Use of oxygen sensors for the non destructive measurement of oxygen in packaged food and beverage products and its impact on product quality and shelf life

The principal objective of this thesis was to investigate the ability of reversible optical O2 sensors to be incorporated into food/beverage packaging systems to continuously monitor O2 levels in a non-destructive manner immediately postpackaging and over time. Residual levels of O2 present in packs can negatively affect product quality and subsequently, product shelf-life, especially for O2-sensitive foods/beverages. Therefore, the ability of O2 sensors to continuously monitor O2 levels present within food/beverage packages was considered commercially relevant in terms of identifying the consequences of residual O2 on product safety and quality over time. Research commenced with the development of a novel range of O2 sensors based on phosphorescent platinum and palladium octaethylporphyrin-ketones (OEPk) in nano-porous high density polyethylene (HDPE), polypropylene (PP) polytetrafluoroethylene (PTFE) polymer supports. Sensors were calibrated over a temperature range of -10°C to +40°C and deemed suitable for food and beverage packaging applications. This sensor technology was used and demonstrated itself effective in determining failures in packaging containment. This was clearly demonstrated in the packaging of cheese string products. The sensor technology was also assessed across a wide range of packaged products; beer, ready-to-eat salad products, bread and convenience-style, muscle-based processed food products. The O2 sensor technology performed extremely well within all packaging systems. The sensor technology adequately detected O2 levels in; beer bottles prior to and following pasteurisation, modified atmosphere (MA) packs of ready-to-eat salad packs as respiration progressed during product storage and MA packs of bread and convenience-style muscle-based products as mycological growth occurred in food packs over time in the presence and absence of ethanol emitters. The use of the technology, in conjunction with standard food quality assessment techniques, showed remarkable usefulness in determining the impact of actual levels of O2 on specific quality attributes. The O2 sensing probe was modified, miniaturised and automated to screen for the determination of total aerobic viable counts (TVC) in several fish species samples. The test showed good correlation with conventional TVC test (ISO:4833:2003), analytical performance and ruggedness with respect to variation of key assay parameters (probe concentration and pipetting volume). Overall, the respirometric fish TVC test was simple to use, possessed a dynamic microbial range (104-107 cfu/g sample), had an accuracy of +/- one log(cfu/g sample) and was rapid. Its ability to assess highly perishable products such as fish for total microbial growth in <12 hr demonstrates commercial potential.

Atomic layer deposition of interface control layers for the fabrication of III/V MOS devices

