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1.  Predicting lymph node output efficiency using systems biology 
Journal of theoretical biology  2013;335:169-184.
Dendritic cells (DCs) capture pathogens and foreign antigen (Ag) in peripheral tissues and migrate to secondary lymphoid tissues, such as lymph nodes (LNs), where they present processed Ag as MHC-bound peptide (pMHC) to naïve T cells. Interactions between DCs and T cells result, over periods of hours, in activation, clonal expansion and differentiation of antigen-specific T cells, leading to primed cells that can now participate in immune responses. Two-photon microscopy (2PM) has been widely adopted to analyze lymphocyte dynamics and can serve as a powerful in vivo assay for cell trafficking and activation over short length and time scales. Linking biological phenomena between vastly different spatiotemporal scales can be achieved using a systems biology approach. We developed a 3D agent-based cellular model of a LN that allows for the simultaneous in silico simulation of T cell trafficking, activation and production of effector cells under different antigen (Ag) conditions. The model anatomy is based on in situ analysis of LN sections (from primates and mice) and cell dynamics based on quantitative measurements from 2PM imaging of mice. Our simulations make three important predictions. First, T cell encounters by DCs and T cell receptor (TCR) repertoire scanning are more efficient in a 3D model compared with 2D, suggesting that a 3D model is needed to analyze LN function. Second, LNs are able to produce primed CD4+T cells at the same efficiency over broad ranges of cognate frequencies (from 10−5 to 10−2). Third, reducing the time that naïve T cells are required to bind DCs before becoming activated will increase the rate at which effector cells are produced. This 3D model provides a robust platform to study how T cell trafficking and activation dynamics relate to the efficiency of T cell priming and clonal expansion. We envision that this systems biology approach will provide novel insights for guiding vaccine development and understanding immune responses to infection.
doi:10.1016/j.jtbi.2013.06.016
PMCID: PMC3783027  PMID: 23816876
Agent based model; 3D; Priming; Effector; T cells
2.  Microenvironments in tuberculous granulomas are delineated by distinct populations of macrophage subsets and expression of nitric oxide synthase and arginase isoforms 
Macrophages in granulomas are both anti-mycobacterial effector and host cell for Mycobacterium tuberculosis(M.tb), yet basic aspects of macrophage diversity and function within the complex structures of granulomas remain poorly understood. To address this, we examined myeloid cell phenotypes and expression of enzymes correlated with host defense in macaque and human granulomas. Macaque granulomas had upregulated inducible and endothelial nitric oxide synthase (iNOS and eNOS) and arginase (Arg1 and Arg2) expression and enzyme activity compared to non-granulomatous tissue. Immunohistochemical analysis indicated macrophages adjacent to uninvolved normal tissue were more likely to express CD163, while epithelioid macrophages in regions where bacteria reside strongly expressed CD11c, CD68 and HAM56. Calprotectin-positive neutrophils were abundant in regions adjacent to caseum. iNOS, eNOS, Arg1 and Arg2 proteins were identified in macrophages and localized similarly in granulomas across species, with greater eNOS expression and ratio of iNOS:Arg1 expression in epithelioid macrophages, as compared to cells in the lymphocyte cuff. iNOS, Arg1 and Arg2 expression in neutrophils was also identified. The combination of phenotypic and functional markers support that macrophages with anti-inflammatory phenotypes localized to outer regions of granulomas while the inner regions were more likely to contain macrophages with pro-inflammatory, presumably bactericidal, phenotypes. Together these data support the concept that granulomas have organized microenvironments that balance anti-microbial anti-inflammatory responses to limit pathology in the lungs.
doi:10.4049/jimmunol.1300113
PMCID: PMC3746594  PMID: 23749634
3.  Monocyte-derived IL-5 reduces TNF production by M. tuberculosis-specific CD4 T cells during SIV/M. tuberculosis co-infection1 
HIV-infected individuals are significantly more susceptible to tuberculosis (TB) than HIV-uninfected individuals. Although it is established that HIV reduces M. tuberculosis-specific T cell responses, the causes of this dysfunction are not known. We used the cynomolgus macaque model of TB to demonstrate that ex vivo SIV reduces the frequency of M. tuberculosis-specific TNF and IFN-γ producing T cells within 24hrs post-infection. In vivo, T cell IFN-γ responses in granulomas from animals with SIV/M. tuberculosis co-infection were lower than SIV-negative animals with active TB. The SIV effects on inhibition of T cell responses were primarily on antigen presenting cells and not the T cells directly. Specifically, reductions in the frequency of TNF-producing M. tuberculosis-specific CD4 T cells were caused, at least in part, by SIV-induced production of monocyte derived IL-5.
