Biology subjects

Lee, M. R.

Publications and source records attributed to Lee, M. R..

6 recordsLinked to original sources

bioRxiv2026

Diverse root fungal endophytes mediate plant access to soil nutrients

Plant roots are broadly colonized by endophytic fungi with saprotrophic capabilities, but our understanding of whether they function in ways that are beneficial or detrimental to the host remains limited to model organisms. We hypothesized that endophytic fungi broadly affect plant access to soil nutrients, particularly organic forms that are typically not directly available to the plant. To address this, we paired 41 fungal endophytes with switchgrass (Panicum virgatum L.) and provided either inorganic or organic forms of nitrogen (N) and phosphorus (P). We evaluated how the fungi affected plant tissue N and P as well as plant growth. We also examined if these outcomes could be predicted from fungal phylogenetic relationships, in vitro traits of the fungi, or characteristics of the habitat from which fungi were isolated. There was substantial variation in both plant N (0.05-0.63%) and P (0.02-0.10%) acquisition that depended on the interaction of fungus and nutrient treatment. More fungi were beneficial for plant N than for P and shoot nutrients generally increased more than root nutrients from fungal associations. However, fungal effects on plant nutrients were not predicted by fungal traits, habitat traits, or fungal phylogenetic relationships. This unpredictability highlights a key challenge for incorporating endophytes into nutrient management strategies. Improving our ability to predict endophyte impacts on host nutrient acquisition will require identifying the mechanisms underlying observed beneficial effects and scaling up to realistic, diverse root microbial communities.

ecology↗

bioRxiv2026

Fatty acid biosynthesis inhibitors fabimycin and triclosan trigger distinct resistance mutations in FabI and potently kill Gram-negative pathogens

In the effort to develop efficacious antibacterials that engage targets for which there is no pre-existing resistance, inhibition of the enoyl-acyl carrier protein reductase FabI has shown promise, with triclosan and fabimycin as representative members of the two major drug classes that show activity against important bacterial pathogens. Here, we use a morbidostat and whole genome sequencing to comprehensively evaluate the resistance profiles that arise in pathogenic bacteria in response to these FabI inhibitors. When assessed against E. coli, fabimycin and triclosan were found to induce primarily non-overlapping resistance profiles leading to minimal cross-resistance between the two compounds. Furthermore, in vivo evaluation of the prominent resistant mutants indicates poor fitness, with the most fit mutant still susceptible to fabimycin. Collectively, these results suggest the combination use of two antibiotics that engage different positions on the same target as a means to kill pathogenic bacteria and limit resistance.

microbiology↗

bioRxiv2025

Direct and diffuse cross-kingdom interactions in plant microbiome assembly

Studies of plant-associated microbial communities consistently indicate a role for classic assembly mechanisms, such as environmental and host filters, but often leave substantial unexplained variation. Biotic interactions within microbial communities may help to fill this gap, specifically cross-kingdom interactions between fungi and bacteria, as these are increasingly found to be important to both assembly and function. We hypothesized that direct interactions between bacteria and fungi are an important driver of composition in low-diversity leaf habitats, where pairwise interactions are more likely. In high-diversity root habitats, we expected diffuse, indirect interactions to be more relevant to composition. To test these hypotheses, we characterized bacterial and fungal communities of switchgrass (Panicum virgatum L.) leaves and roots at 14 sites spanning mountain to coastal ecoregions of North Carolina, USA. We analyzed putative direct and diffuse interactions using ecological network inference and partitioned variance explained in microbial community composition by spatial, environmental, and biotic interactions. We found that cross-kingdom biotic interactions contributed to microbial community structure. The largest improvements to variance explained (5-11%) were from direct interactions, except for root fungal communities where diffuse interactions (7.5%) explained more than double that of direct interactions (2.8%). These contributions were comparable to those from environmental and spatial factors. The joint effects of putative biotic interactions and environmental conditions also contributed to the explained variation, highlighting the importance of environmental tracking in microbes. These findings suggest that using network inference for identifying cross-kingdom ecological interactions can improve our fundamental understanding of how plant-associated microbiomes assemble, which is also directly relevant to applied efforts such as the effective development of synthetic communities.

ecology↗

bioRxiv2023

Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Alterations in Epithelial Integrity

To identify mechanisms underlying the growth of ductal carcinoma in situ (DCIS) and properties that lead to progression to invasive cancer, we performed single-cell RNA-sequencing (scRNA-seq) on DCIS lesions and matched synchronous normal breast tissue. Using inferred copy number variations (CNV), we identified neoplastic epithelial cells from the clinical specimens which contained a mixture of DCIS and normal ducts. Phylogenetic analysis based on the CNVs demonstrated intratumoral clonal heterogeneity was associated with significant gene expression differences. We also classified epithelial cells into mammary cell states and found that individual genetic clones contained a mixture of cell states suggesting an ongoing pattern of differentiation after neoplastic transformation. Cell state proportions were significantly different based on estrogen receptor (ER) expression with ER-DCIS more closely resembling the distribution in the normal breast, particularly with respect to cells with basal characteristics. Using deconvolution from bulk RNA-seq in archival DCIS specimens, we show that specific alterations in cell state proportions are associated with progression to invasive cancer. Loss of an intact basement membrane (BM) is the functional definition of invasive breast cancer (IBC) and scRNA-seq data demonstrated that ongoing transcription of key BM genes occurs in specific subsets of epithelial cell states. Examining BM in archival microinvasive breast cancers and an in vitro model of invasion, we found that passive loss of BM gene expression due to cell state proportion alterations is associated with loss of the structural integrity of the duct leading to an invasive phenotype. Our analyses provide detailed insight into DCIS biology. SIGNIFICANCESingle cell analysis reveals that preinvasive breast cancer is comprised of multiple genetic clones and there is substantial phenotypic diversity both within and between these clones. Ductal carcinoma in situ (DCIS) of the breast is a non-invasive condition commonly identified through mammographic screening. A primary diagnosis of DCIS carries little mortality risk on its own, but its presence is a risk factor for subsequent clonally related invasive breast cancer (IBC) (1-5).

