Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

The human leukocyte antigen (HLA) locus plays a critical role in complex traits spanning autoimmune and infectious diseases, transplantation, and cancer. While coding variation in HLA genes has been extensively documented, regulatory genetic variation modulating HLA expression levels has not been comprehensively investigated. Here, we mapped expression quantitative trait loci (eQTLs) for classical HLA genes across 1,073 individuals and 1,131,414 single cells from three tissues, using personalized reference genomes to mitigate technical confounding. We identified cell-type-specific cis-eQTLs for every classical HLA gene. Modeling eQTLs at single-cell resolution revealed that many eQTL effects are dynamic across cell states even within a cell type. HLA-DQ genes exhibit particularly cell-state-dependent effects within myeloid, B, and T cells. Dynamic HLA regulation may underlie important interindividual variability in immune responses.

Photoionization of atoms described by Fermi Molecular Dynamics: toward a firmer theoretical basis

The application of Fermi Molecular Dynamics (FMD) to the modeling of the photoionization of atoms by a short pulse of long wavelength laser radiation is examined in detail. Depression of the single ionization threshold to values of the electric field strength below the classical over-the-barrier threshold, a common occurrence in FMD, is shown to arise from the preexcitation of bound electrons into a continuum of unphysical low-lying excited states. A connection is made to analogous calculations performed with the quantum Hamilton-Jacobi equation, in which the time-dependent quantum potential ($Q$) plays a role similar to that played in FMD by the so-called Heisenberg potential (V H). Replacement of (V H) by Q in the FMD equations of motion results in a large reduction in the number of excitations to unphysical bound states, while producing no essential change in the photoionization probability.