Bioresource and Agricultural Engineering Commons^™

Robotic Technologies For High-Throughput Plant Phenotyping: Contemporary Reviews And Future Perspectives, Abbas Atefi, Yufeng Ge, Santosh Pitla, James Schnable

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Phenotyping plants is an essential component of any effort to develop new crop varieties. As plant breeders seek to increase crop productivity and produce more food for the future, the amount of phenotype information they require will also increase. Traditional plant phenotyping relying on manual measurement is laborious, time-consuming, error-prone, and costly. Plant phenotyping robots have emerged as a high-throughput technology to measure morphological, chemical and physiological properties of large number of plants. Several robotic systems have been developed to fulfill different phenotyping missions. In particular, robotic phenotyping has the potential to enable efficient monitoring of changes in plant traits …

Comparison Of Promoter, Dna Vector, And Cationic Carrier For Efficient Transfection Of Hmscs From Multiple Donors And Tissue Sources, Tyler Kozisek, Andrew Hamann, Luke Samuelson, Miguel Fudolig, Angela K. Pannier

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Human mesenchymal stem cells (hMSCs) are primary cells with high clinical relevance that could be enhanced through genetic modification. However, gene delivery, particularly through nonviral routes, is inefficient. To address the shortcomings of nonviral gene delivery to hMSCs, our lab has previously demonstrated that pharmacological “priming” of hMSCs with clinically approved drugs can increase transfection in hMSCs by modulating transfection-induced cytotoxicity. However, even with priming, hMSC transfection remains inefficient for clinical applications. This work takes a complementary approach to addressing the challenges of transfecting hMSCs by systematically investigating key transfection parameters for their effect on transgene expression. Specifically, we investigated …

Modeling Vadose Zone Hydrology [Lecture Notes], Derek M. Heeren, Dean E. Eisenhauer

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Modeling Vadose Zone Hydrology is a graduate-level course offered biennially in the Department of Biological Systems Engineering. Topics included hydraulic properties of porous media, application of Darcy's Law in variably saturated media, hydrologic and transport processes in the vadose zone, and solution of steady and unsteady flow problems using numerical techniques. A graphical approach for characterizing vertical one-dimensional problems with energy head profiles was emphasized. Common one-dimensional flow and transport problems were solved analytically. The course was taught using a combination of lecture notes and PowerPoint presentations. The lecture notes from 2021, captured using the Microsoft Whiteboard app with a …

Uavs For Vegetation Monitoring: Overview And Recent Scientific Contributions, Ana I. De Castro, Yeyin Shi, Joe Mari Maja, Jose M. Peña

Department of Agricultural and Biological Systems Engineering: Faculty Publications

This paper reviewed a set of twenty-one original and innovative papers included in a special issue on UAVs for vegetation monitoring, which proposed new methods and techniques applied to diverse agricultural and forestry scenarios. Three general categories were considered: (1) sensors and vegetation indices used, (2) technological goals pursued, and (3) agroforestry applications. Some investigations focused on issues related to UAV flight operations, spatial resolution requirements, and computation and data analytics, while others studied the ability of UAVs for characterizing relevant vegetation features (mainly canopy cover and crop height) or for detecting different plant/crop stressors, such as nutrient content/deficiencies, water …

Early Detection Of Encroaching Woody Juniperus Virginiana And Its Classification In Multi-Species Forest Using Uas Imagery And Semantic Segmentation Algorithms, Lin Wang, Yuzhen Zhou, Qiao Hu, Zhenghong Tang, Yufeng Ge, Adam Smith, Tala Awada, Yeyin Shi

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Woody plant encroachment into grasslands ecosystems causes significantly ecological destruction and economic losses. Effective and efficient management largely benefits from accurate and timely detection of encroaching species at an early development stage. Recent advances in unmanned aircraft systems (UAS) enabled easier access to ultra-high spatial resolution images at a centimeter level, together with the latest machine learning based image segmentation algorithms, making it possible to detect small-sized individuals of target species at early development stage and identify them when mixed with other species. However, few studies have investigated the optimal practical spatial resolution of early encroaching species detection. Hence, we …