The continued advancement of metal oxide semiconductor field effect transistor (MOSFET) technology has shifted the focus from Si/SiO2 transistors towards high-κ/III-V transistors for high performance, faster devices. This has been necessary due to the limitations associated with the scaling of the SiO2 thickness below ~1 nm and the associated increased leakage current due to direct electron tunnelling through the gate oxide. The use of these materials exhibiting lower effective charge carrier mass in conjunction with the use of a high-κ gate oxide allows for the continuation of device scaling and increases in the associated MOSFET device performance. The high-κ/III-V interface is a critical challenge to the integration of high-κ dielectrics on III-V channels. The interfacial chemistry of the high-κ/III-V system is more complex than Si, due to the nature of the multitude of potential native oxide chemistries at the surface with the resultant interfacial layer showing poor electrical insulating properties when high-κ dielectrics are deposited directly on these oxides. It is necessary to ensure that a good quality interface is formed in order to reduce leakage and interface state defect density to maximise channel mobility and reduce variability and power dissipation. In this work, the ALD growth of aluminium oxide (Al2O3) and hafnium oxide (HfO2) after various surface pre-treatments was carried out, with the aim of improving the high-κ/III-V interface by reducing the Dit – the density of interface defects caused by imperfections such as dangling bonds, dimers and other unsatisfied bonds at the interfaces of materials. A brief investigation was performed into the structural and electrical properties of Al2O3 films deposited on In0.53Ga0.47As at 200 and 300oC via a novel amidinate precursor. Samples were determined to experience a severe nucleation delay when deposited directly on native oxides, leading to diminished functionality as a gate insulator due to largely reduced growth per cycle. Aluminium oxide MOS capacitors were prepared by ALD and the electrical characteristics of GaAs, In0.53Ga0.47As and InP capacitors which had been exposed to pre-pulse treatments from triethyl gallium and trimethyl indium were examined, to determine if self-cleaning reactions similar to those of trimethyl aluminium occur for other alkyl precursors. An improved C-V characteristic was observed for GaAs devices indicating an improved interface possibly indicating an improvement of the surface upon pre-pulsing with TEG, conversely degraded electrical characteristics observed for In0.53Ga0.47As and InP MOS devices after pre-treatment with triethyl gallium and trimethyl indium respectively. The electrical characteristics of Al2O3/In0.53Ga0.47As MOS capacitors after in-situ H2/Ar plasma treatment or in-situ ammonium sulphide passivation were investigated and estimates of interface Dit calculated. The use of plasma reduced the amount of interface defects as evidenced in the improved C-V characteristics. Samples treated with ammonium sulphide in the ALD chamber were found to display no significant improvement of the high-κ/III-V interface. HfO2 MOS capacitors were fabricated using two different precursors comparing the industry standard hafnium chloride process with deposition from amide precursors incorporating a ~1nm interface control layer of aluminium oxide and the structural and electrical properties investigated. Capacitors furnished from the chloride process exhibited lower hysteresis and improved C-V characteristics as compared to that of hafnium dioxide grown from an amide precursor, an indication that no etching of the film takes place using the chloride precursor in conjunction with a 1nm interlayer. Optimisation of the amide process was carried out and scaled samples electrically characterised in order to determine if reduced bilayer structures display improved electrical characteristics. Samples were determined to exhibit good electrical characteristics with a low midgap Dit indicative of an unpinned Fermi level

Synthesis and evaluation of novel quinolines and quinazolinediones as potential anti-cancer agents

This thesis outlines the design and effectuation of novel chemical routes towards a nascent class of functionalised quinoline-5,8-diones and the expansion of a series of contemporary quinazolinediones towards an innovative family of pyridinoquinazolinetetrone derivatives. This fragment based approach is envisaged to lead to advancements in the three scaffolds, expanding the SAR pool of both quinolines and quinazolinediones with subsequent evaluation of chemotherapeutic potential as well as furnishing a new class of tricycle for biological investigation. Development of novel quinoline-5,8-diones is provided for by expanding on existing methodology. Using a variety of nucleophiles on a critical intermediate, a broad range of novel compounds was afforded allowing chemotherapeutic potential to be assessed, while also serving as intermediates for accomplishing novel pyridinoquinazolinetetrone congeners. In order to incorporate functionality into our quinazolinedione template, an efficient synthetic strategy was constructed which provided a robust route to effectuate a highly derivatised pyrimidinedione ring. As derivatisation of this template is unreported our chief priority was to synthesise a range of diverse quinazolinediones. The application of annulation methodology using functionalised precursors provided a library of N-3 derivatised quinazolinedione analogues. These, along with their N-1 functionalised derivatives provide a wide scope from which to construct a series of pyridinoquinazolinetetrone derivatives while also serving as a unique class of molecules whose biological potential is uncharted. Although the actualisation of the pyridinoquinazolinetetrone was ultimately unsuccessful, our work has led to the development of novel quinoline-5,8-diones which were found to possess excellent anti-cancer activity when assessed by the NCI screen. Of the quinazolinediones synthesised eight compounds were accepted for screening by the NCI. Results from the single-dose tests however indicated that these compounds possessed little cytotoxic activity at 10 μM. The development of this novel template in conjunction with the highly active quinolinediones serves as an excellent rostrum for future synthetic endeavours.

