Biology subjects

Singer, J. R.

Publications and source records attributed to Singer, J. R..

4 recordsLinked to original sources

bioRxiv2026

Participant-specific macromolecule information improves quantification of GABA-edited spectra at 3T

Purpose: To evaluate the effects of different MM fitting strategies on gamma-aminobutyric acid (GABA) estimates using MEGA-PRESS at 3T. Methods: Thirteen healthy individuals were scanned in the parietal lobe and centrum semiovale. GABA-edited scans were performed at TE=64ms (GABA+MMs) and TE=80ms (MM-suppressed GABA). MM-edited spectra were acquired using MEGA-PRESS with an inversion pre-pulse. MM peaks at 3.0 (MM3.0), 2.05 (MM2.05), and 0.94 (MM0.94) ppm were parameterized to form five MM basis categories. Cohort-mean/individual MM basis sets were constructed with all MM peaks combined (MMtogether), or with MM2.05 fit separately from MM0.94+MM3.0 (MM2+1). Simulated-MM bases were scaled by a participant-specific MM0.94/MM3.0 amplitude-ratio estimated from 64-224 transients. Fit quality numbers (FQNs) between the five MM parameterization methods were calculated to compare fit quality. Intraclass and Pearson's correlations were calculated to assess for agreement of GABA concentrations between the MM-suppressed GABA scan and the GABA+ scan with MMs fit out. Results: GABA concentrations derived from fitting with simulated-/individual-MM bases and MM2.05 fit separately lead to good--excellent agreements and high correlations with MM-suppressed GABA concentrations. Fit quality was significantly (51--63%) worse when fit with the MMtogether methods. GABA concentrations derived from fitting with a simulated MM basis demonstrated strong agreement with MM-suppressed GABA concentrations even when estimating the MM0.94/MM3.0 amplitude-ratio from a reduced number of transients (64--112). Conclusion: A participant-specific MM basis with MM2.05 excluded/fit separately yielded accurate GABA concentrations and superior fits. An accurate estimation of the MM0.94/MM3.0 amplitude-ratio can be achieved from a short 3-minute MM scan.

bioengineering↗

bioRxiv2026

The iron-binding siderophore enterobactin is required for the response of multi-drug resistant Klebsiella pneumoniae to zinc limitation

To persist during infection Klebsiella pneumoniae must overcome nutrient iron and zinc limitation imposed by the host immune system through a process called nutritional immunity. Secreted small molecule siderophores are a major virulence determinant of Klebsiella pneumoniae pathogenesis and are presumed to overcome nutritional immunity by binding iron for bacterial acquisition. In this work, we set out to identify how a multi-drug resistant K. pneumoniae grows in zinc limited environments. Using unbiased transcriptomics, proteomics, and an arrayed transposon screen, we identified that synthesis and uptake of the siderophore enterobactin is required to allow for growth in low zinc conditions. Iron-specific chelators did not replicate this phenotype and addition of supplemental iron through heme in growth media could not complement severe growth defects of enterobactin mutant K. pneumoniae experiencing zinc limitation. Finally, zinc starvation induced enterobactin production independent of the canonical zinc uptake regulator (Zur) transcription factor suggesting an unidentified regulatory mechanism by which Gram-negative pathogens may respond to zinc stress. Together, these studies expand the role of enterobactin beyond iron regulation and highlight a previously unreported link between iron and zinc homeostasis in Klebsiella pneumoniae.

microbiology↗

bioRxiv2026

Barrier Immune Memory is Promoted by Intestinal Epithelial Cell Presentation of Injected Bacterial Antigens

The contributions of antigen compartmentalization to recognition differences between CD4 and CD8 T cells have long been appreciated, but little is known of how subcellular localization of different antigens expressed by a single pathogen impacts T cell immunity. By tracking a clonal CD4 T cell response to its cognate epitope shuttled between different virulence proteins of the enteropathogenic bacterium, Citrobacter rodentium (Cr), we find a remarkable bias in the magnitude and quality of the response contingent on whether antigen remains bacterially associated or is introduced into intestinal epithelial cells colonized by the bacterium. Only proteins injected into the cytosol of colonocytes via the type 3 secretion system (T3SS) of Cr were found to recruit robust antigen-specific T cell responses to the infected mucosa and give rise to CD4 resident memory T (Trm) cells that populate the mucosal epithelium--and this required direct presentation of these antigens by infected epithelial cells. Single-cell transcriptomic analyses revealed that sustained, bidirectional epithelial-T cell communication was required both to elicit epithelial barrier-protective T cell help and to promote transcriptional networks that program a tissue-residency rather than central memory fate. These results establish a central role for antigen presentation by non-professional APCs in controlling memory fate decisions by CD4 T cells, with important implications for development of successful mucosal vaccines.

immunology↗

bioRxiv2021

A Non-redundant Role for T cell-derived IL-22 in Antibacterial Defense of Colonic Crypts

IL-22 is a key cytokine in immune defense against pathogens at barrier sites. In response to enteric attaching and effacing bacteria, IL-22 produced by type 3 innate lymphoid cells (ILC3s) is thought to be important early for induction of antimicrobial peptides (AMPs) that protect intestinal epithelial cells (IECs) in advance of T cell-derived IL-22 that arises later. Yet, the basis for a requirement for both innate and adaptive IL-22-producing immune cells in protecting the intestinal mucosa is unknown. Here, using novel mice that both report IL-22 expression and can be targeted for its lineage-specific deletion, we show that mice with deficiency of IL-22 targeted to innate immune cells, including ILC3s, have impaired STAT3 activation of surface colonic IECs colonized by bacteria early in infection. In contrast, mice with IL-22 deficiency limited to T cells have complete loss of STAT3 activation in IECs lining colonic crypts and fail to protect the crypts from bacterial invasion late despite ongoing production of IL-22 from ILC3s. T cell-derived IL-22 is required for upregulation of many host-protective genes by crypt IECs, including those encoding AMPs, neutrophil-recruiting chemokines, and mucins and mucin-related molecules, while also restricting pro-inflammatory genes downstream of IFN{gamma} and TNF signals. Thus, T cell-derived IL-22 is indispensable for antibacterial defense and damage control of intestinal crypts.

immunology↗