1 (HIV-1) transmission is central to developing effective prevention strategies, including a vaccine. We compared phenotypic and genetic variation in HIV-1 env genes from subjects in acute/early infection and subjects with chronic infections in the context of subtype C heterosexual transmission. We found that the transmitted viruses all used CCR5 and required high levels of CD4 to infect target cells, suggesting selection for replication in T cells and not macrophages after transmission. In addition, the transmitted viruses were more likely to use a maraviroc-sensitive conformation of CCR5, perhaps identifying a feature of the target T cell. We confirmed an earlier observation that the transmitted viruses were, on average, modestly underglycosylated relative to the viruses from chronically infected subjects. This difference was most pronounced in comparing the viruses in acutely infected men to those in chronically infected women. These features of the transmitted virus point to selective pressures during the transmission event. We did not observe a consistent difference either in heterologous neutralization sensitivity or in sensitivity to soluble CD4 between the two groups, suggesting similar conformations between viruses from acute and chronic infection. However, the presence or absence of glycosylation sites had differential effects on neutralization sensitivity for different antibodies. We suggest that the occasional absence of glycosylation sites encoded in the conserved regions of env, further reduced in transmitted viruses, could expose specific surface structures on the protein as antibody targets. PMID:23616655

Ping, Li-Hua; Joseph, Sarah B.; Anderson, Jeffrey A.; Abrahams, Melissa-Rose; Salazar-Gonzalez, Jesus F.; Kincer, Laura P.; Treurnicht, Florette K.; Arney, Leslie; Ojeda, Suany; Zhang, Ming; Keys, Jessica; Potter, E. Lake; Chu, Haitao; Moore, Penny; Salazar, Maria G.; Iyer, Shilpa; Jabara, Cassandra; Kirchherr, Jennifer; Mapanje, Clement; Ngandu, Nobubelo; Seoighe, Cathal; Hoffman, Irving; Gao, Feng; Tang, Yuyang; Labranche, Celia; Lee, Benhur; Saville, Andrew; Vermeulen, Marion; Fiscus, Susan; Morris, Lynn; Karim, Salim Abdool; Haynes, Barton F.; Shaw, George M.; Korber, Bette T.; Hahn, Beatrice H.; Cohen, Myron S.; Montefiori, David; Williamson, Carolyn

2013-01-01

354

The Stem of Vesicular Stomatitis Virus G Can Be Replaced With the HIV-1 Env Membrane-Proximal External Region Without Loss of G Function or Membrane-Proximal External Region Antigenic Properties.  

PubMed

Abstract The structure of the HIV-1 envelope membrane-proximal external region (MPER) is influenced by its association with the lipid bilayer on the surface of virus particles and infected cells. To develop a replicating vaccine vector displaying MPER sequences in association with membrane, Env epitopes recognized by the broadly neutralizing antibodies 2F5, 4E10, or both were grafted into the membrane-proximal stem region of the vesicular stomatitis virus (VSV) glycoprotein (G). VSV encoding functional G-MPER chimeras based on G from the Indiana or New Jersey serotype propagated efficiently, although grafting of both epitopes (G-2F5-4E10) modestly reduced replication and resulted in the acquisition of one to two adaptive mutations in the grafted MPER sequence. Monoclonal antibodies 2F5 and 4E10 efficiently neutralized VSV G-MPER vectors and bound to virus particles in solution, indicating that the epitopes were accessible in the preattachment form of the G-MPER chimeras. Overall, our results showed that the HIV Env MPER could functionally substitute for the VSV G-stem region implying that both perform similar functions even though they are from unrelated viruses. Furthermore, we found that the MPER sequence grafts induced low but detectable MPER-specific antibody responses in rabbits vaccinated with live VSV, although additional vector and immunogen modifications or use of a heterologous prime-boost vaccination regimen will be required to increase the magnitude of the immune response. PMID:24597516

Lorenz, Ivo C; Nguyen, Hanh T; Kemelman, Marina; Lindsay, Ross W; Yuan, Maoli; Wright, Kevin J; Arendt, Heather; Back, Jaap Willem; DeStefano, Joanne; Hoffenberg, Simon; Morrow, Gavin; Jurgens, Christy K; Phogat, Sanjay K; Zamb, Timothy J; Parks, Christopher L

2014-11-01

355

The amino acid substitutions rtP177G and rtF249A in the reverse transcriptase domain of hepatitis B virus polymerase reduce the susceptibility to tenofovir.  

PubMed

Long term antiviral therapy with nucleoside/nucleotide analogs have been routinely used to treat chronic hepatitis B virus (HBV) infection but may lead to the emergence of drug-resistant viral mutants. However, the HBV resistance mutations for tenofovir (TDF) remain controversial. It is speculated that the genetic barrier for TDF resistance may be high for HBV. We asked whether selected amino acid substitutions in HBV polymerase may reduce susceptibility to TDF. A series of amino acids in HBV polymerase were selected based on bioinformatics analysis for mutagenesis. The replication competence and susceptibility to TDF of the mutated HBV clones were determined both in vitro and in vivo. nineteen mutations in HBV polymerase were included and impaired the replication competence of HBV genome in different degrees. The mutations at rtL77F (sS69C), rtF88L (sF80Y), and rtP177G (sR169G) also significantly affected HBsAg expression. The HBV mutants with rtP177G and rtF249A were found to have reduced susceptibility to TDF in vitro with a resistance index of 2.53 and 12.16, respectively. The testing in in vivo model based on the hydrodynamic injection revealed the antiviral effect of TDF against wild type and mutated HBV genomes and confirmed the reduced the susceptibility of mutant HBV to TDF. PMID:23261845

Qin, Bo; Budeus, Bettina; Cao, Liang; Wu, Chunchen; Wang, Yun; Zhang, Xiaoyong; Rayner, Simon; Hoffmann, Daniel; Lu, Mengji; Chen, Xinwen

2013-02-01

356

Development of Reverse Transcription (RT)-PCR and Real-Time RT-PCR Assays for Rapid Detection and Quantification of Viable Yeasts and Molds Contaminating Yogurts and Pasteurized Food Products  

