Vertically Aligned Nanocomposites in Magnetic Thin Films

With the advent of ferromagnetic materials for magnetic memory among other applications, increased attention has been given to understanding the properties of these ferromagnets. Here, a vertically aligned nanocomposite (VAN) system is examined for ferromagnetism and the tuning of its magnetic properties. Specifically, different compositions of (CoFe2O4)x : (CeO2)1-x , grown by pulsed laser deposition (PLD) are tested for varying properties. Growth of different compositions of the VANs allows for an understanding of how exactly the system is different than conventional ferromagnetic materials. This new system, utilizing a combination of two phases as opposed to the thoroughly explored single phase scheme, yields interesting results that can open the door for more ferromagnet applications

Development of a Real-Time Microchip PCR System for Portable Plant Disease Diagnosis

Rapid and accurate detection of plant pathogens in the field is crucial to prevent the proliferation of infected crops. Polymerase chain reaction (PCR) process is the most reliable and accepted method for plant pathogen diagnosis, however current conventional PCR machines are not portable and require additional post-processing steps to detect the amplified DNA (amplicon) of pathogens. Real-time PCR can directly quantify the amplicon during the DNA amplification without the need for post processing, thus more suitable for field operations, however still takes time and require large instruments that are costly and not portable. Microchip PCR systems have emerged in the past decade to miniaturize conventional PCR systems and to reduce operation time and cost. Real-time microchip PCR systems have also emerged, but unfortunately all reported portable real-time microchip PCR systems require various auxiliary instruments. Here we present a stand-alone real-time microchip PCR system composed of a PCR reaction chamber microchip with integrated thin-film heater, a compact fluorescence detector to detect amplified DNA, a microcontroller to control the entire thermocycling operation with data acquisition capability, and a battery. The entire system is 25 × 16 × 8 cm(3) in size and 843 g in weight. The disposable microchip requires only 8-µl sample volume and a single PCR run consumes 110 mAh of power. A DNA extraction protocol, notably without the use of liquid nitrogen, chemicals, and other large lab equipment, was developed for field operations. The developed real-time microchip PCR system and the DNA extraction protocol were used to successfully detect six different fungal and bacterial plant pathogens with 100% success rate to a detection limit of 5 ng/8 µl sample

Sensing & Monitoring Pollinators: From Agent-Based Modeling to Live Sensing

144 pagesThe introduction of digital technology has revolutionized agricultural systems by giving growers the ability to constantly monitor and manage their fields via comprehensive, large-scale data collection and decision support systems. While many avenues have been explored with different sensors, data management platforms, and machine learning, few works have taken a close look at incorporating pollinators into this new, growing infrastructure. With over 80\% of flowering plants requiring some form of animal pollination, the pollinator plays a key role in global agricultural food production. Pollinators in general adapt well to an evolving environment and adeptly navigate and forage by necessity. They have been shown to explore large, complex areas in search of food and resources. Of all pollinators, the honey bee is especially important with millions of colonies in the United States and contributing billions to the global economy. While the importance of honey bees has garnered it significant interest in the past, with many methods attempting to sense and track its behavior, and indirectly its effects on yield, prior works are invasive, large, or require line of sight. Other works have looked to bypass the requirement of instrumenting the pollinator itself by placing sensors such as video and acoustic devices in the environment to gather data. Although this method is limited by the number of devices deployed and area surveyed and is largely manual in data gathering and analysis, sensors placed in the environment have shown promise for gathering interesting information. In this thesis, I will propose solutions in line with both of these research directions. Adding to the tracking of managed pollinators, I will present a comprehensive foraging simulation platform that leverages an innovative flight recorder for monitoring managed pollinators. This simulation produces honey bee flight paths based on parameters found by an extensive literature search and live observation combined with modified robotic path planning algorithms. Paths are sampled by the sensor model and then processed to produce foraging activity and high-level obstacle maps. This simulation platform further provides a tool for modelling the real-life functionality of such a system and also explores sensor design tradeoffs. Adding to the tracking of pollinators by sensors in the environment, I will present two works: 1) a simulation of the feasibility of pollinator monitoring with typical agricultural robots. 2). a low-cost, portable, and user-friendly system for acoustically detecting pollinators in the field. The result of these works is a new direction for pollinator monitoring and digital agriculture in general that provides a new avenue for exploring system design in this space.2024-09-0

