Environmental Engineering Commons^™

Antibiotic Resistance Gene Profile Changes In Cropland Soil After Manure Application And Rainfall, Morgan Meyers, Lisa Durso, John E. Gilley, Heidi Waldrip, Lana Castleberry, Amy Millmier Schmidt

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Land application of manure introduces gastrointestinal microbes into the environment, including bacteria carrying antibiotic resistance genes (ARGs). Measuring soil ARGs is important for active stewardship efforts to minimize gene flow from agricultural production systems; however, the variety of sampling protocols and target genes makes it difficult to compare ARG results between studies. We used polymerase chain reaction (PCR) methods to characterize and/or quantify 27 ARG targets in soils from 20 replicate, long-term no-till plots, before and after swine manure application and simulated rainfall and runoff. All samples were negative for the 10 b-lactamase genes assayed. For tetracycline resistance, only source …

A Role For Nanoparticles In Treating Traumatic Brain Injury, Badrul Alam Bony, Forrest M. Kievit

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Traumatic brain injury (TBI) is one of the main causes of disability in children and young adults, as well as a significant concern for elderly individuals. Depending on the severity, TBI can have a long-term impact on the quality of life for survivors of all ages. The primary brain injury can result in severe disability or fatality, and secondary brain damage can increase the complexities in cellular, inflammatory, neurochemical, and metabolic changes in the brain, which can last decades post-injury. Thus, survival from a TBI is often accompanied by lifelong disabilities. Despite the significant morbidity, mortality, and economic loss, there …

Time-Domain And Frequency-Domain Reflectometry Type Soil Moisture Sensor Performance And Soil Temperature Effects In Fine- And Coarse-Textured Soils, Y. Zhu, S. Irmak, A. J. Jhala, M. C. Vuran, A. Diotto

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The performances of six time-domain reflectometry (TDR) and frequency-domain reflectometry (FDR) type soil moisture sensors were investigated for measuring volumetric soil-water content (θ_v) in two different soil types. Soil-specific calibration equations were developed for each sensor using calibrated neutron probe-measured θ_v. Sensors were also investigated for their performance response in measuring θ_v to changes in soil temperature. The performance of all sensors was significantly different (P<0.05) than the neutron probe-measured θ_v, with the same sensor also exhibiting variation between soils. In the silt loam soil, the 5TE sensor had the lowest root mean squared error (RMSE) of 0.041 …

The Development Of The Infews-Er: A Virtual Resource Center For Transdisciplinary Graduate Student Training At The Nexus Of Food, Energy, And Water, Luis F. Rodriguez, Anna-Maria Marshall, Dan Cotton, Richard K. Koelsch, Jacek Koziel, Deanne Meyer, Dan Steward, Jill Heemstra, Anand Padmanabahn, John Classen, Nathan J. Meyer, Benjamin L. Ruddell, Sean M. Ryan, Ximing Cai, Emad Habib, Peter D. Saundry

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Problems at the nexus of Food, Energy and Water Systems (FEWS) are among the most complex challenges we face. Spanning simple to complex temporal, geographic, social, and political framings, the questions raised at this nexus require multidisciplinary if not transdisciplinary approaches. Answers to these questions must draw from engineering, the physical and biological sciences, and the social sciences. Practical solutions depend upon a wide community of stakeholders, including industry, policymakers, and the general public. Yet there are many obstacles to working in a transdisciplinary environment: unfamiliar concepts, specialized terminology, and countless “blind” spots. Graduate education occurs in disciplinary ‘silos’, often …

Agenator: An Open Source Computer-Controlled Dry Aging System For Beef, Soon Kiat Lau, Felipe Azevedo Ribeiro, Jeyamkondan Subbiah, Chris R. Calkins