Exploration Of The Sludge Biodiesel Pathway, Zachary Christman

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Wastewater sludge is an overlooked source of fat, oil, and grease (FOG) that could be converted into biodiesel. The United States produces about 8 million tons of sludge per year. The disposal cost for this amount of sludge is about 2 billion US dollars. The widespread availability and low cost of sludge compared to other biodiesel raw materials make it an economical choice for a renewable fuel. Using sludge as a raw material can produce 25 to 30 mg per gram of fatty acid methyl ester (FAME); the main component of biodiesel. Sludge biodiesel has the potential of transforming a …

Sensor-Based Nitrogen Management On Non-Irrigated Corn Based Systems In Nebraska, Samantha L. Teten

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Optimizing nitrogen (N) fertilizer applications in corn to reduce environmental impacts while maintaining producer profitability remains a challenge due to spatial and temporal variability in crop yield potential and soil N dynamics. In response to these challenges, active crop canopy sensors and imagery systems have been studied to test the performance of vegetative index-based N management, but adoption has been low. There is also a lack of field-scale research evaluating this technology in water-limiting environments.

The evaluation of two sensor-based N management techniques was completed at nine non-irrigated sites in Eastern Nebraska. The first sensor-based N management technique evaluated an …

Control System For Variable-Orifice Mechatronic Spray Nozzle For Regulation Of Application Rate And Droplet Size Spectra, Rodney Rohrer

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Traditional fixed-orifice spray nozzles are selected for flow rate and droplet spectra required for a given pesticide application. Although limited variation in flow can be achieved by adjusting system pressure, this can adversely affect spray quality. Other nozzle configurations, such as Pulse Width Modulated (PWM) nozzles or passive variable-orifice designs, are intended to maintain consistent droplet size and spray pattern as flow rate is changed but those too have limitations.

A variable-orifice nozzle modified by Luck (2012) can span multiple droplet spectra and offers independent control of flow and droplet size; however, an advanced control system must be developed to …

Challenges And Opportunities In Precision Irrigation Decision-Support Systems For Center Pivots, Jingwen Zhang, Kaiyu Guan, Bin Peng, Chongya Jiang, Wang Zhou, Yi Yang, Ming Pan, Trenton Franz, Derek M. Heeren, Daran R. Rudnick, Olufemi P. Abimbola, Hyungsuk Kimm, Kelly Caylor, Stephen Good, Madhu Khanna, John Gates, Yaping Cai

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Irrigation is critical to sustain agricultural productivity in dry or semi-dry environments, and center pivots, due to their versatility and ruggedness, are the most widely used irrigation systems. To effectively use center pivot irrigation systems, producers require tools to support their decision-making on when and how much water to irrigate. However, currently producers make these decisions primarily based on experience and/or limited information of weather. Ineffective use of irrigation systems can lead to overuse of water resources, compromise crop productivity, and directly reduce producers’ economic return as well as bring negative impacts on environmental sustainability. In this paper, we surveyed …

Preclinical Development Of Single Walled Carbon Nanotube-Based Optical Biosensors, Eric M. Hofferber

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

High resolution, long-term monitoring of key biological analytes would improve patient outcomes by providing earlier detection of disease states and improved efficacy of treatment. One class of biosensors that have gained much attention in recent years are optical biosensors. Optical probes are attractive biosensors due to their noninvasive nature of detection, as certain light can pass through tissue, water, and blood. Single walled carbon nanotubes (SWNT) are a specific type of optical biosensor that fluoresce in the near infrared range of the electromagnetic spectrum and offer unparalleled spatial and temporal resolution. SWNT have been applied as biosensors in vitro, …

Evaluating Evapotranspiration Values In Rwanda Using The Fao-56 Pm, Turc, And Hargreaves-Samani Equations, Elizabeth Uwase