Comparison of fungal and bacterial genomic DNA extracted by a variety of methods with or without the use of liquid nitrogen, phenol and chloroform.

<p><i>Fusarium oxysporum</i> f. sp. <i>lycopersici</i> (FOL) and <i>Pseudomona syringae</i> pv. <i>syringae</i> (<i>Pss</i>) genomic DNA was isolated from 50 mg of wet fungal and bacterial biomass, respectively.^a</p>b<p>Modifications as described in the materials and methods (section 2.2).</p>c<p>Values are the means of three biological replicates ± SE.</p

Gel electrophoresis result to verify the portable real-time microchip PCR system.

<p>The picture shows strong bands of <i>B. glumae</i> DNA (150 ng/sample), <i>Fv</i> DNA (50 ng/sample), and <i>Pss</i> B728a DNA (75 ng/sample) amplified using the real-time PCR microchip system (sample 1 to 10). <i>Fv</i> DNA 50 ng/samples amplified using a conventional PCR machine and water were used as control (sample 11 to 13).</p

Photograph of the portable real-time microchip PCR system.

<p>(A) The portable real-time microchip PCR system controlled by an MCU and powered by a battery. The entire size is 16×28×9 cm³, and the total weight is 843 g. (B) The LCD of the MCU board displays several information about the real time PCR such as the number of cycle, current PCR step, current temperature, fluorescence intensity, the increasing amount of the present cycle’s fluorescence intensity compared to the first cycle’s fluorescence intensity, and the graph showing the trace of the fluorescence intensity of each cycle.</p

Pathogens tested with the real-time microchip PCR system.

<p>Pathogens tested with the real-time microchip PCR system.</p

Illustration of the portable real-time microchip PCR system.

<p>(A) An overview of the real-time microchip PCR system, including a PCR microchip, a fluorescence detector housing coupled to an LED and a PMT, a cooling fan to accelerate cooling, and a microcontroller unit (MCU) for thermocycle control and fluorescence signal acquisition. (B) The PCR microchip is composed of a heater layer and a reaction chamber layer bonded together. The widest line of the heater is located at the center of the chamber, and the widths gets bigger by 1.25 times from the outermost trace to the center trace, thus are 1280, 1600, 2000, and 2500 µm. The gap between the spiral heater lines is 630 µm. The diameter and depth of the circular reaction chamber is 7.8 mm and 80 µm, respectively. White dotted line in the image shows the location of the reaction chamber and the inlet/outlet. (C) Schematic of the compact fluorescence detector housing and optical components inside the housing.</p

Performance of the portable real-time microchip PCR system using different concentrations of <i>Fv</i> DNA.

<p>(A) Amplication plot of PMT voltage output over the thermocycle number. Using 300, 180, 100, 50, 12, and 5 ng/sample, the Cq was 18, 19, 20, 22, 24, and 29, respectively (enlarged graph shows the Cq). The error bar of the negative control (0 ng) is the standard deviation. (B) Correlation graph of the DNA amount and the Cq (R²>0.947).</p

Simulated temperature profile of the microchip.

<p>(A) COMSOL Multiphysics® simulation showing uniform temperature distribution in the PCR chamber region when heated to 94°C (White dotted line shows the position of the reaction chamber). (B) Temperature profile across A-A’ shows the uniformity of the temperature in the chamber region of the PCR microchip within 1°C variation when the PCR microchip is heated to 94°C.</p