Biology subjects

Boehm, A.

Publications and source records attributed to Boehm, A..

9 recordsLinked to original sources

bioRxiv2026

Ticks and tickborne diseases in the upper Midwestern United States: role for citizen science in assessing exposure risk

Tickborne diseases are a significant burden in many parts of the world. In the upper Midwestern United States, Lyme disease is the most common tickborne disease. It is carried by Ixodes scapularis. This vector can also transmit the pathogens causing anaplasmosis, babesiosis, ehrlichiosis, and several more tickborne diseases in this region. There is also concern for other tick species, such as Amblyomma americanum, that are expanding their ranges northward. We launched a citizen science passive tick surveillance program in 2024 to investigate tick species ranges in the upper Midwest, as well as the pathogens carried by I. scapularis. We received over 12,000 ticks in the first two years of this program, primarily from Wisconsin. While we received submissions of adult A. americanum outside of their endemic range, we did not see evidence of establishment in our study area. We measured pathogen prevalence in adult female I. scapularis (n=707) and observed 51% positivity for Borrelia burgdorferi, 9% for Babesia microti, 9% for Anaplasma phagocytophilum, and 3% for Ehrlichia muris eauclairensis. Multiple pathogens were identified in 14% of tested specimens, and significant associations were observed between B. burgdorferi and B. microti, and B. burgdorferi and E. muris eauclairensis. Pathogen prevalences varied across time and geography. Our results can begin to inform risk assessment for tickborne diseases in our region. A non-technical version of this document with interactive maps is available here: https://storymaps.arcgis.com/stories/8008c9d710b5400599f3c6cf88b2c546 Our online data dashboard is available here: redcap.link/TICS

microbiology↗

bioRxiv2025

Importance of a heat snap in RT-PCR quantification of rotavirus double-stranded RNA in wastewater

Quantification of copies of double stranded RNA using RT-PCR methods may require denaturation of the double stranded structure using an initial high temperature incubation followed by rapid cooling, herein called "heat snap". Papers in the literature that report rotavirus RNA concentrations in fecal and environmental samples do not consistently report the use of such a "heat snap". In this study, we quantified rotavirus RNA in diverse environmental samples (wastewater solids, wastewater, and drainage samples) using digital RT-PCR methods with and without a heatsnap. Concentrations were higher in samples by a factor of 125 when a heat snap was applied. This was consistent across sample types, and across laboratories and PCR instrumentation. We recommend a heat snap be used when enumerating double stranded RNA from rotavirus and other viruses in environmental samples.

molecular biology↗

bioRxiv2025

Deep learning-based image quantification of epithelial cell shapes and its application to polycystic kidney disease

Cell shape is a fundamental determinant of tissue architecture and organ function. In epithelial tissues, cytoskeletal organization and tight junctions regulate cell geometry, shaping functional tissue units. Disruption of these mechanisms may cause diseases such as autosomal dominant polycystic kidney disease (ADPKD), in which cyst formation is characterized by abnormal regulation of epithelial cell shape. The mechanisms of cystogenesis remain incompletely understood, highlighting the need for robust, high-throughput methods to quantify the morphology of epithelial cells. Here, we present a fully automated, deep learning-based image analysis pipeline to quantify epithelial cell shape and tight junction morphology from immunofluorescence images. Our approach employs a U-Net convolutional neural network for accurate segmentation of fluorescence labeled tight junctions. We introduce novel algorithms to quantify overall cell shape and tight junction morphology, as well as to estimate cytoskeletal traction at shared cell borders. Our analysis pipeline objectively identifies subtle morphogenetic changes associated with disease-related mutations, applied to a genetically modified Madin-Darby Canine Kidney cell model of ADPKD. The method enables high-throughput, standardized analysis, reduces observer bias, and facilitates comparison across experiments. We further demonstrate the pipelines generalizability by applying it to Drosophila egg chamber epithelia. Our results establish a robust and scalable framework for analyzing cell shape and mechanical interactions in epithelial tissues, with broad applications in phenotypic screening, disease modeling, and morphogenesis research. Author SummaryThe shape of epithelial cells is critical for organ function. In the kidney, properly shaped epithelial cells assemble to tubules ensuring efficient waste excretion as well as body electrolyte and water balance. Disruption of cell shape regulation can lead to diseases such as autosomal dominant polycystic kidney disease (ADPKD), characterized by cyst formation and displacement of normal kidney tissue. Traditionally, analysis of epithelial cell morphology has relied on manual, low-throughput methods, which are time-consuming and prone to error. To overcome these limitations, we developed a fully automated, artificial intelligence-based pipeline that rapidly and reliably quantifies cell shape and junctional organization from microscopic images. We validated our approach using a cellular model of ADPKD, demonstrating clear differences in cell shape and junctional structure between normal and mutant cells harboring mutations in PKD-related genes. Our method enables efficient, objective analysis of large datasets and provides a powerful tool for understanding the mechanisms underlying cell shape regulation in health and disease.

