Several types of cell death including apoptosis, necroptosis and autophagic cell death play diverse roles in different biological processes. In addition to its essential roles in development and metabolism, programmed cell death is indispensable for host immunity. Interestingly, current research shows that these processes are connected but the nature and extent of the crosstalk between host defense and programmed cell death still remains an area of great interest. The NFkB factor Relish is best characterized as a crucial component of Drosophila Imd pathway, which generates immune responses by producing antimicrobial peptides following Gram-negative bacterial infection. In this dissertation, I demonstrate a novel role of Relish in developmentally programmed cell death. During metamorphosis, Drosophila salivary glands are degraded by the collective actions of caspase-dependent and autophagic cell death. Here I show that Relish mutants displayed improper salivary gland degradation and the persistence of salivary gland cell fragments. Expression of Relish in salivary glands rescued this phenomenon. Among the upstream components of the Imd pathway, mutants in the bacterial peptidoglycan receptors, PGRP-LC and-LE also exhibited similar defects in gland degradation, but surprisingly none of the other Imd pathway components examined had any such effect. As both Relish and PGRPs are critical for host defense against bacterial infection, our next concern was the role of host microflora in salivary gland degradation. However, observation of normal salivary gland cell death in axenic flies ruled out the possible involvement of microbiota. Robust genetic analyses proved that Relish-mediated cell death occurs in caspase-independent but autophagy-dependent manner. Moreover, expressions of either active version of Relish or PGRP-LC resulted in the premature gland degradation and induction of autophagy. Finally, I show that Relish controls autophagy by regulating the expression of Atg1, a core component of the autophagy pathway. Together these findings suggest the existence of a novel pathway, which connects immune response factors to developmentally programmed cell death.

Unlike mammals, plants do not have specific immune cells. However, plants can still recognize pathogens and defend themselves. They do that by recognizing microbial-associated molecular patterns (MAMPs) and secreted pathogen proteins, called effectors. MAMP-triggered immunity (MTI) relies on recognition of MAMPs by leucine-rich repeats (LRRs) pattern-recognition receptors (PRRs). The best-studied LRR PRR is Flagellin-Sensitive 2 (Fls2), the receptor of a 22-amino acid long epitope of bacterial flagellin, called flg22. In this project, alleles of FLS2 of different tomato cultivars were sequenced and compared to each other to get insight into natural selection acting on FLS2 and to identify residues important for ligand binding. This information may be used in the future to engineer Fls2 for improved ability to recognize flagellin. MTI can be suppressed by effectors secreted by bacteria into plant cells through the type III secretion system. On the other hand, plants are equipped with repertoires of resistance proteins, which can recognize some pathogen effectors. If a pathogen carries an effector that is recognized, effector-triggered immunity (ETI) is activated and the plant is resistant. Here, eggplant breeding lines were screened for their ability to activate ETI upon recognition of effectors of the soil borne pathogen Ralstonia solanacearum, a causative agent of bacterial wilt. Four effectors were found to trigger plant defenses in some of the lines. This is the first step in cloning the genes coding for the responsible resistance proteins. These genes may be used in the future for engineering tomato and potato for resistance to bacterial wilt. / Master of Science in Life Sciences

Both humans and mice display an age-related decline in immunity. Reduced generation of mature B cells may be a contributing factor due to reduced entry of mature B cells with novel B cell receptors and specificity for pathogens into the mature B cell pool. In aged mice the numbers of B cell precursors within the bone marrow are diminished; there is a severe reduction in numbers of pre-B cells and an increase in numbers of re-circulated mature B cells. Other defects in developing B cells include reduced expression of rag1 and rag2 when measured in total bone marrow precursor populations. In the pro-B cell stage of development rag expression is essential to the process of V(D)J recombination and the generation of pre-B cells. It was not known prior to this work if rag levels were lower in pro-B cells. In Chapter 2 I show that rag2 expression is reduced in pro-B cells of aged mice. The reduction in rag2 expression is correlated with a loss of V(D)J recombinase activity in pro-B cells and reduced numbers of pre-B cells. This suggests that in aged mice the reduction in rag2 expression is sufficient to result in reduced V(D)J recombinase activity and reduced generation of pre-B cells, thus contributing to fewer pre-B cells in aged mice. Furthermore, I have shown that the loss of rag2expression and recombinase activity in pro-B cells are the result of age-associated defects in the bone marrow-microenvironment as opposed to cell-intrinsic defects in developing precursors. In Chapter 3 of this thesis I examine genetic influences on age-related defects in murine B cell development and correlations between bone marrow B cell subsets and peripheral T cell subsets. It was known that longevity and age-related defects in T cell subsets are influenced by genetic differences between strains of inbred mice. The impact of genetic polymorphisms on age-related defects in B cell development had not been previously assessed. Nor was it known if these defects were correlated with age-related changes in peripheral T cell subsets. Here I present evidence that B cell subsets in the bone marrow are influenced by genetic polymorphisms between mice strains. Genetic polymorphisms on Chromosomes 15 and 19 were found to influence the frequency of re-circulated and pre-B cells in the bone marrow of aged mice. Frequencies of bone marrow B cell subsets were compared with peripheral T cell subsets. Interestingly, an association between the frequency of pre-B cells was not observed with either re-circulated B cells in the bone marrow nor peripheral T cell subsets. However the frequency of pre-B cells was inversely correlated with the frequency of B220intIgM+cells, a subset that was found to correlate with more advanced age-related T cell defects. In addition, frequencies of re-circulated B cells in the bone marrow were found to be associated with less advanced age-related defects in peripheral T cell subsets. These observations indicate that defects in B cell development, including reduced rag2 expression and V(D)J recombinase activity, are the result of changes in the aged murine bone marrow microenvironment. In addition, a genetic polymorphism located on Chromosome 19 influences the frequency of pre-B cells in aged mice. Furthermore the frequencies of B cell precursors in aged mice are not correlated with peripheral T cell subsets, but are correlated with frequencies of B220intIgM+ cells in the bone marrow. These observations advance our understanding of age-related defects in murine B cell development and may lead to identification of genes that influence B cell development in aged mice and humans as well as to help devise therapeutics aimed at restoring humoral immunity in aged individuals.

