Life Sciences Commons^™

Do Coffee Agroforestry Systems Always Improve Soil Carbon Stocks Deeper In The Soil?—A Case Study From Turrialba, Costa Rica, Nilovna Chatterjee, P. K. Ramachandran Nair, Vimala D. Nair, Abhishek Bhattacharjee, Elias De Melo Virginio Filho, Rheinhold G. Muschler, Martin R.A. Noponen

Department of Agronomy and Horticulture: Faculty Publications

Shaded perennial agroforestry systems (AFS) are regarded as desirable land‐use practices that improve soil carbon sequestration. However, most studies assume a positive correlation between above ground and below ground carbon without considering the effect of past and current land management, textural variations (silt and clay percentage), and such other site‐specific factors that have a major influence on the extent of soil C sequestration. We assessed SOC stock at various depths (0–10, 10–30, 30–60, and 60–100 cm) in shaded perennial coffee (Coffea arabica L.) AFS in a 17‐ year‐old experimental field at the Centro Agronómico Tropical de Investigación y Enseñanza, (9°53′44′′ …

Connectivity Differences Between Gulf War Illness (Gwi) Phenotypes During A Test Of Attention, Tomas Clarke, Jessie Jamieson, Patrick Malone, Rakib U. Rayhan, Stuart Washington, John W. Vanmeter, James N. Baraniuk

Department of Mathematics: Faculty Publications

One quarter of veterans returning from the 1990–1991 Persian Gulf War have developed Gulf War Illness (GWI) with chronic pain, fatigue, cognitive and gastrointestinal dysfunction. Exertion leads to characteristic, delayed onset exacerbations that are not relieved by sleep. We have modeled exertional exhaustion by comparing magnetic resonance images from before and after submaximal exercise. One third of the 27 GWI participants had brain stem atrophy and developed postural tachycardia after exercise (START: Stress Test Activated Reversible Tachycardia). The remainder activated basal ganglia and anterior insulae during a cognitive task (STOPP: Stress Test Originated Phantom Perception). Here, the role of attention …

Remediating Soil For Successful Vegetation Establishment Along Nebraska Highways, Shad Mills, Martha Mamo, Walt Schacht, Humberto Blanco-Canqui

Nebraska Department of Transportation: Research Reports

Vegetation along roadsides is important to prevent soil erosion, provide habitat, and filter water running off the road. Vegetation close to the pavement along highways in Nebraska does not readily establish and persist. It is thought that the sodium and bulk density are the driving factors behind the lack of vegetation. After a construction project the shoulder is seeded into the compacted soil, and during winter salts can accumulate in the soil because of deicing agents being used. The purpose of our study was to determine if the sodium and bulk density are the driving factors of the vegetation cover. …

Establishment Of Wildflower Islands To Enhance Roadside Health And Aesthetics, Walter Schacht, Judy Wu-Smart

Nebraska Department of Transportation: Research Reports

Wildflowers are crucial in the ecological function of the low-input roadside plant communities in terms of water andnutrient cycling, nutrient inputs such as nitrogen, total plant canopy cover, stand longevity, and provision of habitat for numerous small animals. Further, wildflowers provide critical foraging and nesting resources for birds, insects, and other wildlife. Unfortunately, habitat loss from agricultural and urban development has led to rapid population declines in wild bees and other pollinators across the US, thereby jeopardizing not only food production but also the sustainability of our natural landscapes (Kearns & Inouye, 1997). One way to mitigate wild bee decline …

Pi‑Plat: A High‑Resolution Image‑Based 3d Reconstruction Method To Estimate Growth Dynamics Of Rice Inflorescence Traits, Jaspreet Sandhu, Feiyu Zhu, Puneet Paul, Tian Gao, Balpreet K. Dhatt, Yufeng Ge, Paul E. Staswick, Hongfeng Yu, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Background: Recent advances in image-based plant phenotyping have improved our capability to study vegetative stage growth dynamics. However, more complex agronomic traits such as inflorescence architecture (IA), which predominantly contributes to grain crop yield are more challenging to quantify and hence are relatively less explored. Previous efforts to estimate inflorescence-related traits using image-based phenotyping have been limited to destructive end-point measurements. Development of non-destructive inflorescence phenotyping platforms could accelerate the discovery of the phenotypic variation with respect to inflorescence dynamics and mapping of the underlying genes regulating critical yield components.