PubMed Central

Reverse transcriptase PCR (RT-PCR) and real-time RT-PCR assays have been used to detect and quantify actin mRNA from yeasts and molds. Universal primers were designed based on the available fungal actin sequences, and by RT-PCR they amplified a specific 353-bp fragment from fungal species involved in food spoilage. From experiments on heat-treated cells, actin mRNA was a good indicator of cell viability: viable cells and cells in a nonculturable state were detected, while no signal was observed from dead cells. The optimized RT-PCR assay was able to detect 10 CFU of fungi ml?1 in pure culture and 103 and 102 CFU ml?1 in artificially contaminated yogurts and pasteurized fruit-derived products, respectively. Real-time RT-PCR, performed on a range of spoiled commercial food products, validated the suitability of actin mRNA detection for the quantification of naturally contaminating fungi. The specificity and sensitivity of the procedure, combined with its speed, its reliability, and the potential automation of the technique, offer several advantages to routine analysis programs that assess the presence and viability of fungi in food commodities. PMID:12839789

Bleve, Gianluca; Rizzotti, Lucia; Dellaglio, Franco; Torriani, Sandra

2003-01-01

357

Dynamo transformation of the collisional R-T in a weakly ionized plasma  

NASA Astrophysics Data System (ADS)

Theoretical prediction of a new kind of normal mode behaviour of electro-mechanical nature was first time reported by Dwivedi and Das in 1992 in the context of mesospheric modeling of observed neutral induced turbulence. Local dynamo action (due to relative neutral flow) governs the basic physical principle for linear excitation of the neutral induced low frequency instability (NILF) in mesospheric plasma, which comprises of weakly ionized inhomogeneous gas confined by the external gravity and ambient magnetic field. The present contribution offers physical explanation in terms of dynamo transformation of neutral drag effect as a source to understand complete suppression of the usual collisional R-T and in turn linear driving of the NILF. It is therefore emphasized, worth calling it as the dynamo instability.

Dwivedi, C. B.

2000-11-01

358

The Elusive Soft Emission from Hard X-ray Symbiotic System RT Cru  

NASA Astrophysics Data System (ADS)

RT Cru is a fascinating member of a new class of hard X-ray emitting symbiotic binaries showing X-ray emission extending to over 50keV. While its hard X-ray emission has been studied in detail, the soft component of the spectrum, including flares, remains elusive, since previous observations have focused on the high-energy regime. We propose Chandra HRC-S/LETG observations to determine the spatial, spectral, and temporal characteristics of the source of the soft X-ray emission with a goal to establish the origin of the soft component, and determine whether and how it is tied to the hard component. Determining the origin of the soft emission is a crucial piece of the puzzle to understanding the geometry, energetics, and the environment of WD accretion in this class of symbiotic systems.

Karovska, Margarita

2014-09-01

359

Long-term starspot activity of short-period RS Canum Venaticorum stars. II - RT Andromedae  

NASA Astrophysics Data System (ADS)

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.

Zeilik, M.; Cox, D. A.; de Blasi, C.; Rhodes, M.; Budding, E.

1989-10-01

360

Multiplex RT-PCR for the Detection of Leukemia-Associated Translocations  

PubMed Central

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

Salto-Tellez, Manuel; Shelat, Suresh G.; Benoit, Bernice; Rennert, Hanna; Carroll, Martin; Leonard, Debra G.B.; Nowell, Peter; Bagg, Adam

2003-01-01

361

No Control Genes Required: Bayesian Analysis of qRT-PCR Data  

PubMed Central

Background Model-based analysis of data from quantitative reverse-transcription PCR (qRT-PCR) is potentially more powerful and versatile than traditional methods. Yet existing model-based approaches cannot properly deal with the higher sampling variances associated with low-abundant targets, nor do they provide a natural way to incorporate assumptions about the stability of control genes directly into the model-fitting process. Results In our method, raw qPCR data are represented as molecule counts, and described using generalized linear mixed models under Poisson-lognormal error. A Markov Chain Monte Carlo (MCMC) algorithm is used to sample from the joint posterior distribution over all model parameters, thereby estimating the effects of all experimental factors on the expression of every gene. The Poisson-based model allows for the correct specification of the mean-variance relationship of the PCR amplification process, and can also glean information from instances of no amplification (zero counts). Our method is very flexible with respect to control genes: any prior knowledge about the expected degree of their stability can be directly incorporated into the model. Yet the method provides sensible answers without such assumptions, or even in the complete absence of control genes. We also present a natural Bayesian analogue of the “classic” analysis, which uses standard data pre-processing steps (logarithmic transformation and multi-gene normalization) but estimates all gene expression changes jointly within a single model. The new methods are considerably more flexible and powerful than the standard delta-delta Ct analysis based on pairwise t-tests. Conclusions Our methodology expands the applicability of the relative-quantification analysis protocol all the way to the lowest-abundance targets, and provides a novel opportunity to analyze qRT-PCR data without making any assumptions concerning target stability. These procedures have been implemented as the MCMC.qpcr package in R. PMID:23977043

Matz, Mikhail V.; Wright, Rachel M.; Scott, James G.