doi:10.4049/jimmunol.1202043
PMCID: PMC3677169  PMID: 23690470
4.  “Of Mice and Men”: Arginine Metabolism in Macrophages 
doi:10.3389/fimmu.2014.00479
PMCID: PMC4188127  PMID: 25339954
arginase; human macrophage; macrophage polarization; nitric oxide synthase; macrophage activation
5.  Nitric Oxide Synthase: Non-Canonical Expression Patterns 
Science can move ahead by questioning established or canonical views and, so it may be with the enzymes, nitric oxide synthases (NOS). Nitric oxide (NO) is generated by NOS isoforms that are often described by their tissue-specific expression patterns. NOS1 (nNOS) is abundant in neural tissue, NOS2 is upregulated in activated macrophages and known as inducible NOS (iNOS), and NOS3 (eNOS) is abundant in endothelium where it regulates vascular tone. These isoforms are described as constitutive or inducible, but in this perspective we question the broad application of these labels. Are there instances where “constitutive” NOS (NOS1 and NOS3) are inducibly expressed; conversely, are there instances where NOS2 is constitutively expressed? NOS1 and NOS3 inducibility may be linked to post-translational regulation, making their actual patterns activity much more difficult to detect. Constitutive NOS2 expression has been observed in several tissues, especially the human pulmonary epithelium where it may regulate airway tone. These data suggest that expression of the three NOS enzymes may include non-established patterns. Such information should be useful in designing strategies to modulate these important enzymes in different disease states.
doi:10.3389/fimmu.2014.00478
PMCID: PMC4191211  PMID: 25346730
NOS1; NOS2; NOS3; iNOS; eNOS; nNOS; nitric oxide; nitric oxide synthase
6.  CD4 Regulatory T cells in a Cynomolgus Macaque Model of Mycobacterium tuberculosis Infection123 
The Journal of infectious diseases  2010;202(4):533-541.
Background
Mycobacterium tuberculosis (M. tuberculosis) infection in humans results in either latent infection or active tuberculosis (TB). We sought to determine whether a higher frequency of regulatory T cells predispose an individual toward active disease or whether the Tregs develop in response to active disease.
Methods
In cynomolgus macaques infected with a low dose M. tuberculosis approximately 50% develop primary TB and 50% present with latent infection. 41 animals were followed for 6-8 months to correlate the frequency of Foxp3+ cells in peripheral blood and airways with outcome of infection.
Results
In all animals, the frequency of Tregs (CD4+Foxp3+) in peripheral blood rapidly decreased and simultaneously increased in the airways. Latently infected monkeys had a significantly higher frequency of Tregs in peripheral blood prior to infection and during early infection than those that developed active disease. Monkeys with active disease had increased Tregs in PBMC as they developed disease.
Conclusions
Our data suggest that increased Tregs in active disease occur in response to more inflammation, rather than act as a causative factor in progression to active disease.
doi:10.1086/654896
PMCID: PMC3683560  PMID: 20617900
Mycobacterium tuberculosis; Regulatory T cells; non-human primate
7.  Monocyte-Derived IL-5 Reduces TNF Production by Mycobacterium tuberculosis–specific CD4 T Cells during SIV/M. tuberculosis Coinfection 
The Journal of Immunology Author Choice  2013;190(12):6320-6328.
HIV-infected individuals are significantly more susceptible to tuberculosis (TB) than uninfected individuals. Although it is established that HIV reduces Mycobacterium tuberculosis–specific T cell responses, the causes of this dysfunction are not known. We used the cynomolgus macaque model of TB to demonstrate that ex vivo SIV reduces the frequency of M. tuberculosis–specific TNF and IFN-γ–producing T cells within 24 h after infection. In vivo, T cell IFN-γ responses in granulomas from animals with SIV/M. tuberculosis coinfection were lower than SIV-negative animals with active TB. The SIV effects on the inhibition of T cell responses were primarily on APCs and not the T cells directly. Specifically, reductions in the frequency of TNF-producing M. tuberculosis–specific CD4 T cells were caused, at least in part, by SIV-induced production of monocyte derived IL-5.