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Evapotranspiration (ET) is an important component of the hydrologic cycle and involves exchange of water between the surrounding water bodies, soil, crop surfaces, and the atmosphere. Therefore, this research was aimed at determining ET and its trend across Rwanda using climatic data measured at five sites. Equations were used to calculate ET using extra-terrestrial radiations, solar radiations, evapotranspiration using the FAO-56 guidelines - Turc method (1961) and Hargreaves-Samani (HS) method (1983). The obtained data from the weather stations were analyzed using the two methods and graphs were plotted for visualization. The average monthly reference evapotranspiration for both equations ranges from …

Utilizing Digital Image Processing And Two‑Source Energy Balance Model For The Estimation Of Evapotranspiration Of Dry Edible Beans In Western Nebraska, Wei‑Zhen Liang, Isabella Possignolo, Xin Qiao, Kendall Dejonge, Suat Irkmak, Derek M. Heeren, Daran Rudnick

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Having an accurate yet simple method to estimate crop evapotranspiration ( ET_C) is a vital component of reliable irrigation scheduling. In this study, two versions of the two-source energy balance (TSEB) model: the TSEB model with the Priestley–Taylor equation (TSEB-PT) and the Penman–Monteith equation (TSEB-PM), were used to estimate ET_C of dry edible beans in western Nebraska. Compared with previous studies, this study is unique in that a Visual Basic software—Crop Canopy Image Analyzer (CCIA) was developed to process digitally captured RGB canopy images to obtain necessary canopy cover (CC) parameters for the TSEB models such as …

Unconventional Agriculture: An Exploration Of Hydroponics And Aquaponics And Their Role As A Solution To Food Scarcity, Kai Meacham

Honors Program: Senior Projects (Public)

Unconventional agriculture includes methods of farming that are defined by unique farming practices and a focus on sustainability. Unconventional agriculture can take many forms, including hydroponic systems and aquaponic systems. These two systems are unique in the sense that they are soilless methods of growing plants. Both of these systems require careful monitoring because they do not have soil to act as a buffer and help maintain normal levels. Though these two systems are very similar they have some key differences in how they function, which ultimately leads to differing advantages and disadvantages of both systems. Additionally, these systems have …

Comparative Study Of Human Pluripotent Stem Cell-Derived Endothelial Cells In Hydrogel-Based Culture Systems, Zhanqi Wang, Fuxing Zuo, Qing Liu, Xuesheng Wu, Qian Du, Yuguo Lei, Zhangmin Wu, Haishuang Lin

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Human pluripotent stem cell (hPSC)-derived endothelial cells (ECs) are promising cell sources for drug discovery, tissue engineering, and studying or treating vascular diseases. However, hPSC-ECs derived from different culture methods display different phenotypes. Herein, we made a detailed comparative study of hPSC-ECs from three different culture systems (e.g., 2D, 3D PNIPAAm-PEG hydrogel, and 3D alginate hydrogel cultures) based on our previous reports. We expanded hPSCs and differentiated them into ECs in three culture systems. Both 3D hydrogel systems could mimic an in vivo physiologically relevant microenvironment to protect cells from shear force and prevent cell agglomeration, leading to a high …

Development Of An Internet Of Things (Iot) Enabled Novel Wireless Multi Sensor Network For Infield Crop Monitoring, Nipuna Chamara

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Multispectral imaging systems on satellite, aerial, and ground platforms are used commonly to monitor in-field crops in precision agriculture by farmers and researchers. Limited spatial and temporal resolution and weather dependence of the data collection are two main disadvantages of these methods. In-field sensor networks can continuously monitor environmental and plant physiological parameters by leveraging low-power computation and long-range communication technologies. We built and tested a novel sensor network equipped with soil moisture, multispectral and RGB imaging sensors in an experimental soybean field at Eastern Nebraska Research and Extension Center, NE, USA. 10 down-looking and 1 up-looking sensor node were …

