Life Sciences Commons^™

Contaminant Transport Mechanisms And Source Tracking In Karst Groundwater Systems Under Agricultural Land Use, Shreya Pandey

Masters Theses & Specialist Projects

Karst areas in general face severe groundwater contamination problems that can degrade their water quality. In comparison to other landscapes, groundwater within karst regions is more susceptible to contamination. The situation gets worse when agriculture is practiced in these karst regions, because the nutrients and bacteria like nitrates and E. coli (Escherichia coli) are released into the groundwater systems which contaminate the water quality of those karst groundwater systems. This research aims to study the impacts of these contaminants, specifically nitrates and E. coli., by identifying the contaminant transport mechanisms and source tracking of these contaminants in the groundwater under …

Estate Planning: Stepped-Up Tax Basis, Anastasia Meyer

Center for Agricultural Profitability

A key consideration in estate planning is the transfer of assets to the next generation as 98% of farms are family owned and operated. Additionally, active operators or retired farmers own 75% of U.S. farmland (AgAmerica, 2023). As the average age of an operator increases, there is going to be a large transfer of farmland and other assets in the future whether by gifting, selling, or passing the farm to the next generation through inheritance.

Stepped-up basis is a tax provision that allows the value of an inherited asset to be adjusted to its fair market value at the time …

Robust Hydropower Planning Balances Energy Generation, Carbon Emissions And Sediment Connectivity In The Mekong River Basin, M. Tangi, Rafael Schmitt, Rafael M. Almeida, S. Bossi, Alexander S. Flecker, F. Sala, A. Castelletti

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

We present a framework for strategic dam planning under uncertainty, which includes GHG emissions mitigation as a novel objective. We focus on the Mekong River Basin, a fast‐developing region heavily relying on river‐derived ecosystem services. We employ a multi‐objective evolutionary algorithm to identify strategic dam portfolios for different hydropower expansion targets, using process‐related and statistical models to derive indicators of sediment supply disruption and GHG emissions. We introduce a robust optimization approach that explores variations in optimal portfolio compositions for more than 5,000 state‐of‐ the‐world configurations, regarding sediment origins and trapping and GHG emissions. Thus, we can rank dam projects' …

Research Trends In Production, Separation, And Identification Of Bioactive Peptides From Fungi – A Critical Review, Tanvir Ahmed, Angéla Juhász, Utpal Bose, Netsanet Shiferaw Terefe, Michelle L. Colgrave

Research outputs 2022 to 2026

Fungal-derived bioactive peptides (BPs) are increasingly attracting significant academic and industry research interest due to their high-quality protein content and potential environmentally friendly credentials. Fungi encompass a diverse range of species, some of which remain underexplored with demonstrated the ability to synthesise complex peptides with unique and potent bioactivities. While some recent reviews have focused on fungal protein sources and BPs, there remains a knowledge gap in the technologies and methods used to produce, isolate, and identify BPs from various fungal species. This article critically evaluates the strengths, challenges, and future directions of the recent methods and technologies employed in …

Peptidomics Analysis Of In Vitro Digested Wheat Breads: Effect Of Genotype And Environment On Protein Digestibility And Release Of Celiac Disease And Wheat Allergy Related Epitopes, Mélanie Lavoignat, Angéla Juhász, Utpal Bose, Thierry Sayd, Christophe Chambon, Miguel Ribeiro, Gilberto Igrejas, Sébastien Déjean, Catherine Ravel, Emmanuelle Bancel

Research outputs 2022 to 2026

Wheat proteins can trigger immunogenic reactions due to their resistance to digestion and immunostimulatory epitopes. Here, we investigated the peptidomic map of partially digested bread samples and the fingerprint of epitope diversity from 16 wheat genotypes grown in two environmental conditions. Flour protein content and composition were characterized; gastric and jejunal peptides were quantified using LC-MS/MS, and genotypes were classified into high or low bread protein digestibility. Differences in flour protein content and peptide composition distinguish high from low digestibility genotypes in both growing environments. No common peptide signature was found between high- and low-digestible genotypes; however, the celiac or …