2013-01-01

362

RT-qPCR Normalization Genes in the Red Alga Chondrus crispus  

PubMed Central

Chondrus crispus is a common red macroalga living on the rocky shores of the North Atlantic Ocean. It has a long research history, being a major source of carrageenan, a thickener widely used in the food industry, but also for physiological and ecological studies. To establish it as a model for red algae, its genome has been sequenced, allowing the development of molecular tools such as quantification of gene expression, including RNAseq and RT-qPCR. To determine appropriate genes for RT-qPCR normalization, the expression of 14 genes was monitored in 18 conditions using two sets of algal samples: samples from the sequenced strain, cultured and stressed in laboratory conditions and C. crispus collected on the shore and stressed in situ. The expression stability of the genes between the samples was evaluated by comparing the Ct range and using the programs geNorm and NormFinder. The candidate genes encoded translation related proteins (initiation factors IF4A-1 and IF4A-2, elongation factor EF1? and eRF3, an eukaryotic polypeptide chain release factor), cytoskeleton proteins (two ?-tubulins, ?-tubulin and actin), enzymes involved in the pentose phosphate pathway (glucose 6-phosphate deshydrogenase), protein recycling process (ubiquitin and ubiquitin-conjugating enzyme) and glycolysis (isocitrate dehydrogenase). The two sets of samples showed different expression patterns. Most of the genes were stable in the algae cultivated in the laboratory, whereas environmental samples showed a more important variation in gene expression. When analyzing the two sets separately, the ranking of the most stables genes were different from one method to another. When considering all samples, the two statistical methods were concordant, revealing translation initiation factor 4A-2 and eukaryotic polypeptide chain release factor 3 as pertinent normalization genes. This study highlights thus the importance of testing reference genes according to the experiments as well as the genetic and physiological background of the organism. PMID:24498277

Kowalczyk, Nathalie; Rousvoal, Sylvie; Herve, Cecile; Boyen, Catherine; Collen, Jonas

2014-01-01

363

Genes and channels: patch/voltage-clamp analysis and single-cell RT-PCR.  

PubMed

Technological advances in electrophysiology and molecular biology in the last two decades have led to great progress in ion channel research. The invention of the patch-clamp recording technique has enabled the characterization of the biophysical and pharmacological properties of single channels. Rapid progress in the development of molecular biology techniques and their application to ion channel research led to the cloning, in the 1980s, of genes encoding all major classes of voltage- and ligand-gated ionic channels. It has become clear that operationally defined channel types represent extended families of ionic channels. Several experimental approaches have been developed to test whether there is a correlation between the detection of particular ion channel subunit mRNAs and the electrophysiological response to a pharmacological or electrical stimulus in a cell. In one method, whole-cell patch-clamp recording is performed on a cell in culture or tissue-slice preparation. The biophysical and pharmacological properties of the ionic channels of interest are characterized and the cytoplasmic contents of the recorded cell are then harvested into the patch pipette. In a variant of this method, the physiological properties of a cell are characterized with a two-electrode voltage clamp and, following the recording, the entire cell is harvested for its RNA. In both methods, the RNA from a single cell is reverse-transcribed into cDNA by a reverse transcriptase and subsequently amplified by the polymerase chain reaction, i.e. by the so-called single-cell/reverse transcription/polymerase chain reaction method (SC-RT-PCR). This review presents an analysis of the results of work obtained by using a combination of whole-cell patch-clamp recording or two-electrode voltage clamp and SC-RT-PCR with emphasis on its potential and limitations for quantitative analysis. PMID:11151442

Sucher, N J; Deitcher, D L; Baro, D J; Warrick, R M; Guenther, E

2000-12-01

364

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

NASA Technical Reports Server (NTRS)

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.

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

2012-01-01

365

Evaluating the Impacts of NASA/SPoRT Daily Greenness Vegetation Fraction on Land Surface Model and Numerical Weather Forecasts  

NASA Technical Reports Server (NTRS)

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.

Bell, Jordan R.; Case, Jonathan L.; Molthan, Andrew L.

2011-01-01

366

Development of a quantitative Light Cycler real-time RT-PCR for detection of avian reovirus.  

PubMed

A robust, ultrasensitive, and accurate quantitative assay was developed for avian reovirus (ARV) with the Light Cycler SYBR Green-based real-time reverse transcription-PCR (real-time LC RT-PCR). The assay exhibited high specificity as all negative controls and other avian pathogens, such as Newcastle disease virus (NDV), infectious bronchitis virus (IBV), infectious bursal disease virus (IBDV), avian influenza virus (AIV), and mycoplasma synovia (MS), failed to show any positive detection. A minimum of 39 copies/microl of ARV genomic RNA could be detected by the assay. By dilution analysis, the real-time LC RT-PCR developed in this study was 3-log more sensitive than the conventional RT-PCR for the detection of ARV. The vaccine and field isolates of ARV were detected by the real-time LC RT-PCR. As a result of the high sensitivity and specificity of the assay with a relatively rapid and simple procedure, the real-time LC RT-PCR will be useful as a routine assay for the clinical diagnosis of ARV infection. PMID:16300834

Ke, Guan M; Cheng, Hsueh L; Ke, Liang Y; Ji, Wen T; Chulu, Julius L C; Liao, Ming H; Chang, Tien J; Liu, Hung J

2006-04-01

367

Increase in rT3 serum levels observed during extended Alaskan field operations of Naval personnel.  

PubMed

Members of a US Navy Special Warfare platoon had blood samples drawn by venipuncture and other baseline measurements carried out prior to departure for a three-month period of field operations in Alaska. Assays of serum reverse triiodothyronine (rT3), free thyroxine (fT3), free T4 (fT4), and thyroid stimulating hormone (TSH) were subsequently done at the Naval Medical Research Institute (NMRI), Bethesda, Maryland. In the field and at baseline, hematocrits and urine specific gravities were also measured to track hydration status, and body weights and fat were recorded to track nutritional status. After plasma volume change and weight change corrections, an approximate 30% increase in serum rT3 level and 20% decrease in free T3 level over 76 days of cold exposure were recorded. The necessity for an rT3 kinetic study is indicated. The mean residence time for rT3 in the circulation is about 8 hours with respect to about 36 hours for free T3, so rT3 kinetic studies would be advantageous with respect to long term cold exposure of military personnel. PMID:8936697

McCormack, P D; Reed, H L; Thomas, J R; Malik, M J

1996-01-01

368

Digital-Direct-RT-PCR: a sensitive and specific method for quantification of CTC in patients with cervical carcinoma  