Determination Of Vadose Zone And Saturated Zone Nitrate Lag Times Using Long-Term Groundwater Monitoring Data And Statistical Machine Learning, Martin J. Wells, Troy E. Gilmore, Natalie Nelson, John K. Bohlke

Department of Agricultural and Biological Systems Engineering: Faculty Publications

In this study, we explored the use of statistical machine learning and long-term groundwater nitrate monitoring data to estimate vadose zone and saturated zone lag times in an irrigated alluvial agricultural setting. Unlike most previous statistical machine learning studies that sought to predict groundwater nitrate concentrations within aquifers, the focus of this study was to leverage available groundwater nitrate concentrations and other environmental variables to determine mean regional vertical velocities (transport rates) of water and solutes in the vadose zone and saturated zone (3.50 and 3.75 m yr−1 , respectively). The statistical machine learning results are consistent with two primary …

Role Of Nadþ In Regulating Cellular And Metabolic Signaling Pathways, Sara Amjad, Sabah Nisar, Ajaz A. Bhat, Ab Rauf Shah, Michael P. Frenneaux, Khalid Fakhro, Mohammad Haris, Ravinder Reddy, Zoltan Patay, Joseph Baur, Puneet Bagga

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Background: Nicotinamide adenine dinucleotide (NAD⁺), a critical coenzyme present in every living cell, is involved in a myriad of metabolic processes associated with cellular bioenergetics. For this reason, NAD⁺ is often studied in the context of aging, cancer, and neurodegenerative and metabolic disorders.

Scope of review: Cellular NAD⁺ depletion is associated with compromised adaptive cellular stress responses, impaired neuronal plasticity, impaired DNA repair, and cellular senescence. Increasing evidence has shown the efficacy of boosting NAD⁺ levels using NAD⁺ precursors in various diseases. This review provides a comprehensive understanding into the role of NAD^{+ …}

Historical Contingency In Microbial Resilience To Hydrologic Perturbations, Hyun-Seob Song, James C. Stegen, Emily B. Graham, Timothy D. Scheibe

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Development of reliable biogeochemical models requires a mechanistic consideration of microbial interactions with hydrology. Microbial response to and its recovery after hydrologic perturbations (i.e., resilience) is a critical component to understand in this regard, but generally difficult to predict because the impacts of future events can be dependent on the history of perturbations (i.e., historical contingency). Fundamental issues underlying this phenomenon include how microbial resilience to hydrologic perturbations is influenced by historical contingency and how their relationships vary depending on the characteristics of microbial functions. To answer these questions, we considered a simple microbial community composed of two species that …

Common Unit Conversions For Irrigation, Dean E. Eisenhauer, Derrel L. Martin, Derek M. Heeren, Glenn J. Hoffman

Open Learning Resources, General/Selected

A fact sheet that includes common unit conversions for irrigation in international system of units (SI) and United States customary system of units (USCS).

Includes units for: length, area, volume, flow, weight and mass, pressure, crop yield, temperature, and the United States public land survey system.

Quantification Of Nitric Oxide Concentration Using Single-Walled Carbon Nanotube Sensors, Jakob Meier, Joseph Stapleton, Eric M. Hofferber, Abigail Haworth, Stephen D. Kachman, Nicole M. Iverson

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Nitric oxide (NO), a free radical present in biological systems, can have many detrimental effects on the body, from inflammation to cancer. Due to NO’s short half-life, detection and quan- tification is difficult. The inability to quantify NO has hindered researchers’ understanding of its impact in healthy and diseased conditions. Single-walled carbon nanotubes (SWNTs), when wrapped in a specific single-stranded DNA chain, becomes selective to NO, creating a fluorescence sensor. Unfortunately, the correlation between NO concentration and the SWNT’s fluorescence intensity has been difficult to determine due to an inability to immobilize the sensor without altering its properties. Through the …

