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Biology subjects

Johnson, A. J.

Publications and source records attributed to Johnson, A. J..

20 records · Page 2Linked to original sources

Conditional silencing of H-2Db class I molecule expression on dendritic cells modulates the protective and pathogenic kinetics of virus-antigen specific CD8 T cell responses during Theiler’s Virus infection

Theilers murine encephalomyelitis virus (TMEV) infection of the central nervous system is rapidly cleared in C57BL/6 mice by an anti-viral CD8 T cell response restricted by the MHC class I molecule, H-2Db. While the CD8 T cell response against neurotropic viruses is well characterized, the identity and function of the antigen presenting cell(s) involved in this process is(are) less well defined. To address this gap in knowledge, we developed a novel C57BL/6 H-2Db conditional knockout mouse that expresses an H-2Db transgene in which the transmembrane domain locus is flanked by LoxP sites. We crossed these H-2Db LoxP mice with MHC class I-deficient mice expressing Cre-recombinase under either the CD11c or LysM promoter in order to silence H-2Db restricted antigen presentation predominantly in dendritic cells or macrophages, respectively. Upon challenge with intracranial TMEV infection, we observe that CD11c+ APCs are critical for early priming of CD8 T cells against the immunodominant TMEV peptide VP2121-130 presented in the context of the H-2Db molecule. This stands in stark contrast to later time points post TMEV infection where CD11c+ APCs appear dispensable for the activation of antigen-specific T cells; the functionality of these late-arising antiviral CD8 T cells is reflected in the restoration of viral control at later time points. These late-arising CD8 T cells also retain their capacity to induce blood-brain barrier disruption. In contrast, when H-2Db restricted antigen presentation was selectively silenced in LysM+ APCs there was no overt impact on the priming of Db:VP2121-130 epitope-specific CD8 T cells, although a modest reduction in immune cell entry into the CNS was observed. This work establishes a model system which enables critical dissection of MHC class I restricted antigen presentation to T cells, revealing cell specific and temporal features involved in the generation of antiviral CD8 T cell responses. Employing this novel system, we established CD11c+ cells as a pivotal driver of acute, but not later-arising, antiviral CD8 T cell responses against the TMEV immunodominant epitope VP2121-130, with functional implications both for T cell-mediated viral control and immunopathology.

immunology↗

Flavor-Cyber-Agriculture: Optimization of plant metabolites in an open-source control environment through surrogate modeling

Food production in conventional agriculture faces numerous challenges such as reducing waste, meeting demand, maintaining flavor, and providing nutrition. Contained environments under artificial climate control, or cyber-agriculture, could in principle be used to meet many of these challenges. Through such environments, phenotypic expression of the plant---mass, edible yield, flavor, and nutrients---can be actuated through a "climate recipe," where light, water, nutrients, temperature, and other climate and ecological variables are optimized to achieve a desired result. This paper describes a method for doing this optimization for the desired result of flavor by combining cyber-agriculture, metabolomic phenotype (chemotype) measurements, and machine learning. In a pilot experiment, (1) environmental conditions, i.e. photoperiod and ultraviolet (UV) light (known to affect production of flavor-active molecules in edible plants) were applied under different regimes to basil plants (Ocimum basilicum) growing inside a hydroponic farm with an open-source design; (2) flavor-active volatile molecules were measured in each plant using gas chromatography-mass spectrometry (GC-MS); and (3) symbolic regression was used to construct a surrogate model of this chemistry from the input environmental variables, and this model was used to discover new combinations of photoperiod and UV light to increase this chemistry. These new combinations, or climate recipes, were then implemented in the hydroponic farm, and several of them resulted in a marked increase in volatiles over control. The process also led to two important insights: it demonstrated a "dilution effect", i.e. a negative correlation between weight and desirable chemical species, and it discovered the surprising effect that a 24-hour photoperiod of photosynthetic-active radiation, the equivalent of all-day light, induces the most flavor molecule production in basil. In this manner, surrogate optimization through machine learning can be used to discover effective recipes for cyber-agriculture that would be difficult and time-consuming to find using hand-designed experiments.

plant biology↗