Despite advances in the treatment of HIV-1 a cure remains elusive. A significant barrier to the eradication of the virus from an infected individual is a pool of cells infected with transcriptionally silent proviruses. A key pillar of the strategy to eradicate latent viruses has been called 'kick and kill', whereby the latent virus is stimulated to transcribe rendering the host cell vulnerable to eradication by cytotoxic T cells. Optimising the reactivation signal is therefore critical to this approach. Here the established model system of latency 'J-lat' is used to probe optimum reactivation signals. Single clones are observed to respond to maximal stimulation with a single agent with a fixed proportion of cells. Here it is shown that this proportion can be overcome by dosing with two agents in combination and critically that maximum synergies between agents occur at concentrations of agents close to those achieved in vivo. The role of SETDB1 recruitment by the recently described HUSH complex is examined using shRNA knockdowns of these proteins. Knockdown does not increase expression from the majority of J-lat clones tested. Viral factors which influence silencing and reactivation from latency have not been explored to the same extent. Here mutations affecting the binding of splicing factors to HIV-1 mRNA were cloned into laboratory viruses. A reduction in splice factor binding is seen to change the use of splice junctions required for the production of Tat mRNA; in turn this alters the rate at which proviruses are silenced. In addition the threshold for transcription in response to stimulation is increased in mutants with reduced splice factor binding.

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Salmonella enterica serovar Typhimurium (S. Typhimurium) is an important human pathogen. The Centers for Disease Control and Prevention (CDC) estimates that 1,027,561 people become ill with nontyphoidal Salmonellosis annually, and S. Typhimurium is one of the most common disease causing serovars. Quantification of the true number of cases of salmonellosis is hampered by the presence of a carrier state. These carriers are animals and humans that carry the pathogens for a variable period of time without showing any clinical signs. One of the biggest barriers to controlling and preventing salmonellosis in a population is identification of these carriers. Identifying these latent carriers of chronic infections is vital to preventing such disease transmission and creating avenues for novel control and treatments. In my dissertation research, we developed a cell culture model to study latent Salmonella infections. By activating human monocytes with retinoic acid and vitamin D3, we were able to isolate Salmonella from such cells 45 days after inoculation. We subsequently used this model to identify genes that were upregulated in this chronic infection model. We found that aceA, a gene that codes for isocitrate lyase, is significantly upregulated on days 10 and 30 post infection. Isocitrate lyase is part of the glyloxylate cycle. Some bacterial species have developed a mechanism to utilize acetone as a carbon source to synthesize tricarboxylic acid (TCA) cycle intermediates. This anaplerotic reaction allows organisms to conserve carbon and use alternative carbon sources. This cycle is one way in which bacteria can adapt and survive in an intracellular environment. This intracellular survival is key to latent infections persisting within a host. It is biologically plausible that, in order to survive in a latent state, S. Typhimurium would up-regulate genes that would facilitate intracellular survival. After establishing the cell culture model, we tested the hypothesis that aceA is upregulated in latent infections of S. Typhimurium in a mouse model. We orally challenged mice that were resistant to Salmonella infection, collected their feces, and collected tissue specimens at several time points up to 135 days post-challenge. These samples were cultured and tested using quantitative polymerase chain reaction (qPCR). The qPCR results showed that tissue samples from inoculated mice had increased aceA expression 95 days after challenge. Finally, we examined whether aceA expression could be detected in cattle lymph node samples. Supra-mammary lymph nodes from 40 dairy cattle and mesenteric lymph nodes from 100 culled cattle were sampled and submitted for culture and qPCR. None of the supra-mammary lymph nodes were positive for Salmonella via culture or aceA qPCR; however, 11 mesenteric lymph nodes showed increased aceA expression in qPCR compared to 5 culture positive lymph nodes. Further research is necessary, but these results demonstrate some of the advantages of using genetic primers to identify latent Salmonella infections in clinically normal cattle. In addition, the assay may be able to differentiate between latent and active salmonellosis, and could be used to provide targeted drug delivery. / Doctor of Philosophy / Salmonella enterica serovar Typhimurium (S. Typhimurium) is an important human pathogen. Determining the true number of cases of salmonellosis is made more difficult because of the presence of a carrier state. These carriers are animals and humans that carry the pathogens for a variable period of time without showing any clinical signs. Identifying these latent carriers of chronic infections is vital to preventing such disease transmission and creating avenues for novel control and treatments. In my dissertation research, we looked at genetic markers from an offshoot of the TCA cycle, the glyoxylate pathway. We used these markers to test the hypothesis that these glyoxylate pathway genes would be upregulated in latent S. Typhimurium infections. Our research involved developing a cell culture model, then using the results from the cell culture model to inform a mouse model, and then a cattle lymph node diagnostic study. The cell culture model indicated that the gene for isocitrate lyase, aceA, is significantly upregulated compared to housekeeping genes. We found the presence of aceA in chronically infected mice, as well as cattle lymph node samples. Further research is necessary, but these results demonstrate some of the advantages of using genetic primers to identify latent Salmonella infections in clinically normal cattle.