doi:10.4049/jimmunol.1202043
PMCID: PMC3677169  PMID: 23690470
8.  Comparison of the Effects of Pathogenic Simian Human Immunodeficiency Virus Strains SHIV-89.6P and SHIV-KU2 in Cynomolgus Macaques 
Factors explaining why human immunodeficiency virus (HIV) enhances the risk of reactivated tuberculosis (TB) are poorly understood. Unfortunately, experimental models of HIV-induced reactivated TB are lacking. We examined whether cynomolgus macaques, which accurately model latent TB in humans, could be used to model pathogenesis of HIV infection in the lungs and associated lymph nodes. These experiments precede studies modeling the effects of HIV infection on latent TB. We infected two groups of macaques with chimeric simian–human immunodeficiency viruses (SHIV-89.6P and SHIV-KU2) and followed viral titers and immunologic parameters including lymphocytes numbers and phenotype in the blood, bronchoalveolar lavage cells, and lymph nodes over the course of infection. Tissues from the lungs, liver, kidney, spleen, and lymph nodes were similarly examined at necropsy. Both strains produced dramatic CD4+ T cell depletion. Plasma titers were not different between viruses, but we found more SHIV-89.6P in the lungs. Both viruses induced similar patterns of cell activation markers. SHIV-89.6P induced more IFN-γ expression than SHIV-KU2. These results indicate SHIV-89.6P and SHIV-KU2 infect cynomolgus macaques and may be used to accurately model effects of HIV infection on latent TB.
doi:10.1089/aid.2007.0238
PMCID: PMC3311977  PMID: 18366326
9.  Simian Immunodeficiency Virus-Induced Changes in T Cell Cytokine Responses in Cynomolgus Macaques with Latent Mycobacterium tuberculosis Infection Are Associated with Timing of Reactivation 
Understanding the early immunologic events accompanying reactivated tuberculosis (TB) in HIV-infected individuals may yield insight into causes of reactivation and improve treatment modalities. We used the cynomolgus macaque (Macaca fascicularis) model of HIV–Mycobacterium tuberculosis coinfection to investigate the dynamics of multifunctional T cell responses and granuloma T cell phenotypes in reactivated TB. CD4+ and CD8+ T cells expressing Th1 cytokines (IFN-γ, IL-2, TNF) and Th2 cytokines (IL-4 and IL-10) were followed from latent M. tuberculosis infection to reactivation after coinfection with a pathogenic SIV. Coinfected animals experienced increased Th1 cytokine responses to M. tuberculosis Ags above the latent-response baseline 3–5 wk post-SIV infection that corresponded with peak plasma viremia. Th2 cytokine expression was not Ag specific, but strong, transient IL-4 expression was noted 4–7 wk post-SIV infection. Animals reactivating <17 wk post-SIV infection had significantly more multifunctional CD4+ T cells 3–5 wk post-SIV infection and more Th2-polarized and fewer Th0-, Th1-polarized CD8+ T cells during weeks 1–10 post-SIV infection than animals reactivating >26 wk post-SIV infection. Granuloma T cells included Th0-, Th1-, and Th2-polarized phenotypes but were particularly rich in cytolytic (CD107+) T cells. When combined with the changes in peripheral blood T cells, these factors indicate that events during acute HIV infection are likely to include distortions in proinflammatory and anti-inflammatory T cell responses within the granuloma that have significant effects on reactivation of latent TB. Moreover, it appears that mycobacteria-specific multifunctional T cells are better correlates of Ag load (i.e., disease status) than of protection.
doi:10.4049/jimmunol.1003773
PMCID: PMC3311978  PMID: 21317393
10.  Reactivation of Latent Tuberculosis in Cynomolgus Macaques Infected with SIV Is Associated with Early Peripheral T Cell Depletion and Not Virus Load 
PLoS ONE  2010;5(3):e9611.
HIV-infected individuals with latent Mycobacterium tuberculosis (Mtb) infection are at significantly greater risk of reactivation tuberculosis (TB) than HIV-negative individuals with latent TB, even while CD4 T cell numbers are well preserved. Factors underlying high rates of reactivation are poorly understood and investigative tools are limited. We used cynomolgus macaques with latent TB co-infected with SIVmac251 to develop the first animal model of reactivated TB in HIV-infected humans to better explore these factors. All latent animals developed reactivated TB following SIV infection, with a variable time to reactivation (up to 11 months post-SIV). Reactivation was independent of virus load but correlated with depletion of peripheral T cells during acute SIV infection. Animals experiencing reactivation early after SIV infection (<17 weeks) had fewer CD4 T cells in the periphery and airways than animals reactivating in later phases of SIV infection. Co-infected animals had fewer T cells in involved lungs than SIV-negative animals with active TB despite similar T cell numbers in draining lymph nodes. Granulomas from these animals demonstrated histopathologic characteristics consistent with a chronically active disease process. These results suggest initial T cell depletion may strongly influence outcomes of HIV-Mtb co-infection.