cancer biology↗

bioRxiv2022

Single-cell Landscape Analysis of the Circulating Human B Cell Pool under Selective Pressure of Allogeneic Stem Cell Transplantation

Alloreactivity can drive autoimmune syndromes. After allogeneic hematopoietic stem cell transplantation (allo-HCT) chronic graft-versus-host disease (cGVHD), a B cell-mediated autoimmune-like syndrome, commonly occurs. Because donor-derived B cells continually develop under selective pressure from host alloantigens, aberrant B Cell Receptor (BCR)-activation and IgG production can emerge and contribute to cGVHD pathobiology. To better understand molecular programing of B cells under selective pressure of alloantigens, we performed scRNA-Seq analysis on high numbers of purified B cells from allo-HCT patients. An unsupervised analysis revealed 10 clusters, distinguishable by signature genes for maturation, activation and memory. We found striking transcriptional differences in the memory B cell compartment after allo-HCT compared to healthy or infected individuals. To identify intrinsic properties when B-cell tolerance is lost after allo-HCT, we then assessed clusters for differentially expressed genes (DEGs) between patients with vs. without autoimmune-like manifestations (Active cGVHD vs. No cGVHD, respectively). DEGs were found in Active cGVHD in both naive and BCR-activated clusters, suggesting functional diversity. Some DEGs were also differentially expressed across most clusters, suggesting common molecular programs that may promote B cell plasticity. Our study of human allo-HCT and cGVHD provides new understanding of B-cell memory in the face of chronic alloantigen stimulation. One Sentence SummaryOur scRNA-Seq study of purified B cells after allo-HCT clarifies molecular differences in human B cell subsets when immune tolerance is lost or maintained. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/512162v4_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@5c452eorg.highwire.dtl.DTLVardef@1c1d34borg.highwire.dtl.DTLVardef@171310org.highwire.dtl.DTLVardef@e4bf15_HPS_FORMAT_FIGEXP M_FIG C_FIG The circulating human B cell compartment under the selective pressure of allogeneic hematopoietic stem cell transplantation (Allo-HCT) has an intrinsically altered memory B cell pool. In allo-HCT, genetically disparate donor stem and progenitor cells engraft, regenerating a new peripheral B cell compartment in the host. During ongoing B lymphopoiesis and diversification, selective pressure from alloantigens and other extrinsic factors, including B Cell Activating Factor (BAFF), result in either B cell maturation and immune tolerance (No Chronic GVHD) or altered B cell homeostasis and autoimmune manifestations (Active Chronic GVHD). B cells within defined subsets in patients with Active GVHD have distinct intrinsic programs delineated by differentially expressed genes (DEGs). Some DEGs occur across nearly all B cell subsets ( Differentially Expressed Broadly), while other DEGs are more restricted within only one or a few B cell subsets ( Naive, BCR-activated, or Memory). We affirm altered trajectories for diversification (blue arrow) and enrichment of an atypical memory B cell (ABC) pool, with intrinsic differences when chronic GVHD occurs.

immunology↗

bioRxiv2020

Pursuing the Mechanisms Underlying Alcohol-Induced Changes in the Ghrelin System: New Insights from Preclinical and Clinical Investigations

Ghrelin is a gastric-derived peptide hormone with demonstrated impact on alcohol intake and craving, but the reverse side of this bidirectional link, i.e., the effects of alcohol on the ghrelin system, remains to be fully established. To characterize the downstream effects of alcohol on the ghrelin system, we examined the following: (1) plasma ghrelin levels across four human laboratory alcohol administration experiments with non-treatment seeking, heavy-drinking participants, (2) expression of ghrelin, ghrelin receptor, and ghrelin-O-acyltransferase (GOAT) genes (GHRL, GHSR, and MBOAT4, respectively) in human post-mortem brain tissue from individuals with alcohol use disorder (AUD) vs. controls, (3) plasma ghrelin levels in Ghsr knockout and wild-type rats following intraperitoneal (i.p.) ethanol administration, (4) effect of ethanol on ghrelin secretion from gastric mucosa cells ex vivo and GOAT enzymatic activity in vitro, and (5) plasma ghrelin levels in rats following i.p. ethanol administration vs. an iso-caloric sucrose solution. Peripheral acyl- and total ghrelin levels significantly decreased following acute ethanol administration in humans. No difference in GHRL, GHSR, and MBOAT4 mRNA expression in the brain was observed between AUD vs. control post-mortem samples. In rats, acyl-ghrelin levels significantly decreased following i.p. ethanol administration in both genotype groups (Ghsr knockout and wild-type), while des-acyl-ghrelin was not affected by ethanol. No effect of ethanol was observed ex vivo on ghrelin secretion from gastric mucosa cells or in vitro on GOAT acylation activity. Lastly, we observed different effects of i.p. ethanol and sucrose solution on acyl- and des-acyl-ghrelin in rats despite administering amounts with equivalent caloric value. Ethanol acutely decreases peripheral ghrelin concentrations in humans and rats, and our findings suggest that this effect does not occur through interaction with ghrelin-secreting gastric mucosal cells, the ghrelin receptor, or the GOAT enzyme. Moreover, this effect does not appear to be proportional to caloric load. Our findings, therefore, suggest that ethanol does not suppress circulating ghrelin through direct interaction with the ghrelin system, or in proportion to the caloric value of alcohol, and may differentially affect ghrelin acylation and ghrelin peptide secretion.

physiology↗