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Dry aging of beef is a process where beef is exposed to a controlled environment with the ultimate goal of drying the beef to improve its quality and value. Comprehensive investigations into the effects of various environmental conditions on dry aging are crucial for understanding and optimizing the process, but the lack of affordable equipment focused on data collection makes it difficult to do so. The Agenator was thus developed as an open source system with a suite of features for investigating dry aging such as: measuring and recording relative humidity, temperature, mass, air velocity, and fan rotational speed; precise …

Patellar Tendon Morphology In Trans-Tibial Amputees Utilizing A Prosthesis With A Patellar-Tendonbearing Feature, Kai-Yu Ho, Michelle Harty, Jessica Kellogg, Kelly Teter, Szu-Ping Lee, Yu-Jen Chang, Gregory Bashford

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A patellar-tendon-bearing (PTB) bar is a common design feature used in the socket of trans-tibial prostheses to place load on the pressure-tolerant tissue. As the patellar tendon in the residual limb is subjected to the perpendicular compressive force not commonly experienced in normal tendons, it is possible for tendon degeneration to occur over time. The purpose of this study was to compare patellar tendon morphology and neovascularity between the residual and intact limbs in trans-tibial amputees and healthy controls. Fifteen unilateral trans-tibial amputees who utilized a prosthesis with a PTB feature and 15 age- and sex- matched controls participated. Sonography …

Design Of Plant Protection Uav Variable Spray System Based On Neural Networks, Sheng Wen, Quanyong Zhang, Xuanchun Yin, Yubin Lan, Jiantao Zhang, Yufeng Ge

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Recently, unmanned aerial vehicles (UAVs) have rapidly emerged as a new technology in the fields of plant protection and pest control in China. Based on existing variable spray research, a plant protection UAV variable spray system integrating neural network based decision making is designed. Using the existing data on plant protection UAV operations, combined with artificial neural network (ANN) technology, an error back propagation (BP) neural network model between the factors affecting droplet deposition is trained. The factors affecting droplet deposition include ambient temperature, ambient humidity, wind speed, flight speed, flight altitude, propeller pitch, nozzles pitch and prescription value. Subsequently, …

Rapeseed Seedling Stand Counting And Seeding Performance Evaluation At Two Early Growth Stages Based On Unmanned Aerial Vehicle Imagery, Biquan Zhao, Jian Zhang, Chenghai Yang, Guangsheng Zhou, Youchun Ding, Yeyin Shi, Dongyan Zhang, Jing Xie, Qingxi Liao

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The development of unmanned aerial vehicles (UAVs) and image processing algorithms for field-based phenotyping offers a non-invasive and effective technology to obtain plant growth traits such as canopy cover and plant height in fields. Crop seedling stand count in early growth stages is important not only for determining plant emergence, but also for planning other related agronomic practices. The main objective of this research was to develop practical and rapid remote sensing methods for early growth stage stand counting to evaluate mechanically seeded rapeseed (Brassica napus L.) seedlings. Rapeseed was seeded in a field by three different seeding devices. A …

Grain Yield, Crop And Basal Evapotranspiration, Production Functions And Water Productivity Response Of Drought-Tolerant And Non-Drought-Tolerant Maize Hybrids Under Different Irrigation Levels, And Population Densities: Part I. In Western Nebraska's Semi-Arid Environments, Ali T. Mohammed, Suat Irmak, William Kranz, Simon Van Donk, C. Dean Yonts

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Grain yield, crop evapotranspiration (ETc), basal evapotranspiration (ETb), ETc-yield production functions (ETYPF), and crop water use efficiency (CWUE) response of three drought-tolerant (DT) and one non-drought-tolerant (NDT) maize (Zea mays L.) hybrids to two plant population densities (PPDs) [84,000 plants ha-1 (high PPD) and 59,300 plants ha-1 (low PPD)] and three irrigation levels were researched at two semi-arid locations: North Platte (WCREC) and Scottsbluff (MAL), Nebraska, in 2010, 2011, and 2012. The irrigation levels were fully irrigated (FIT), early cutoff (ECOT), and rainfed (RFT). Precipitation in 2010 was above average, 2011 was a normal year, and 2012 was one of …

System For Optimizing Fed-Batch Hydrolysis Of Biomass, Chao Tai, Deepak R. Keshwani

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Provided herein is a system for optimizing the fed-batch hydrolysis of biomass.

