Biology subjects

Lee, S. T.

Publications and source records attributed to Lee, S. T..

3 recordsLinked to original sources

bioRxiv2024

The Rodent Electronic Nicotine Delivery System: Description and Validationof an Apparatus for Nose-Only E-Cigarette Aerosol Inhalation in Freely Moving Rats

Tobacco use is the leading cause of death globally and in the U.S. After decades of decline, driven by decreases in combusted tobacco use, nicotine product use has increased due to Electronic Nicotine Delivery Systems, also known as e-cigarettes or vapes. Preclinical models of nicotine self-administration can serve as important lodestars in the search for effective intervention and prevention tactics. Current variants of the task have substantial limitations, however. Therefore, we created the Rodent Electronic Nicotine Delivery System, a novel low-cost non-proprietary nose-only preclinical model of nicotine aerosol self-administration. We confirmed that RENDS sequesters nicotine aerosol in the nose port by measuring fine particulate matter (PM < 2.5 microns) generated by e-cigarettes. We also showed that rats robustly self-administer flavored nicotine aerosol, resulting in high blood levels of cotinine (the major nicotine metabolite) and spontaneous somatic withdrawal symptoms. Thus, we provide strong validation of the operation and function of the RENDS, opening the door to an open-source preclinical aerosol model of nicotine self-administration that is relatively low cost. Four existing operant chambers can be retrofitted with the RENDS for less than $325/chamber. All RENDS diagrams and plans for custom designed components are on Open Science Framework (https://osf.io/x2pqf/?view_only=775b55435b8e428f98e6da384ef7889d).

animal behavior and cognition↗

bioRxiv2020

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and their intriguing patterns of site specificity amidst the lack of dispersal limitation. Yet, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among the taxa that belong to recently discovered branches of microbial life. Here we assembled metagenomes from daily tongue and dental plaque samples from multiple individuals and reconstructed 790 non-redundant genomes, 43 of which resolved to TM7 that formed six monophyletic clades distinctly associated either with plaque or with tongue. Both pangenomic and phylogenomic analyses grouped tongue-specific TM7 clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 grouped together with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and the mobilome of the cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of human associated microbes. Additionally, we report that prophages are widespread amongst oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.

microbiology↗

bioRxiv2016

High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes

Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits. Here we used shotgun metagenomics to reconstruct 97 metagenome-assembled genomes (MAGs) from fecal samples of a single donor and followed their distribution in two FMT recipients to identify microbial populations with different colonization properties. Our analysis of the occurrence and distribution patterns post-FMT revealed that 22% of the MAGs transferred from the donor to both recipients and remained abundant in their guts for at least eight weeks. Most MAGs that successfully colonized the recipient gut belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales and colonization success was negatively correlated with the number of genes related to sporulation. Although our dataset showed a link between taxonomy and the ability of a MAG to colonize the recipient gut, we also identified MAGs with different colonization properties that belong to the same taxon, highlighting the importance of genome-resolved approaches to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems for mechanistic insights.

microbiology↗