Results: The major objective of this study is to evaluate …

Association Of Serum Γ-Tocopherol Levels With Mortality: The Multiethnic Cohort Study, Weiwen Chai, Gertraud Maskarinec, Adrian A. Franke, Kristine R. Monroeuniversity Of Southern California, Song-Yi Park, Laurence N. Kolonel, Lynne R. Wilkens, Loïc Le Marchand, Robert V. Cooney

Department of Nutrition and Health Sciences: Faculty Publications

Background/Objectives—γ-Tocopherol has unique properties that protect against nitrogen oxide-mediated cellular damage. To elucidate the potential role of γ-tocopherol in the aging process, we examined the associations of serum γ-tocopherol levels with all-cause and cause-specific mortality.

Subjects/Methods—Among participants in the biorepository subcohort of the Multiethnic Cohort Study, pre-cancer diagnostic serum γ-tocopherol levels were measured in a subset of 3904 men and 4461 women. Of these, 22.7% of men and 13.5% of women died during a mean follow- up time of 9.6±2.6 years. Hazard ratios (HRs) and 95% confidence intervals (95%CIs) for mortality associated with γ-tocopherol were estimated by Cox proportional hazards …

Antimicrobial Peptide Identification Using Multi-Scale Convolutional Network, Xin Su, Jing Xu, Yanbin Yin, Xiongwen Quan, Han Zhang

Department of Food Science and Technology: Faculty Publications

Background: Antibiotic resistance has become an increasingly serious problem in the past decades. As an alternative choice, antimicrobial peptides (AMPs) have attracted lots of attention. To identify new AMPs, machine learning methods have been commonly used. More recently, some deep learning methods have also been applied to this problem.

Results: In this paper, we designed a deep learning model to identify AMP sequences. We employed the embedding layer and the multi-scale convolutional network in our model. The multi-scale convolutional network, which contains multiple convolutional layers of varying filter lengths, could utilize all latent features captured by the multiple convolutional layers. …

Chloroviruses, James L. Van Etten, Irina V. Agarkova, David D. Dunigan

Nebraska Center for Virology: Faculty Publications

Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 …

Divergent Phenotypic Response Of Rice Accessions To Transient Heat Stress During Early Seed Development, Puneet Paul, Balpreet K. Dhatt, Jaspreet Sandhu, Waseem Hussain, Larissa Irvin, Gota Morota, Paul E. Staswick, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Increasing global surface temperatures is posing a major food security challenge. Part of the solution to address this problem is to improve crop heat resilience, especially during grain development, along with agronomic decisions such as shift in planting time and increasing crop diversification. Rice is a major food crop consumed by more than 3 billion people. For rice, thermal sensitivity of reproductive development and grain filling is well-documented, while knowledge concerning the impact of heat stress (HS) on early seed development is limited. Here, we aim to study the phenotypic variation in a set of diverse rice accessions for elucidating …

Diary Of A Service Dog (Dropout), Kristen An Horton, Heidi Anne Horton Pittman

Zea E-Books Collection

My name is Granger. I am a Labrador Retriever. I want to be a service dog. It is not always easy. This is my story. (Human's note: The most important take away is that the public, children and adults, need to learn how to not interact with service dogs. As Granger says, “I’m cute. I’m working. Please ignore me.”)

Management Controls The Net Greenhouse Gas Outcomes Of Growing Bioenergy Feedstocks On Marginally Productive Croplands, Virginia L. Jin, Marty Schmer, Catherine E. Stewart, Robert B. Mitchell, Candiss O. Williams, Brian J. Wienhold, Gary Varvel, Ronald F. Follett, John Kimble, Kenneth P. Vogel

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Bio-based energy is key to developing a globally sustainable low-carbon economy. Lignocellulosic feedstock production on marginally productive croplands is expected to provide substantial climate mitigation benefits, but long-term field research comparing greenhouse gas (GHG) outcomes during the production of annual versus perennial crop-based feedstocks is lacking. Here, we show that long-term (16 years) switchgrass (Panicum virgatum L.) systems mitigate GHG emissions during the feedstock production phase compared to GHG-neutral continuous corn (Zea mays L.) under conservation management on marginally productive cropland. Increased soil organic carbon was the major GHG sink in all feedstock systems, but net agronomic GHG outcomes …

Representative Economic Budgets For Nebraska Cow Herds, Glennis Mcclure, Jay Parsons

Cornhusker Economics

In 2017, the University of Nebraska-Lincoln Institute of Agricultural and Natural Resources (IANR) and Nebraska Extension made a commitment to implement a multidisciplinary Beef Systems Initiative (BSI). BSI is administered by the Center for Grassland Studies and is comprised of six projects designed to develop and support implementation of beef production systems that optimize feed resource use, natural resource conservation, and producer success in Nebraska through improved management of perennial grasslands and systems of integrated crop-beef cattle production. In addition to BSI, a parallel project funded by the Foundation for Food and Agriculture Research (FFAR) is studying the best practices …

