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McElrone, Andrew J.

Publications and source records attributed to McElrone, Andrew J..

8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Red Wine Fermentation Alters Grape Seed Morphology and Internal Porosity

During wine fermentation, grape berry components, including seeds, undergo extensive physical and chemical changes that result in the release of flavonoids, such as tannins, from seeds into wine. Understanding changes in seed morphology during fermentation is crucial for aiding the development of accurate prediction models for flavonoid extraction during winemaking, which enhances fermentation management and ensures consistency in wines from year to year. High-resolution x-ray microcomputed tomography (x-ray μCT) was used to investigate the effect of red wine fermentation on changes in grape seed morphology. Using a PyTorch-based implementation of a fully convolutional network with a Resnet-101 backbone for semantic segmentation of x-ray μCT images, we quantified extensive alteration to grape seed structure during fermentation. Image analyses revealed the development of a pore network breaking apart the seed endosperm by the end of fermentation, leading to an increase in surface area. Fermentation significantly altered grape seed morphology. Such alterations could enable transport of seed flavonoids from inside the endosperm and integument to outside the seed. Further research on the physical processes occurring in seeds during wine fermentation is necessary to build better physiochemical models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Anatomy of an agricultural antagonist: Feeding complex structure and function of three xylem sap‐feeding insects illuminated with synchrotron‐based 3D imaging

Abstract Many insects feed on xylem or phloem sap of vascular plants. Although physical damage to the plant is minimal, the process of insect feeding can transmit lethal viruses and bacterial pathogens. Disparities between insect‐mediated pathogen transmission efficiency have been identified among xylem sap‐feeding insects; however, the mechanistic drivers of these trends are unclear. Identifying and understanding the structural factors and associated integrated functional components that may ultimately determine these disparities are critical for managing plant diseases. Here, we applied synchrotron‐based X‐ray microcomputed tomography to digitally reconstruct the morphology of three xylem sap‐feeding insect vectors of plant pathogens: Graphocephala atropunctata (blue‐green sharpshooter; Hemiptera, Cicadellidae) and Homalodisca vitripennis (glassy‐winged sharpshooter; Hemiptera, Cicadellidae), and the spittlebug Philaenus spumarius (meadow spittlebug; Hemiptera, Aphrophoridae). The application of this technique revealed previously undescribed anatomical features of these organisms, such as key components of the salivary complex. The visualization of the 3D structure of the precibarial valve led to new insights into the mechanism of how this structure functions. Morphological disparities with functional implications between taxa were highlighted as well, including the morphology and volume of the cibarial dilator musculature responsible for extracting xylem sap, which has implications for force application capabilities. These morphological insights will be used to target analyses illuminating functional differences in feeding behavior.

3D imaging↗
DOE OSTI2022

A workflow for segmenting soil and plant X-ray computed tomography images with deep learning in Google’s Colaboratory

X-ray micro-computed tomography (X-ray μCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray μCT images, using low-cost resources in Google’s Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Maximum CO 2 diffusion inside leaves is limited by the scaling of cell size and genome size

Maintaining high rates of photosynthesis in leaves requires efficient movement of CO 2 from the atmosphere to the mesophyll cells inside the leaf where CO 2 is converted into sugar. CO 2 diffusion inside the leaf depends directly on the structure of the mesophyll cells and their surrounding airspace, which have been difficult to characterize because of their inherently three-dimensional organization. Yet faster CO 2 diffusion inside the leaf was probably critical in elevating rates of photosynthesis that occurred among angiosperm lineages. Here we characterize the three-dimensional surface area of the leaf mesophyll across vascular plants. We show that genome size determines the sizes and packing densities of cells in all leaf tissues and that smaller cells enable more mesophyll surface area to be packed into the leaf volume, facilitating higher CO 2 diffusion. Measurements and modelling revealed that the spongy mesophyll layer better facilitates gaseous phase diffusion while the palisade mesophyll layer better facilitates liquid-phase diffusion. Our results demonstrate that genome downsizing among the angiosperms was critical to restructuring the entire pathway of CO 2 diffusion into and through the leaf, maintaining high rates of CO 2 supply to the leaf mesophyll despite declining atmospheric CO 2 levels during the Cretaceous.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Xylem network connectivity and embolism spread in grapevine( Vitis vinifera L.)