Computational modeling of defects in nanoscale device materials

This PhD thesis concerns the computational modeling of the electronic and atomic structure of point defects in technologically relevant materials. Identifying the atomistic origin of defects observed in the electrical characteristics of electronic devices has been a long-term goal of first-principles methods. First principles simulations are performed in this thesis, consisting of density functional theory (DFT) supplemented with many body perturbation theory (MBPT) methods, of native defects in bulk and slab models of In0.53Ga0.47As. The latter consist of (100) - oriented surfaces passivated with A12O3. Our results indicate that the experimentally extracted midgap interface state density (Dit) peaks are not the result of defects directly at the semiconductor/oxide interface, but originate from defects in a more bulk-like chemical environment. This conclusion is reached by considering the energy of charge transition levels for defects at the interface as a function of distance from the oxide. Our work provides insight into the types of defects responsible for the observed departure from ideal electrical behaviour in III-V metal-oxidesemiconductor (MOS) capacitors. In addition, the formation energetics and electron scattering properties of point defects in carbon nanotubes (CNTs) are studied using DFT in conjunction with Green’s function based techniques. The latter are applied to evaluate the low-temperature, low-bias Landauer conductance spectrum from which mesoscopic transport properties such as the elastic mean free path and localization length of technologically relevant CNT sizes can be estimated from computationally tractable CNT models. Our calculations show that at CNT diameters pertinent to interconnect applications, the 555777 divacancy defect results in increased scattering and hence higher electrical resistance for electron transport near the Fermi level.

The Cultural Dimensions of the Vietnamese Private Entrepreneurship

In this essay, we explore cultural impacts on the private entrepreneurship in the post-Doi Moi Vietnam. Some important aspects of the traditional cultural values of the Vietnamese society are explored in conjunction with the socio-economic changes over the past two decades. Traditional cultural values continue to have strong impacts on the Vietnamese society, and to a large extent to adversely affect the entrepreneurial spirit of the community. Typical constraints private entrepreneurs face may have roots in the cultural facet as legacy of the Confucian society, such as relationship-based bank credit. Low quality business education is both victim and culprit of the long-standing tradition that looks down on the role of private entrepreneurship in the country.

It Takes Two to Tango: Entrepreneurship and Creativity in Troubled Times – Vietnam 2012

Strikingly, most literature suggests that market competition will push firms to take creativity/innovation seriously as matter of death or survival. Using the data, we examined creativity methods (Napier and Nilsson, 2008; Napier, 2010) in conjunction with three influential cultural values – namely risk tolerance, relationship, and dependence on resources – to assess how they influence decisions of entrepreneurs.The primary objective of this study focuses on perceived values of entrepreneurship and creativity in business conducted within a turbulent environment. Our initial hypothesis is that a typical entrepreneurial process carries with it “creativity-enabling elements.” In a normal situation, when businesses focus more on optimizing their resources for commercial gains, perceptions about values of entrepreneurial creativity are usually vague. However, in difficult times and harsh competition, the difference between survival and failure may be creativity. This paper also examines many previous findings on both entrepreneurship and creativity and suggests a highly possible “organic growth” of creativity in an entrepreneurial environment and reinforcing value of entrepreneurship when creativity power is present. In other words, we see each idea reinforcing the other. We use data from a survey of sample Vietnamese firms during the chaotic economic year 2012 to learn about the ‘entrepreneurshipcreativity nexus.’ A data set of 137 responses qualified for a statistical examination was obtained from an online survey, which started on February 16 and ended May 24, 2012, sent to local entrepreneurs and corporate managers using social networks. The authors employed categorical data analysis (Agresti, 2002; Azen & Walker, 2011). Statistical analyses confirm that for business operation, the creativity and entrepreneurial spirit could hardly be separate; and, this is not only correct with entrepreneurial firm, but also well established companies. The single most important factor before business startup and during early implementation in Vietnam is what we call “connection/relationship.” However, businesspeople are increasingly aware of the need of creativity/innovation. In fact, we suggest that creativity and entrepreneurial spirit cannot be separated in entrepreneurial firms as well as established companies.

Co-regulation of nuclear respiratory factor-1 by NFkappaB and CREB links LPS-induced inflammation to mitochondrial biogenesis.

