Biology subjects

Davis, M. A.

Publications and source records attributed to Davis, M. A..

6 recordsLinked to original sources

bioRxiv2025

Applying environmental DNA metabarcoding to calculate an index of biotic integrity for freshwater fish

Multi-metric indices like the Index of Biotic Integrity (IBI) are important biomonitoring tools for Clean Water Act compliance in the United States (US) but have also been implemented worldwide across many taxonomic groups. Environmental DNA (eDNA) metabarcoding could complement IBIs by increasing detection sensitivity for rare taxa while also reducing monitoring costs. To date, no studies have examined the efficacy of using eDNA metabarcoding to calculate IBIs in the US. Here, we used eDNA metabarcoding to calculate a fish-based IBI for streams and rivers of the Tennessee River Basin in northern Alabama, US. We collected water samples from 50 stream and river sites across a gradient of land use intensity, extracted eDNA from these samples, and sequenced the eDNA using vertebrate-specific primers. We compared our eDNA-IBI to a previous fish-IBI implemented by the state of Alabama using conventional sampling, as well as predicted biological condition of these streams from the US Environmental Protection Agency (EPA) based on a benthic macroinvertebrate multi-metric index (BMMI). We found a highly significant, positive relationship between the eDNA-IBI and fish-IBI for the same streams but a weaker, non-significant positive relationship between the eDNA-IBI and BMMI. Notably, the former was recovered despite eDNA-IBI sampling being conducted nine years after the conventional fish sampling at slightly different locations, the fish-IBI having used greater sampling effort throughout the year (including spring and autumn rather than only summer sampling), and a lack of reference DNA sequences that prevented eDNA detection for some species detected by conventional fish sampling. Accordingly, our study provides a baseline for how an eDNA-IBI may work relative to multi-metric indices calculated from conventional sampling, which can be improved through future directions identified and discussed in our paper.

molecular biology↗

bioRxiv2025

Strengthening Antisense Oligonucleotide-Mediated Anti-Tumor Immunity via Metal-Organic Framework Nanoparticles

Overexpression of checkpoint proteins, such as programmed death ligand one (PD-L1), prevents immune recognition and enables cancer growth. Current monoclonal antibodies that block PD-L1 tend to be fragile, unable to penetrate tumors, and target cancer at later stages, thus leading to inconsistent patient outcomes. Antisense oligonucleotides (ASOs) provide an alternative to decrease PD-L1 expression, but require frequent high dosing due to fast degradation, rapid clearance, and poor cell uptake. To overcome these issues, we harnessed biocompatible metal-organic framework (MOF) nanoparticles, porous nanomaterials comprising metal nodes and organic linkers, to deliver ASOs. Encapsulating ASOs into MOFs enhances their stability and protection during intracellular delivery, leading to reduced PD-L1 expression and downstream immune recognition. Herein, we synthesized three distinct PD-L1-specific ASOs and loaded them individually into zirconium-based nano-sized NU-1000 MOFs, averaging [~]80% encapsulation efficiency. Release of encapsulated ASOs was sustained up to 7 days ex cellulo. MOF encapsulation increased ASO potency and reduced PD-L1 expression[~] 3-fold and 2-fold in triple negative breast cancer EMT6 and melanoma B16-F10 cells, respectively. We evaluated the impact of MOF-delivered ASOs on PD-L1-expressing immune cells, where we observed ca. 12-fold increases in dendritic cell co-stimulatory marker expression, and amplified T cell activation and proliferation compared to untreated cells (4-fold and 10-fold, respectively). Notably, these changes drove a 3-fold increase in tumor caspase-3 expression, a key mediator for apoptosis. This research highlights how MOFs can be harnessed to bypass ASO limitations without requiring sequence modifications, and offers a broadly applicable platform for improved oligonucleotide delivery for various genes of interest.

bioengineering↗

bioRxiv2025

An intranasal, NLC-delivered self-amplifying RNA vaccine establishes protective immunity against pre-pandemic H5N1 and H7N9 influenza

Seasonal and pandemic influenzas are continuous threats to human health, requiring rapid development of vaccines to multiple evolving viral strains. New RNA vaccine technologies have the adaptability and manufacturability to facilitate pandemic preparedness but have limited flexibility in their route of administration, reducing the ability to establish local protective immune responses such as respiratory mucosal immunity. Here, we describe monovalent and bivalent self-amplifying RNA (saRNA) vaccines against A/Vietnam/1203/2004 H5N1 and A/Anhui/2013 H7N9. These saRNA vaccines express either H5 or H7 hemagglutinin and are formulated with a nanostructured lipid carrier (NLC) that permits both intramuscular (IM) and intranasal (IN) dosing. In mice, IM vaccination established systemic humoral and cellular responses but no detectable mucosal response, while IN administration induced robust systemic and mucosal immunity. The saRNA-NLC vaccines provided complete protection against morbidity and mortality in ferret challenge models, establishing this intranasally-administered saRNA-NLC vaccine platform as a potential pandemic response tool. ONE SENTENCE SUMMARYA self-amplifying RNA-NLC vaccine, delivered intranasally, induces robust mucosal immunity in mice and protects against H5N1 and H7N9 in ferrets