Nucleic Acid Delivery To Mesenchymal Stem Cells: A Review Of Nonviral Methods And Applications, Andrew Hamann, Albert Nguyen, Angela K. Pannier

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Background: Mesenchymal stem cells (MSCs) are multipotent stem cells that can be isolated and expanded from many tissues, and are being investigated for use in cell therapies. Though MSC therapies have demonstrated some success, none have been FDA approved for clinical use. MSCs lose stemness ex vivo, decreasing therapeutic potential, and face additional barriers in vivo, decreasing therapeutic efficacy. Culture optimization and genetic modification of MSCs can overcome these barriers. Viral transduction is efficient, but limited by safety concerns related to mutagenicity of integrating viral vectors and potential immunogenicity of viral antigens. Nonviral delivery methods are safer, though limited …

Actual Evapotranspiration And Crop Coefficients Of Irrigated Lowland Rice (Oryza Sativa L.) Under Semiarid Climate, Koffi Djaman, Daran R. Rudnick, Yonnelle D. Moukoumbi, Abdoulaye Sow, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Lowland irrigated rice is the predominant crop produced in the Senegal River Valley characterized by very low annual rainfall, high temperatures, and low relative humidity. The Senegal River is shared by Senegal, Mali, Mauritania, and Guinea, and serves as the main source of irrigation water for the adopted double rice cropping system. Developing appropriate resource management strategies might be the key factor for the sustainability of rice production in the region. This study aims to estimate rice seasonal evapotranspiration (ETa), irrigation water requirement, and to develop rice growth stage specific crop coefficients (Kc) to improve rice water productivity. Field experiments …

Narrow Grass Hedge Effects On Microbial Transport Following Variable Applications Of Beef Cattle Manure, Lisa M. Durso, John E. Gilley, Dave B. Marx, Brian L. Woodbury

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The effectiveness of a 1.4 m wide grass hedge in reducing microbial transport following manure application was examined in this study. Beef cattle manure was applied to 0.75 m wide by 4.0 m long plots established on an Aksarben silty clay loam located in southeast Nebraska. Manure was added at rates required to meet none or the 1-, 2-, or 4-year nitrogen requirements for corn. The transport of phages, total coliforms, E. coli, and enterococci was measured for three 30 min simulated rainfall events, which were separated by approximately 24 h intervals. The narrow grass hedge reduced total counts of …

Minimal Interspecies Interaction Adjustment (Miia): Inference Of Neighbor-Dependent Interactions In Microbial Communities, Hyun-Seob Song, Joon-Yong Lee, Shin Haruta, William C. Nelson, Dong-Yup Lee, Stephen R. Lindemann, Jim K. Fredrickson, Hans C. Bernstein

Department of Agricultural and Biological Systems Engineering: Faculty Publications

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more …

High-Speed, High-Frequency Ultrasound, In Utero Vector-Flow Imaging Of Mouse Embryos, Jeffrey A. Ketterling, Orlando Aristizabal, Billy Y. S. Yiu, Daniel H. Turnbull, Colin K. L. Phoon, Alfred C. H. Yu, Ronald H. Silverman

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Real-time imaging of the embryonic murine cardiovascular system is challenging due to the small size of the mouse embryo and rapid heart rate. High-frequency, linear-array ultrasound systems designed for small-animal imaging provide high-frame-rate and Doppler modes but are limited in regards to the field of view that can be imaged at fine-temporal and -spatial resolution. Here, a plane-wave imaging method was used to obtain high-speed image data from in utero mouse embryos and multi-angle, vector-flow algorithms were applied to the data to provide information on blood flow patterns in major organs. An 18-MHz linear array was used to acquire plane-wave …

