Increasing use of iron oxide nanoparticles in medicine and environmental remediation has led to concerns regarding exposure of these nanoparticles to the public. However, limited studies are available to evaluate their effects on the environment, in particular on plants and food crops. Here, we investigated the effects of positive (PC) and negative (NC) charged iron oxide (Fe₂O₃) nanoparticles (IONPs) on the physiology and reproductive capacity of Arabidopsis thaliana at concentrations of 3 and 25 mg/L. The 3 mg/L treated plants did not show evident effects on seeding and root length. However, the 25 mg/L treatment resulted in reduced seedling (positive-20% and negative-3.6%) and root (positive-48% and negative-negligible) length. Interestingly, treatment with polyethylenimine (PEI; IONP-PC coating) also resulted in reduced root length (39%) but no change was observed with polyacrylic acid (PAA; IONP-NC coating) treatment alone. However, treatment with IONPs at 3 mg/L did lead to an almost 5% increase in aborted pollen, a 2%–6% reduction in pollen viability and up to an 11% reduction in seed yield depending on the number of treatments. Interestingly, the treated plants did not show any observable phenotypic changes in overall size or general plant structure, indicating that environmental nanoparticle contamination could go dangerously unnoticed.

Symbiotic microbiota can help its host to overcome nutritional challenges, which is consistent with a holobiont theory of evolution. Our project investigated the effects produced by the microbiota community, acquired from the environment and horizontal transfer, on metabolic traits related to obesity. The study applied a novel approach of raising Drosophila melanogaster, from ten wild-derived genetic lines on naturally fermented peaches, preserving genuine microbial conditions. Larvae raised on the natural and standard lab diets were significantly different in every tested phenotype. Frozen peach food provided nutritional conditions similar to the natural ones and preserved key microbial taxa necessary for survival and development. On the peach diet, the presence of parental microbiota increased the weight and development rate. Larvae raised on each tested diet formed microbial communities distinct from each other. The effect that individual microbial taxa produced on the host varied significantly with changing environmental and genetic conditions, occasionally to the degree of opposite correlations.

Coastal areas are the most biologically productive and undoubtedly among the most complex ecosystems. Algae are responsible for most of the gross primary production in these coastal regions. However, despite the critical importance of algae for the global ecosystem, the biodiversity of many algal groups is understudied, partially due to the high complexity of morphologically identifying algal species. The current study aimed to take advantage of the recently developed technology for biotic community assessment through the high-throughput sequencing (HTS) of environmental DNA (eDNA), known as the “eDNA metabarcoding”, to characterize littoral algal communities in the Northern Gulf of Mexico (NGoM). This study demonstrated that eDNA metabarcoding, based on the universal plastid amplicon (UPA) and part of the large nuclear ribosomal subunit (LSU) molecular markers, could successfully differentiate coastal biotic communities among littoral zones and geographical locations along the shoreline of the NGoM. The statistical significance of separation between biotic communities was partially dependent on the dissimilarity calculation metric; thus, the differentiation of algal community structure according to littoral zones was more distinct when phylogenetic distances were incorporated into the diversity analysis. Current work demonstrated that the relative abundance of algal species obtained with eDNA metabarcoding matches previously established zonation patterns for these species. In addition, the present study detected molecular signals of 44 algal species without previous reports for the Gulf of Mexico, thus providing an important, molecular-validated baseline of species richness for this region.

Background & Aims: Intrahepatic biliary epithelial cell (BEC) heterogeneity remains challenging to define. Here, we sought to identify BEC subpopulations and biomarkers in mouse liver. Methods: We performed scRNA-seq on Sox9EGFP+ liver epithelium from mice subjected to bile duct ligation (BDL) and sham controls. A machine learning algorithm, NSForest, identified minimal, multi-gene signatures for BEC subpopulations. These metagenes and were validated using hybridization chain reaction (HCR) FISH in tissue sections from wild-type mice and on primary BECs expanded in vitro. Metagenes were used to match BDL subpopulations to their corresponding sham subpopulations for differential gene expression (DGE) analysis. Results: We identified 4 BEC subpopulations in sham controls, each associated with 1-2 gene metagenes. Spatial localization of metagene-defined BEC subpopulations by HCR FISH revealed heterogeneous cellular composition of intrahepatic bile ducts. BECs belonging to a given subpopulation were most likely to have neighbors of the same identity, forming homogenous cellular compartments within ducts. BDL downregulated subpopulation-specific genes and upregulated a damage-associated gene set. BDL samples also included a proliferative subpopulation not found in sham controls, which contained populations enriched for three of the four metagenes. All BEC subpopulations were also found in monolayers in vitro, where they clustered spatially with BECs of the same subtype. Conclusions: Novel metagene biomarkers of BEC subpopulations facilitated spatial localization of BECs in situ, identified subpopulation specific injury responses, and confirmed that BEC heterogeneity is preserved in vitro. The presence of locally homogenous BEC neighborhoods in vitro suggests some degree of BEC organization may be epithelial-autonomous.

Intrahepatic bile ducts (IHBDs) form a complex hierarchical network essential for liver function. Remodeling and expansion of this network during ductular reaction (DR) is a hallmark of liver disease that can be a key indicator of disease severity. Conventional histology fails to capture the full extent of IHBD structural changes following injury due to the complex 3D organization of the IHBD network which limits understanding of DR, especially in human tissue. A major barrier to leveraging 3D imaging as a diagnostic tool is the absence of standardized pipelines for IHBD imaging and analysis. Here, we establish a robust 3D IHBD imaging and analysis workflow and apply it to both mouse and human liver tissues. This pipeline enables quantification of tissue and individual duct (“segment”) level features and identifies features of invasive and noninvasive DR. In mouse models, we uncover regional phenotypes, including IHBD diverticula following duct blockage and the formation of anastomosed clusters after hepatocellular injury. Finally, we apply our 3D imaging and analysis workflow to quantify IHBD networks in human liver tissue. This work deepens our understanding of IHBD architecture in homeostasis and injury and lays the groundwork for advanced phenotyping of IHBD morphologies in mice and humans with relevance to next-generation experimental and diagnostic approaches to liver disease.