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<p>We are all born germ-free. Soon after birth, microbes colonize our body’s surfaces, with the intestine housing the highest density of microbes on earth. Most of us remain blissfully unaware of this co-existence because inflammatory responses to the indigenous microbes are normally not triggered. Nonetheless, intestinal microbes are true educators of our immune system, which is exemplified by the immature immune system observed in germ-free animals. Accumulating evidence suggests that microbial exposure and/or composition impacts on immune regulation. As an example, isotype switch to immunoglobulin E (IgE) is normally very tightly regulated such that in healthy individuals and mice, serum levels are maintained at very low levels. In contrast, total serum IgE levels are elevated in germ-free mice, indicating that in the absence of microbes the regulatory pathway that maintains IgE at basal levels is disrupted. We hypothesize that in the absence of stimuli from the resident intestinal bacteria the immune system does not receive adequate educational signals. We showed that in germ-free mice class switch recombination (CSR) to IgE occurred at intestinal mucosal lymphoid sites a few weeks after birth. IgE levels then remained at elevated levels throughout life, even when intestinal bacteria were introduced after weaning. In the first part of this thesis, the mechanisms involved in this hygiene-induced IgE were investigateted. In a second part, the immunoregulatory role of commensal bacteria was extended to a model of autoimmunity.</p> <p>Collectively these results demonstrate a new dimension of the impact of intestinal symbionts on the immune system: they dictate baseline immune system regulation. Elucidating the mechanisms whereby microbes induce immunoregulatory pathways may give insights into the increasing prevalence of allergic- and autoimmune diseases.</p> / Doctor of Philosophy (PhD)

A heat-stable soluble inhibitor of T cell proliferation was demonstrated in splenic and peritoneal macrophage (Mφ) culture supernatants. Concentrated supernatants were prostaglandin E₂ (PGE₂)-free and yet inhibited proliferation in the mixed lymphocyte reaction (MLR) and mitogen assays. The high mw inhibitory factor was apparently >67 kd, as shown by S-200 Sephacryl chromatography and gel electrophoresis. DEAE-Cellulose chromatography suggested that the pl of the inhibitory factor was < 7.7. lsoelectric focusing revealed that the Mφ-mediated inhibitory activity differed in charge, with a pl of 6.5-7.6 for normal hosts and 4.0-6.0 for tumor bearing hosts (TBH). Normal and TBH Mφ supernatants showed different hydroxylapatite fractionation, with the latter being resistant to proteolytic enzymes but sensitive to neuraminidase. Lectins such as wheat germ agglutinin, concanavalin A, Ricin communi: and Bandeirea simplicifolia were not useful in affinity purification of the high mw inhibitory monokine. Sugar-BSA conjugates suggested that inhibitory activity was vested in a terminal ßl,4 linked galactose. The inhibitory activity was apparently hydrophobic and heat·stable, but heat-stability was lost if supernatants were boiled at an acidic pH. The high mw monokine inhibited the proliferation of P388D₁ and A4A cells, but enhanced the proliferation of BW 5147.3 cells. Time course addition to the MLR revealed that PGE; may be required for inhibitory activity to be manifested early (0 and 24 hr) but not if the high molecular weight (mw) inhibitor was added late (>48 hr). Indomethacin blocked activity of the inhibitory factor early in the MLR using normal host T cells and augmented the proliferation of TBH T cells in the MLR. Both normal and TBH Mo supernatants suppressed the generation of interleukin 2 but with a dose- and time·dependent difference. Cell cycle analysis of mitogen- stimulated cells revealed that TBH M<p supernatants enhanced cell cycle progression at 42 hr, but that both normal and TBH Mφ supernatants suppressed the number of cells in S phase at 66 hr. To determine the phenotype of Mφ that produced the high mw inhibitor, Mφ were modulated with anti-Mac-1, -2, or -3 monoclonal antibodies (mAb) or depleted with mAb plus complement and cultured with or without indomethacin. P388D₁; cells, used as a control, revealed that the anti-Mac mAb were reacting specifically and not via Fc receptors. Culture supernatants added to the MLR showed that the Mφ suppressor phenotype shifted from Mac-3⁺ in the normal host to Mac-2⁺ in the TBH. Production of PGE₂ was susceptible to indomethacin, but in general the relative production of PGE₂ by the Mφ subpopulations remained the same. Depletion of Mac-1⁺ Mφ caused a higher increase in PGE₂; production than did activation, suggesting that Mac-1⁺ Mcp down-regulated PGE; production. In contrast, no Mac-1* Mrp-mediated regulatory function occurred in the TBH. Mac-2⁺ Mφ were the primary producers of PGE; in the TBH, but not in the normal host. Thus, immunosuppression in the TBH was at least partly due to the inability of Mac-1⁺ and/or Mac-3⁺ Mφ to control production of PGE; by Mac-2⁺ Mφ, which then acts in conjunction with the high mw inhibitor to stop T cell proliferation. / Ph. D.