PubMed Central

The detection of circulating tumour cells (CTC) in cancer patients may be useful for therapy monitoring and prediction of relapse. A sensitive assay based on HPV-oncogene transcripts which are highly specific for cervical cancer cells was established. The Digital-Direct-RT-PCR (DD-RT-PCR) combines Ficoll-separation, ThinPrep-fixation and one-step RT-PCR in a low-throughput digital-PCR format enabling the direct analysis and detection of individual CTC without RNA isolation. Experimental samples demonstrated a sensitivity of one HPV-positive cell in 500,000 HPV-negative cells. Spike-in experiments with down to 5 HPV-positive cells per millilitre EDTA-blood resulted in concordant positive results by PCR and immunocytochemistry. Blood samples from 3 of 10 CxCa patients each contained a single HPV-oncogene transcript expressing CTC among 5 to 15*105?MNBC. Only 1 of 7 patients with local but 2 of 3 women with systemic disease had CTC. This highly sensitive DD-RT-PCR for the detection of CTC may also be applied to other tumour entities which express tumour-specific transcripts. Abbreviations: CTC – circulating tumour cells, CxCa – cervical cancer, DD-RT-PCR – Digital-Direct Reverse Transcriptase PCR, HPV – Human Papilloma Virus, MNBC – mononuclear blood cells, ICC – immunocytochemistry. PMID:24496006

Pfitzner, Claudia; Schroder, Isabel; Scheungraber, Cornelia; Dogan, Askin; Runnebaum, Ingo Bernhard; Durst, Matthias; Hafner, Norman

2014-01-01

369

2005 Nature Publishing Group Protection of macaques from vaginal SHIV  

E-print Network

), with seroconversion after 14­35 days. Inhibitor-treated animals remaining plasma RNA-negative and antibody-negative and a subsequent compound, BMS- 388043, were successfully tested for safety in humans, and more potent, related (refs 12, 13). The infection rate for our stock in control animals was 9 out of 9 (Fig. 1). Plasma

Cai, Long

370

SMART LIGHTING ENGINEERING RESEARCH CENTER Dr. Shiv Kalyanaraman  

E-print Network

envisage a future model of leasing public transportation via a service similar to telecom/ cell phone Energy meets Smarter Transportation: The Energy-Transportation Nexus & Personalized Public Transportation The rapidly growing global use of LEDs in automotive lighting, traffic signals and streetlights is creating

Linhardt, Robert J.

371

Molecular detection of thyroglobulin mRNA transcripts in peripheral blood of patients with thyroid disease by RT-PCR  

PubMed Central

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

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

372

SiC\\/Si 3N 4 nano\\/micro-composite — processing, RT and HT mechanical properties  

Microsoft Academic Search

Two SiC\\/Si3N4 nano\\/micro composites were prepared from a starting mixture of crystalline ?-Si3N4, amorphous SiNC, Y2O3 and\\/or Al2O3. The composite material for room temperature (RT) application has high strength of 1200 MPa, Weibull modulus of 19 and moderate fracture toughness of 7 MPa m1\\/2. The composite for high temperature (HT) application, without Al2O3 has RT strength of 710 MPa and

P. Šajgal??k; M. Hnatko; F. Lofaj; P. Hvizdoš; J. Dusza; P. Warbichler; F. Hofer; R. Riedel; E. Lecomte; M. J. Hoffmann

2000-01-01

373

Comparison of karyotype analysis and RT-PCR for AML1\\/ETO in 204 unselected patients with AML  

Microsoft Academic Search

The chromosomal translocation t(8;21) (q22;q22) is often associated with acute myeloid leukemia with maturation (AML-M2)\\u000a and can be detected by a reverse transcription-polymerase chain reaction (RT-PCR) for the AML1\\/ETO fusion mRNA. We investigated\\u000a the prevalence of t(8;21) and AML1\\/ETO in 204 unselected patients with AML and compared the results of cytogenetic analysis\\u000a with these of RT-PCR. Fifteen of 204 AML

M. Mitterbauer; R. Kusec; I. Schwarzinger; O. A. Haas; K. Lechner; U. Jaeger

1998-01-01

374

Identification and validation of reference genes for quantitative RT-PCR normalization in wheat  

PubMed Central

Background Usually the reference genes used in gene expression analysis have been chosen for their known or suspected housekeeping roles, however the variation observed in most of them hinders their effective use. The assessed lack of validated reference genes emphasizes the importance of a systematic study for their identification. For selecting candidate reference genes we have developed a simple in silico method based on the data publicly available in the wheat databases Unigene and TIGR. Results The expression stability of 32 genes was assessed by qRT-PCR using a set of cDNAs from 24 different plant samples, which included different tissues, developmental stages and temperature stresses. The selected sequences included 12 well-known HKGs representing different functional classes and 20 genes novel with reference to the normalization issue. The expression stability of the 32 candidate genes was tested by the computer programs geNorm and NormFinder using five different data-sets. Some discrepancies were detected in the ranking of the candidate reference genes, but there was substantial agreement between the groups of genes with the most and least stable expression. Three new identified reference genes appear more effective than the well-known and frequently used HKGs to normalize gene expression in wheat. Finally, the expression study of a gene encoding a PDI-like protein showed that its correct evaluation relies on the adoption of suitable normalization genes and can be negatively affected by the use of traditional HKGs with unstable expression, such as actin and ?-tubulin. Conclusion The present research represents the first wide screening aimed to the identification of reference genes and of the corresponding primer pairs specifically designed for gene expression studies in wheat, in particular for qRT-PCR analyses. Several of the new identified reference genes outperformed the traditional HKGs in terms of expression stability under all the tested conditions. The new reference genes will enable more accurate normalization and quantification of gene expression in wheat and will be helpful for designing primer pairs targeting orthologous genes in other plant species. PMID:19232096

Paolacci, Anna R; Tanzarella, Oronzo A; Porceddu, Enrico; Ciaffi, Mario

2009-01-01

375

Implementation and commissioning of an integrated micro-CT/RT system with computerized independent jaw collimation  

