Integrative Plant Science Professional Masters Projects

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    Non-invasive detection of nitrogen deficiency in Cannabis sativa using Raman spectroscopy
    Antoszewski, Graham (2023)
    Proper crop management requires rapid detection methods of abiotic and biotic stresses to ensure plant health and final product yield. Hemp (Cannabis sativa L.) is an emerging economically and environmentally sustainable crop, capable of yielding extensive biomass with low input. Nitrogen deficiency in hemp significantly reduces plant growth, affecting photosynthetic capacity and leading to a precipitous drop in overall biomass. A real-time, non- destructive detection method, such as Raman spectroscopy, is therefore critical to identify nitrogen deficiency in living hemp plant tissue for fast crop remediation. A two-part hydroponic experiment was conducted to investigate portable Raman spectroscopy as a viable hemp nitrogen deficiency detection method, and to compare the technique’s predictive ability against a hand- held SPAD chlorophyll meter. Raman scans show characteristic spectral markers indicating nitrogen deficiency corresponding to vibrational modes of carotenoids, an essential pigment for photosynthesis. Raman spectra and SPAD were used to train separate nitrogen deficiency discrimination models. Findings show a Raman-based model can consistently predict nitrogen within 4 days of deficiency treatment onset across trials, while SPAD could only differentiate nitrogen deficiency in the second trial when deficiency was more visible. Raman spectroscopy is capable of identifying nitrogen deficiency prior to visible symptoms in hemp. Implications of the research go beyond nitrogen deficiency – it bolsters the repertoire of plant stresses in which Raman spectroscopy provides non-invasive chemical information to hemp cultivators.
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    Automatic Segmentation of Crops in UAV Images
    Zheng, Yuanyuan (2023)
    Remote sensing imagery has been increasingly utilized in agricultural production due to its convenience and cost-effectiveness. However, traditional methods for crop segmentation require significant time and manual effort. Therefore, this research proposed the use of threshold segmentation and deep learning techniques to achieve automatic crop segmentation in UAV images and evaluated their performance. Specifically, this research utilized image threshold segmentation, a custom UNet network, Deeplabv3+ and segment anything model(SAM) with multiple prompts. The results showed that the Intersection over Union (IoU) for threshold segmentation was 0.58. The IoU for UNet was 0.70, and for DeepLabV3+ it was 0.76. The IoU achieved by SAM with points prompt was 0.89, demonstrating superior crop segmentation performance. However, the masks generated using SAM automatic mask generation and a bounding box with a point prompt couldn’t segment crops effectively.
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    Apply Immuno-FISH in Zea Maize
    Wen, Xin (2023)
    The process of meiosis, a fundamental mechanism in plant sexual reproduction, orchestrates the creation of germ cells with genetically diverse homologous chromosomes, primarily through the intricate event of crossing-over (CO). CO plays a pivotal role in promoting genetic variation by enabling the exchange of genetic material among chromosomes. Despite DNA Double Strand Breaks (DSBs) initiating chromosome recombination, not all DSB events culminate in COs. This study seeks to revolutionize the CO process in plants to expedite plant breeding and produce novel genotypes harboring traits unattainable through traditional methods. In pursuit of this goal, transgenic Zea mays lines have been developed, introducing a bespoke recombinant protein, Cas9:SPO11. This engineered protein is adept at guiding DSBs to precise chromosome regions during meiosis, imparting a degree of control over the recombination landscape. Our hypothesis posits that these targeted regions, under the influence of Cas9:SPO11, experience heightened recombination rates compared to their wild-type counterparts. The innovation lies in the potential to channel recombination events towards desired genomic loci, thereby creating new avenues for directed trait incorporation. The present study is poised to investigate the anticipated increase in CO events at the designated target loci in the transgenic lines when contrasted with the natural recombination pattern of wild-type maize. This investigation hinges on a multimodal approach, combining the power of Immuno-Fluorescent in situ Hybridization (Immuno-FISH) with protein immunolabeling. These techniques afford visualization of chromosome dynamics, elucidating the spatial and temporal aspects of the recombination process. The research aligns with a significant body of literature emphasizing the indispensability of CO in generating genetic diversity and facilitating adaptive evolution. Moreover, the role of DSBs as initiators of recombination events has been underscored by studies in various organisms, including model plant species. The exploration of CRISPR-Cas9 technology in the context of enhancing recombination dynamics is an emerging avenue, with diverse applications ranging from basic research to agricultural innovation. As the scope of plant breeding broadens to address contemporary challenges, such as climate resilience and nutritional enhancement, the ability to strategically modulate recombination events offers an enticing proposition. The outcomes of this study could revolutionize crop improvement strategies, allowing for the accelerated development of plant varieties with desirable traits. Ultimately, this research underscores the potential of leveraging genetic recombination mechanisms to usher in a new era of precision agriculture.
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    A Non-invasive Guide to Approximating the Ages of Historical Trees in the Northeastern Landscape
    Zier, Jenna (2023)
    Understanding the ages of trees and their historical significance has the potential to encourage the public to think critically about the resiliency of plants in the natural world. A common method for approximating the ages of trees used in public gardens is dendrochronology coring. The main issue with this technique is that it requires that the tree be cored to get this data, opening it up to diseases or pests. This process also requires professional equipment that is not accessible to the general public. As people begin to learn how to determine the age of a tree without cutting into it, they may become less likely to remove it from their home lawns. What if we could all learn how to approximate the ages of the trees around us in a simple, practical way? Children and adults could learn the same method and alter the way they think about historical trees. Trees can have their ages approximated using several different best practices including the examination of certain characteristics distinctive to old trees, as well as using a formula by the International Society of Arboriculture. By utilizing methodologies from highly respected public gardens, as well as best practices from other professionals in the field, a comprehensive public guide to aging significant trees when historical records are not present was created to promote the appreciation for legacy trees. We should all strive to gain a better perspective on the magnitude of our natural environment, but in a simple, digestible way. This guide will be shared with public gardens to try to impact the appreciation of historical trees by the public.