bioinformatics↗

bioRxiv2024

Bacterial Wastewater-Based Epidemiology Using Surface-Enhanced Raman Spectroscopy and Machine Learning

Wastewater-based epidemiology (WBE) is a powerful tool for monitoring community disease occurrence, but current methods for bacterial detection suffer from limited scalability, the need for a priori knowledge of the target organism, and the high degree of genetic similarity between different strains of the same species. Here, we show that surface-enhanced Raman spectroscopy (SERS) can be a scalable, label-free method for detection of bacteria in wastewater. We preferentially enhance Raman signal from bacteria in wastewater using positively-charged plasmonic gold nanorods (AuNRs) that electrostatically bind to the bacterial surface. Transmission cryoelectron microscopy (cryoEM) confirms that AuNRs bind selectively to bacteria in this wastewater matrix. We spike the bacterial species Staphylococcus epidermidis, Staphylococcus aureus, Serratia marcescens, and Escerichia coli and AuNRs into filter-sterilized wastewater, varying the AuNR concentration to achieve maximum signal across all pathogens. We then collect 540 spectra from each species, and train a machine learning (ML) model to identify bacterial species in wastewater. For bacterial concentrations of 109 cells/mL, we achieve an accuracy exceeding 85%. We also demonstrate that this system is effective at environmentally-realistic bacterial concentrations, with a limit of bacterial detection of 104 cells/mL. These results are a key first step toward a label-free, high-throughput platform for bacterial WBE.

bioengineering↗

bioRxiv2023

Adsorption of respiratory syncytial virus (RSV), rhinovirus, SARS-CoV-2, and F+ bacteriophage MS2 RNA onto wastewater solids from raw wastewater

Despite the wide adoption of wastewater surveillance, more research is needed to understand the fate and transport of viral genetic markers in wastewater. This information is essential for the interpretation of wastewater surveillance data and the development of mechanistic models that link wastewater measurements to the number of individuals shedding virus. In this study, we examined the solid-liquid partitioning behavior of four viruses in wastewater: SARS-CoV-2, respiratory syncytial virus (RSV), rhinovirus (RV), and F+ coliphage/MS2. We used two approaches to achieve this: we (1) conducted laboratory partitioning experiments using lab-grown viruses and (2) examined the distribution of endogenous viruses in wastewater. Partition experiments were conducted at 4{degrees}C and 22{degrees}C; wastewater samples were spiked with varying concentrations of each virus and stored for three hours to allow the system to equilibrate. Solids and liquids were separated via centrifugation and viral RNA concentrations were quantified using reverse-transcription-digital droplet PCR (RT-ddPCR). For the distribution experiment, wastewater samples were collected from six wastewater treatment plants and processed without spiking exogenous viruses; viral RNA concentrations were measured in wastewater solids and liquid. Overall, RNA concentrations were higher in solids than the liquid fraction of wastewater by approximately 3-4 orders of magnitude. Partition coefficients (KF) from laboratory experiments were determined using the Freundlich model and ranged from 2,000-270,000 ml{middle dot}g-1 across viruses and temperature conditions. Distribution coefficients (Kd) determined from endogenous wastewater viruses were consistent with results from laboratory experiments.Further research is needed to understand how virus and wastewater characteristics might influence the partition of viral genetic markers in wastewater. SynopsisWe examined the solid-liquid partitioning behavior of SARS-CoV-2, RSV, RV, and F+coliphage/MS2 RNA in wastewater influent. Overall, partition/distribution coefficients were similar across viruses and temperature conditions.

microbiology↗

bioRxiv2023

Phenotypic plasticity and genetic differentiation drive troglomorphic character development in European cave loach

Using a cross-fostering experiment, we provide evidence for the contribution of both genetic differentiation and phenotypic plasticity to troglomorphic character development in the recently discovered cave form of Barbatula barbatula, an evolutionarily young lineage and first cavefish described in Europe, the northernmost record. We established reproducing populations of cave- and surface-dwelling loaches to produce cave, surface, and hybrid offspring and reared the F1 fish in a common garden setting in total darkness (DD) to simulate cave conditions as well as under the natural photoperiod (DL). We observed significant differences in the occurrence and extent of typical troglomorphic target characters among the offspring groups. Regardless of rearing conditions, cave fish exhibited smaller eyes, lighter body coloration, longer barbels, and larger olfactory epithelium than seen in surface fish. Hybrids in both rearing conditions generally showed an intermediate level of these traits. Surface and hybrid DD fish differed from the DL groups, resembling the cave fish phenotype in several traits, including eye size and body pigmentation. In contrast, cave and hybrid DL fish groups resembled surface fish phenotypes. Results confirmed that troglomorphic traits arise from heritable genetic differentiation of cave from surface forms and that phenotypic plasticity contributes to the process of adaptation to novel light conditions.

evolutionary biology↗

bioRxiv2020

Targeting CSF-1 ameliorates experimental autoimmune encephalomyelitis by depleting inflammatory monocytes and microglia in the central nervous system without affecting quiescent microglia.

