Biology subjects

Smith, J. T.

Publications and source records attributed to Smith, J. T..

At least 19 recordsLinked to original sources

bioRxiv2026

Indole-3-propionic acid nano-prodrugs sustain increased lymphoid exposure and alleviate experimental autoimmune arthritis

Chronic inflammatory diseases, including rheumatoid arthritis (RA), currently require sustained control of inflammation. Although long-acting therapies can reduce dosing frequency, those that rely on systemic immunosuppression may still compromise protective immunity. Microbiota-derived metabolites offer a complementary starting point for immune modulation through naturally occurring host-microbe signals. Indole-3-propionic acid (IPA), a gut microbial tryptophan metabolite naturally present in human circulation, has newly recognized immunoregulatory activity, yet its effects across disease contexts and its potential for therapeutic use remain incompletely defined. Here, we developed polymeric IPA nano-prodrugs (pIPANP) by conjugating IPA to a methacrylamide polymer through ester linkages and formulating the polymer into injectable nanoparticles. Following subcutaneous administration of fluorescently-labeled pIPANP, injection-site fluorescence remained detectable for at least 35 days, with labeled material detected in multiple lymph nodes. LC-MS/MS confirmed higher lymph-node IPA concentrations in mice treated with the pIPANPs compared to free IPA control at every sampled time point over 14 days. In collagen antibody-induced arthritis (CAIA), pIPANPs reduced clinical disease severity and paw swelling under both prophylaxis and therapeutic administration. pIPANP treatment increased the relative representation of CD11cCD103CD11b- cells with a conventional dendritic cell (cDC)1-associated phenotype and reduced costimulatory-marker frequencies in both CD11cCD103 and CD11cCD11b populations, most prominently in hock-draining lymph nodes. These changes were accompanied by increased PD-1 and IFN-{gamma} frequencies among CD4 and CD8 T cells. Fluorescent nanoparticle tracking showed preferential association with several myeloid populations, while single-cell profiling revealed divergent interferon-response signatures across splenic populations. These findings reveal arthritis-associated immunomodulatory activity of polymeric IPA and support its further development as a microbiome-inspired, long-acting approach to inflammatory arthritis.

bioengineering↗

bioRxiv2026

Exclusion of fire and grazing does not reduce annual grass invasion in a sagebrush steppe ecosystem

Disturbance is widely recognized as a catalyst of invasion, but growing evidence suggests even protected communities are susceptible to severe infestation. We used k[i]pukas--naturally isolated patches of minimally-disturbed vegetation surrounded by lava flows--as a large-scale natural experiment to test the long-term biotic resistance of protected sagebrush ecosystems threatened by Bromus tectorum and other invasive annual grasses. Employing a robust causal inference approach combining matching with regression adjustment, we compared protected communities within k[i]pukas to otherwise similar communities exposed to contemporary disturbance regimes. Despite their near-total protection from fire and livestock grazing, k[i]pukas were extensively invaded by annual grasses (18.9 {+/-} 0.28% cover), with abundance comparable to or slightly exceeding disturbed sites (16.7 {+/-} 0.29% cover). These findings challenge the notion that protection from disturbance confers effective long-term resistance to invasion, instead demonstrating that invaders can establish, proliferate, and drive ecosystem transformation where favorable abiotic conditions prevail. Our findings reveal the limits of passive protection as a conservation strategy, suggesting active management may be necessary to prevent ecosystem degradation by aggressive invaders.

ecology↗

bioRxiv2026

Shifting Resilience: Trends and Predictors of Mesic Resource Productivity in Western U.S. Rangelands

