Biology subjects

Donnelly, J. P.

Publications and source records attributed to Donnelly, J. P..

5 recordsLinked to original sources

bioRxiv2026

3D Visualization and Proteomic Analysis of Human Cardiac Transthyretin Amyloidosis Tissue Reveals Microangiopathy and Capillary Occlusion

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSTransthyretin amyloidosis (ATTR) is a progressive, degenerative disease affecting the heart and other organ systems, as well as the peripheral, autonomic, and central nervous systems. Although pharmacological and genetic evidence establishes aggregation as a driver of ATTR pathology, the mechanism by which aggregation compromises post-mitotic tissue function is poorly understood. We utilized bottom-up proteomics on wild-type (WT) human cardiac (WT/WT genotype) and V122I human cardiac (V122I/WT genotype) tissue, combined with tissue clearing technology to create an optically transparent tissue architecture to visualize three-dimensional relationships, to better understand TTR cardiomyopathy (CM). MethodsFlash-frozen 0.5 mm cardiac tissue slices from human subjects with end-stage WT-TTR CM, end-stage V122I CM, and slices from an age-matched human control were used for these experiments. Fibril extraction from diseased tissue followed published protocols. Strong denaturant-mediated proteome tissue extraction on samples from each subject facilitated bottom-up proteomics by using liquid chromatography (LC)-mass spectrometry (MS)/MS. Tissue clearing was performed on 0.5 mm cardiac slices utilizing a lauryl sulfate-based lipid removal strategy. Slices were stained using indirect immunofluorescence with antibodies to protein targets identified by proteomics. We used an antibody to non-native TTR and AmyTracker 480 (an oligothiophene dye that binds to amyloid fibrils) to image TTR deposits. ATTR fibrils were characterized structurally using cryogenic electron microscopy (cryo-EM) followed by helical reconstruction. ResultsProteomic cardiac analysis afforded high spectral counts for transthyretin (TTR) and proteins typically associated with amyloid fibrils, e.g. serum amyloid P (APCS). Fibril and cardiac homogenate proteomics revealed high levels of angiogenic and hemostatic proteins, including those composing the complement and coagulation cascades. 3D imaging revealed loss of normal microvascular architecture in CM samples with regions of hyper- and hypovascularization. Microvascular obstruction by capillary thrombosis was also observed in CM. ATTR fibrils adopted the common spearhead fold and were decorated with collagen VI (COLVI), an extracellular matrix component. ConclusionsWe hypothesize that ATTR CM is a microangiopathy driven by capillary bed thrombo-inflammation and dysregulated angiogenic revascularization. Phenotypic convergence of WT ATTR CM and V122I ATTR CM was observed via proteomics, 3D imaging, and ex vivo fibril characterization by cryo-EM. We provide evidence of capillary thrombosis in ex vivo ATTR CM tissue. Vasodilation and increased capillary permeability expose components of the vascular basement membrane (VBM) to misfolded TTR. These components are known to promote TTR aggregation and stabilize amyloid fibrils in the extracellular space. Congestion of the VBM prevents appropriate revascularization, reducing cardiac exertional capacity over time, leading to heart failure. Our ATTR CM heart tissue proteomics data shows significant overlap with the proteomic profiles of human AD brain tissues, revealing key amyloid, coagulation, complement, and angiogenesis proteins being changed in amyloidoses.

pathology↗

bioRxiv2025

Helical Reconstruction of Amyloids in cryoSPARC

Amyloid-mediated proteotoxicity underlies more than 50 human diseases. Cryo-electron microscopy (cryo-EM) analyses have yielded hundreds of in vitro and patient-derived amyloid structures, establishing direct links between filament morphologies and specific pathological conditions. Despite the growing popularity of the processing software cryoSPARC for single-particle analyses, RELION remains the dominant software platform for performing helical reconstruction of amyloid structures, highlighting an area for further development. Here, we present comprehensive processing guidelines for helical reconstruction of helical amyloids using cryoSPARC. Through systematic re-processing and validation of publicly deposited datasets, we demonstrate current capabilities and identify key limitations, emphasizing the need for amyloid-specific parameter optimization within cryoSPARC workflows. Our findings showcase a potential for developing unsupervised processing workflows to meet the demanding throughput requirements of time-resolved in vitro studies and largescale compound screening initiatives, thereby accelerating therapeutic drug development. Ultimately, our goal is to shift the focus of amyloid cryo-EM from computationally intensive processing challenges toward addressing fundamental biological questions that enhance our capacity for treatment discovery. O_FIG O_LINKSMALLFIG WIDTH=110 HEIGHT=200 SRC="FIGDIR/small/680389v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1f2e9fcorg.highwire.dtl.DTLVardef@dfb6f5org.highwire.dtl.DTLVardef@164a2c3org.highwire.dtl.DTLVardef@1f9c570_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Beneficial 'inefficiencies' of western ranching: Flood-irrigated hay production sustains wetland systems by mimicking historic hydrologic processes