A Model For The Prediction Of Antimicrobial Resistance In Escherichia Coli Based On A Comparative Evaluation Of Fatty Acid Profiles, Randal S. Stahl, Bledar Bisha, Sebabrata Mahapatra, Jeffrey C. Chandler

USDA Wildlife Services: Staff Publications

Antimicrobial resistance is a threat to agricultural production and public health. In this proof-of-concept study, we investigated predicting antimicrobial sensitive/resistant (S/R) phenotypes and host sources of Escherichia coli (n = 128) based on differential fatty acid abundance. Myristic (14:0), pentadecanoic acid (15:0), palmitic (16:0), elaidic (18:19) and steric acid (18:0) were significantly different (α = 0.05) using a two-way ANOVA for predicting nalidixic acid, ciprofloxacin, aztreonam, cefatoxime, and ceftazidime S/R phenotypes. Additionally, analyses of palmitoleic (16:1), palmitic acid (16:0), methyl palmitate (i-17:0), and cis-9,10-methyleneoctadecanoic acid (19:0Δ) showed these markers were significantly different (α = 0.05) between isolates obtained from cattle …

Genetic Taster Status As A Mediator Of Neural Activity And Swallowing Mechanics In Healthy Adults, Angela M. Dietsch, Ross M. Westemeyer, William G. Pearson Jr., Douglas H. Schultz

Center for Brain, Biology, and Behavior: Faculty and Staff Publications

As part of a larger study examining relationships between taste properties and swallowing, we assessed the influence of genetic taster status (GTS) on measures of brain activity and swallowing physiology during taste stimulation in healthy men and women. Twenty-one participants underwent videofluoroscopic swallowing study (VFSS) and functional magnetic resonance imaging (fMRI) during trials of high-intensity taste stimuli. The precisely formulated mixtures included sour, sweet-sour, lemon, and orange taste profiles and unflavored controls. Swallowing physiology was characterized via computational analysis of swallowing mechanics plus other kinematic and temporal measures, all extracted from VFSS recordings. Whole-brain analysis of fMRI data assessed blood …

Treehoppers (Hemiptera: Aetalionidae And Membracidae) From Madre De Dios Region, Peru, Chung-Ping Lin, Munetoshi Maruyama, Jo-Fan Wang, Paige E. Miller, Caroline S. Chaboo

Department of Entomology: Faculty Publications

A list of treehoppers (Aetalionidae and Membracidae) is presented from Madre de Dios region at the southeastern Amazon basin in Peru. The treehopper specimens were collected as by-catch in a survey of the beetles in the Villa Carmen Biological Station and Los Amigos Biological Station. The list comprises 44 species, 31 genera, 16 tribes and 9 subfamilies. Ten genera are new records to Peru. The images of representative specimens of each identified species and genera are provided to facilitate the identification of the local treehopper fauna.

Resumen: Se presenta una lista de los membrácidos (Aetalionidae y Membracidae) de la región …

A Self-Marker-Like Protein Governs Hemocyte Allorecognition In Halocynthia Roretzi, Masaki Ema, Taizo Okada, Miki Takahashi, Masato Uchiyama, Hideo Kubo, Hideaki Moriyama, Hitoshi Miyakawa, Midori Matsumoto

School of Biological Sciences: Faculty Publications

Background: Self-incompatibility, fusion/non-fusion reactions, and contact reactions (CRs) have all been identified as allorecognition phenomena in ascidians. CR is a reaction characteristic of the hemocytes of Halocynthia roretzi, whereby they release phenol oxidase (PO) upon contact with non-self hemocytes. Thus, these cells may represent a primitive form of the vertebrate immune system. In the present study, we focused on the CR of H. roretzi hemocytes and sought to identify self-marker proteins that distinguish between self and non-self cells.