The increasing healthcare burden of type 1 diabetes (T1D) makes finding preventive or therapeutic strategies a global priority. This chronic disease is characterized by the autoimmune destruction of the insulin-producing β cells. This destruction leads to poorly controlled blood glucose and accompanying life threatening acute and chronic complications. The role of viral infections as initiating factors for T1D is probable, but contentious. Therefore, my goal is to better characterize the effects of viral infection on human β cells in their function of producing insulin and to define innate immune gene responses in β cells upon viral infection. These aspects were evaluated in various platforms including mice engrafted with primary human islets, cultured primary human islets, β cells derived from human stem cells, and a human β cell line. Furthermore, the contributions of cell-type specific innate immune responses are evaluated in flow cytometry-sorted primary human islet cells. Taken together, the results from these studies provide insights into the mechanisms of the loss of insulin production in β cells during virus infection, and characterize the antiviral innate immune responses that may contribute to the autoimmune destruction of these cells in T1D.

The immune response to an infection is determined by a number of factors, which also affect the generation of memory T cells afterwards. The immune response can also affect the stability of the pre-existing memory populations. The memory developed after an infection can influence the response to subsequent infections with unrelated pathogens. This heterologous immunity may deviate the course of disease and alter the disease outcome. The generation and stability of memory CD8 T cells and the influence of the history of infections on subsequent heterologous infections are studied in this thesis using different viral infection sequences. Previous studies using mice lacking individual immunoproteasome catalytic subunits showed only modest alterations in the CD8 T cell response to lymphocytic choriomeningitis virus (LCMV). In this study, I found that the CD8 T cell response to LCMV was severely impaired in mice lacking all three catalytic subunits of the immunoproteasome, altering the immunodominance hierarchy of the CD8 T cell response and CD8 T cell memory. Adoptive transfer experiments suggested that both inefficient antigen presentation and altered T cell repertoire contribute to the reduction of the CD8 T cell response in the immunoproteasome knockout mice. Immune responses generated during infections can reduce pre-existing memory T cell populations. Memory CD8 T cells have been shown to be reduced by subsequent heterologous infections. In this study, I re-examined the phenomenon using immune mice infected with LCMV, murine cytomegalovirus (MCMV) and vaccinia virus (VACV) in different infection sequences. I confirmed that memory CD8 T cells were reduced by heterologous infections, and showed that LCMV-specific memory CD4 T cells were also reduced by heterologous infections. Reduction of the memory CD8 T cells is thought to be the result of apoptosis of memory CD8 T cells associated with the peak of type I interferon early during infection. I showed that memory CD4 T cells were similarly driven to apoptosis early during infection; however, Foxp3+ CD4+ regulatory T cells were relatively resistant to virus infection-induced apoptosis, and were stably maintained during LCMV infection. The stability of Treg cells during viral infections may explain the relatively low incidence of autoimmunity associated with infections. The history of infections can deviate the course of disease and affect the disease outcome, but this heterologous immunity is not necessarily reciprocal. Previous studies have shown the effects of heterologous immunity during acute infections. In this thesis, I showed that the history of LCMV infection led to higher viral titers during persistent MCMV infection, caused more severe immunopathology at the beginning of infection, and reduced the number of MCMV-specific inflationary memory CD8 T cells after the period of memory inflation. In a different context of infection, the history of LCMV infection can be beneficial. LCMV-immune mice have been shown to have lower viral titers after VACV infection, but VACV-immune mice are not protected during LCMV infection. I found that memory CD8 T cells generated from LCMV and VACV infections were phenotypically different, but the differences could not explain the nonreciprocity of heterologous immunoprotection. By increasing the number of crossreactive VACV A11R198-205-specific memory CD8 T cells, however, I showed that some VACV-immune mice displayed reduced viral titers upon LCMV challenge, suggesting that the low number of potentially cross-reactive CD8 T cells in VACV-immune mice may be part of the reasons for the non-reciprocity of immunoprotection between LCMV and VACV. Further analysis deduced that both number of potentially cross-reactive memory CD8 T cells and the private specificity of memory CD8 T cell repertoire played a part in determining the outcome of heterologous infections.