The nuclear respiratory factor-1 (NRF1) gene is activated by lipopolysaccharide (LPS), which might reflect TLR4-mediated mitigation of cellular inflammatory damage via initiation of mitochondrial biogenesis. To test this hypothesis, we examined NRF1 promoter regulation by NFκB, and identified interspecies-conserved κB-responsive promoter and intronic elements in the NRF1 locus. In mice, activation of Nrf1 and its downstream target, Tfam, by Escherichia coli was contingent on NFκB, and in LPS-treated hepatocytes, NFκB served as an NRF1 enhancer element in conjunction with NFκB promoter binding. Unexpectedly, optimal NRF1 promoter activity after LPS also required binding by the energy-state-dependent transcription factor CREB. EMSA and ChIP assays confirmed p65 and CREB binding to the NRF1 promoter and p65 binding to intron 1. Functionality for both transcription factors was validated by gene-knockdown studies. LPS regulation of NRF1 led to mtDNA-encoded gene expression and expansion of mtDNA copy number. In cells expressing plasmid constructs containing the NRF-1 promoter and GFP, LPS-dependent reporter activity was abolished by cis-acting κB-element mutations, and nuclear accumulation of NFκB and CREB demonstrated dependence on mitochondrial H(2)O(2). These findings indicate that TLR4-dependent NFκB and CREB activation co-regulate the NRF1 promoter with NFκB intronic enhancement and redox-regulated nuclear translocation, leading to downstream target-gene expression, and identify NRF-1 as an early-phase component of the host antibacterial defenses.

Analytic expressions for the constitutive parameters of magnetoelectric metamaterials

Electromagnetic metamaterials are artificially structured media typically composed of arrays of resonant electromagnetic circuits, the dimension and spacing of which are considerably smaller than the free-space wavelengths of operation. The constitutive parameters for metamaterials, which can be obtained using full-wave simulations in conjunction with numerical retrieval algorithms, exhibit artifacts related to the finite size of the metamaterial cell relative to the wavelength. Liu showed that the complicated, frequency-dependent forms of the constitutive parameters can be described by a set of relatively simple analytical expressions. These expressions provide useful insight and can serve as the basis for more intelligent interpolation or optimization schemes. Here, we show that the same analytical expressions can be obtained using a transfer-matrix formalism applied to a one-dimensional periodic array of thin, resonant, dielectric, or magnetic sheets. The transfer-matrix formalism breaks down, however, when both electric and magnetic responses are present in the same unit cell, as it neglects the magnetoelectric coupling between unit cells. We show that an alternative analytical approach based on the same physical model must be applied for such structures. Furthermore, in addition to the intercell coupling, electric and magnetic resonators within a unit cell may also exhibit magnetoelectric coupling. For such cells, we find an analytical expression for the effective index, which displays markedly characteristic dispersion features that depend on the strength of the coupling coefficient. We illustrate the applicability of the derived expressions by comparing to full-wave simulations on magnetoelectric unit cells. We conclude that the design of metamaterials with tailored simultaneous electric and magnetic response-such as negative index materials-will generally be complicated by potentially unwanted magnetoelectric coupling. © 2010 The American Physical Society.

The impact of anxiety-inducing distraction on cognitive performance: a combined brain imaging and personality investigation.