Mesic resources, the late-season herbaceous vegetation found in riparian areas and wet meadows, provide disproportionately important forage and habitat across western U.S. rangelands, yet their response to climatic variability and anthropogenic influences remains poorly understood. Using a 40-year Landsat time series (1984-2024), we quantified trends in late-season productivity (NDVI) across 4.5 million hectares of the sagebrush biome and applied random forest models to distinguish between temporal and spatial predictors of mesic resource productivity. We identified a fundamental shift in how mesic resources respond to drought: from 1984 to 2004, mesic productivity was strongly correlated with drought severity (Palmer Drought Severity Index, R{superscript 2} = 0.92), but this relationship weakened substantially in the next two decades (2005-2024; R{superscript 2} = 0.28), during which time productivity increased despite persistent aridity. Temporal modeling identified rising atmospheric CO2 concentrations as the strongest predictor of this shift, consistent with enhanced plant water-use efficiency under CO2 fertilization. Spatially, large agricultural valley floodplains act as anthropogenic refugia, sustaining productive mesic resources through flood irrigation and subsequent groundwater recharge into late summer. These findings suggest that human water management and physiological shifts in vegetation are currently buffering mesic systems against meteorological drought throughout U.S. rangelands. However, this apparent buffering is spatially heterogeneous and may mask vulnerability to groundwater depletion, shifts in precipitation regimes, and woody encroachment. Sustaining these vital ecosystems will require conservation approaches that go beyond climate monitoring to include balanced management considering both agricultural and ecological water needs and constraints.

ecology↗

bioRxiv2025

Predicting Human Pharmacokinetic Parameters of Drugs using a Multi-Tissue Chip Platform Integrating Liver, Kidney, and Skeletal Muscle Microphysiological Systems

Accurate prediction of human pharmacokinetic (PK) parameters remains a critical challenge in drug discovery. While simple in vitro assays provide insight into discrete metabolic processes, they cannot recapitulate the complex multi-organ interactions that involve absorption, distribution, metabolism, and excretion (ADME) processes. This limitation has perpetuated a heavy reliance on animal experimentation to predict integrated outcomes like hepatic and renal clearance in humans. In this study, we developed a multi-tissue chip (MTC) to evaluate the PK parameters of intravenously (IV) administered drugs. The MTC platform provides continuous oxygenation through media recirculation and interconnects three MPSs (liver, kidney, skeletal muscle) to study drug metabolism, excretion and distribution within a single in vitro system. The functionality of each MPS was characterized for more than 15 days with single- and multi-tissue chips. A diverse set of drugs from all extended clearance classification system (ECCS) classes with various clearance mechanisms was evaluated on the MTCs and on-chip PK parameters were evaluated, such as hepatic metabolism, uptake, and disposition, tubular secretion and reabsorption, and muscle distribution. These PK parameters were successfully correlated to clinical parameters for IV drugs: hepatic clearance (CLH), renal clearance (CLR), volume of distribution (VD) and then these parameters were extrapolated to human drug exposures using physiologically-based pharmacokinetic (PBPK) modeling. This study demonstrated that the MTC platform could deliver accurate prediction for clinical pharmacokinetics of intravenously administered small molecules without the need for animal studies.

bioengineering↗

bioRxiv2025

A 0.6-meter resolution canopy height and structure model for the contiguous United States

Above-ground vertical structure is a critical variable for ecosystem monitoring, carbon accounting, and land management. However, the high cost and limited coverage of airborne lidar hinder its widespread application. To address this, we developed NAIP-CHM, a 0.6-meter resolution canopy height and structure model (CHM) covering the contiguous United States, derived from National Agriculture Imagery Program (NAIP) aerial imagery. Unlike forestry-specific models that exclude human-made features, NAIP-CHM characterizes the full vertical structure of the landscape including vegetation, buildings, and infrastructure. We utilized a U-Net convolutional neural network with attention mechanisms and environmental conditioning, training and validating the model with a peer-reviewed, publicly available dataset of 22.8 million co-registered NAIP imagery and lidar-derived CHM pairs, with stratified sampling to ensure robustness in open-canopy ecosystems. The model achieved a pixel-wise root mean square error (RMSE) of 2.28 meters and an r2 of 0.87. Forested sites alone produced an r2 of 0.82 and RMSE of 3.82 meters. We provide the dataset, source code, and cloud-based tools to enable broad application without requiring specialized computational resources.