SciTech Connect

Purpose: To design, construct, and commission a set of computer-controlled motorized jaws for a micro-CT/RT system to perform conformal image-guided small animal radiotherapy.Methods: The authors designed and evaluated a system of custom-built motorized orthogonal jaws, which allows the delivery of off-axis rectangular fields on a GE eXplore CT 120 preclinical imaging system. The jaws in the x direction are independently driven, while the y-direction jaws are symmetric. All motors have backup encoders, verifying jaw positions. Mechanical performance of the jaws was characterized. Square beam profiles ranging from 2 × 2 to 60 × 60 mm{sup 2} were measured using EBT2 film in the center of a 70 × 70 × 22 mm{sup 3} solid water block. Similarly, absolute depth dose was measured in a solid water and EBT2 film stack 50 × 50 × 50 mm{sup 3}. A calibrated Farmer ion chamber in a 70 × 70 × 20 mm{sup 3} solid water block was used to measure the output of three field sizes: 50 × 50, 40 × 40, and 30 × 30 mm{sup 2}. Elliptical target plans were delivered to films to assess overall system performance. Respiratory-gated treatment was implemented on the system and initially proved using a simple sinusoidal motion phantom. All films were scanned on a flatbed scanner (Epson 1000XL) and converted to dose using a fitted calibration curve. A Monte Carlo beam model of the micro-CT with the jaws has been created using BEAMnrc for comparison with the measurements. An example image-guided partial lung irradiation in a rat is demonstrated.Results: The averaged random error of positioning each jaw is less than 0.1 mm. Relative output factors measured with the ion chamber agree with Monte Carlo simulations within 2%. Beam profiles and absolute depth dose curves measured from the films agree with simulations within measurement uncertainty. Respiratory-gated treatments applied to a phantom moving with a peak-to-peak amplitude of 5 mm showed improved beam penumbra (80%–20%) from 3.9 to 0.8 mm.Conclusions: A set of computer-controlled motorized jaws for a micro-CT/RT system were constructed with position reliably better than a tenth of a millimeter. The hardware system is ready for image-guided conformal radiotherapy for small animals with capability of respiratory-gated delivery.

Jensen, Michael D. [Department of Medical Biophysics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada)] [Department of Medical Biophysics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Hrinivich, W. Thomas; Jung, Jongho A. [Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada)] [Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Holdsworth, David W. [Imaging Research Laboratories, Robarts Research Institute, 100 Perth Drive, London, Ontario N6A 5K8 (Canada) [Imaging Research Laboratories, Robarts Research Institute, 100 Perth Drive, London, Ontario N6A 5K8 (Canada); Department of Medical Biophysics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Department of Surgery, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Drangova, Maria [Imaging Research Laboratories, Robarts Research Institute, 100 Perth Drive, London, Ontario N6A 5K8, Canada and Department of Medical Biophysics, The University of Western Ontario 1151 Richmond Street, London, Ontario N6A 3K7 (Canada)] [Imaging Research Laboratories, Robarts Research Institute, 100 Perth Drive, London, Ontario N6A 5K8, Canada and Department of Medical Biophysics, The University of Western Ontario 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Chen, Jeff [Department of Physics and Engineering, London Regional Cancer Program, London Health Sciences Centre, 800 Commissioners Road East, London, Ontario N6A 5W9 (Canada) [Department of Physics and Engineering, London Regional Cancer Program, London Health Sciences Centre, 800 Commissioners Road East, London, Ontario N6A 5W9 (Canada); Department of Medical Biophysics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Department of Oncology, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Wong, Eugene [Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada) [Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Department of Medical Biophysics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Department of Oncology, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7 (Canada); Department of Physics and Engineering, London Regional Cancer Program, London Health Sciences Centre, 800 Commissioners Road East, London, Ontario N6A 5W9 (Canada)

2013-08-15

376

The impact of flattening-filter-free beam technology on 3D conformal RT  

PubMed Central

Background The removal of the flattening filter (FF) leads to non-uniform fluence distribution with a considerable increase in dose rate. It is possible to adapt FFF beams (flattening-filter-free) in 3D conformal radiation therapy (3D CRT) by using field in field techniques (FiF). The aim of this retrospective study is to clarify whether the quality of 3D CRT plans is influenced by the use of FFF beams. Method This study includes a total of 52 CT studies of RT locations that occur frequently in clinical practice. Dose volume targets were provided for the PTV of breast (n=13), neurocranium (n=11), lung (n=7), bone metastasis (n=10) and prostate (n=11) in line with ICRU report 50/62. 3D CRT planning was carried out using FiF methods. Two clinically utilized photon energies are used for a Siemens ARTISTE linear accelerator in FFF mode at 7MVFFF and 11MVFFF as well as in FF mode at 6MVFF and 10MVFF. The plan quality in relation to the PTV coverage, OAR (organs at risk) and low dose burden as well as the 2D dosimetric verification is compared with FF plans. Results No significant differences were found between FFF and FF plans in the mean dose for the PTV of breast, lung, spine metastasis and prostate. The low dose parameters V5Gy and V10Gy display significant differences for FFF and FF plans in some subgroups. The DVH analysis of the OAR revealed some significant differences. Significantly more fields (1.9 – 4.5) were necessary in the use of FFF beams for each location (p<0.0001) in order to achieve PTV coverage. All the tested groups displayed significant increases (1.3 – 2.2 times) in the average number of necessary MU with the use of FFF beams (p<0.001). Conclusions This study has shown that the exclusive use of a linear accelerator in FFF mode is feasible in 3D CRT. It was possible to realize RT plans in comparable quality in typical cases of clinical radiotherapy. The 2D dosimetric validation of the modulated fields verified the dose calculation and thus the correct reproduction of the characteristic FFF parameters in the planning system that was used. PMID:23725479

2013-01-01

377

Assistant Professor, Dept. od Civil Engineering, Univ. of Tehran, P.O. Box 11365-4563, Tehran, Iran; Fax 98-21-661024 Professor, Dept. of Civil, Struc. & Env. Engrg, State Univ. of New York at Buffalo, 130 Ketter Hall, Buffalo, New York  

E-print Network

-4563, Tehran, Iran; Fax 98-21-661024 2 Professor, Dept. of Civil, Struc. & Env. Engrg, State Univ. of New York at Buffalo, 130 Ketter Hall, Buffalo, New York SEISMIC PERFORMANCE OF DIAPHRAGMS IN SLAB-ON-GIRDER STEEL damage during earthquakes. This paper presents the results from an experimental work to investigate

