Biology subjects

Barnes, E. M.

Publications and source records attributed to Barnes, E. M..

5 recordsLinked to original sources

bioRxiv2026

Glyoxal induces DNA-Protein Crosslinking in Cells

Glyoxal (GO) is a small, highly reactive molecule that is produced naturally in cells during normal metabolism and can also come from processed foods and oxidative stress. Because of its high reactivity, glyoxal can modify DNA and proteins to form harmful products called advanced glycation end-products (AGEs), which have been linked to diseases such as diabetes, cancer, and aging. Although glyoxal is known to modify DNA and proteins, it is not well understood whether it can form DNA-protein crosslinks (DPCs), a type of DNA damage in which proteins become permanently attached to DNA. In this study, we investigated glyoxal induced DPC formation in HeLa cells using biochemical assays and mass spectrometry-based proteomics experiments. We observed that glyoxal exposure elevated cellular DPC formation in a concentration- and time-dependent manner. Cells with reduced SPRTN expression accumulated higher levels of DPCs, suggesting that SPRTN plays an important role in repairing glyoxal induced DNA damage. Proteomics experiments revealed 469 proteins exhibited elevated DNA association in glyoxal-treated samples, including histones and other proteins involved in chromatin organization, DNA replication, DNA repair, and gene expression. In-vitro experiments confirmed that glyoxal can directly crosslink DNA with histone proteins. Overall, this study provides the first evidence that glyoxal forms DNA-protein crosslinks in human cells. These findings provide a foundation for future studies on the chemical structure, biological effects and repair of glyoxal induced DNA-protein crosslinks and their possible role in human disease.

biochemistry↗

bioRxiv2025

Isotope Dilution nanoLC-MS/MS Quantitation of Methylglyoxal DNA-Protein Crosslinks: Formation and Repair in Human Cells

DNA-protein crosslinks (DPCs) represent a prevalent form of DNA damage that form when cellular proteins become covalently trapped to DNA strands upon exposure to various endogenous and exogenous agents. Methylglyoxal, is an endogenous metabolite that reacts with guanine and adenine bases in DNA and RNA, as well as cysteine, arginine and lysine residues in proteins, generating advanced glycation end-products (AGEs) including DPCs. These modifications have been linked to human disease, including cancer, liver disease, diabetes, and neurodegenerative disorders. Herein, we present a mass spectrometry method for quantifying MGO-induced DNA-protein crosslinks (DPCs) in human cells. We prepared an isotope 15N213C6-dG-MGO-Lys internal standard to develop a quantitative LC-MS/MS method for detecting and quantifying the formation and repair of dG-MGO-Lys DPCs in cells. Genomic DNA was extracted, subjected to sequential protease and nuclease digestion, purified by offline HPLC, and analyzed by LC-MS/MS. The methods standard curve showed a strong linear relationship across a concentration range of 10-1000 fmol (R2 = 0.9994). The method achieved limits of detection (LOD) and quantification (LOQ) of 10 and 20 fmol, respectively. Inhibition of proteasome and SPRTN activity revealed that SPRTN functions as a predominant proteolytic enzyme in MGO DPC repair. Overall, this analytical approach can offer valuable insights into the relevance of DPCs in diseases linked to elevated MGO levels.

cancer biology↗

bioRxiv2021

Preferential associations of soil fungal taxa under mixed compositions of eastern American tree species

Soil fungi are vital to forest ecosystem functions, in part through their role mediating tree responses to environmental factors, as well as directly through effects on resource cycling. While the distribution of these key taxa may vary with a suite of abiotic and biotic factors, the relative role of host species identity on soil fungal community composition and function remains unresolved. In this study, we used a combination of amplicon sequencing and enzymatic assays to assess soil fungal composition and associated function under three tree species, Quercus rubra, Betula nigra, and Acer rubrum, planted individually and in all combinations in a greenhouse, with added fungal inoculum collected below mature field trees. Across treatments, fungal communities were dominated by the phylum Ascomycota, followed by Basidiomycota and Mortierellomycota. Nonetheless, fungal communities differed between each of the solo planted treatments, suggesting at least some taxa may associate preferentially with these tree species. Additionally, fungal community composition under mixed sapling treatments broadly differed from solo saplings. The data also suggests that there were larger enzymatic activities in the solo treatments as compared with all mixed treatments. This difference may be due to the greater relative abundance of saprobic taxa found in the solo treatments. This study provides evidence of the importance of tree identity on soil microbial communities and functional changes to forest soils.

ecology↗

bioRxiv2021

Priority effects among amphibian microbes lead to varying levels of Bd infection

Priority effects in host-associated microbiomes can influence not only community composition and structure, but also community functions, such as disease resistance. However, evidence for these priority effects remains scarce. Past studies suggest that amphibian protection from chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis (Bd), is related to antifungal bacterial composition on host skin. Priority effects in these bacterial communities may influence susceptibility to Bd, but this possibility has not been tested. Using in vitro microcosms, we demonstrated that priority effects can influence interactions among amphibian-associated microbes. We observed strong priority effects irrespective of high antifungal ability such that the Bd-inhibitory potential of two strongly inhibitory bacterial species did not always produce higher levels of Bd-inhibition. This result suggests that interactions may be more complex than previously thought. Additionally, our results suggest that priority effects between commensal and pathogenic taxa can be either facilitatory or inhibitory, with the strength and direction of this effect dependent on the composition of the community. Thus, changes in assembly may lead to varying levels of Bd infection, influencing how we might augment amphibian-associated microbiomes to conserve taxa currently at risk of extinction.

ecology↗

bioRxiv2020

Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs

0A growing focus in microbial ecology is understanding of how beneficial microbiome function is created and maintained through both stochastic and deterministic assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species pools in the soil and local communities of an amphibian host. To address this, we compared the microbiomes of over 200 Plethodon cinereus salamanders along a 65km land-use gradient in the greater New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that if soil functions as the main regional species pool to amphibian skin, variation in skin microbial community composition would correlate with changes seen in soil. We found that salamanders share many microbial taxa with their soil environment but that these two microbiomes exhibit key differences, especially in the relative abundances of the bacteria phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varied with changes in land-use associated factors such as canopy cover, impervious surface, and concentrations of the soil elements Al, Ni, and Hg, creating site-specific compositions. In addition, high dissimilarity among individual amphibian microbiomes across and within sites suggest that both stochastic and deterministic mechanisms guide assembly of microbes onto amphibian skin, with likely consequences in disease preventative function.

ecology↗