The receptor for colony stimulating factor 1 (CSF-1R) is important for the survival and function of myeloid cells that mediate pathology during experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS). CSF-1 and IL-34, the ligands of CSF-1R, have similar bioactivities but distinct tissue and context-dependent expression patterns, suggesting that they have different roles. This could be the case in EAE, given that CSF-1 expression is upregulated in the CNS, while IL-34 remains constitutively expressed. We found that targeting CSF-1 with neutralizing mAb halted ongoing EAE, with efficacy superior to CSF-1R inhibitor BLZ945, whereas IL-34 neutralization had no effect, suggesting that pathogenic myeloid cells were maintained by CSF-1, not IL-34. Both anti-CSF-1- and BLZ945-treatment greatly reduced numbers of monocyte-derived cells and microglia in the CNS. However, anti-CSF-1 selectively depleted inflammatory microglia and monocytes in inflamed CNS areas, whereas BLZ945 depleted virtually all myeloid cells, including quiescent microglia, throughout the CNS. Anti-CSF-1 treatments reduced the size of demyelinated lesions, and microglial activation in the grey matter. Lastly, we found that bone marrow-derived immune cells were the major mediators of CSF-1R-dependent pathology, while microglia played a lesser role. Our findings suggest that targeting CSF-1 could be effective in ameliorating MS pathology, while preserving the homeostatic functions of myeloid cells, thereby minimizing risks associated with total ablation of CSF-1R-dependent cells. Significance StatementMultiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE), are autoimmune diseases characterized by accumulation of myeloid immune cells into the central nervous system (CNS). Both harmful and beneficial myeloid cells are present in EAE/MS, and a goal of MS therapy is to preferentially remove harmful myeloid cells. The receptor for CSF-1 (CSF-1R) is found on myeloid cells and it is important for their survival. CSF-1R can bind two ligands, CSF-1 and IL-34, but is unknown whether their functions in EAE/MS differ. We found that blocking CSF-1 depleted only harmful myeloid cells in the CNS and suppressed EAE, whereas blocking IL-34 had no effect. Thus, we propose that blocking CSF-1 could be a novel therapy for MS.

immunology↗

bioRxiv2020

Quantitative PCR assays to detect humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge) in marine water samples

Monitoring aquatic species by identification of environmental DNA (eDNA) is becoming more common. In order to obtain quantitative datasets for individual species, species-specific quantitative PCR (qPCR) assays are required. Here, we present detailed methodology of qPCR assay design and testing, including in silico, in vitro, and in vivo testing, and comment on the challenges associated with assay design and performance. We use the presented methodology to design assays for three important marine organisms common in the California Current Ecosystem (CCE): humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge). All three assays have excellent sensitivity and high efficiencies ranging from 92% to 99%. However, specificities of the assays varied from species-specific in the case of common murre to the genus-specific shortbelly rockfish assay, to the humpback whale assay which cross-amplified with other two other whale species, including one in a different family. All assays detected their associated targets in complex environmental water samples.

molecular biology↗

bioRxiv2020

Structural manipulations of a shelter resource reveal underlying preference functions in a shell-dwelling cichlid fish

Many animals can modify the environments in which they live, thereby changing the selection pressures they experience. A common example of such niche-construction is the use, creation, or modification of environmental resources for use as nests or shelters. Because these resources often have correlated structural elements, it can be difficult to disentangle the relative contribution of these elements to resource choice, and the preference functions underlying niche-construction behaviour remain hidden. Here, we present an experimental paradigm that uses 3D-scanning, -modelling, and -printing to create replicas of structures that differ with respect to key structural attributes. We show that a niche-constructing, shelldwelling cichlid fish, Neolamprologus multifasciatus, has strong open-ended preference functions for exaggerated shell replicas. Fish preferred shells that were fully intact and either enlarged, lengthened, or had widened apertures. Shell intactness was the most important structural attribute, followed by shell length, then aperture width. We disentangle the relative roles of different shell attributes, which are tightly correlated in the wild, but nevertheless differentially influence shelter choice and therefore niche construction in this species. We highlight the broad utility of our approach when compared to more traditional methods (e.g. two-choice tasks) for studying animal decision-making in a range of contexts.

evolutionary biology↗