Bruneau, Michel

378

Microhard MHX 2420 Orbital Performance Evaluation Using RT Logic T400CS  

NASA Technical Reports Server (NTRS)

A major upfront cost of building low cost Nanosatellites is the communications sub-system. Most radios built for space missions cost over $4,000 per unit. This exceeds many budgets. One possible cost effective solution is the Microhard MHX2420, a commercial off-the-shelf transceiver with a unit cost under $1000. This paper aims to support the Nanosatellite community seeking an inexpensive radio by characterizing Microhard's performance envelope. Though not intended for space operations, the ability to test edge cases and increase average data transfer speeds through optimization positions this radio as a solution for Nanosatellite communications by expanding usage to include more missions. The second objective of this paper is to test and verify the optimal radio settings for the most common cases to improve downlinking. All tests were conducted with the aid of the RT Logic T400CS, a hardware-in-the-loop channel simulator designed to emulate real-world radio frequency (RF) link effects. This study provides recommended settings to optimize the downlink speed as well as the environmental parameters that cause the link to fail.

Kearney, Stuart; Lombardi, Mark; Attai, Watson; Oyadomari, Ken; Al Rumhi, Ahmed Saleh Nasser; Rakotonarivo, Sebastien; Chardon, Loic; Gazulla, Oriol Tintore; Wolfe, Jasper; Salas, AlbertoGuillen; DeWald, Jon; Alena, Richard

2012-01-01

379

Real time RT-PCR assays for detection and typing of African horse sickness virus.  

PubMed

Although African horse sickness (AHS) can cause up to 95% mortality in horses, naïve animals can be protected by vaccination against the homologous AHSV serotype. Genome segment 2 (Seg-2) encodes outer capsid protein VP2, the most variable of the AHSV proteins. VP2 is also a primary target for AHSV specific neutralising antibodies, and consequently determines the identity of the nine AHSV serotypes. In contrast VP1 (the viral polymerase) and VP3 (the sub-core shell protein), encoded by Seg-1 and Seg-3 respectively, are highly conserved, representing virus species/orbivirus-serogroup-specific antigens. We report development and evaluation of real-time RT-PCR assays targeting AHSV Seg-1 or Seg-3, that can detect any AHSV type (virus species/serogroup-specific assays), as well as type-specific assays targeting Seg-2 of the nine AHSV serotypes. These assays were evaluated using isolates of different AHSV serotypes and other closely related orbiviruses, from the 'Orbivirus Reference Collection' (ORC) at The Pirbright Institute. The assays were shown to be AHSV virus-species-specific, or type-specific (as designed) and can be used for rapid, sensitive and reliable detection and identification (typing) of AHSV RNA in infected blood, tissue samples, homogenised Culicoides, or tissue culture supernatant. None of the assays amplified cDNAs from closely related heterologous orbiviruses, or from uninfected host animals or cell cultures. PMID:24721971

Bachanek-Bankowska, Katarzyna; Maan, Sushila; Castillo-Olivares, Javier; Manning, Nicola M; Maan, Narender Singh; Potgieter, Abraham C; Di Nardo, Antonello; Sutton, Geoff; Batten, Carrie; Mertens, Peter P C

2014-01-01

380

Effect of shear on R-T mixing at low and medium Atwood numbers  

NASA Astrophysics Data System (ADS)

Combined RT and KH instabilities are studied at three different Atwood numbers using the gas channel facility at TAMU. In the experiment, two gas streams of different densities (heavy over light) flowing parallel to each other are initially separated by a thin splitter plate. At the end of the splitter plate the two fluids are allowed to mix and the Rayleigh-Taylor instability develops. Simultaneous 3 wire and cold wire anemometry (S3WCA) is used to measure velocities and densities at different locations along and across the channel. Temperature is used as a marker to identify the streams and density is calculated from the temperature measured using a temperature probe with a constant current anemometer. High resolution digital imaging is performed to measure mixing heights and growth rates by injecting smoke into one of the streams and collecting the scattered light from the fog particles illuminated by the back lighting of the channel. Experiments are performed at Atwood numbers 0.04, 0.1 and 0.3. At these Atwood numbers, effect of shear is studied by varying the velocity of one the top stream. Initial conditions are characterized at the interface right after the splitter plate using S3WCA. Different parameters obtained from these measurements including, molecular mixing parameter ?, u', v', w' rms profiles, velocity correlations, vertical turbulent mass flux ?'v' and their effect on mixing growth rate are discussed.

Akula, Bhanesh; Ranjan, Devesh

2011-11-01

381

Detection of human enteric viruses in stream water with RT-PCR and cell culture.  

USGS Publications Warehouse

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 with traditional cell culture and Escherichia coli membrane filtration assays. The study incorporated multiple quality controls and included a control for virus recovery during the sampling procedure as well as controls to detect potentially false-negative and false-positive data. Poliovirus recovery ranged from 16 to 65% and was variable, even in samples collected within the same stream. All five sites were positive for viruses by both molecular and cell culture-based virus assays. Enteroviruses, reoviruses, rotaviruses, and hepatitis A viruses were detected, but the use of the quality controls proved critical for interpretation of the molecular data. All sites showed evidence of faecal contamination, and culturable viruses were detected in four samples that would have met the US Environmental Protection Agency's recommended E. coli guideline for safe recreational water.

Denis-Mize, K.; Fout, G. S.; Dahling, D. R.; Francy, D. S.

2004-01-01

382

Diagnostic evaluation of RT-PCR-ELISA for the detection of rabies virus.  

