In Vivo validation of a bioinformatics based tool to identify reduced replication capacity in HIV-1.

Although antiretroviral drug resistance is common in treated HIV infected individuals, it is not a consistent indicator of HIV morbidity and mortality. To the contrary, HIV resistance-associated mutations may lead to changes in viral fitness that are beneficial to infected individuals. Using a bioinformatics-based model to assess the effects of numerous drug resistance mutations, we determined that the D30N mutation in HIV-1 protease had the largest decrease in replication capacity among known protease resistance mutations. To test this in silico result in an in vivo environment, we constructed several drug-resistant mutant HIV-1 strains and compared their relative fitness utilizing the SCID-hu mouse model. We found HIV-1 containing the D30N mutation had a significant defect in vivo, showing impaired replication kinetics and a decreased ability to deplete CD4+ thymocytes, compared to the wild-type or virus without the D30N mutation. In comparison, virus containing the M184V mutation in reverse transcriptase, which shows decreased replication capacity in vitro, did not have an effect on viral fitness in vivo. Thus, in this study we have verified an in silico bioinformatics result with a biological assessment to identify a unique mutation in HIV-1 that has a significant fitness defect in vivo

Stem-cell-based gene therapy for HIV infection.

Despite the enormous success of combined anti-retroviral therapy, HIV infection is still a lifelong disease and continues to spread rapidly worldwide. There is a pressing need to develop a treatment that will cure HIV infection. Recent progress in stem cell manipulation and advancements in humanized mouse models have allowed rapid developments of gene therapy for HIV treatment. In this review, we will discuss two aspects of HIV gene therapy using human hematopoietic stem cells. The first is to generate immune systems resistant to HIV infection while the second strategy involves enhancing anti-HIV immunity to eliminate HIV infected cells

Initial Virological and Immunologic Response to Highly Active Antiretroviral Therapy Predicts Long-Term Clinical Outcome

Little is known about the long-term clinical outcomes for human immunodeficiency virus (HIV)-infected patients who have received highly active antiretroviral therapy (HAART). Determining factors associated with long-term clinical outcomes early in the course of treatment may allow modifications to be made for patients who are at a greater risk of treatment failure. To evaluate these factors, we studied 213 HIV-infected patients who had received HAART for at least 115 weeks. In the univariate analysis, virological response, which was measured as the change in virus load from baseline at month 3 of treatment, was the single best predictor of clinical outcome (relative hazard, 0.722; P = .001), independent of virological suppression. In the multivariate analysis, virological response and immunologic response, which was measured as an increase in CD4 cell count of >200 cells/mm^3, resulted in better prediction of clinical outcomes than did use of either variable alone (P = .02). Our results indicate that changes in virus load and immunologic response together are good predictors of clinical outcome and can be assessed after the initiation of HAART, which would allow clinicians to identify patients early in the course of therapy who are at greater risk of negative outcome

A new perspective when examining maize fertilizer nitrogen use efficiency, incrementally

For maize (Zea mays L.), nitrogen (N) fertilizer use is often summarized from field to global scales using average N use efficiency (NUE). But expressing NUE as averages is misleading because grain increase to added N diminishes near optimal yield. Thus, environmental risks increase as economic benefits decrease. Here, we use empirical datasets obtained in North America of maize grain yield response to N fertilizer (n = 189) to create and interpret incremental NUE (iNUE), or the change in NUE with change in N fertilization. We show for those last units of N applied to reach economic optimal N rate (EONR) iNUE for N removed with the grain is only about 6%. Conversely stated, for those last units of N applied over 90% is either lost to the environment during the growing season, remains as inorganic soil N that too may be lost after the growing season, or has been captured within maize stover and roots or soil organic matter pools. Results also showed iNUE decrease averaged 0.63% for medium-textured soils and 0.37% for fine-textured soils, attributable to fine-textured soils being more predisposed to denitrification and/or lower mineralization. Further analysis demonstrated the critical nature growing season water amount and distribution has on iNUE. Conditions with too much rainfall and/or uneven rainfall produced low iNUE. Producers realize this from experience, and it is uncertain weather that largely drives insurance fertilizer additions. Nitrogen fertilization creating low iNUE is environmentally problematic. Our results show that with modest sub-EONR fertilization and minor forgone profit, average NUE improvements of ~10% can be realized. Further, examining iNUE creates unique perspective and ideas for how to improve N fertilizer management tools, educational programs, and public policies and regulations

An Uncharged Amine in the Transition State of the Ribosomal Peptidyl Transfer Reaction