A Comparison Of Tracheal Intubation Using Direct Laryngoscope And Video Laryngoscope In The Sellick And Trendelenburg Position With That Using Direct Laryngoscope In The Supine Sniffing Position: A Randomized Controlled Trial, Yun-Jeong Chae, Jung-Yoon Moon, Min-Gyu Lee, Han-Bum Joe

Student and Faculty Publications

Background: Tracheal intubation in the Sellick and Trendelenburg position (ST position) can prevent pulmonary aspiration but increase the difficulty of tracheal intubation. We compared tracheal intubation using video and direct laryngoscopy in the ST position with direct laryngoscopy in the supine sniffing position to evaluate the overall intubation performance. Methods: One hundred and twenty patients were randomly assigned to three groups: direct laryngoscope in the supine sniffing position (control), direct laryngoscope in the ST position (ST direct), and video laryngoscope in the ST position (ST video). The primary outcome was the intubation time; secondary outcomes included the first …

Developing A Hyperspectral Remote Sensing-Based Algorithm To Diagnose Potato Moisture For Water-Saving Irrigation, Qiqige Suyala, Zhuoling Li, Zhenxin Zhang, Liguo Jia, Mingshou Fan, Youping Sun, Haifeng Xing

Plants, Soils, and Climate Faculty Publications

Appropriate water supply is crucial for high-yield and high-quality potato tuber production. However, potatoes are mainly planted in arid and semi-arid regions in China, where the precipitation usually cannot meet the water demand throughout the growth period. In view of the actual situation of water shortage in these areas, to monitor the water status of potato plants timely and accurately and thus precisely control the irrigation are of significance for water-saving management of potatoes. Hyperspectral remote sensing has unique advantages in diagnosing crop water stress. In this paper, the canopy spectral reflectance and plant water content were measured under five …

Exploring The Pdz, Duf, And Lim Domains Of Pdlim5 In Dendrite Branching, Yogesh Srivastava, Maxsam Donta, Lydia L Mireles, Adriana Paulucci-Holthauzen, Leilei Shi, Mark T Bedford, M Neal Waxham, Pierre D Mccrea

Student and Faculty Publications

The branched architecture of neuronal dendrites is a key factor in how neurons form ordered networks and discoveries continue to be made identifying proteins and protein-protein interactions that direct or execute the branching and extension of dendrites. Our prior work showed that the molecular scaffold Pdlim5 and delta-catenin, in conjunction, are two proteins that help regulate the branching and elongation of dendrites in cultured hippocampal neurons and do so through a phosphorylation-dependent mechanism triggered by upstream glutamate signaling. In this report we have focused on Pdlim5's multiple scaffolding domains and how each contributes to dendrite branching. The three identified regions …

The F Plasmid Conjutome: The Repertoire Of E Coli Proteins Translocated Through An F-Encoded Type Iv Secretion System, Abu Amar M Al Mamun, Kimberley Kissoon, Yang Grace Li, Erin Hancock, Peter J Christie

Student and Faculty Publications

Bacterial conjugation systems pose a major threat to human health through their widespread dissemination of mobile genetic elements (MGEs) carrying cargoes of antibiotic resistance genes. Using the Cre Recombinase Assay for Translocation (CRAfT), we recently reported that the IncFV pED208 conjugation system also translocates at least 16 plasmid-encoded proteins to recipient bacteria. Here, we deployed a high-throughput CRAfT screen to identify the repertoire of chromosomally encoded protein substrates of the pED208 system. We identified 32 substrates encoded by the Escherichia coli W3110 genome with functions associated with (i) DNA/nucleotide metabolism, (ii) stress tolerance/physiology, (iii) transcriptional regulation, or (iv) toxin inhibition. …