Factors Related To Intra-Tendinous Morphology Of Achilles Tendon In Runners, Kai-Yu Ho, Ari Baquet, Yu-Jen Chang, Lung-Chang Chien, Michelle Harty, Gregory Bashford, Kornelia Kulig

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The purpose of this study was to determine and explore factors (age, sex, anthropometry, running and injury/pain history, tendon gross morphology, neovascularization, ankle range of motion, and ankle plantarflexor muscle endurance) related to intra-tendinous morphological alterations of the Achilles tendon in runners. An intra-tendinous morphological change was defined as collagen fiber disorganization detected by a low peak spatial frequency radius (PSFR) obtained from spatial frequency analysis (SFA) techniques in sonography. Ninety-one runners (53 males and 38 females; 37.9 ± 11.6 years) with 8.8 ± 7.3 years of running experience participated. Height, weight, and waist and hip circumferences were recorded. Participants …

Early Prediction Of Soybean Traits Through Color And Texture Features Of Canopy Rgb Imagery, Wenan Yuan, Nuwan Kumara Wijewardane, Shawn Jenkins, Geng Bai, Yufeng Ge, George L. Graef

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Global crop production is facing the challenge of a high projected demand, while the yields of major crops are not increasing at sufficient speeds. Crop breeding is an important way to boost crop productivity, however its improvement rate is partially hindered by the long crop generation cycles. If end-season crop traits such as yield can be predicted through early-season phenotypic measurements, crop selection can potentially be made before a full crop generation cycle finishes. This study explored the possibility of predicting soybean end-season traits through the color and texture features of early-season canopy images. Six thousand three hundred and eighty-three …

Metabolic Compounds Within The Porcine Uterine Environment Are Unique To The Type Of Conceptus Present During The Early Stages Of Blastocyst Elongation, Sophie C. Walsh, Jeremy R. Miles, Linxing Yao, Corey D. Broeckling, Lea A. Rempel, Elane C. Wright-Johnson, Angela K. Pannier

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The objective of this study was to identify metabolites within the porcine uterine milieu during the early stages of blastocyst elongation. At Days 9, 10, or 11 of gestation, reproductive tracts of White cross‐bred gilts (n = 38) were collected immediately following harvest and flushed with Roswell Park Memorial Institute‐1640 medium. Conceptus morphologies were assessed from each pregnancy and corresponding uterine flushings were assigned to one of five treatment groups based on these morphologies: (a) uniform spherical (n = 8); (b) heterogeneous spherical and ovoid (n = 8); (c) uniform ovoid (n = 8); (d) heterogeneous …

Optimization Of Process Parameters And Fermentation Strategy For Xylanase Production In A Stirred Tank Reactor Using A Mutant Aspergillus Nidulans Strain, Asmaa Abdella, Fernando Segato, Mark R. Wilkins

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The present work studied the optimization of aeration rate, agitation rate and oxygen transfer and the use of various batch fermentation strategies for xylanase production from a recombinant Aspergillus nidulans strain in a 3 L stirred tank reactor. Maximum xylanase production of 1250 U/mL with productivity of 313 U/mL/day was obtained under an aeration rate of 2 vvm and an agitation rate of 400 rpm using batch fermentation. The optimum volumetric oxygen transfer coefficient (kLa) for efficient xylanase production was found to be 38.6 h1. Fed batch mode and repeated batch fermentation was also performed with kLa was 38.6 h1. …

Optimization Of Process Parameters And Fermentation Strategy For Xylanase Production In A Stirred Tank Reactor Using A Mutant Aspergillus Nidulans Strain, Asmaa Abdella, Fernando Segato, Mark R. Wilkins

