Urbanization can result in shifts in abiotic and biotic factors, including temperature, pollution, habitat type, pathogens, and diet, among others. These shifts can, in turn, shape the ecological and evolutionary trajectory of urban wildlife. The gut microbiota has the potential to mediate host-environment interactions, especially in the context of diet and disease, and thus may […]
Partitioning the roots of interactions between microbes (PRISM): environment-supplied resources versus species-produced mediators
Microbial species in a community can metabolically interact through competition for resources present in the environment, as well as inhibition or facilitation by metabolites produced by other species. Understanding the relative contribution of these two types of interaction will help us modulate bacterial interactions more effectively. Our work focuses on partitioning the impact of metabolites […]
A Tissue Microenvironment Analogous to Certain Tumor Microenvironments Facilitates HIV Persistence
The HIV reservoir that establishes early upon infection and persists in tissues remains the primary barrier to a functional cure. While progress has been made to study the reservoir in blood compartments and specific cell types, knowledge gaps remain on the tissue microenvironment that facilitates persistence. The development of a novel immunoPET/CT-guided spatial transcriptomics pipeline […]
A decrease in specific health-associated commensals is linked to progressive periodontal tissue destruction independent of dysbiotic community profiles
Periodontitis is a chronic inflammatory disease associated with dysbiotic microbial communities that leads to destruction of the tooth-supporting tissues. The transition from host-microbial periodontal homeostasis to disease remains poorly understood. The murine ligature-induced periodontitis model was employed to characterize the temporal dynamics of the subgingival microbiome and host tissue features. Ligatures were placed in C57BL/6N […]
Partitioning the roots of interactions between microbes (PRISM): environment-supplied resources versus species-produced mediators
Microbial species in a community can metabolically interact through competition for resources present in the environment, as well as inhibition or facilitation by metabolites produced by other species. Understanding the relative contribution of these two types of interaction will help us modulate bacterial interactions more effectively. Our work focuses on partitioning the impact of metabolites […]
Dietary and gut microbial variation among urban and rural populations of house mice (Mus musculus domesticus)
Urbanization can result in shifts in abiotic and biotic factors, including temperature, pollution, habitat type, pathogens, and diet, among others. These shifts can, in turn, shape the ecological and evolutionary trajectory of urban wildlife. The gut microbiota has the potential to mediate host-environment interactions, especially in the context of diet and disease, and thus may […]
The Unified Human Virome Database: A toolkit for expanded human virome analysis
Current approaches for computationally analyzing viruses within human microbiomes often rely on databases largely composed of fragmented viral genomes from gastrointestinal samples, limiting identification of viruses exclusively found outside the gastrointestinal tract and analyses requiring high-quality genomes. To address these issues, we created the Unified Human Virome Database (UHVDB), comprising 575,497 high-quality, annotated viral genomes […]
A Tissue Microenvironment Analogous to Certain Tumor Microenvironments Facilitates HIV Persistence
The HIV reservoir that establishes early upon infection and persists in tissues remains the primary barrier to a functional cure. While progress has been made to study the reservoir in blood compartments and specific cell types, knowledge gaps remain on the tissue microenvironment that facilitates persistence. The development of a novel immunoPET/CT-guided spatial transcriptomics pipeline […]
Systematic benchmarking of small variant calling pipelines for long-read RNA sequencing data
Background: Long-read RNA sequencing (lrRNA-seq) enables transcript-resolved variant detection, but systematic and neutral evaluations of small variants calling pipelines remain limited. The performance of existing tools across sequencing technologies, alignment strategy, variant caller choice, genomic contexts and downstream haplotype phasing is not fully understood. Results: Here, we systematically benchmark four lrRNA-seq variant callers (Clair3-RNA, DeepVariant, […]
Phage terminase recognition by the bacterial immune sensors Avs2 and Upx
Prokaryotes employ diverse defense strategies to detect and halt the progression of phage infection. Multiple defense systems sense phage proteins through direct binding, including antiviral STAND NTPases (Avs), which oligomerize upon target recognition to induce programmed cell death. The widespread Avs2 family was previously shown to detect the large terminase subunit of tailed phages, but […]
A chimeric human-mouse lung vascular model using induced pluripotent stem cells reveals insights into the pathogenesis of BMPR2-related pulmonary hypertension
Advances in tissue biology have revealed remarkable transcriptomic heterogeneity of endothelial cells between and within organ systems. This necessitates more precise models of organ-specific endothelium to understand the pathogenesis of genetic vascular disorders, such as pulmonary hypertension (PH), where gene-disease associations have implicated endothelial cell dysfunction as a key driver of disease pathogenesis. Towards this […]
Type 1-polarized DC immunotherapeutic contains heterogeneous populations with IL-12p70 production restricted to a rare subset
Monocyte-derived DC therapies programmed for robust IL-12p70 production have been associated with favorable outcomes in cancer clinical trials. However, clinical responses remain inconsistent even under standardized protocols, and the cellular basis for this variability is unknown. We leveraged single-cell multiomics to characterize two widely used DC platforms, the high-IL-12p70-producing alpha-Type-1-polarized DC (DC1) and the IL-12p70-deficient […]