Identifying Genes Linked To Variation In Metabolic And Whole Plant Phenotypes Using Data From Genome Resequencing, Transcriptomics, And Metabolic Profiling Of A Field-Grown Maize Diversity Panel, Ramesh Kanna Mathivanan

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

Maize metabolism is highly complex and influenced by genetic variation, yet the specific genes contributing to this variation and their links to non-metabolic traits remain less understood. To address this knowledge gap, we identified genes involved in maize metabolic variation and linked them to non-metabolic traits. We utilized a quadruplicate dataset of whole genome resequencing, transcriptomic, metabolic, and whole plant phenotype data from a single common field experiment of 660 diverse maize inbred lines. Leaf samples were collected shortly before flowering and analyzed using GC-MS for 26 metabolites. A Resampling Model Inclusion Probability Genome-Wide Association Study (RMIPGWAS) of approximately 2.6 …

Consumer Perceptions And Preferences For Utah Fresh And Packaged Fruit, Makaylie Langford, Kynda R. Curtis, Marcelo Pignatari

All Current Publications

In this fact sheet, we discuss the results of a 2023 study examining Utah consumer perceptions and preferences for Utah fresh and packaged fruit products. Study data were collected online via a Qualtrics survey, and 384 Utah adults completed the survey. Utah consumer food behaviors and attitudes, including participation in food and agricultural tourism activities, are discussed. We analyze the most consumed fruits and the preferred purchasing options for various fruit types, such as packaged, frozen, canned, and fresh. Additionally, we explore the factors influencing consumers’ decisions when buying fruit and review the product information they rely on. Overall, the …

Fruit Consumption Indicators: Who Consumes More Fruit In Utah?, Makaylie Langford, Kynda R. Curtis

All Current Publications

This fact sheet discusses fruit consumption patterns in Utah, exploring the key demographic and socioeconomic factors linked to increased fruit intake. Fruit growers and marketers can use this information to design effective promotional campaigns targeting consumers more likely to purchase fruit and fruit products.

Utah Fruit Growers Assessment Results Overview, Makaylie Langford, Kynda R. Curtis

All Current Publications

Fruit growers throughout Utah manage operations of varying sizes and sell their fruit products fresh or processed through various direct-to-consumer and wholesale markets. In early winter 2023, researchers conducted an online survey via Qualtrics to better understand the fruit products under production, current marketing methods, grower concerns, and future business interests. This fact sheet provides an overview of the survey results.

Utah Consumer Preferences And Willingness To Pay For Specialty Labeled Fruit Products, Kynda R. Curtis, Makaylie Langford, Marcelo Pignatari

All Current Publications

In this fact sheet, we discuss the results of a 2023 study examining Utah consumer preferences and willingness to pay (WTP) for fruit products labeled local (Utah’s Own™), organic, and GMO-free. We discuss and compare survey respondents' past consumption, awareness, preferences, and attitudes toward these labeling programs. Additionally, we examine consumer WTP values for each of these labels for three fruit varieties and fresh and dried products, namely fresh apples, strawberries, and dried tart cherries.

Pocket Gophers, Mark Nelson, S. Nicole Frey, Earl Creech, Kalen Taylor, Jacob Hadfield, Linden Greenhalgh, Cory Farnsworth, Jody Gale, Melanie Heaton, Justin Wyatt Clawson, Steve Price

All Current Publications

Pocket gophers can damage agriculture and human development infrastructure. In agricultural fields, pocket gophers cause conflicts by directly consuming plants, destroying plants when their soil mounds cover them, and causing premature loss of field stands such as alfalfa, necessitating expensive alfalfa stand replacement. They can chew through electrical, internet, and other utility cables, damaging irrigation pipes, and compromising the integrity of canals and ditch banks. They also cause significant damage to lawns and gardens in urban areas. Understanding pocket gopher habits, especially the burrow system, is the key to effective control. Management methods include trapping, hand or mechanical baiting, fumigation, …