ecology↗

bioRxiv2025

Efagins evolved independently to target the enterococcal cell wall

Enterococci are major causes of multidrug-resistant infections, and antimicrobials with fundamentally new mechanisms of action are urgently needed. We identify a new class of antibacterial agents, termed efagins, which are chromosomally encoded, phage-related nanomachines that recognize cell wall carbohydrate receptors and inhibit subsets of E. faecalis, E. faecium and other enterococci selectively--a key reason they evaded prior detection. Five natural variants with distinct targeting profiles were identified - four related by sequence divergence, while one appears to have arisen through recombination of the targeting domain, likely from a phage donor. Operons encoding the corresponding carbohydrate receptors are highly variable, accounting for targeting specificity. The efagin targeting domain can be engineered to reprogram them toward alternative receptors, providing a pathway for filling critical coverage gaps. These findings advance efagins as new selective antibacterials with promise for addressing infection and spread of multidrug-resistant enterococcal infection.

microbiology↗

bioRxiv2025

Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species

The ability to detect and reconstruct plasmids from genome assemblies is crucial for studying the evolution and spread of antimicrobial resistance and virulence in bacteria. Though long-read sequencing technologies have made reconstructing plasmids easier, most (97%) of the bacterial genome assemblies in the public domain are generated from short-read data. Work to compare plasmid reconstruction tools has focused primarily on E. coli, leaving gaps in our understanding of how well these tools perform on other, less well-characterized, taxa. Using high quality assemblies as ground truth, we benchmarked 12 plasmid detection tools (which identify plasmid contigs in assemblies) and four plasmid reconstruction tools (which group contigs from the same plasmid together). We tested their ability to characterize diverse plasmids from short-read assemblies representing a wide range of Enterobacterales and Enterococcus species, including newly discovered and poorly characterized species collected from non-human hosts. Plasmer, PlasmidEC, PlaScope, and gplas2 were the highest-scoring plasmid detection tools, performing well for both Enterobacterales and enterococci. The two major determinants of accurate plasmid detection were representation in plasmid databases - with Enterobacterales plasmids being more easily detected than those from enterococci - and assembly contiguity, which was also key for successful plasmid reconstruction. Gplas2 performed best for plasmid reconstruction; however, less than half of plasmids were perfectly reconstructed, suggesting that substantial room for improvement remains in this class of tools. Key MessagesO_LIThe ability to detect and reconstruct plasmids from short-read assemblies is crucial to study the spread of antimicrobial resistance and virulence genes in bacteria. C_LIO_LIMost past comparisons of tools for plasmid detection and reconstruction have focused on plasmids from well-characterized E. coli; therefore, we broadened our benchmarking set to include plasmids from diverse Enterobacterales and Enterococcus species, collected from a wide range of hosts. C_LIO_LIWe compared the predictions of 12 recent plasmid detection and four plasmid reconstruction tools on short read assemblies, against a truth set generated from high-quality hybrid assemblies. C_LIO_LIPlasmer, PlasmidEC, PlaScope, and gplas2 were the highest-scoring plasmid detection tools. C_LIO_LIGplas2 was the highest-scoring tool for plasmid reconstruction; the quality of plasmid reconstruction was mainly determined by assembly fragmentation, with plasmids in more contiguous assemblies being easier to reconstruct. C_LI

bioinformatics↗

bioRxiv2025

Estimating rangeland fractional cover and canopy gap size class with Sentinel-2 imagery

Rangelands are extensive ecosystems, providing important ecosystem services while undergoing continuous change. As a result, improved monitoring technologies can help better characterize vegetation change. Satellite remote sensing has proven effective in this regard, tracking vegetation dynamics at broad and fine scales. We leveraged the spatial, spectral, and temporal resolution of Sentinel-2 satellites to estimate fractional cover and canopy gap across rangelands of the western United States. We produced annual, 10 m spatial resolution estimates of fractional cover and canopy gap size class for years 2018 to 2024. Fractional cover estimates include that of common plant functional types (annual forb and grass, bareground, littler, perennial forb and grass, shrub, tree) and select genera (including invasive annual grass species, pinyon-juniper species, and sagebrush species); canopy gap size classes include gap sizes 25 to 50, 51 to 100, 101 to 200, and greater than 200 cm. We make these data available as Cloud Optimized GeoTIFFs, organized as 75x75 km tiles covering the 17 western states of the United States.

ecology↗

bioRxiv2024

Multiscale analysis and functional validation of the cellular and genetic determinants of skeletal disease

