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PublicationEvaluating Neural Radiance Fields for 3D Plant Geometry Reconstruction in Field Conditions(Science Partner Journals, 2024-09-09)We evaluate different Neural Radiance Field (NeRF) techniques for the 3D reconstruction of plants in varied environments, from indoor settings to outdoor fields. Traditional methods usually fail to capture the complex geometric details of plants, which is crucial for phenotyping and breeding studies. We evaluate the reconstruction fidelity of NeRFs in 3 scenarios with increasing complexity and compare the results with the point cloud obtained using light detection and ranging as ground truth. In the most realistic field scenario, the NeRF models achieve a 74.6% F1 score after 30 min of training on the graphics processing unit, highlighting the efficacy of NeRFs for 3D reconstruction in challenging environments. Additionally, we propose an early stopping technique for NeRF training that almost halves the training time while achieving only a reduction of 7.4% in the average F1 score. This optimization process substantially enhances the speed and efficiency of 3D reconstruction using NeRFs. Our findings demonstrate the potential of NeRFs in detailed and realistic 3D plant reconstruction and suggest practical approaches for enhancing the speed and efficiency of NeRFs in the 3D reconstruction process.
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PublicationAn Undergraduate Course in CRISPR/Cas9-Mediated Gene Editing in Zebrafish(Mary Ann Liebert, 2024-04-11)We have developed a one-credit, semester-long research experience for undergraduate students that involves the use of CRISPR/Cas9 to edit genes in zebrafish. The course is available to students at all stages of their undergraduate training and can be taken up to four times. Students select a gene of interest to edit as the basis of their semester-long project. To select a gene, exploration of developmental processes and human disease is encouraged. As part of the course, students use basic bioinformatic tools, design guide RNAs, inject zebrafish embryos, and analyze both the molecular consequences of gene editing and phenotypic outcomes. Over the ten years we have offered the course, enrollment has grown from less than 10 students to over 60 per semester. Each year we choose a different gene editing strategy to explore based on recent publications of gene editing methodologies. These have included making CRISPants, targeted integrations, and large gene deletions. Here, we present how we structure the course and our assessment of the course over the last three years.
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PublicationAgGym: An agricultural biotic stress simulation environment for ultra-precision management planning( 2024-09-01)Agricultural production requires careful management of inputs such as fungicides, insecticides, and herbicides to ensure a successful crop that is high-yielding, profitable, and of superior seed quality. Current state-of-the-art field crop management relies on coarse-scale crop management strategies, where entire fields are sprayed with pest and disease-controlling chemicals, leading to increased cost and sub-optimal soil and crop management. To overcome these challenges and optimize crop production, we utilize machine learning tools within a virtual field environment to generate localized management plans for farmers to manage biotic threats while maximizing profits. Specifically, we present AgGym, a modular, crop and stress agnostic simulation framework to model the spread of biotic stresses in a field and estimate yield losses with and without chemical treatments. Our validation with real data shows that AgGym can be customized with limited data to simulate yield outcomes under various biotic stress conditions. We further demonstrate that deep reinforcement learning (RL) policies can be trained using AgGym for designing ultra-precise biotic stress mitigation strategies with potential to increase yield recovery with less chemicals and lower cost. Our proposed framework enables personalized decision support that can transform biotic stress management from being schedule based and reactive to opportunistic and prescriptive. We also release the AgGym software implementation as a community resource and invite experts to contribute to this open-sourced publicly available modular environment framework.
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PublicationTagging the tjp1a gene in zebrafish with mRFP using biotin homology arms(Mary Ann Liebert, 2024-04-11)Tjp1a and other tight junction and adherens proteins play important roles in cell-cell adhesion, scaffolding and forming seals between cells in epithelial and endothelial tissues. In this study, we labeled Tjp1a of zebrafish with the red fluorescent tag (mRFP) using CRISPR/Cas9-mediated targeted integration of biotin-labeled PCR generated templates. Labeling Tjp1a with RFP allowed us to follow membrane and junctional dynamics of epithelial and endothelial cells throughout zebrafish embryo development. For targeted integration, we used short 35 bp homology arms on each side of the Cas9 genomic target site at the C-terminal of the coding sequence in tjp1a. Through PCR using 5’ biotinylated primers containing the homology arms, we generated a double-stranded template for homology directed repair containing a flexible linker followed by RFP. Cas9 protein was complexed with the tjp1a gRNA prior to mixing with the repair template and microinjected into one-cell zebrafish embryos. We confirmed and recovered a precise integration allele at the desired site at the tjp1a C-terminus. Examination of fluorescence reveals RFP cell-cell junctional labeling using confocal imaging. We are currently using this stable tjp1a-mRFPis86 line to examine the behavior and interactions between cells during vascular formation in zebrafish.
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PublicationOne-Step Spark Plasma Erosion Processing of Carbon-Coated Sn-Si Nanoparticles for Lithium-Ion Battery Anodes(Multidisciplinary Digital Publishing Institute, 2024-09-10)High density portable energy storage is desirable owing to the energy requirements of portable electronics and electric vehicles. The Li-ion battery’s high energy density could be even further improved through the utilization of alternative materials (instead of carbon) for the anode, such as Sn or Si. Nonetheless, the large volume expansion upon lithiation, up to ~300% for Li22Si5, causes pulverization and rapid capacity degradation during cycling. Sn also forms a Li22Sn5 compound with the equivalent stoichiometric Li capacity but with enhanced ductility. Nano-sized Si and Sn have demonstrated distinctive nanoscale properties, facilitating the retention of higher capacities, particularly when coated with carbon, which improves mechanical stability. To date, the methods of synthesizing coated Si, Sn, or Si-Sn alloyed nanoparticles are complicated, costly, and not readily scalable to meet the demands of cost-effective manufacturing. Spark plasma erosion in a hydrocarbon dielectric has been explored as a one-step process to produce Sn-Si alloy nanoparticles coated with a thin carbon film, offering a scalable and cost-effective processing route. The resulting Sn-Si particles exhibited a bi-modal size distribution at ~5 nm and ~500 nm and were carbon-coated, as intended, from the hydrocarbon dielectric breakdown. The spark-eroded nanoparticles were thoroughly characterized using TEM/EDS, XPS, AES, SSNMR, and TGA, and their improved electrochemical performance was assessed through half-cell experiments.