Fruit Production And Opportunities For Growers In Utah, Makaylie Langford, Kynda R. Curtis

All Current Publications

This fact sheet discusses the state of the fruit industry in Utah, its impact on the Utah economy, as well as current challenges the fruit industry faces and opportunities for fruit growers moving forward. These challenges and opportunities underscore the importance of fruit to the state’s economy, as growers navigate urbanization, competition, and consumer preferences for locally grown produce. Fostering collaboration between consumers and growers will ensure a commitment to local agriculture and community support.

Analyzing The Relationship Between Dose And Geometric Agreement Metrics For Auto-Contouring In Head And Neck Normal Tissues, Barbara Marquez, Zachary T Wooten, Ramon M Salazar, Christine B Peterson, David T Fuentes, T J Whitaker, Anuja Jhingran, Julianne Pollard-Larkin, Surendra Prajapati, Beth Beadle, Carlos E Cardenas, Tucker J Netherton, Laurence E Court

Student and Faculty Publications

This study aimed to determine the relationship between geometric and dosimetric agreement metrics in head and neck (H&N) cancer radiotherapy plans. A total 287 plans were retrospectively analyzed, comparing auto-contoured and clinically used contours using a Dice similarity coefficient (DSC), surface DSC (sDSC), and Hausdorff distance (HD). Organs-at-risk (OARs) with ≥200 cGy dose differences from the clinical contour in terms of Dmax (D0.01cc) and Dmean were further examined against proximity to the planning target volume (PTV). A secondary set of 91 plans from multiple institutions validated these findings. For 4995 contour pairs across 19 OARs, 90% had a DSC, sDSC, …

Twenty-Three Years Of Pcr-Based Seafood Authentication Assay Development: What Have We Learned?, Maleeka Singh, Robert G. Young, Rosalee S. Hellberg, Robert H. Hanner, Maria G. Corradini, Jeffrey M. Farber

Food Science Faculty Articles and Research

Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA-based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer-probe pairs used for DNA …

Twenty-Three Years Of Pcr-Based Seafood Authentication Assay Development: What Have We Learned?, Maleeka Singh, Robert G. Young, Rosalee S. Hellberg, Robert H. Hanner, Maria G. Corradini, Jeffrey M. Garber

Food Science Faculty Articles and Research

Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA-based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer-probe pairs used for DNA …

Terminating A Verbal Farmland Lease In Nebraska, Jessica J. Groskopf, J. David Aiken

Center for Agricultural Profitability

Some farm leases are not written but are verbal or "handshake" agreements. Because nothing is in writing, the parties may have different recollections of their agreement, making lease disputes more difficult to resolve. The most common legal issue associated with verbal farm leases is how a lease may legally be terminated. For verbal leases in Nebraska, six months advance notice must be given to legally terminate the lease. In contrast, the termination of a written lease is determined by the terms of the written lease. If the lease does not address termination, the lease automatically terminates on the last day …

A Cooperative High Precision Dredge Survey To Assess The Mid-Atlantic Sea Scallop Resource Area In 2021 And 2022, Sally Roman, Carter Lin, David Rudders

Reports

For the sea scallop, Placopecten magellanicus, current and accurate information related to the abundance and distribution of adult and juvenile scallops is essential for effective management of the resource. Scallop management is a combination of input and output controls, with a focus on spatial area management. The continued prosperity of the scallop resource and fishery is dependent on both periodic and large incoming year classes, as well as a mechanism to delineate the scale of a recruitment event and subsequently monitor the growth and abundance of these scallops over time.