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    Evaluating Propagation Techniques for Cannabis Sativa L. Cultivation: A Comparitive Analysis of Soilless Methods and Aeroponic Parameters
    Weingarten, Matt (2023)
    Given the rapid growth of the industrial Cannabis sector, the necessity for a reliable source of starter plant with limited genetic variation and efficient growth is crucial to achieving reliable and successful cultivation results. This study presents a multi-faceted experiment series analyzing propagation techniques for evaluating proficiency in growth and development of Cannabis plants. The research encompasses various (1) soilless propagation methods ((i) aeroponics, (ii) horticultural foam, and (iii) rockwool) and (2) transplant timings, (3) aeroponic spray intervals, and (4) aeroponic reservoir nutrient concentrations to elucidate their impact on rooting and growth parameters amongst two cultivars. It was found that aeroponics can provide as or more effective root development and plant growth than soilless propagation substrates. Further, continuous spray intervals compared to intermittent and optimized nutrient concentrations result in better promotion of root initiation and plant growth in aeroponics. The effects of experimental treatment often depended on cultivar and sampling day. Cultivators should assess their specific genetics to pinpoint the optimal conditions for propagation. These findings offer valuable insights into how various propagation techniques and growth parameters can be tailored to enhance the cultivation process. These results hold critical implications for cultivators intending to achieve premium harvests through efficient propagule methods and optimization strategies in the competitive Cannabis industry.
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    Nowhere Else on Earth: An Interpretive Toolkit for Ex-Situ Conservation of Sri Lanka's Endemic Flora
    Lee, Mary (2023)
    In 2017, Nature Plants published the most comprehensive inventory of botanic garden living collections that has been conducted to date. The analysis found that botanic gardens worldwide house roughly 30% of all formally recognized plant species. Furthermore, the data revealed a substantial discrepancy in the ratio of plants native to temperate regions versus those native to tropical. Approximately 76% of the plant species not currently accessioned by any garden are native to tropical areas. Within this subset of tropical plants, there are substantiated concerns that endemic plants might more easily become endangered or extinct as other stressors compound with their already restricted distribution scale. Sri Lanka’s landscape is teeming with floristic species, a trait that may be the result of evolution in terrestrial solitude. As of 2020, 863 angiosperms were considered endemic to the island. Of these 863 endemics, 625 (approximately 73% of the total endemic island plants) were classified as threatened. I have fully executed the design process and interpretive planning for a conservatory display, a venture rooted in the belief that humans are primed to feel an attachment to the things we can directly experience and understand. Above retention of fact or reiteration of experience, I hope the exhibit will facilitate a chance for the lens through which they engage with local flora to become more intentional.
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    Winter Ornaments of Nature: A Sustainable Approach to Creating a Winter and Early Spring Display at Botanic Gardens
    Koh, Sean (2023)
    Botanic gardens and arboreta in the Northeast, especially those in USDA hardiness zones 3-7 experience long cold winters which can deprive them of visitorship during the colder months from late October to mid April due to their dormant landscapes. Seasonal displays, notably winter and early spring botanical displays offer great opportunities to create interest and a reason for visitors to visit botanic gardens during these colder dormant months. Information gathered from 6 botanic gardens was used to inform and develop a protocol for creating a prototype of a winter and early spring display at Cornell Botanic Gardens. This prototype and protocol serves as a model for botanic gardens as to how they can create a sustainably-developed botanical display in the winter and early spring months.
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    Breeding Safe and Climate-Resilient Lettuce (Lactuca Sativa) via Genome Editing
    Hu, Xinwen (2023)
    UV sterilization can solve the safety concern of lettuce that has been repeatedly recalled due to deadly Escherichia Coli and/or Listeria monocytogenes contamination. However, the strong UV radiation could damage lettuce development and induce senescence. It is also known that climate change will negatively impact lettuce growth and development by inducing, for example, senescence, and breeding lettuce resilient to climate change is much needed. This research project aims to address these grand challenges by using the CRISPR/CAS9 genome-editing tool. Briefly, a senescence-master regulator has been found to mediate all adverse environment (including UV radiation)-induced senescence, and knocking out the gene will render the new lettuce germplasm resistant to UV sterilization and many other adverse environmental conditions. Toward the goals, this project has used the related binary vector for knocking out the master regulator gene in lettuce and has transferred the binary vector into lettuce leaf tissues and cotyledons via agrobacterium-mediated transformation. The edited lettuce lines will most likely be resistant to strong UV sterilization (thus safer lettuce) and changing climate.
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    Arbuscular Mycorrhizae Fungi Symbiotic Relationships with Vitis vinifera Cultivar Pinot Noir
    Jones, Lloyd C. (2023)
    A field trial was conducted to evaluate the symbiotic relationship between Arbuscular Mycorrhizal Fungi (AMF) and Vitis vinifera cultivar Pinot noir with commercial inoculation. Pinot noir grapevines were planted and inoculated with MycoApply® Endo-granular in early summer, 2019. MycoApply® Endo is a granular product containing 4 species of fungi (Glomus intraradices, Glomus mossae, Glomus aggregatum, and Glomus etunicatum). The purpose was to evaluate the proposed benefits of the commercially sold fungi and differences between two rootstocks compared to the control. The experiments were conducted in the Finger Lakes AVA at Lansing, NY Cornell University vineyard. The inoculation treatments resulted in greater root length colonization by AMF, but there were no apparent benefits to the vine.