Musculoskeletal diseases are a major health burden. Development of bone-active therapies has been hindered by limited understanding of the cells and genes that regulate the skeleton. We exploited the value of cross-species analysis and developed single-cell methodologies in skeletal tissues to define the critical endosteal compartment that regulates bone turnover. Thirty-four distinct cell types were identified, and disease-relevant cells prioritised by enrichment for rare skeletal disorder genes and bone mineral density-associated genes in an extended UK Biobank GWAS. Functional validation was undertaken in over one thousand genetically modified mouse models. Endothelial and vascular smooth muscle cells were identified as novel skeletal disease-relevant cells alongside osteoblast, chondrocyte and osteoclast cell lineages. Hundreds of cell-specific genes with unappreciated roles in skeletal pathophysiology were identified. This comprehensive cellular and molecular framework underpins skeletal physiology and disease, and will help prioritise new therapeutic targets to accelerate development of novel therapies to treat musculoskeletal disease.

genetics↗

bioRxiv2024

A Novel Technique for Fluorescence Lifetime Tomography

Fluorescence lifetime imaging has emerged as a powerful tool for quantitatively assessing the molecular environment of live tissues in vivo. While fluorescence lifetime microscopy (FLIM) is a mature field, achieving effective 3D imaging in deep tissues has remained a significant challenge due to high scattering. In this study, we present a deep neural network-based approach, referred to as AUTO-FLI, which enables both 3D intensity and quantitative lifetime reconstructions at centimeters depth. This Deep Learning (DL)-based method incorporates an in silico framework to accurately generate fluorescence lifetime data for training and validation. The performance of this novel DL model is further validated with experimental data acquired on an anatomically accurate mouse-mimicking phantom. The results demonstrate that AUTO-FLI can provide precise 3D quantitative estimates of both intensity and lifetime distributions in highly scattering media. This method holds great promise for fluorescence lifetime-based molecular imaging at both the mesoscopic and macroscopic scales, with potential applications for pre-clinical translational research and fluorescence-guided surgery.

bioengineering↗

bioRxiv2024

Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data

Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool for understanding gene function across diverse cells. Recently, this has included the use of allele-specific expression (ASE) analysis to better understand how variation in the human genome affects RNA expression at the single-cell level. We reasoned that because intronic reads are more prevalent in single-nucleus RNA-Seq (snRNA-Seq), and introns are under lower purifying selection and thus enriched for genetic variants, that snRNA-seq should facilitate single-cell analysis of ASE. Here we demonstrate how experimental and computational choices can improve the results of allelic imbalance analysis. We explore how experimental choices, such as RNA source, read length, sequencing depth, genotyping, etc., impact the power of ASE-based methods. We developed a new suite of computational tools to process and analyze scRNA-seq and snRNA-seq for ASE. As hypothesized, we extracted more ASE information from reads in intronic regions than those in exonic regions and show how read length can be set to increase power. Additionally, hybrid selection improved our power to detect allelic imbalance in genes of interest. We also explored methods to recover allele-specific isoform expression levels from both long- and short-read snRNA-seq. To further investigate ASE in the context of human disease, we applied our methods to a Parkinsons disease cohort of 94 individuals and show that ASE analysis had more power than eQTL analysis to identify significant SNP/gene pairs in our direct comparison of the two methods. Overall, we provide an end-to-end experimental and computational approach for future studies.

genomics↗

bioRxiv2024

Fluorescence Lifetime Imaging for quantification of targeted drug delivery in varying tumor microenvironments