Acknowledging the importance of accurate, timely, and meaningful information necessary …

In Silico Analysis Of The Rop29 Protein As A Vaccine Candidate Against Toxoplasma Gondii, Amir Karimipour-Saryazdi, Fatemeh Ghaffarifar, Abdolhossein Dalimi, Masoud Foroutan, John Horton, Javid Sadraei

Student and Faculty Publications

The progression of Toxoplasma gondii (T. gondii) invasion is aided by rhoptry proteins (ROPs), which are also crucial for the parasite's survival in host cells. In this study, in silico analysis was performed to examine the various aspects of the ROP29 protein, such as physicochemical properties, potential T- and B-cell epitopes, and other significant features. The research revealed that there were 55 possible sites for posttranslational modification in the ROP29 protein. The secondary structure of the ROP29 protein consists of a random coil, an alpha-helix, and an extended strand, which account for 49.69%, 36.81%, and 13.50%, respectively. Moreover, …

Detection Of Diffusely Abnormal White Matter In Multiple Sclerosis On Multiparametric Brain Mri Using Semi-Supervised Deep Learning, Benjamin C Musall, Refaat E Gabr, Yanyu Yang, Arash Kamali, John A Lincoln, Michael A Jacobs, Vi Ly, Xi Luo, Jerry S Wolinsky, Ponnada A Narayana, Khader M Hasan

Student and Faculty Publications

In addition to focal lesions, diffusely abnormal white matter (DAWM) is seen on brain MRI of multiple sclerosis (MS) patients and may represent early or distinct disease processes. The role of MRI-observed DAWM is understudied due to a lack of automated assessment methods. Supervised deep learning (DL) methods are highly capable in this domain, but require large sets of labeled data. To overcome this challenge, a DL-based network (DAWM-Net) was trained using semi-supervised learning on a limited set of labeled data for segmentation of DAWM, focal lesions, and normal-appearing brain tissues on multiparametric MRI. DAWM-Net segmentation performance was compared to …

Martian Atmospheric Hydrogen And Deuterium: Seasonal Changes And Paradigm For Escape To Space, John T Clarke, Majd Mayyasi, Dolon Bhattacharyya, Jean-Yves Chaufray, Nicolas Schneider, Bruce Jakosky, Roger Yelle, Franck Montmessin, Michael Chaffin, Shannon Curry, Justin Deighan, Sonal Jain, Jean-Loup Bertaux, Eryn Cangi, Matteo Crismani, Scott Evans, Sumedha Gupta, Franck Lefevre, Greg Holsclaw, Daniel Lo, William Mcclintock, Michael Stevens, Ian Stewart, Shane Stone, Paul Mahaffy, Mehdi Benna, Meredith Elrod

Student and Faculty Publications

Mars' water history is fundamental to understanding Earth-like planet evolution. Water escapes to space as atoms, and hydrogen atoms escape faster than deuterium giving an increase in the residual D/H ratio. The present ratio reflects the total water Mars has lost. Observations with the Mars Atmosphere and Volatile Evolution (MAVEN) and Hubble Space Telescope (HST) spacecraft provide atomic densities and escape rates for H and D. Large increases near perihelion observed each martian year are consistent with a strong upwelling of water vapor. Short-term changes require processes in addition to thermal escape, likely from atmospheric dynamics and superthermal atoms. Including …

Revision Of Trachyderines Related To Sphaenothecus From North America With Description Of Three New Genera, And New Species Of Lophalia Casey, 1912, Mannophorus Leconte, 1854, And Ischnocnemis Thomson, 1864 (Coleoptera: Cerambycidae: Cerambycinae: Trachyderini), Bryan K. Eya

Insecta Mundi

The genera Lophalia Casey, 1912, Mannophorus LeConte, 1854 and Ischnocnemis Thomas, 1864 (Coleoptera: Cerambycidae: Cerambycinae: Trachyderini) are recharacterized by providing additional morphological features to enhance the delineation of these genera. Two species, Lophalia cribricollis Bates, 1892 and Ischnocnemis luteicollis (Bates, 1885), are transferred to a new genus Lophaliamorpha Eya with Lophaliamorpha luteicollis (Bates) new combination as the type species. Ischnocnemis skillmani Chemsak and Hovore, 2010 is transferred to a new genus Paramannophorus Eya with Paramannophorus skillmani (Chemsak and Hovore) new combination as the type species. A new genus Microteroschema is created to accommodate two additional species from Mexico: Microteroschema parvum …