Abstract Xylem networks are vulnerable to the formation and spread of gas embolisms that reduce water transport. Embolisms spread through interconduit pits, but the three-dimensional (3D) complexity and scale of xylem networks means that the functional implications of intervessel connections are not well understood. Here, xylem networks of grapevine (Vitis vinifera L.) were reconstructed from 3D high-resolution X-ray micro-computed tomography (microCT) images. Xylem network performance was then modeled to simulate loss of hydraulic conductivity under increasingly negative xylem sap pressure simulating drought stress conditions. We also considered the sensitivity of xylem network performance to changes in key network parameters. We found that the mean pit area per intervessel connection was constant across 10 networks from three, 1.5-m stem segments, but short (0.5 cm) segments fail to capture complete network connectivity. Simulations showed that network organization imparted additional resistance to embolism spread beyond the air-seeding threshold of pit membranes. Xylem network vulnerability to embolism spread was most sensitive to variation in the number and location of vessels that were initially embolized and pit membrane vulnerability. Our results show that xylem network organization can increase stem resistance to embolism spread by 40% (0.66 MPa) and challenge the notion that a single embolism can spread rapidly throughout an entire xylem network.

Wason, Jay↗
DOE OSTI2020

Xylella fastidiosa causes transcriptional shifts that precede tylose formation and starch depletion in xylem

Abstract Pierce's disease (PD) in grapevine ( Vitis vinifera ) is caused by the bacterial pathogen Xylella fastidiosa . X. fastidiosa is limited to the xylem tissue and following infection induces extensive plant‐derived xylem blockages, primarily in the form of tyloses. Tylose‐mediated vessel occlusions are a hallmark of PD, particularly in susceptible V. vinifera . We temporally monitored tylose development over the course of the disease to link symptom severity to the level of tylose occlusion and the presence/absence of the bacterial pathogen at fine‐scale resolution. The majority of vessels containing tyloses were devoid of bacterial cells, indicating that direct, localized perception of X. fastidiosa was not a primary cause of tylose formation. In addition, we used X‐ray computed microtomography and machine‐learning to determine that X. fastidiosa induces significant starch depletion in xylem ray parenchyma cells. This suggests that a signalling mechanism emanating from the vessels colonized by bacteria enables a systemic response to X. fastidiosa infection. To understand the transcriptional changes underlying these phenotypes, we integrated global transcriptomics into the phenotypes we tracked over the disease spectrum. Differential gene expression analysis revealed that considerable transcriptomic reprogramming occurred during early PD before symptom appearance. Specifically, we determined that many genes associated with tylose formation (ethylene signalling and cell wall biogenesis) and drought stress were up‐regulated during both Phase I and Phase II of PD. On the contrary, several genes related to photosynthesis and carbon fixation were down‐regulated during both phases. These responses correlate with significant starch depletion observed in ray cells and tylose synthesis in vessels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Anatomical and hydraulic responses to desiccation in emergent conifer seedlings

Premise The young seedling life stage is critical for reforestation after disturbance and for species migration under climate change, yet little is known regarding their basic hydraulic function or vulnerability to drought. Here, we sought to characterize responses to desiccation including hydraulic vulnerability, xylem anatomical traits, and impacts on other stem tissues that contribute to hydraulic functioning. Methods Larix occidentalis , Pseudotsuga menziesii , and Pinus ponderosa (all ≤6 weeks old) were imaged using x‐ray computed microtomography during desiccation to assess seedling biomechanical responses with concurrently measured hydraulic conductivity ( k s ) and water potential ( Ψ ) to assess vulnerability to xylem embolism formation and other tissue damage. Results In non‐stressed samples for all species, pith and cortical cells appeared circular and well hydrated, but they started to empty and deform with decreasing Ψ which resulted in cell tearing and eventual collapse. Despite the severity of this structural damage, the vascular cambium remained well hydrated even under the most severe drought. There were significant differences among species in vulnerability to xylem embolism formation, with 78% xylem embolism in L. occidentalis by Ψ of −2.1 MPa, but only 47.7% and 62.1% in P. ponderosa and P. menziesii at −4.27 and −6.73 MPa, respectively. Conclusions Larix occidentalis seedlings appeared to be more susceptible to secondary xylem embolism compared to the other two species, but all three maintained hydration of the vascular cambium under severe stress, which could facilitate hydraulic recovery by regrowth of xylem when stress is relieved.

Miller, Megan L.↗