Modeling And Prioritizing Interventions Using Pollution Hotspots For Reducing Nutrients, Atrazine And E. Coli Concentrations In A Watershed, Olufemi P. Abimbola, Aaron R. Mittelstet, Tiffany Messer, Elaine Berry, Anna Van Griensven

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Excess nutrients and herbicides remain two major causes of waterbody impairment globally. In an attempt to better understand pollutant sources in the Big Sandy Creek Watershed (BSCW) and the prospects for successful remediation, a program was initiated to assist agricultural producers with the implementation of best management practices (BMPs). The objectives were to (1) simulate BMPs within hotspots to determine reductions in pollutant loads and (2) to determine if water-quality standards are met at the watershed outlet. Regression-based load estimator (LOADEST) was used for determining sediment, nutrient and atrazine loads, while artificial neural networks (ANN) were used for determining E. …

Antibiotic Resistance Genes In Swine Manure Slurry As Affected By Pit Additives And Facility Disinfectants, Maria C. Hall, Jon Duerschner, John E. Gilley, Amy Schmidt, Shannon Bartelt-Hunt, Daniel D. Snow, Kent M. Eskridge, Xu Li

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Manure storage facilities are critical control points to reduce antibiotic resistance genes (ARGs) in swine manure slurry before the slurry is land applied. However, little is known about how exogenous chemicals entering the manure storage facilities may affect the fate of ARGs. The objective of this study was to analyze the impact of six commonly used pit additives and four facility disinfectants on the concentration of ARGs in swine manure slurry. Bench scale reactors, each containing approximately 50 L of liquid swine manure, were dosed with additives or disinfectants and were sampled for 40 days. Seven antibiotic resistance genes along …

Differential Survival Of Non-O157 Shiga Toxigenic Escherichia Coli In Simulated Cattle Feedlot Runoff, Lisa M. Durso, John E. Gilley, Daniel N. Miller

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Environmental survival time is important when evaluating adverse health outcomes from foodborne pathogens. Although outbreaks associated with manure-impacted irrigation or runoff water are relatively infrequent, their broad scope, regulatory importance, and severe health outcomes highlight the need to better understand the environmental survival of manure-borne pathogens. Shiga toxigenic Escherichia coli (STEC) are excreted in feces and persist in the environment until they die or recolonize a new host. Surface waters contaminated with manure-borne STEC can infect humans through drinking and recreational water use or irrigated crops that are minimally cooked. In this study, manure-impacted water microcosms mimicking beef cattle feedlot …

Editorial: Predictive Modeling Of Human Microbiota And Their Role In Health And Disease, Hyun-Seob Song, Stephen R. Lindemann, Dong-Yup Lee

Department of Agricultural and Biological Systems Engineering: Faculty Publications

No abstract provided.

The Nanotheranostic Researcher’S Guide For Use Of Animal Models Of Traumatic Brain Injury, Brandon Z. Mcdonald, Connor C. Gee, Forrest M. Kievit

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Traumatic brain injury (TBI) is currently the leading cause of injury-related morbidity and mortality worldwide, with an estimated global cost of USD 400 billion annually. Both clinical and preclinical behavioral outcomes associated with TBI are heterogeneous in nature and influenced by the mechanism and frequency of injury. Previous literature has investigated this relationship through the development of animal models and behavioral tasks. However, recent advancements in these methods may provide insight into the translation of therapeutics into a clinical setting. In this review, we characterize various animal models and behavioral tasks to provide guidelines for evaluating the therapeutic efficacy of …

Frontier: Discipline-Based Education Research To Advance Authentic Learning In Agricultural And Biological Engineering, Heidi A. Diefes-Dux

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Discipline-based education research (DBER) is research activity aimed at investigating “learning and teaching in a discipline from a perspective that reflects the discipline’s priorities, worldview, knowledge, and practices” for the purpose of producing research-based evidence to improve education in that discipline. DBER arose out of concerns about the quality of post-secondary science education. Physics, chemistry, engineering, biology, geosciences, and astronomy education each have unique DBER histories in the U.S. that date back to the late 1800s or early 1900s when colleges and university systems were expanding and formalizing. The DBER fields accelerated in the 1950s and 1960s as a result …

