Generation and characterization of a SIVmac239 clone corrected at four suboptimal nucleotides.

BACKGROUND: SIVmac239 is a commonly used virus in non-human primate models of HIV transmission and pathogenesis. Previous studies identified four suboptimal nucleotides in the SIVmac239 genome, which putatively inhibit its replicative capacity. Since all four suboptimal changes revert to the optimal nucleotide consensus sequence during viral replication in vitro and in vivo, we sought to eliminate the variability of generating these mutations de novo and increase the overall consistency of viral replication by introducing the optimal nucleotides directly to the infectious molecular clone. RESULTS: Using site directed mutagenesis of the full-length/nef-open SIVmac239 clone, we reverted all four nucleotides to the consensus/optimal base to generate SIVmac239Opt and subsequently tested its infectivity and replicative capacity in vitro and in vivo. In primary and cell line cultures, we observed that the optimized virus displayed consistent modest but not statistically significant increases in replicative kinetics compared to wild type. In vivo, SIVmac239Opt replicated to high peak titers with an average of 1.2 × 10(8) viral RNA copies/ml at day 12 following intrarectal challenge, reaching set-point viremia of 1.2 × 10(6) viral RNA copies/ml by day 28. Although the peak and set point viremia means were not statistically different from the original "wild type" SIVmac239, viral load variation at set point was greater for SIVmac239WT compared to SIVmac239Opt (p = 0.0015) demonstrating a greater consistency of the optimized virus. Synonymous mutations were added to the integrase gene of SIVmac239Opt to generate a molecular tag consisting of ten genetically distinguishable viral variants referred to as SIVmac239OptX (Del Prete et al., J Virol. doi: 10.1128/JVI.01026-14 , 2014). Replication dynamics in vitro of these optimized clones were not statistically different from the parental clones. Interestingly, the consistently observed rapid reversion of the primer binding site suboptimal nucleotide is not due to viral RT error but is changed post-integration of a mismatched base via host proofreading mechanisms. CONCLUSIONS: Overall, our results demonstrate that SIVmac239Opt is a functional alternative to parental SIVmac239 with marginally faster replication dynamics and with increased replication uniformity providing a more consistent and reproducible infection model in nonhuman primates.

CD40 expression in renal cell carcinoma is associated with tumor apoptosis, CD8(+) T cell frequency and patient survival.

The co-stimulatory molecule, CD40, is expressed in renal cell carcinoma (RCC) and a variety of inflammatory diseases in the kidney. We investigated the relationship between tumor-associated CD40 expression, immune milieu of the tumor microenvironment, tumor stage and survival of patients with RCC. The expression of CD40, TUNEL and CD8 in human renal cell carcinomas was analyzed by immunohistochemistry performed on tissue samples obtained at the time of surgery. Computer-assisted quantitation of protein expression was used to analyze results in connection with patient survival and tumor stage. We show for the first time that tumor-associated CD40 expression is associated with prolonged survival in RCC patients. Tumor apoptosis (TUNEL) and CD8 immunostaining were also associated with patient survival. No relation was observed between CD40 expression and tumor stage. Our results suggest CD40 may be a prognostic biomarker indicative of prolonged RCC patient survival. Strategies that up-regulate CD40 expression in some RCC patients may thus improve survival, supporting further studies of agonistic CD40 antibodies in RCC.

Chr 19(A/J) modifies tumor resistance in a sex- and parent-of-origin-specific manner.

Neurofibromatosis type 1 (NF1) is one of the most common human genetic diseases affecting the nervous system and predisposes individuals to cancer, including peripheral nerve sheath tumors (PNSTs) and astrocytomas. Modifiers in the genetic background affect the severity of the disease and we have previously mapped two modifier loci, Nstr1 and Nstr2, that influence resistance to PNSTs in the Nf1-/+;Trp53-/+cis mouse model of NF1. We report here the analysis of Nstr1 in isolation from other epistatic loci using a chromosome substitution strain, and further show that a modifier locus (or loci) on chromosome 19 influences resistance to both PNSTs and astrocytomas. This modifier locus interacts with sex, resulting in sex-specific modification of tumors. Allele variability on chromosome 19 affects both the timing and the penetrance of the growth of different tumor types associated with NF1, specifically PNSTs and astrocytoma. These results indicate that modifiers of cancer susceptibility interact and affect tumorigenesis under different genetic conditions and demonstrate the power of chromosome substitution strains to study genetic modifiers.