PubMed

Rabies is primarily a disease of terrestrial and airborne mammals. In most cases, rabies is diagnosed primarily on the basis of clinical symptoms and signs, and a corroborative history of or evidence of an animal bite, death of an animal and incomplete or no vaccination following exposure. The facility for laboratory diagnosis and confirmation of rabies is available in only a few institutions in India. Diagnostic tests using conventional assays like fluorescent antibody test (FAT) are unreliable at times, despite the clinical diagnosis. Currently, there are a number of molecular tests that can be used to complement conventional tests in rabies diagnosis. We have developed and evaluated an RT-PCR-ELISA using a panel of brain tissue samples from rabies suspected animals of various species. This assay was able to detect rabies virus genome in all the 43 samples that were previously tested positive for rabies. Moreover this assay was shown to be 100 % sensitive and specific in detecting the rabies virus genome in post-mortem brain tissue samples from different species of animals. Our pilot study shows the potential of this assay as an alternative diagnostic test when the samples are unsuitable for use in FAT and also a supplementary test to FAT. In addition, the region of nucleoprotein gene amplified using this assay can be used for the molecular investigation of geographical origin of the field strains. PMID:24426319

Aravindhbabu, R P; Manoharan, S; Ramadass, P

2014-01-01

383

Assessment of a novel real-time pan-flavivirus RT-polymerase chain reaction.  

PubMed

Outbreaks of West Nile virus (WNV) have occurred intermittently in regions around the Mediterranean coast, and the virus may have become established in Northern Italy and Romania, with reported intermittent outbreaks in Spain, Hungary, and France. WNV has also spread rapidly throughout the Americas since its introduction into New York in 1999. This capacity to emerge in new geographical locations and to spread rapidly together with the current increase in incidence of other flaviviruses such as tick-borne encephalitis virus, dengue virus, and Usutu virus has prompted us to design a novel pan-flavivirus RT-polymerase chain reaction for the purpose of surveillance for a range of flaviviruses. The assay utilizes degenerate primers targeting the flavivirus NS5 gene (RNA-dependent RNA polymerase) and detects a range of flaviviruses, including WNV. A small panel of WNV bird samples obtained from the United States has been shown to be detected using this assay. The amplicon generated is of sufficient size to provide sequence data to confirm the identity of the virus detected and undertake limited phylogenetic analysis. Testing using this assay has shown its ability to detect a range of tick-borne flaviviruses, particularly louping ill virus that is endemic in areas of the United Kingdom. The assay has been used to survey 160 bird samples and 1000 mosquito samples from the United Kingdom and found no evidence for WNV. PMID:20854019

Johnson, Nicholas; Wakeley, Philip R; Mansfield, Karen L; McCracken, Fiona; Haxton, Ben; Phipps, Lawrence Paul; Fooks, Anthony R

2010-10-01

384

Detection of GRB 090618 with RT-2 Experiment Onboard the Coronas-Photon Satellite  

E-print Network

We present the results of an analysis of the prompt gamma-ray emission from GRB 090618 using the RT-2 Experiment onboard the Coronas-Photon satellite. GRB 090618 shows multiple peaks and a detailed study of the temporal structure as a function of energy is carried out. As the GRB was incident at an angle of 77 degree to the detector axis, we have generated appropriate response functions of the detectors to derive the spectrum of this GRB. We have augmented these results using the publicly available data from the Swift BAT detector and show that a combined spectral analysis can measure the spectral parameters quite accurately. We also attempt a spectral and timing analysis of individual peaks and find evidence for a systematic change in the pulse emission characteristics for the successive pulses. In particular, we find that the peak energy of the spectrum, E_p, is found to monotonically decrease with time, for the successive pulses of this GRB.

Rao, A R; Hingar, M K; Agrawal, V K; Chakrabarti, S K; Nandi, A; Debnath, D; Kotoch, T B; Sarkar, R; Chidambaram, T R; Vinod, P; Sreekumar, S; Kotov, Y D; Buslov, A S; Yurov, V N; Tyshkevich, V G; Arkhangelskij, A I; Zyatkov, R A; Naik, Sachindra

2010-01-01

385

An inexpensive and portable microchip-based platform for integrated RT-PCR and capillary electrophoresis.  

PubMed

We present an inexpensive, portable and integrated microfluidic instrument that is optimized to perform genetic amplification and analysis on a single sample. Biochemical reactions and analytical separations for genetic analysis are performed within tri-layered glass-PDMS microchips. The microchip itself consists of integrated pneumatically-actuated valves and pumps for fluid handling, a thin-film resistive element that acts simultaneously as a heater and a temperature sensor, and channels for capillary electrophoresis (CE). The platform is comprised of high voltage circuitry, an optical assembly consisting of a laser diode and a charged coupled device (CCD) camera, circuitry for thermal control, and mini-pumps to generate vacuum/pressure to operate the on-chip diaphragm-based pumps and valves. Using this microchip and instrument, we demonstrate an integration of reverse transcription (RT), polymerase chain reaction (PCR), and capillary electrophoresis (CE). The novelty of this system lies in the cost-effective integration of microfluidics, optics, and electronics to realize a fully portable and inexpensive system (on the order of $1000 in component costs) for performing both genetic amplification and analysis - the basis of many medical diagnostics. We believe that this combination of portability, cost-effectiveness and performance will enable more accessible healthcare. PMID:18299747

Kaigala, Govind V; Hoang, Viet N; Stickel, Alex; Lauzon, Jana; Manage, Dammika; Pilarski, Linda M; Backhouse, Christopher J

2008-03-01

386

Optical and UV spectroscopy of the peculiar RS CVn system, RT Lacertae  

NASA Technical Reports Server (NTRS)

Spectra in the H-alpha and H-beta regions of the peculiar double-lined RS CVn binary, RT Lacertae, were obtained in the fall of 1984. Limited International Ultraviolet Explorer (IUE) long wavelength low and high resolution spectra were obtained concurrently. The ground based spectra have shown an asymmetry with orbital phase in the H-alpha profile. The H-beta profiles were consistent with the same effect. One hemisphere showed excess emission and the other excess absorption, with a broad Gaussian emission component superposed upon the excess H-alpha line. An improved radial velocity curve, giving a better determined mass ratio and geometry was derived. This combined with the radii implied by the rotational broadening of the spectra, showed one component to be 80 to 90% filling the equilibrium Roche surface. The two-faced nature is, therfore, very likely due to mass transfer from the contact component impacting upon its companion. Low resolution ultraviolet data showed that the supposed cooler component is bluer than its companion. High resolution ultraviolet data taken during secondary eclipse showed Mg II emission strength which decreased more slowly than the area visible. The phase behavior of the low resolution data support the former situation, indicating traditional chromospheric activity.