Evolution Of Three Streambanks Before And After Stabilization And Record Flooding, Matthew Russell, Aaron R. Mittelstet, Tiffany Messer, Jesse T. Korus, R.M. Joeckel

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Stabilization projects are increasingly used to mitigate the effects of anthropogenic streambank erosion, yet the effectiveness of stabilization has been insufficiently measured. Sound monitoring practices inform adjustments in implementation and maintenance, which improve engineered effectiveness. Thus, the objectives of this study were to: 1) measure streambank migration from in three reaches stabilized with wooden jetties following a major flooding event, and 2) quantify deposition around the jetties between pre-flood and post-flood. Streambank deposition was measured in 2019 with a River Surveyor and Global Positioning System (GPS). Bank erosion rates in Reaches 1, 2 and 3 were 0.41, 0.96 and 0.07 …

Assessing Different Plant-Centric Water Stress Metrics For Irrigation Efficacy Using Soil-Plant-Atmosphere-Continuum Simulation, Jingwen Zhang, Kaiyu Guan, Bin Peng, Ming Pan, Wang Zhou, Robert F. Grant, Trenton E. Franz, Daran Rudnick, Derek M. Heeren, Andrew Suyker, Yi Yang, Genghong Wu

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Understanding plant water stress (PWS) in the soil-plant-atmosphere-continuum (SPAC) that connects water supply from soil, water demand from atmosphere, and plant self-regulation is a prerequisite for efficient irrigation in response to water scarcity. Currently, PWS can be defined in various ways, for example, based on environmental factors and/or plant-centric metrics. The environment-based metrics usually do not take plants into consideration. Regarding the existing plant-centric metrics, their interconnections and abilities to capture the physical water constraints from both soil water supply and atmospheric water demand are still unclear. This research investigates the theoretical foundations behind different PWS metrics, and assesses their …

Low-Level Groundwater Atrazine In High Atrazine Usage Nebraska Counties: Likely Effects Of Excessive Groundwater Abstraction, Moses New-Aaron, Olufemi Abimbola, Raheleh Mohammadi, Oluwaseun Famojuro, Zaeema Naveed, Azar Abadi, Jesse E. Bell, Shannon Bartelt-Hunt, Eleanor G. Rogan

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Recent studies observed a correlation between estrogen-related cancers and groundwater atrazine in eastern Nebraska counties. However, the mechanisms of human exposure to atrazine are unclear because low groundwater atrazine concentration was observed in counties with high cancer incidence despite having the highest atrazine usage. We studied groundwater atrazine fate in high atrazine usage Nebraska counties. Data were collected from Quality Assessed Agrichemical Contaminant Nebraska Groundwater, Parameter–Elevation Regressions on Independent Slopes Model (PRISM), and water use databases. Descriptive statistics and cluster analysis were performed. Domestic wells (59%) were the predominant well type. Groundwater atrazine was affected by well depth. Clusters consisting …

Improvements In Sub-Catchment Fractional Snowpack And Snowmelt Parameterizations And Hydrologic Modeling For Climate Change Assessments In The Western Himalayas, Vishal Singh, Francisco Muñoz-Arriola

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The present work proposes to improve estimates of snowpack and snowmelt and their assessment in the steep Himalayan ranges at the sub-catchment scale. Temporal variability of streamflow and the associated distribution of accumulated snow in catchments with glacier presence in the Himalayas illustrates how changes in snowpack and snowmelt can affect the water supply for local water management. The primary objective of this study is to assess the role of elevation, temperature lapse rate (TLR), and precipitation lapse rate (PLR) in the computation of snowpack (or snowfall) and snowmelt in sub-catchments of the Satluj River basin. Modeling of snowpack and …