RationaleTrastuzumab (TZM) is a monoclonal antibody that targets the human epidermal growth factor receptor (HER2) and is clinically used for the treatment of HER2-positive breast tumors. However, the tumor microenvironment can limit the access of TZM to the HER2 targets across the whole tumor and thereby compromise TZMs therapeutic efficacy. An imaging methodology that can non-invasively quantify the binding of TZM-HER2, which is required for therapeutic action, and distribution within tumors with varying tumor microenvironments is much needed. MethodsWe performed near-infrared (NIR) fluorescence lifetime (FLI) Forster Resonance Energy Transfer (FRET) to measure TZM-HER2 binding, using in vitro microscopy and in vivo widefield macroscopy, in HER2 overexpressing breast and ovarian cancer cells and tumor xenografts, respectively. Immunohistochemistry was used to validate in vivo imaging results. ResultsNIR FLI FRET in vitro microscopy data show variations in intracellular distribution of bound TZM in HER2-positive breast AU565 and AU565 tumor-passaged XTM cell lines in comparison to SKOV-3 ovarian cancer cells. Macroscopy FLI (MFLI) FRET in vivo imaging data show that SKOV-3 tumors display reduced TZM binding compared to AU565 and XTM tumors, as validated by ex vivo immunohistochemistry. Moreover, AU565/XTM and SKOV-3 tumor xenografts display different amounts and distributions of TME components, such as collagen and vascularity. Therefore, these results suggest that SKOV-3 tumors are refractory to TZM delivery due to their disrupted vasculature and increased collagen content. ConclusionOur study demonstrates that FLI is a powerful analytical tool to monitor the delivery of antibody drug tumor both in cell cultures and in vivo live systems. Especially, MFLI FRET is a unique imaging modality that can directly quantify target engagement with potential to elucidate the role of the TME in drug delivery efficacy in intact live tumor xenografts.

cancer biology↗

bioRxiv2023

A Novel Milli-fluidic Liver Tissue Chip with continuous Recirculation for Predictive pharmacokinetics Applications

A crucial step in lead selection during drug development is accurate estimation and optimization of hepatic clearance using in vitro methods. However, current methods are limited by factors such as lack of physiological relevance, short culture/incubation times that are not consistent with drug exposure patterns in patients, use of drug absorbing materials, and evaporation during long-term incubation. To address these technological needs, we developed a novel milli-fluidic human liver tissue chip (LTC) that was designed with continuous media recirculation and optimized for hepatic cultures using human primary hepatocytes. Here, we characterized the LTC using a series of physiologically relevant metrics and test compounds to demonstrate that we could accurately predict the PK of both low and high clearance compounds. The non-biological characterization indicated that the cyclic olefin copolymer (COC)-based LTC exhibited negligible evaporation and minimal non-specific binding of drugs of varying ionic states and lipophilicity. Biologically, the LTC exhibited functional and polarized hepatic culture with sustained metabolic CYP activity for at least 15 days. This long-term culture was then used for drug clearance studies for low and high-clearance compounds for at least 12 days and clearance was estimated for a range of compounds with high in vitro in vivo correlation (IVIVC). We also demonstrated that LTC can be induced by rifampicin, and the culture age had insignificant effect on depletion kinetic and predicted clearance value. Thus, we used advances in bioengineering to develop a novel purpose-built platform with high reproducibility and minimal variability to address unmet needs for PK applications.

pharmacology and toxicology↗

bioRxiv2023

The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance in Enterobacterales

Carbapenem-resistant Enterobacterales (CRE) are important pathogens that can develop resistance via multiple molecular mechanisms, including hydrolysis or reduced antibiotic influx. Identifying these mechanisms can improve pathogen surveillance, infection control, and patient care. We investigated, both phenomenologically and mechanistically, how resistance mechanisms influence the carbapenem inoculum effect (IE), a phenomenon where inoculum size affects antimicrobial susceptibility testing (AST). We demonstrated that any of seven different carbapenemases were sufficient to impart a meropenem IE when transformed into a laboratory strain of Escherichia coli. Across 106 clinical CRE isolates spanning 6 genera and 12 species, the carbapenem IE strictly depended on resistance mechanism: all 36 carbapenemase-producing CRE (CP-CRE) exhibited a clear IE, whereas 43 porin-deficient CRE displayed none. 27 isolates with both carbapenemase production and porin deficiency exhibited high-level resistance at all inocula, and still displayed an IE, albeit smaller in magnitude than CP-CRE with intact porins. Mechanistically, we found that clinical CP-CRE release carbapenemase activity into culture supernatant to protect other cells. Further, this released activity markedly increased upon exposure to lethal antibiotic doses, functionally consistent with altruism. Concerningly, 50% and 24% of CP-CRE isolates changed susceptibility classification to meropenem and ertapenem, respectively, across the allowable inoculum range in clinical testing guidelines. The meropenem IE, and the ratio of ertapenem to meropenem minimal inhibitory concentration (MIC) at standard inoculum, reliably identified CP-CRE. Understanding how resistance mechanisms affect AST could improve diagnosis and guide therapies for CRE infections. ImportanceInfections caused by carbapenem-resistant Enterobacterales (CRE) pose significant threats to patients and public health worldwide. Carbapenem resistance can occur through several molecular mechanisms, including enzymatic hydrolysis by carbapenemases and reduced influx via porin mutations. Identifying carbapenemase-producing isolates could enable tailored antibiotic selection to improve patient outcomes, and infection control measures to prevent further carbapenemase transmission. In a large collection of CRE isolates, we found that only carbapenemase-producing CRE exhibit an inoculum effect, in which their measured resistance varies markedly with cell density, which risks misdiagnosis. Further, this inoculum effect occurs under conditions where bacteria release carbapenemases to the community upon exposure to antibiotic that results in cell death, functionally consistent with altruism. Measuring this inoculum effect, or integrating other data from routine antimicrobial susceptibility testing, enhances carbapenem resistance detection, paving the way for more effective strategies to combat this growing public health crisis.