BACKGROUND: Previous investigations revealed that the impact of task-irrelevant emotional distraction on ongoing goal-oriented cognitive processing is linked to opposite patterns of activation in emotional and perceptual vs. cognitive control/executive brain regions. However, little is known about the role of individual variations in these responses. The present study investigated the effect of trait anxiety on the neural responses mediating the impact of transient anxiety-inducing task-irrelevant distraction on cognitive performance, and on the neural correlates of coping with such distraction. We investigated whether activity in the brain regions sensitive to emotional distraction would show dissociable patterns of co-variation with measures indexing individual variations in trait anxiety and cognitive performance. METHODOLOGY/PRINCIPAL FINDINGS: Event-related fMRI data, recorded while healthy female participants performed a delayed-response working memory (WM) task with distraction, were investigated in conjunction with behavioural measures that assessed individual variations in both trait anxiety and WM performance. Consistent with increased sensitivity to emotional cues in high anxiety, specific perceptual areas (fusiform gyrus--FG) exhibited increased activity that was positively correlated with trait anxiety and negatively correlated with WM performance, whereas specific executive regions (right lateral prefrontal cortex--PFC) exhibited decreased activity that was negatively correlated with trait anxiety. The study also identified a role of the medial and left lateral PFC in coping with distraction, as opposed to reflecting a detrimental impact of emotional distraction. CONCLUSIONS: These findings provide initial evidence concerning the neural mechanisms sensitive to individual variations in trait anxiety and WM performance, which dissociate the detrimental impact of emotion distraction and the engagement of mechanisms to cope with distracting emotions. Our study sheds light on the neural correlates of emotion-cognition interactions in normal behaviour, which has implications for understanding factors that may influence susceptibility to affective disorders, in general, and to anxiety disorders, in particular.

Nonlinear oscillator metamaterial model: numerical and experimental verification.

We verify numerically and experimentally the accuracy of an analytical model used to derive the effective nonlinear susceptibilities of a varactor-loaded split ring resonator (VLSRR) magnetic medium. For the numerical validation, a nonlinear oscillator model for the effective magnetization of the metamaterial is applied in conjunction with Maxwell equations and the two sets of equations solved numerically in the time-domain. The computed second harmonic generation (SHG) from a slab of a nonlinear material is then compared with the analytical model. The computed SHG is in excellent agreement with that predicted by the analytical model, both in terms of magnitude and spectral characteristics. Moreover, experimental measurements of the power transmitted through a fabricated VLSRR metamaterial at several power levels are also in agreement with the model, illustrating that the effective medium techniques associated with metamaterials can accurately be transitioned to nonlinear systems.

Transcription factors MYOCD, SRF, Mesp1 and SMARCD3 enhance the cardio-inducing effect of GATA4, TBX5, and MEF2C during direct cellular reprogramming.

Transient overexpression of defined combinations of master regulator genes can effectively induce cellular reprogramming: the acquisition of an alternative predicted phenotype from a differentiated cell lineage. This can be of particular importance in cardiac regenerative medicine wherein the heart lacks the capacity to heal itself, but simultaneously contains a large pool of fibroblasts. In this study we determined the cardio-inducing capacity of ten transcription factors to actuate cellular reprogramming of mouse embryonic fibroblasts into cardiomyocyte-like cells. Overexpression of transcription factors MYOCD and SRF alone or in conjunction with Mesp1 and SMARCD3 enhanced the basal but necessary cardio-inducing effect of the previously reported GATA4, TBX5, and MEF2C. In particular, combinations of five or seven transcription factors enhanced the activation of cardiac reporter vectors, and induced an upregulation of cardiac-specific genes. Global gene expression analysis also demonstrated a significantly greater cardio-inducing effect when the transcription factors MYOCD and SRF were used. Detection of cross-striated cells was highly dependent on the cell culture conditions and was enhanced by the addition of valproic acid and JAK inhibitor. Although we detected Ca(2+) transient oscillations in the reprogrammed cells, we did not detect significant changes in resting membrane potential or spontaneously contracting cells. This study further elucidates the cardio-inducing effect of the transcriptional networks involved in cardiac cellular reprogramming, contributing to the ongoing rational design of a robust protocol required for cardiac regenerative therapies.