immunology↗

bioRxiv2023

A Cellular Platform for Production of C4 Monomers

Living organisms carry out a wide range of remarkable functions, including the synthesis of thousands of simple and complex chemical structures for cellular growth and maintenance. The manipulation of this reaction network has allowed for the genetic engineering of cells for targeted chemical synthesis, but it remains challenging to alter the program underlying their fundamental chemical behavior. By taking advantage of the unique ability of living systems to use evolution to find solutions to complex problems, we have achieved ~95% theoretical yield of three C4 commodity chemicals, n-butanol, 1,3-butanediol, and 4-hydroxy-2-butanone. Genomic sequencing of the evolved strains identified pcnB and rpoBC as two gene loci that are able to alter carbon flow by remodeling the transcriptional landscape of the cell, highlighting the potential of synthetic pathways as a tool to identify metabolic control points.

synthetic biology↗

bioRxiv2021

BeeDNA: microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities

Pollinators are imperiled by global declines that can reduce plant reproduction, erode essential ecosystem services and resilience, and drive economic losses. Monitoring pollinator biodiversity trends is key for adaptive conservation and management, but conventional surveys are often costly, time consuming, and require taxonomic expertise. Environmental DNA (eDNA) metabarcoding surveys are booming due to their rapidity, non-invasiveness, and cost efficiency. Microfluidic technology allows multiple primer sets from different markers to be used in eDNA metabarcoding for more comprehensive species inventories whilst minimizing biases associated with individual primer sets. We evaluated microfluidic eDNA metabarcoding for pollinator community monitoring by introducing a bumblebee colony to a greenhouse flower assemblage and sampling natural flower plots. We collected nectar draws, flower swabs, or whole flower heads from four flowering species, including two occurring in both the greenhouse and field. Samples were processed using two eDNA isolation protocols before amplification with 15 primer sets for two markers (COI and 16S). Microfluidic eDNA metabarcoding detected the target bumblebee and greenhouse insects as well as common regional arthropods. Pollinator detection was maximized using whole flower heads preserved in ATL buffer and extracted with a modified Qiagen(R) DNeasy protocol for amplification with COI primers. eDNA surveillance could enhance pollinator assessment by detecting protected and endangered species and being more applicable to remote, inaccessible locations, whilst reducing survey time, effort, and expense. Microfluidic eDNA metabarcoding requires optimization to address remaining efficacy concerns but this approach shows potential in revealing complex networks underpinning critical ecosystem functions and services, enabling more accurate assessments of ecosystem resilience.

ecology↗

bioRxiv2020

Metapopulation Connectivity in Voles (Microtus sp.) as a Gauge for Tallgrass Prairie Restoration in Midwestern North America

Applying quantifiable metrics to validate the success of restoration efforts is crucial for ongoing management programs in anthropogenically fragmented habitats. Estimates of dispersal can provide such baseline data because they measure not only the extent to which restored patches are colonized and interconnected, but also their metapopulation source/sink dynamics. In this context, we estimated dispersal and population connectivity among prairie (Microtus ochrogaster; N=231) and meadow vole (M. pennsylvanicus; N=83), sampled from eight restored plots at five tallgrass prairie sites embedded within the agricultural matrix of midwestern North America. Our expectation was that extensive distances separating these restored habitats (i.e., 48-246 km) would spatially isolate vole metapopulations, resulting in significant genetic differentiation. We first used molecular taxonomy to validate the field-identifications of all sampled individuals, then used pairwise FST derived from 15 microsatellite DNA loci to estimate genetic connectivity among the species-delimited study populations. Metapopulation stability was gauged by assessing migration rates and deriving effective population sizes (Ne). We also calculated relatedness values (r) as a potential surrogate for contact in prairie vole, a primary vector for Lyme disease. Molecular species-assignments contravened field-identifications in 25% of samples (11 prairie/67 meadow) and identified two instances of species-hybridization (0.6%). Local effects (i.e., population crash/drought) were manifested at two sites, as documented by significant temporal declines in Ne and r. Overall, high migration rates and non-significant (10/15) pairwise FST values underscored elevated metapopulation connectivity. A single site that recorded five significant FST values also displayed significant r-values indicating the inadvertent sampling of closely related individuals. This highlights the close social groupings among cooperatively-breeding prairie vole that can exacerbate Lyme disease transmission. Thus, while elevated population connectivity aligns with prairie restoration goals, it also reinforces a need in adaptive management to evaluate environmental matrices for their permeability to vector-borne diseases.

ecology↗