Ranching in the American West has long relied on riparian ecosystems to grow grass-hay to feed livestock in winter and during drought. Producers seasonally flood grasslands for hay production using stream diversions and low-tech flood-irrigation on riparian floodplains. Inundation mimics natural processes that sustain riparian vegetation and recharge groundwater. The recent doubling in use of more efficient irrigation approaches, such as center-pivot sprinklers, threatens to accelerate climate change impacts by unintentionally decoupling more inefficient, traditional practices that sustain riparian systems. To address this information gap, we developed an exhaustive spatial inventory of grass-hay production and combined it with monthly surface water distributions modeled from satellite data. Surface water data were classified by wetland hydroperiod and used to estimate the proportion of wetlands supported by grass-hay production in the Intermountain West, USA. Elevation and proportion of grass-hay relative to other irrigated lands were enumerated to examine differences in their positions and abundance within landscapes. Lastly, we overlaid the delineated grass-hay wetlands with LANDFIRE pre-Euro-American Settings layer to quantify the efficacy of flood irrigation in mimicking the conservation of historical riparian processes. Findings suggest that inefficient grass-hay irrigation mirrored the timing of natural hydrology, concentrating [~]93% of flooded grasslands in historical riparian ecosystems, affirming that at large scales, this ranching practice, in part, mimics floodplain processes sustaining wetlands and groundwater recharge. Despite representing only 2.5% of irrigated lands, grass-hay operations supported a majority (58%)of temporary wetlands, a rare and declining habitat for wildlife in the Intermountain West. Tolerance for colder temperatures confined grass-hay production to upper watershed reaches where higher value crops are constrained by growing degree days. This novel understanding of grass-hay agroecology highlights the vital role of working ranches in the resilience and stewardship of riparian systems.

ecology↗

bioRxiv2023

Flood-irrigated agriculture mediates climate-induced wetland scarcity for summering sandhill cranes in western North America

Documenting a species extent is often the first step in understanding its ecology and is critical to informing conservation planning. Basic information about species distributions is lacking in many regions of the world, forcing natural resource managers to answer complex ecological questions with incomplete data. Information gaps are compounded by climate change, driving resource bottlenecks that can act as new and powerful demographic constraints on fauna. Here, we reconstructed greater sandhill crane (Antigone canadensis tabida) summering range in western North America using movement data from 120 GPS-tagged individuals to determine how landscape composition shaped their distributions. Landscape variables developed from remotely sensed data were combined with bird locations using cloud computing and machine learning to model distribution probabilities. Additionally, land-use practices and land ownership were summarized within summer range as a measure of use dependence. Wetland variables identified as important predictors of bird distributions were also evaluated in a post hoc analysis using satellite imagery to measure the long-term (1984-2022) effects of climate-driven surface water drying. Wetlands and associated agricultural practices accounted for 1.2% of the summer range but were key predictors of greater sandhill crane occurrence. Bird distributions were patterned primarily by riparian floodplains that concentrated water, wetlands, and flood-irrigated agriculture in otherwise arid and semi-arid landscapes. Findings highlighted the critical role of private lands in greater sandhill crane ecology as they accounted for 78% of predicted distributions. Wetland drying observed in portions of the range from 1984 to 2022 represented an emerging ecological bottleneck that could limit future greater sandhill crane summer range. Study outcomes provide novel insight into the significance of ecosystem services provided by flood-irrigated agriculture that supported nearly 60% of the wetland resources used by birds. Findings suggest greater sandhill cranes function as an umbrella species for agroecology and climate change adaptation strategies seeking to reduce agricultural water use through improved efficiency while also maintaining distinct flood-irrigation practices supporting greater sandhill cranes and other wetland-dependent wildlife. To inform conservation design, we make our wetland and sandhill crane summering distributions publicly available as interactive web-based mapping tools.

systems biology↗

bioRxiv2022

Functional wetland loss drives emerging risks to waterbird migration networks

Migratory waterbirds (i.e., shorebirds, wading birds, and waterfowl) rely on a diffuse continental network of wetland habitats to support annual life cycle needs. Emerging threats of climate and land-use change raise new concerns over the sustainability of these habitat networks as water scarcity triggers cascading ecological effects impacting wetland habitat availability. Here we use important waterbird regions in Oregon and California, USA, as a model system to examine patterns of landscape change impacting wetland habitat networks in western North America. Wetland hydrology and flooded agricultural habitats were monitored monthly from 1988 to 2020 using satellite imagery to quantify the timing and duration of inundation--a key delimiter of habitat niche values associated with waterbird use. Trends were binned by management practice and wetland hydroperiods (semi-permanent, seasonal, and temporary) to identify differences in their climate and land-use change sensitivity. Wetland results were assessed using 33 waterbird species to detect nonlinear effects of network change across a diversity of life cycle and habitat needs. Pervasive loss of semi-permanent wetlands was an indicator of systemic functional decline. Shortened hydroperiods caused by excessive drying transitioned semi-permanent wetlands to seasonal and temporary hydrologies--a process that in part counterbalanced concurrent seasonal and temporary wetland losses. Expansion of seasonal and temporary wetlands associated with closed-basin lakes offset wetland declines on other public and private lands, including wildlife refuges. Diving ducks, black terns, and grebes exhibited the most significant risk of habitat decline due to semi-permanent wetland loss that overlapped important migration, breeding, molting, and wintering periods. Shorebirds and dabbling ducks were beneficiaries of stable agricultural practices and top-down processes of functional wetland declines that operated collectively to maintain habitat needs. Outcomes from this work provide a novel perspective of wetland ecosystem change affecting waterbirds and their migration networks. Understanding the complexity of these relationships will become increasingly important as water scarcity continues to restructure the timing and availability of wetland resources.

ecology↗