Online gaming is rapidly growing as an entertainment choice, as it provides players with a high variety in genres, affordability, ubiquity and also real-time online interactions. However, slow networks or congestion can cause perceivable network latency and make players suffer from a degraded gameplay experience. Latency compensation techniques have been developed to combat the negative effects of network latency, but more understanding of latencies affects and latency compensations benefits are still needed. Our project studied the degradation of different game actions with latency and how player prediction - a classic latency compensation technique - affects gameplay in a 2D platformer. We designed and implemented an original 2D platformer with player prediction implemented for player movement actions, then invited players to play our game under different network and latency compensation conditions. Based on the subjective and objective data collected, we found that 2D platformers are sensitive to even modest amounts of network latency. Player prediction helped players have fewer deaths below 200ms of latency, but at 400ms and above its benefits were outweighed by its disadvantages to visual consistency.

Eradication of latent human immunodeficiency virus (HIV) infection is a global health challenge. Reactivation of HIV latency and killing of virus-infected cells, the so-called “kick and kill” or “shock and kill” approaches, are a popular strategy for HIV cure. While antiretroviral therapy (ART) halts HIV replication by targeting multiple steps in the HIV life cycle, including viral entry, integration, replication, and production, it cannot get rid of the occult provirus incorporated into the host-cell genome. These latent proviruses are replication-competent and can rebound in cases of ART interruption or cessation. In general, a very small population of cells harbor provirus, serve as reservoirs in ART-controlled HIV subjects, and are capable of expressing little to no HIV RNA or proteins. Beyond the canonical resting memory CD4+ T cells, HIV reservoirs also exist within tissue macrophages, myeloid cells, brain microglial cells, gut epithelial cells, and hematopoi-etic stem cells (HSCs). Despite a lack of active viral production, latently HIV-infected subjects con-tinue to exhibit aberrant cellular signaling and metabolic dysfunction, leading to minor to major cellular and systemic complications or comorbidities. These include genomic DNA damage; telo-mere attrition; mitochondrial dysfunction; premature aging; and lymphocytic, cardiac, renal, he-patic, or pulmonary dysfunctions. Therefore, the arcane machineries involved in HIV latency and its reversal warrant further studies to identify the cryptic mechanisms of HIV reservoir formation and clearance. In this review, we discuss several molecules and signaling pathways, some of which have dual roles in maintaining or reversing HIV latency and reservoirs, and describe some evolving strategies and possible approaches to eliminate viral reservoirs and, ultimately, cure/eradicate HIV infection.

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In human infection, herpes simplex virus (HSV) navigates two distinct life cycles; lytic and latent. The latent cycle takes place in sensory neurons, and is characterized as a dormant period punctuated by stress-induced episodes of viral reactivation. Understanding the mechanisms by which HSV latency and reactivation occur has been hindered by the lack of a model that faithfully recapitulates the environment of a human sensory neuron. Systems ranging from rat neurons to human fibroblasts have been developed to host HSV latency, however few available models have been able to investigate the role of human neuron-specific factors. To address this need, human medulloblastoma tumour cell lines, which derive from neuronal precursor cells, were differentiated and examined for their ability to host the HSV latency-reactivation cycle—in a manner similar to the differentiated PC-12 cell model. ONS-76 and UW228 medulloblastoma cell lines were screened for differentiation capacity. The differentiated cells were demonstrated to possess neuronal character as several neuron-specific proteins were found to be expressed. Differentiated ONS-76 cells were not compatible with hosting HSV latency, however, infection with a viral mutant impaired for lytic cycle initiation exhibited a deviant pattern of gene expression that resembles what has been observed in reactivation. Differentiated UW228 cells were found to host a low frequency, stable infection with the HSV mutant, characterized by the absence of infectious virus and viral lytic gene expression in the presence of persisting viral DNA. This DNA could further be induced to re-enter the lytic cycle through heat shock treatment and removal of differentiating agents from cell cultures. These results depict differentiated medulloblastoma cells as a novel tool in the study of HSV latency and reactivation, as these cells derive from the central nervous system and provide a new cellular perspective through which HSV biology can be viewed.

Thesis (Ph. D.)--Case Western Reserve University, 2007. / [School of Medicine] Department of Molecular Virology. Includes bibliographical references. Available online via OhioLINK's ETD Center.

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