Continuity and Change on an Urban Houselot: Archaeological Excavation at the 22 West Street Backlot (18AP51) of the Annapolis National Historic District, Anne Arundel County, Maryland

Intensive archaeological investigation was undertaken on an urban backlot in Annapolis, Maryland. Fieldwork was conducted on behalf of Historic Annapolis Foundation for the property's owners, King and Cornwall, Inc. Supplemental documentary research, an evaluation of existing conditions on the property, and below-ground excavation of a 35 X 70 ft. urban backlot were conducted. While the project was not a Section 106 compliance effort, the field methods and rationale for the site's investigation are comparable to those of standard Phase II site evaluations. Historical documentation attested to the fact that the 22 West Street Backlot, located along the western most edge of the Historic District of Annapolis, Maryland, had seen development and occupation since the first quarter of the eighteenth century. A substantial brick structure was known to have occupied the property in a series of altered forms for much of that period. This structure served a variety of purposes over time: a private residence in the eighteenth century, a boarding house in the nineteenth century (known as the National Hotel), a duplex in the early twentieth century, half of which remained in use until the structure was entirely razed in the 1970s after destruction by fire. Recovery and analysis of site formation processes (i.e., both cultural and natural transformations of the buried remains) indicated that sections of the site were disturbed to a depth of six feet. In contrast to what initially seemed a poor prognosis for site integrity, other areas of the backlot revealed numerous intact historical features and deposits. Structural remains from the dwelling and its associated outbuildings, additions, and attendant trash deposits were recovered. What was initiated as a program of limited testing evolved into a larger-scale undertaking that made use of largely hand-excavated units in conjunction with machine-assisted stripping of areas demonstrated to contain from four to six-foot deep sterile layers of fill. The current investigations provided a window into a portion of the city and period in its history not documented archaeologically. Moreover, this project provided valuable insight into the archaeology of the homelot within a lightly industrialized, urban context. Evidence was recovered of shifts in the layout and arrangement of the houselot as well as changing relations between individuals and the workplace--all within an urban context--an issue defined elsewhere in the archaeological literature as a significant one. No further investigations are recommended for the site, however, further analysis and interpretation of materials recovered are ongoing. In the event that the site were to undergo development, monitoring of any construction activity is recommended.

Archaeological Testing at the John Brice II (Jennings-Brice) House, 18AP53, 195 Prince George Street, Annapolis, Maryland

In the fall of 1989, emergency excavation was undertaken in conjunction with restoration work at the John Brice II (Jennings-Brice) House, 18AP53. The exact date of construction for this brick home is problematic, and it was hoped that archaeological investigation could provide conclusive evidence to firmly establish the structure's date of construction. Excavation of one 5 X 5 ft. unit revealed the presence of 10 separate soil layers and four features of note, described in detail below. Unfortunately, no builders trench or similar feature by which we might date the house's construction was recovered. Future plans and possibilities for excavation at the property are outlined with the hopes of performing subsequent work at this rich site. We anticipate a focus on the arrangement and changes in use of the houselot, amassing evidence to support the presence of a vernacular garden on the property during the 18th century, as well as researching refuse disposal patterns, and clues to changing lifeways through the 18th century.

Electronic Techtonics: Thinking at the Interface

This volume originated in HASTAC’s first international conference, “Electronic Techtonics: Thinking at the Interface,” held at Duke University during April 19-21, 2007. “Electronic Techtonics” was the site of truly unforgettable conversations and encounters that traversed domains, disciplines, and media – conversations that explored the fluidity of technology both as interface as well as at the interface. This hardcopy version of the conference proceedings is published in conjunction with its electronic counterpart (found at www.hastac.org). Both versions exist as records of the range and depth of conversations that took place at the conference. Some of the papers in this volume are almost exact records of talks given at the conference, while others are versions that were revised and reworked some time after the conference. These papers are drawn from a variety of fields and we have not made an effort to homogenize them in any way, but have instead retained the individual format and style of each author.

Mechanisms of CD8+ T Cell Mediated Virus Inhibition in HIV-1 Virus Controllers

CD8+ T cells are associated with long term control of virus replication to low or undetectable levels in a population of HIV+ therapy-naïve individuals known as virus controllers (VCs; <5000 RNA copies/ml and CD4+ lymphocyte counts >400 cells/µl). These subjects' ability to control viremia in the absence of therapy makes them the gold standard for the type of CD8+ T-cell response that should be induced with a vaccine. Studying the regulation of CD8+ T cells responses in these VCs provides the opportunity to discover mechanisms of durable control of HIV-1. Previous research has shown that the CD8+ T cell population in VCs is heterogeneous in its ability to inhibit virus replication and distinct T cells are responsible for virus inhibition. Further defining both the functional properties and regulation of the specific features of the select CD8+ T cells responsible for potent control of viremia the in VCs would enable better evaluation of T cell-directed vaccine strategies and may inform the design of new therapies.

