Biology subjects

Lapp, S.

Publications and source records attributed to Lapp, S..

3 recordsLinked to original sources

bioRxiv2025

Automated identification of individual birds by song enables multi-year recapture from passive acoustic monitoring data

Autonomous sensors and machine learning are transforming ecology by enabling large-scale observation of organisms and ecosystems. However, sensor data collected by camera traps, acoustic recorders, and satellites are typically used only to produce detections of unidentified individuals. Tracking individuals over time to study movement, survival, and behavior continues to require invasive and high-effort capture and marking techniques. Here, we introduce an automated, general approach that identifies individual animals from passive acoustic recordings based on individually distinctive vocalizations. Unlike previous approaches, ours can identify individuals in passive acoustic recordings without previously labeled examples of their vocalizations. We apply our approach to a model songbird species (Ovenbird, Seiurus aurocapilla), estimating abundance and annual survival across 126 locations and four years. Our approach identifies individuals with 96% accuracy. We find high Ovenbird apparent annual survival (0.70) and acoustic recapture probability (0.89) across 405 individuals. Our approach can readily be applied to other species with individually distinctive vocalizations using open-source Python implementations. Automated individual identification will broadly unlock the ability to passively recapture individual animals at the massive scale of autonomous sensing, supporting the study of population trajectories and informing proactive ecosystem management to prevent biodiversity loss.

ecology↗

bioRxiv2024

Eosinophils protect against SARS-CoV-2 following a vaccine breakthrough infection

Waning immunity and the emergence of immune evasive SARS-CoV-2 variants jeopardize vaccine efficacy leading to breakthrough infections. We have previously shown that innate immune cells play a critical role in controlling SARS-CoV-2. To investigate the innate immune response during breakthrough infections, we modeled breakthrough infections by challenging low-dose vaccinated mice with a vaccine-mismatched SARS-CoV-2 Beta variant. We found that low-dose vaccinated infected mice had a 2-log reduction in lung viral burden, but increased immune cell infiltration in the lung parenchyma, characterized by monocytes, monocyte-derived macrophages, and eosinophils. Single cell RNA-seq revealed viral RNA was highly associated with eosinophils that corresponded to a unique IFN-{gamma} biased signature. Antibody-mediated depletion of eosinophils in vaccinated mice resulted in increased virus replication and dissemination in the lungs, demonstrating that eosinophils in the lungs are protective during SARS-CoV-2 breakthrough infections. These results highlight the critical role for the innate immune response in vaccine mediated protection against SARS-CoV-2.

immunology↗

bioRxiv2024

Single cell analysis reveals an antiviral network that controls Zika virus infection in human dendritic cells

Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10x Genomics Chromium single cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human moDCs infected with ZIKV at the single cell level. The bystander cells, which lacked detectable viral RNA, expressed an antiviral state that was enriched for genes coinciding predominantly with a type I interferon (IFN) response. Within the infected cells, viral RNA negatively correlated with type I IFN dependent and independent genes (antiviral module). We modeled the ZIKV specific antiviral state at the protein level leveraging experimentally derived protein-interaction data. We identified a highly interconnected network between the antiviral module and other host proteins. In this work, we propose a new paradigm for evaluating the antiviral response to a specific virus, combining an unbiased list of genes that highly correlate with viral RNA on a per cell basis with experimental protein interaction data. Our ZIKV-inclusive scRNA-seq assay will serve as a useful tool to gaining greater insight into the host response to ZIKV and can be applied more broadly to the flavivirus field.

microbiology↗