microbiology↗

bioRxiv2023

Translational control by Trypanosoma brucei DRBD18 contributes to the maintenance of the procyclic state

Trypanosoma brucei occupies distinct niches throughout its life cycle, within both the mammalian and tsetse fly hosts. The immunological and biochemical complexity and variability of each of these environments require a reshaping of the protein landscape of the parasite both to evade surveillance and face changing metabolic demands. Whereas most well-studied organisms rely on transcriptional control as the main regulator of gene expression, post-transcriptional control mechanisms are particularly important in T. brucei, and these are often mediated by RNA-binding proteins. DRBD18 is a T. brucei RNA-binding protein that interacts with ribosomal proteins and translation factors. Here, we tested a role for DRBD18 in translational control. We show that DRBD18 depletion by RNA interference leads to altered polysomal profiles with a specific depletion of heavy polysomes. Ribosome profiling analysis reveals that 101 transcripts change in translational efficiency (TE) upon DRBD18 depletion: 41 exhibit decreased TE and 60 exhibit increased TE. A further 66 transcripts are buffered, i.e. changes in transcript abundance are compensated by changes in TE such that the total translational output is expected not to change. Proteomic analysis validates these data. In DRBD18-depleted cells, a cohort of transcripts that codes for procyclic form-specific proteins is translationally repressed while, conversely, transcripts that code for bloodstream form- and metacyclic form-specific proteins are translationally enhanced. These data suggest that DRBD18 contributes to the maintenance of the procyclic state through both positive and negative translational control of specific mRNAs.

microbiology↗

bioRxiv2023

in vivo quantitative FRET small animal imaging: intensity versus lifetime-based FRET

Forster Resonance Energy Transfer (FRET) microscopy is used in numerous biophysical and biomedical applications to monitor inter- and intramolecular interactions and conformational changes in the 2-10 nm range. FRET is currently being extended to in vivo optical imaging, its main application being in quantifying drug-target engagement or drug release in animal models of cancer using organic dye or nanoparticle-labeled probes. Herein, we compared FRET quantification using intensity-based FRET (sensitized emission FRET analysis with the 3-cube approach using an IVIS imager) and macroscopic fluorescence lifetime (MFLI) FRET using a custom system using a time-gated ICCD, for small animal optical in vivo imaging. The analytical expressions and experimental protocols required to quantify the product fD E of the FRET efficiency E and the fraction of donor molecules involved in FRET, fD, are described in detail for both methodologies. Dynamic in vivo FRET quantification of transferrin receptor-transferrin binding was acquired in live intact nude mice upon intravenous injection of near infrared-labeled transferrin FRET pair and benchmarked against in vitro FRET using hybridized oligonucleotides. Even though both in vivo imaging techniques provided similar dynamic trends for receptor-ligand engagement, we demonstrate that MFLI FRET has significant advantages. Whereas the sensitized emission FRET approach using the IVIS imager required 9 measurements (6 of which are used for calibration) acquired from three mice, MFLI FRET needed only one measurement collected from a single mouse, although a control mouse might be needed in a more general situation. Based on our study, MFLI therefore represents the method of choice for longitudinal preclinical FRET studies such as that of targeted drug delivery in intact, live mice. WHY IT MATTERSFRET measurements in live animals open a unique window into drug-target interaction monitoring, by sensing the close proximity between a donor and acceptor-labeled molecular probes. To perform these measurements, a 3-cube fluorescent intensity measurement strategy can be adopted, as is common for in vitro FRET microscopy studies. However, it is challenging to translate this already cumbersome approach to in vivo small animal imaging. Here, we compare this standard approach, for which we provide a revised analytical framework, to a conceptually much simpler and more powerful one based on fluorescence lifetime measurements. Our results demonstrate that the technical challenge of in vivo fluorescence lifetime macroscopic imaging is well worth surmounting to obtain quantitative, whole-animal information regarding molecular drug-target engagement.