Here we discuss the progress made in elucidating the features and regulation of CD8+ T cell response in virus controllers. We first detail the development of assays to quantify CD8+ T cells' ability to inhibit virus replication. This includes the use of a multi-clade HIV-1 panel which can subsequently be used as a tool for evaluation of T cell directed vaccines. We used these assays to evaluate the CD8+ response among cohorts of HIV-1 seronegative, HIV-1 acutely infected, and HIV-1 chronically infected (both VC and chronic viremic) patients. Contact and soluble CD8+ T cell virus inhibition assays (VIAs) are able to distinguish these patient groups based on the presence and magnitude of the responses. When employed in conjunction with peptide stimulation, the soluble assay reveals peptide stimulation induces CD8+ T cell responses with a prevalence of Gag p24 and Nef specificity among the virus controllers tested. Given this prevalence, we aimed to determine the gene expression profile of Gag p24-, Nef-, and unstimulated CD8+ T cells. RNA was isolated from CD8+ T-cells from two virus controllers with strong virus inhibition and one seronegative donor after a 5.5 hour stimulation period then analyzed using the Illumina Human BeadChip platform (Duke Center for Human Genome Variation). Analysis revealed that 565 (242 Nef and 323 Gag) genes were differentially expressed in CD8+ T-cells that were able to inhibit virus replication compared to those that could not. We compared the differentially expressed genes to published data sets from other CD8+ T-cell effector function experiments focusing our analysis on the most recurring genes with immunological, gene regulatory, apoptotic or unknown functions. The most commonly identified gene in these studies was TNFRSF9. Using PCR in a larger cohort of virus controllers we confirmed the up-regulation of TNFRSF9 in Gag p24 and Nef-specific CD8+ T cell mediated virus inhibition. We also observed increase in the mRNA encoding antiviral cytokines macrophage inflammatory proteins (MIP-1α, MIP-1αP, MIP-1β), interferon gamma (IFN-γ), granulocyte-macrophage colony-stimulating factor (GM-CSF), and recently identified lymphotactin (XCL1).

Our previous work suggests the CD8+ T-cell response to HIV-1 can be regulated at the level of gene regulation. Because RNA abundance is modulated by transcription of new mRNAs and decay of new and existing RNA we aimed to evaluate the net rate of transcription and mRNA decay for the cytokines we identified as differentially regulated. To estimate rate of mRNA synthesis and decay, we stimulated isolated CD8+ T-cells with Gag p24 and Nef peptides adding 4-thiouridine (4SU) during the final hour of stimulation, allowing for separation of RNA made during the final hour of stimulation. Subsequent PCR of RNA isolated from these cells, allowed us to determine how much mRNA was made for our genes of interest during the final hour which we used to calculate rate of transcription. To assess if stimulation caused a change in RNA stability, we calculated the decay rates of these mRNA over time. In Gag p24 and Nef stimulated T cells , the abundance of the mRNA of many of the cytokines examined was dependent on changes in both transcription and mRNA decay with evidence for potential differences in the regulation of mRNA between Nef and Gag specific CD8+ T cells. The results were highly reproducible in that in one subject that was measured in three independent experiments the results were concordant.

This data suggests that mRNA stability, in addition to transcription, is key in regulating the direct anti-HIV-1 function of antigen-specific memory CD8+ T cells by enabling rapid recall of anti-HIV-1 effector functions, namely the production and increased stability of antiviral cytokines. We have started to uncover the mechanisms employed by CD8+ T cell subsets with antigen-specific anti-HIV-1 activity, in turn, enhancing our ability to inhibit virus replication by informing both cure strategies and HIV-1 vaccine designs that aim to reduce transmission and can aid in blocking HIV-1 acquisition.