doi:10.1371/journal.pone.0009611
PMCID: PMC2835744  PMID: 20224771
11.  Transgene expression and silencing in a tick cell line: a model system for functional tick genomics 
The genome project of the blacklegged tick, Ixodes scapularis provides sequence data for testing gene function and regulation in this important pathogen vector. We tested Sleeping Beauty (SB), a Tc1/mariner group transposable element, and cationic lipid-based transfection reagents for delivery and genomic integration of transgenes into I. scapularis cell line ISE6. Plasmid DNA and dsRNA were effectively transfected into ISE6 cells and they were successfully transformed to express a red fluorescent protein (DsRed2) and a selectable marker, neomycin phosphotransferase (NEO). Frequency of transformation was estimated as 1 transformant per 5,000–10,000 cells and cultures were incubated 2 to 3 months in medium containing the neomycin analog G418 in order to isolate transformants. Genomic integration of the DsRed2 transgene was confirmed by inverse PCR and sequencing that demonstrated a TA nucleotide pair inserted between SB inverted/direct repeat sequences and tick genomic sequences, indicating that insertion of the DsRed2 gene into the tick cell genome occurred through the activity of SB transposase. RNAi using dsRNA transcribed from the DsRed2 gene silenced expression of red fluorescent protein in transformed ISE6 cells. SB transposition in cell line ISE6 provides an effective means to explore the functional genomics of I. scapularis.
doi:10.1016/j.ibmb.2008.07.008
PMCID: PMC2581827  PMID: 18722527
Ixodes scapularis; transformation; cell line; RNAi; Sleeping Beauty
12.  Rickettsia peacockii, an endosymbiont of Dermacentor andersoni, does not elicit or inhibit humoral immune responses from immunocompetent D. andersoni or Ixodes scapularis cell lines 
Ixodes scapularis and Dermacentor andersoni cell lines were stimulated with heat killed Escherichia coli and Micrococcus luteus to investigate whether infection by Rickettsia peacockii, an endosymbiont of D. andersoni, modifies humoral immune responses. Radial diffusion assays, western blotting, flow cytometry, and quantitative reverse-transcription PCR were used to determine if expression of bacteriolytic peptides, including lysozyme and defensin, was upregulated by bacterial stimulation or infection with R. peacockii. The I. scapularis line IDE12 upregulated expression of lysozyme and defensin following stimulation. The D. andersoni cell line DAE15 also expressed defensin and lysozyme, but only lysozyme was upregulated by bacterial stimulation. R. peacockii infection alone, or in cells stimulated with bacteria, did not modify defensin or lysozyme expression in either cell line. These results suggest tick endosymbionts may avoid recognition by the tick immune system, and infection may not affect humoral immune responses to bacteria not normally associated with ticks.
doi:10.1016/j.dci.2007.01.011
PMCID: PMC2099254  PMID: 17428539
endosymbiont; immune response; defensin; lysozyme; tick cell culture; rickettsia; real-time PCR; immune evasion
13.  Phagocytosis of the Lyme Disease Spirochete, Borrelia burgdorferi, by Cells from the Ticks, Ixodes scapularis and Dermacentor andersoni, Infected with An Endosymbiont, Rickettsia peacockii  
Tick cell lines were used to model the effects of endosymbiont infection on phagocytic immune responses. The lines tested for their ability to phagocytose the Lyme disease spirochete, Borrelia burgdorferi (Spirochaetales: Spirochaetaceae), were ISE6 and IDE12 from the black-legged tick, Ixodes scapularis Say (Acari: Ixodidae) and DAE15 from the Rocky Mountain wood tick, Dermacentor andersoni Stiles. Rickettsia peacockii (Rickettsiales: Rickettsiaceae), an endosymbiont of D. andersoni, was used as a representative tick endosymbiont. 70–80% of uninfected or R. peacocciz-infected IDE12 and DAE15 cells phagocytosed heat-killed borreliae and 80–90% of IDE12 and DAE15 cells phagocytosed viable spirochetes. ISE6 cells were permissive of spirochetes; less than 1% of these cells phagocytosed borreliae, and spirochetes remained adherent to the cells seven days after inoculation. Cytochalasin B blocked phagocytosis of killed and viable borreliae by IDE12 cells, and prevented phagocytosis of killed spirochetes by DAE15 cells, whereas viable spirochetes successfully invaded cytochalasin-treated DAE15. IDE12 and DAE15 cells degraded borreliae within phagolysosome-like compartments. Time-lapse microscopy showed that DAE15 cells phagocytosed borreliae more rapidly than IDE12 cells. IDE12 and DAE15 cells eliminated most adherent spirochetes within 7 days of inoculation. Thus, endosymbiont infection does not significantly interfere with the phagocytic activity of immunocompetent tick cells.
doi:10.1673/031.007.5801
PMCID: PMC2999452  PMID: 20331397
coiling phagocytosis; tick cell culture; fluorescence microscopy; live cell imaging; vector competency

Results 1-13 (13)