The ribosome has an active site comprised of RNA that catalyzes peptide bond formation. To understand how RNA promotes this reaction requires a detailed understanding of the chemical transition state. Here, we report the Brønsted coefficient of the α-amino nucleophile with a series of puromycin derivatives. Both 50S subunit- and 70S ribosome-catalyzed reactions displayed linear free-energy relationships with slopes close to zero under conditions where chemistry is rate limiting. These results indicate that, at the transition state, the nucleophile is neutral in the ribosome-catalyzed reaction, in contrast to the substantial positive charge reported for typical uncatalyzed aminolysis reactions. This suggests that the ribosomal transition state involves deprotonation to a degree commensurate with nitrogen-carbon bond formation. Such a transition state is significantly different from that of uncatalyzed aminolysis reactions in solution

Engineering Antigen-Specific T Cells from Genetically Modified Human Hematopoietic Stem Cells in Immunodeficient Mice

There is a desperate need for effective therapies to fight chronic viral infections. The immune response is normally fastidious at controlling the majority of viral infections and a therapeutic strategy aimed at reestablishing immune control represents a potentially powerful approach towards treating persistent viral infections. We examined the potential of genetically programming human hematopoietic stem cells to generate mature CD8+ cytotoxic T lymphocytes that express a molecularly cloned, “transgenic” human anti-HIV T cell receptor (TCR). Anti-HIV TCR transduction of human hematopoietic stem cells directed the maturation of a large population of polyfunctional, HIV-specific CD8+ cells capable of recognizing and killing viral antigen-presenting cells. Thus, through this proof-of-concept we propose that genetic engineering of human hematopoietic stem cells will allow the tailoring of effector T cell responses to fight HIV infection or other diseases that are characterized by the loss of immune control

Continuous-mode 448 kHz capacitive resistive monopolar radiofrequency induces greater deep blood flow changes compared to pulsed mode shortwave: a crossover study in healthy adults

This document is the Accepted Manuscript version of the following article: Binoy Kumaran, Anthony Herbland and Tim Watson, ‘Continuous-mode 448 kHz capacitive resistive monopolar radiofrequency induces greater deep blood flow changes compared to pulsed mode shortwave: a crossover study in healthy adults’, European Journal of Physiotheraphy, first published online 20 April 2017. The version of record is available online at doi: http://dx.doi.org/10.1080/21679169.2017.1316310. © 2017 Informa UK Limited, trading as Taylor & Francis Group.Aims: Radiofrequency-based electrophysical agents (EPAs) have been used in therapy practice over several decades (e.g. shortwave therapies). Currently, there is insufficient evidence supporting such EPAs operating below shortwave frequencies. This laboratory-based study investigated the deep physiological effects of 448 kHz capacitive resistive monopolar radiofrequency (CRMRF) and compared them to pulsed shortwave therapy (PSWT). Methods: In a randomized crossover study, 17 healthy volunteers initially received four treatment conditions: high, low and placebo dose conditions receiving 15-min CRMRF treatment and a control condition receiving no intervention. Fifteen participants additionally received high-dose PSWT as fifth condition, for comparison. Pre- and post-treatment measurements of deep blood flow and tissue extensibility were obtained using Doppler ultrasound and sonoelastography. Group data were compared using analysis of variance model. Statistical significance was set at p ≤ .05, 0.8 power, and 95% confidence interval. Results: Significant increases in volume and intensity of deep blood flow were obtained with CRMRF over placebo, control (p = .003) and PSWT (p < .001). No significant changes in blood flow velocity or tissue extensibility were noted for any condition. Conclusions: Deep blood flow changes with CRMRF were more pronounced than that with PSWT, placebo or control. Potential greater therapeutic benefits need to be confirmed with comparative clinical studies.Peer reviewe

LAGraph: Linear algebra, network analysis libraries, and the study of graph algorithms

Graph algorithms can be expressed in terms of linear algebra. GraphBLAS is a library of low-level building blocks for such algorithms that targets algorithm developers. LAGraph builds on top of the GraphBLAS to target users of graph algorithms with high-level algorithms common in network analysis. In this paper, we describe the first release of the LAGraph library, the design decisions behind the library, and performance using the GAP benchmark suite. LAGraph, however, is much more than a library. It is also a project to document and analyze the full range of algorithms enabled by the GraphBLAS. To that end, we have developed a compact and intuitive notation for describing these algorithms. In this paper, we present that notation with examples from the GAP benchmark suite