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The present work studied the optimization of aeration rate, agitation rate and oxygen transfer and the use of various batch fermentation strategies for xylanase production from a recombinant Aspergillus nidulans strain in a 3 L stirred tank reactor. Maximum xylanase production of 1250 U/mL with productivity of 313 U/mL/day was obtained under an aeration rate of 2 vvm and an agitation rate of 400 rpm using batch fermentation. The optimum volumetric oxygen transfer coefficient (kLa) for efficient xylanase production was found to be 38.6 h-1. Fed batch mode and repeated batch fermentation was also performed with kLa was 38.6 h …

Hydrogen Peroxide Sensors For Biomedical Applications, Jakob Meier, Eric M. Hofferber, Joseph A. Stapleton, Nicole M. Iverson

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Hydrogen peroxide (H2O2) is an important molecule within the human body, but many of its roles in physiology and pathophysiology are not well understood. To better understand the importance of H2O2 in biological systems, it is essential that researchers are able to quantify this reactive species in various settings, including in vitro, ex vivo and in vivo systems. This review covers a broad range of H2O2 sensors that have been used in biological systems, highlighting advancements that have taken place since 2015.

Principal Variable Selection To Explain Grain Yield Variation In Winter Wheat From Features Extracted From Uav Imagery, Jiating Li, Arun-Narenthiran Veeranampalayam-Sivakumar, Madhav Bhatta, Nicholas D. Garst, Hannah Stoll, P. Stephen Baenziger, Vikas Belamkar, Reka Howard, Yufeng Ge, Jiating Li

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Background: Automated phenotyping technologies are continually advancing the breeding process. However, collecting various secondary traits throughout the growing season and processing massive amounts of data still take great efforts and time. Selecting a minimum number of secondary traits that have the maximum predictive power has the potential to reduce phenotyping efforts. The objective of this study was to select principal features extracted from UAV imagery and critical growth stages that contributed the most in explaining winter wheat grain yield. Five dates of multispectral images and seven dates of RGB images were collected by a UAV system during the spring growing …

Heterologous Expression And Functional Characterization Of A Gh10 Endoxylanase From Aspergillus Fumigatus Var. Niveus With Potential Biotechnological Application, Josman Velasco, Bianca Oliva, Evandro Jose Mulinari, Leidy Patricia Quintero, Awana Da Silva Lima, Aline Larissa Goncalves, Thiago Augusto Goncalves, Andre Damasio, Fabio Marcio Squina, Adriane Maria Ferreira Milagres, Asmaa Abdella, Mark R. Wilkins, Fernando Segato

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Xylanases decrease the xylan content in pretreated biomass releasing it from hemicellulose, thus improving the accessibility of cellulose for cellulases. In this work, an endo-β-1,4-xylanase from Aspergillus fumigatus var. niveus (AFUMN-GH10) was successfully expressed. The structural analysis and biochemical characterization showed this AFUMN-GH10 does not contain a carbohydrate-binding module. The enzyme retained its activity in a pH range from 4.5 to 7.0, with an optimal temperature at 60°C. AFUMN-GH10 showed the highest activity in beechwood xylan. The mode of action of AFUMNGH10 was investigated by hydrolysis of APTS-labeled xylohexaose, which resulted in xylotriose and xylobiose as the main products. AFUMN-GH10 …

Perceptions Of Vulnerability To Flooding, Hurricanes, And Climate Change On Grand Isle, Louisiana’S Only Inhabited Barrier Island, Lauren Miller

Graduate Student Theses, Dissertations, & Professional Papers

This study used in-depth interviews of permanent residents on Grand Isle, Louisiana, a remote barrier island, to better understand their perceptions of structural flood measures, non-structural responses to flooding and hurricanes, and perceptions of vulnerability to flooding, hurricanes, and climate change on a remote barrier island-Grand Isle, Louisiana. Residents' perceptions regarding the various structural measures implemented by the federal, state, and local government appeared mixed. Non-structural responses to flooding risks implemented at the household, community, state, and federal level continue to strengthen resiliency on Grand Isle. According to interviewees, aspects of environmental, rural, and economic vulnerability on Grand Isle impact …