An Analysis Of The Genus Aleyrodes Latreille (Hemiptera: Sternorrhyncha: Aleyrodidae) In California, With Three Synonymies, Natalia Von Ellenrieder, Raymond J. Gill

Insecta Mundi

Abstract

Based on the examination of an extensive series of specimens and available type material, three out of the six species of Aleyrodes Latreille (Hemiptera: Sternorrhyncha: Aleyrodidae) described from California, A. diasemus Bemis, 1904, A. essigi Penny, 1922, and A. osmaroniae Sampson, 1945, are newly synonymized under A. spiraeoides Quaintance, 1900. The species of Aleyrodes reported from California are keyed and diagnosed based on characters from puparia and male genitalia, and character variability is documented and illustrated.

Resumen

Basado en el examen de una extensa serie de especímenes y material tipo disponible, tres de las seis …

Aposematic-Habitat Correlation In Nearctic Species Of Episyron Schiødte (Hymenoptera: Pompilidae: Pompilinae: Pompilini), Frank E. Kurczewski

Insecta Mundi

Three Nearctic species of Episyron Schiødte (Hymenoptera: Pompilidae: Pompilinae: Pompilini) were examined morphologically, geographically, and ecologically with intent to infer an aposematic correlation with habitat type, protarsal digging rake morphology, and host spider association. Episyron quinquenotatus quinquenotatus (Say) and E. conterminus cressoni (Dewitz), two subspecies with extensive aposematic markings and more and longer protarsal comb spines, were associated with bare or sparsely vegetated sandy soils near water courses. Episyron biguttatus biguttatus (Fabricius), with few aposematic markings and less and shorter protarsal comb spines, was associated with more densely vegetated terrain and gravelly and loamy soils. Three subspecies of Anoplius …

A New Species Of Gaindaphodius Král And Mencl From Nepal (Coleoptera: Scarabaeidae: Aphodiinae), Stefano Ziani

Insecta Mundi

A new species from Nepal, Gaindaphodius marigold (Coleoptera: Scarabaeidae: Aphodiinae), is described, illustrated and compared with G. gainda Král and Mencl, 2024, the only other species in the genus Gaindaphodius Král and Mencl, 2024.

Diapause Specific Proteins Of A Brine Shrimp Form Liquid Droplets Dependent On Salt And Ph Levels, Kolby Sanders, Alex Haydon, Charles Elder, David Grimm, Michael Menze

Undergraduate Research Events

Liquid-Liquid Phase Separation (LLPS) is a process when a polypeptide condenses into a dense and dilute phase in aqueous solutions. Within cells, this process is believed to relate to stress regulation and various cellular processes. Several stress-related proteins found only during the embryonic developmental stage of diapause in the brine shrimp, A. franciscana, have been observed to undergo LLPS in vitro. Our results show that the small heat shock protein (sHSP) p26 has a greater propensity to LLPS under varying salt concentrations compared to LEA6, a late embryogenesis abundant protein (LEA). At a protein concentration of 1.31 mg/ml in …

Effects Of Premortem Stress On Protein Expression, Steak Color, Oxidation, And Myofibrillar Fragmentation Index In The Longissimus Lumborum, Reganne K. Briggs, Jerrad F. Legako, Paul R. Broadway, Jeff A. Carroll, Nicole C. Burdick Sanchez, Nikole E. Ineck, Zachary K. Smith, Ranjith Ramanathan, Kara J. Thornton

Animal, Dairy, and Veterinary Science Faculty Publications

No abstract provided.