biophysics↗

bioRxiv2022

Mapping Tree Cover Expansion in Montana, U.S.A. Rangelands using High-Resolution Historical Aerial Imagery

Worldwide, trees are colonizing rangelands with high conservation value. The introduction of trees into grasslands and shrublands causes large-scale changes in ecosystem structure and function, which have cascading impacts to ecosystem services, biodiversity, and agricultural economies. Satellites are increasingly being used to track tree cover at continental to global scales, but these methods can only provide reliable estimates of change over recent decades. Given the slow pace of tree cover expansion, remote sensing techniques that can extend this historical record provide critical insights into the magnitude of environmental change. Here, we estimate conifer expansion in rangelands of the northern Great Plains, United States, North America, using historical aerial imagery from the mid-20th century and modern aerial imagery. We analyzed 19.3 million hectares of rangelands in Montana, USA, using a convolutional neural network (U-Net architecture) and cloud computing to detect tree features and tree cover change. Our bias-corrected results estimate 3.0 {+/-} 0.2 million hectares of conifer tree cover expansion in Montana rangelands, which accounts for 15.4% of the total study area. Overall accuracy was greater than 91%, but producer accuracy was lower than user accuracy (0.60 vs. 0.88). Nonetheless, the omission errors were not spatially correlated, indicating that the method is reliable for estimating the spatial extent of tree cover expansion. Using the model results in conjunction with historical and modern imagery allows for effective communication of the scale of tree expansion while overcoming the recency effect caused by shifting environmental baselines.

ecology↗

bioRxiv2022

Regional context for balancing sagebrush- and woodland-dependent songbird needs with targeted pinyon-juniper management in the sagebrush biome

Tree expansion among historic grassland and shrubland systems is a global phenomenon, which results in dramatic influences on ecosystem processes and wildlife populations. In the western US, pinyon-juniper woodlands have expanded by as much as six-fold among sagebrush steppe landscapes since the late nineteenth century, with demonstrated negative impacts to the behavior, demography, and population dynamics of species that rely on intact sagebrush rangelands. Notably, greater sage-grouse (Centrocercus urophasianus) are unable to tolerate even low conifer cover, which can result in population declines and local extirpation. Removing expanding conifer cover has been demonstrated to increase sage grouse population growth rates and sagebrush-obligate songbird abundance. However, advances in restoring sagebrush habitats have been met with concern about unintended impacts to species that rely on conifer woodlands, notably the pinyon jay (Gymnorhinus cyanocephalus) whose population declines are distinctive among birds breeding in pinyon-juniper woodlands. We modeled indices to abundance in relation to multi-scale habitat features for nine songbirds reliant on both sagebrush and pinyon-juniper woodlands for breeding. Findings demonstrate that targeted sage grouse habitat restoration under the Sage Grouse Initiative is not at odds with protection of pinyon jay populations. Rather, conifer management has largely occurred in the northern sagebrush ecosystem where models suggest that past cuts likely benefit Brewers sparrow and sage thrasher while avoiding pinyon jay habitat. Extending our spatial modeling further south beyond the sagebrush biome could better equip conservationists with more comprehensive decision-support, particularly where pinyon jays face additional pressures of drought-induced tree mortality.

ecology↗