A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R.

This article describes specific procedures for conducting quality assessment of Affymetrix GeneChip(R) soybean genome data and for performing analyses to determine differential gene expression using the open-source R programming environment in conjunction with the open-source Bioconductor software. We describe procedures for extracting those Affymetrix probe set IDs related specifically to the soybean genome on the Affymetrix soybean chip and demonstrate the use of exploratory plots including images of raw probe-level data, boxplots, density plots and M versus A plots. RNA degradation and recommended procedures from Affymetrix for quality control are discussed. An appropriate probe-level model provides an excellent quality assessment tool. To demonstrate this, we discuss and display chip pseudo-images of weights, residuals and signed residuals and additional probe-level modeling plots that may be used to identify aberrant chips. The Robust Multichip Averaging (RMA) procedure was used for background correction, normalization and summarization of the AffyBatch probe-level data to obtain expression level data and to discover differentially expressed genes. Examples of boxplots and MA plots are presented for the expression level data. Volcano plots and heatmaps are used to demonstrate the use of (log) fold changes in conjunction with ordinary and moderated t-statistics for determining interesting genes. We show, with real data, how implementation of functions in R and Bioconductor successfully identified differentially expressed genes that may play a role in soybean resistance to a fungal pathogen, Phakopsora pachyrhizi. Complete source code for performing all quality assessment and statistical procedures may be downloaded from our web source: http://css.ncifcrf.gov/services/download/MicroarraySoybean.zip.

ASSESSING MERCURY LEVELS IN THE WASTEWATER OF AN AGING RESEARCH LABORATORY BUILDING.

Increasingly stringent restrictions on mercury concentrations in wastewater discharge may be problematic for aging research laboratory facilities. Relatively high levels of mercury compounds may exist and concentrate deep in the plumbing system and their sediments, resulting in elevated wastewater concentrations. This study was conducted to assess total mercury levels in an aging laboratory building wastewater system. Wastewater outflow, sink trap water, and pipe sediment samples were collected from the building. The Jerome 431 Mercury Vapor Analyzer was assessed as a tool for screening lab sink trap drains for mercury deposition. Results revealed that the three day average for mercury discharge from this single structure, if not diluted by other waters, would be above the local total release parameters to the wastewater treatment plant. The sink traps did not contain a majority of the mercury; however, the pipe sediment and outflow samples revealed consistently elevated concentrations.

Application of the granzyme B ELISPOT assay for monitoring cancer vaccine trials.

Granzyme B (GrB) is present in the granules of cytolytic lymphocytes and is a key mediator of cell-mediated target cell death via the granule-mediated pathway. The release of GrB can be used as an indicator of a cytotoxic T lymphocyte response. Herein, we report that the GrB enzyme-linked immunospot assay (ELISPOT) can be used to measure ex vivo antigen-specific cytotoxicity of peripheral blood mononuclear cells from cancer patients vaccinated with a peptide-based cancer vaccine. We compare the reactivity of patients' peripheral blood mononuclear cells in the GrB ELISPOT with reactivity in the tetramer, interferon (IFN)-gamma ELISPOT, and Cr-release assays. Differences in immune response over all assays tested were found between patients and 4 response patterns were observed. Reactivity in the GrB ELISPOT was more closely associated with cytotoxicity in the Cr-release assay than the tetramer or IFN-gamma ELISPOT assays. Moreover, the higher affinity g209-2M peptide (used for vaccination) elicited greater GrB secretion than the native g209 peptide, although this difference was not observed with IFN-gamma secretion. Taken together with the fact that GrB is a specific mediator released by cytotoxic T lymphocytes, these results show that simultaneous use of the GrB ELISPOT assay with other immunologic assays may provide important additional immunologic insight into patient responses to cancer vaccines.