Water Effects On Optical Canopy Sensing For Late-Season Site-Specific Nitrogen Management Of Maize, Tsz Him Lo, Daran Rudnick, Brian Krienke, D. M. Heeren, Yufeng Ge, Tim M. Shaver

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The interpretation of optical canopy sensor readings for determining optimal rates of late-season site-specific nitrogen application to corn (Zea mays L.) can be complicated by spatially variable water sufficiency, which can also affect canopy size and/or pigmentation. In 2017 and 2018, corn following corn and corn following soybeans were subjected to irrigation×nitrogen fertilizer treatments in west central Nebraska, USA, to induce variable water sufficiency and variable nitrogen sufficiency. The vegetation index-sensor combinations investigated were the normalized difference vegetation index (NDVI), the normalized difference red edge index (NDRE), and the reflectance ratio of near infrared minus red edge over near …

Microcontroller Based Granular Urea Application Attachment For Rice Transplanter, Md Towfiqur Rahman, Md Monjurul Alam, Md Mosharraf Hossain, Muhammad Rashed Al Mamun

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Transplanting and fertilizer application for rice production in Bangladesh are tedious, time consuming and laborious task, and mostly done manually. Mechanical transplanting of rice becoming popular in the country in recent years and few machines have been developed for granular urea deep placement, however, having some limitations. Placing granular urea precisely along with rice transplanting, an attempt was under taken to design and fabricate an electronic control granular urea applicator to be attach with a 4-row walk behind type rice transplanter. Fabrication of the electronic granular urea applicator was done in the workshop of the Department of Farm Power and …

Invasion Of The P Elements: Tolerance Is Not Futile, Colin D. Meiklejohn, Justin P. Blumenstiel

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Organisms are locked in an eternal struggle with parasitic DNA sequences that live inside their genomes and wreak havoc on their host’s chromosomes as they spread through populations. To combat these parasites, host species have evolved elaborate mechanisms of resistance that suppress their activity. A new study in Drosophila indicates that, prior to the acquisition of resistance, individuals can vary in their ability to tolerate the activity of these genomic parasites, ignoring or repairing the damage they induce. This tolerance results from variation at genes involved in germline development and DNA damage checkpoints and suggests that these highly conserved cellular …

Cover Crops Have Negligible Impact On Soil Water In Nebraska Maize–Soybean Rotation, J. Burdette Barker, Derek M. Heeren, Katja Koehler-Cole, Charles Shapiro, Humberto Blanco-Canqui, Roger W. Elmore, Christopher A. Proctor, Suat Irmak, Charles A. Francis, Tim M. Shaver, Ali T. Mohammed

Department of Agricultural and Biological Systems Engineering: Faculty Publications

One perceived cost of integrating winter cover cropping in maize (Zea mays L.) and soybean [Glycine max (L.) Merr.] rotation systems is the potential negative impact on soil water storage available for primary crop production. The objective of this 3-year study was to evaluate the effects of winter cover crops on soil water storage and cover crop biomass production following no-till maize and soybean rotations. Locations were near Brule (west-central), Clay Center (south-central), Concord (northeast), and Mead (east-central), Nebraska, United States. Treatments included crop residue only (no cover crop) and a multi-species cover crop mix, both broadcast-seeded before …

Dna Identification Of Polyculture, Andrew Schuler

Energize New Mexico (NSF EPSCoR Track 1 IV)

DNA sequencing of algae polyculture growing in oilfield produced water. It is dominated by the algae species Parachlorella kessleri and Cyanobacterium aponinum.

Portable Flux Tower Deployments Field Campaign Report, M. S. Torn, L Kuepper, S. C. Biraud, D. P. Billesbach

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Contents

Acronyms and Abbreviations...................................................................... iii

1.0 Summary ....................................................... 1

2.0 Results ........................................... 1

3.0 Publications and References ................................................. 2

4.0 Lessons Learned .................................................................... 2