Huenemoerder, D. P.; Barden, S. C.

1985-01-01

387

Real Time RT-PCR Assays for Detection and Typing of African Horse Sickness Virus  

PubMed Central

Although African horse sickness (AHS) can cause up to 95% mortality in horses, naïve animals can be protected by vaccination against the homologous AHSV serotype. Genome segment 2 (Seg-2) encodes outer capsid protein VP2, the most variable of the AHSV proteins. VP2 is also a primary target for AHSV specific neutralising antibodies, and consequently determines the identity of the nine AHSV serotypes. In contrast VP1 (the viral polymerase) and VP3 (the sub-core shell protein), encoded by Seg-1 and Seg-3 respectively, are highly conserved, representing virus species/orbivirus-serogroup-specific antigens. We report development and evaluation of real-time RT-PCR assays targeting AHSV Seg-1 or Seg-3, that can detect any AHSV type (virus species/serogroup-specific assays), as well as type-specific assays targeting Seg-2 of the nine AHSV serotypes. These assays were evaluated using isolates of different AHSV serotypes and other closely related orbiviruses, from the ‘Orbivirus Reference Collection’ (ORC) at The Pirbright Institute. The assays were shown to be AHSV virus-species-specific, or type-specific (as designed) and can be used for rapid, sensitive and reliable detection and identification (typing) of AHSV RNA in infected blood, tissue samples, homogenised Culicoides, or tissue culture supernatant. None of the assays amplified cDNAs from closely related heterologous orbiviruses, or from uninfected host animals or cell cultures. PMID:24721971

Bachanek-Bankowska, Katarzyna; Maan, Sushila; Castillo-Olivares, Javier; Manning, Nicola M.; Maan, Narender Singh; Potgieter, Abraham C.; Di Nardo, Antonello; Sutton, Geoff; Batten, Carrie; Mertens, Peter P. C.

2014-01-01

388

High-throughput microfluidic single-cell RT-qPCR  

PubMed Central

A long-sought milestone in microfluidics research has been the development of integrated technology for scalable analysis of transcription in single cells. Here we present a fully integrated microfluidic device capable of performing high-precision RT-qPCR measurements of gene expression from hundreds of single cells per run. Our device executes all steps of single-cell processing, including cell capture, cell lysis, reverse transcription, and quantitative PCR. In addition to higher throughput and reduced cost, we show that nanoliter volume processing reduced measurement noise, increased sensitivity, and provided single nucleotide specificity. We apply this technology to 3,300 single-cell measurements of (i) miRNA expression in K562 cells, (ii) coregulation of a miRNA and one of its target transcripts during differentiation in embryonic stem cells, and (iii) single nucleotide variant detection in primary lobular breast cancer cells. The core functionality established here provides the foundation from which a variety of on-chip single-cell transcription analyses will be developed. PMID:21808033

White, Adam K.; VanInsberghe, Michael; Petriv, Oleh I.; Hamidi, Mani; Sikorski, Darek; Marra, Marco A.; Piret, James; Aparicio, Samuel; Hansen, Carl L.

2011-01-01

389

High-throughput microfluidic single-cell RT-qPCR.  

PubMed

A long-sought milestone in microfluidics research has been the development of integrated technology for scalable analysis of transcription in single cells. Here we present a fully integrated microfluidic device capable of performing high-precision RT-qPCR measurements of gene expression from hundreds of single cells per run. Our device executes all steps of single-cell processing, including cell capture, cell lysis, reverse transcription, and quantitative PCR. In addition to higher throughput and reduced cost, we show that nanoliter volume processing reduced measurement noise, increased sensitivity, and provided single nucleotide specificity. We apply this technology to 3,300 single-cell measurements of (i) miRNA expression in K562 cells, (ii) coregulation of a miRNA and one of its target transcripts during differentiation in embryonic stem cells, and (iii) single nucleotide variant detection in primary lobular breast cancer cells. The core functionality established here provides the foundation from which a variety of on-chip single-cell transcription analyses will be developed. PMID:21808033

White, Adam K; VanInsberghe, Michael; Petriv, Oleh I; Hamidi, Mani; Sikorski, Darek; Marra, Marco A; Piret, James; Aparicio, Samuel; Hansen, Carl L

2011-08-23

390

Pilot Quality Control Program for Audit RT External Beams at Mexican Hospitals  

SciTech Connect

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.

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

391

The Selection of Low Envelope Glycoprotein Reactivity to Soluble CD4 and Cold during Simian-Human Immunodeficiency Virus Infection of Rhesus Macaques  

PubMed Central

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

McGee, Kathleen; Haim, Hillel; Korioth-Schmitz, Birgit; Espy, Nicole; Javanbakht, Hassan; Letvin, Norman

2014-01-01

392

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 Central

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

Trott, Maria; Weiss, Svenja; Antoni, Sascha; Koch, Joachim; von Briesen, Hagen; Hust, Michael; Dietrich, Ursula

2014-01-01

393

1132 VOLUME 19 NUMBER 11 NOVEMBER 2012 nature structural & molecular biology a rt i c l e s  

E-print Network

1132 VOLUME 19 NUMBER 11 NOVEMBER 2012 nature structural & molecular biology a rt i c l e s Gram a promising target against which to develop antimicrobial therapeutics1. Although all steps in the pathway that accesses its normally bilayer-resident substrate and produces the same product as LpxH but by a different

Stroud, Robert

394

Detection of influenza virus using a lateral flow immunoassay for amplified DNA by a microfluidic RT-PCR chip.  

PubMed

Influenza virus RNA was amplified by a continuous-flow polydimethylsiloxane microfluidic RT-PCR chip within 15-20 min. The amplified influenza virus RNA was observed with the naked eye, as the red color at the test line, using a lateral flow immunoassay within 1 min. PMID:22354200