Results: We initially generated a CR-inducing monoclonal antibody against the complete hemocyte membraneprotein complement (mAb11B16B10). This antibody was identified based on the …

Postharvest Heat Treatments To Inhibit Penicillium Digitatum Growth And Maintain Quality Of Mandarin (Citrus Reticulata Blanco), Diana B. Queb-Gonzalez, Aurelio Lopez-Malo, María E. Sosa-Morales, Rossana Villa-Rojas

Department of Food Science and Technology: Faculty Publications

Use of fungicides is a common practice as a postharvest treatment to control fruit decay. Nowadays, environment-friendly technologies, such as heat treatments, are viable replacements. This study evaluated the effects of post-harvest heat treatments (traditional and microwave-assisted) on mandarins intentionally inoculated with Penicillium digitatum. For the studied heat treatments, the target temperature was 50C, which was held for 2.5 min. After heating, mandarins were cooled and stored at 25C for 13 days. MW treatments effectively prevented mold growth during storage, while HW only delayed it. Control mandarins (without treatment) showed the highest significant weight loss. Neither thermal treatment nor storage …

A Novel And Green Nanoparticle Formation Approach To Forming Low-Crystallinity Curcumin Nanoparticles To Improve Curcumin’S Bioaccessibility, Ali Ubeyitogullari, Ozan Ciftci

Department of Food Science and Technology: Faculty Publications

Health-promoting effects of curcumin are well-known; however, curcumin has a very low bioavailability due to its crystalline structure. The main objective of this study was to develop a novel green nanoparticle formation method to generate low-crystallinity curcumin nanoparticles to enhance the bioavailability of curcumin. Nanoporous starch aerogels (NSAs) (surface area of 60 m2/g, pore size of 20 nm, density of 0.11 g/cm3, and porosity of 93%) were employed as a mold to produce curcumin nanoparticles with the help of supercritical carbon dioxide (SC-CO2). The average particle size of the curcumin nanoparticles was 66 nm. Impregnation into NSAs decreased the crystallinity …

From Field To Film: Mosquito Surveillance And Survey Of Us Adults' Knowledge And Attitudes Towards Arthropod-Borne Disease Vectors, Justine Laviolette

Department of Entomology: Dissertations, Theses, and Student Research

Mosquito-borne disease is a public health challenge that warrants an active surveillance program for the identification of mosquito populations and the education of the public for prevention and protection against disease-transmitting arthropods. The communication of science to the public is necessary to prevent disease, change behavior, and promote a dialog between scientists and the public.

People are accustomed to high quality entertainment, which begs the question, “If we made science more entertaining, would the public be more interested?”

To address these issues, the objectives of this study are: 1) identify mosquito species and abundance at the US Meat Animal Research …

Accrual Accounting And The Farm Business, Part Ii, Tim L. Meyers

Cornhusker Economics

My last Cornhusker Economics article, Accounting Assumptions and the Farm Business (10-16-19) set the foundation for a specific evaluation of the conceptual framework accrual accounting offers the farm or ranch manager. The article addressed cash accounting and hinted at its shortfalls which were rectified by accrual accounting. This article will explain conceptual frameworks, and two accrual accounting principles; namely the revenue recognition principle and the matching principle.

During one of my graduate school experiences, I encountered a professor who seemed to be in love with conceptual frameworks. I chose a framework and tried to use it as instructed, but it …

Deep Kernel And Deep Learning For Genome-Based Prediction Of Single Traits In Multienvironment Breeding Trials, José Crossa, Johannes W.R. Martini, Daniel Gianola, Paulino Pérez-Rodríguez, Diego Jarquin, Philomin Juliana, Osval Antonio Montesinos López, Jaime Cuevas

Department of Agronomy and Horticulture: Faculty Publications

Deep learning (DL) is a promising method for genomic-enabled prediction. However, the implementation of DL is difficult because many hyperparameters (number of hidden layers, number of neurons, learning rate, number of epochs, batch size, etc.) need to be tuned. For this reason, deep kernel methods, which only require defining the number of layers, may be an attractive alternative. Deep kernel methods emulate DL models with a large number of neurons, but are defined by relatively easily computed covariance matrices. In this research, we compared the genome-based prediction of DL to a deep kernel (arc-cosine kernel, AK), to the commonly used …

Structural Basis Of Non-Canonical Transcriptional Regulation By The A-Bound Iron-Sulfur Protein Whib1 In M. Tuberculosis, Tao Wan, Shanren Li, Daisy Guiza Beltran, Andrew Schacht, Lu Zhang, Donald F. Becker, Limei Zhang

Department of Biochemistry: Faculty Publications

WhiB1 is amonomeric iron–sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress inM. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 A° -resolution crystal structure of the [4Fe–4S] cluster-bound (holo- )WhiB1 in complex with the C-terminal domain of the 70-family primary sigma factor A of M. tuberculosis containing the conserved region 4 (A 4). Region 4 of the 70-family primary sigma factors is commonly used by transcription factors …

Plant Hormones Differentially Control The Sub-Cellular Localization Of Plasma Membrane Microdomains During The Early Stage Of Soybean Nodulation, Zhenzhen Qiao, Prince Zogli, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

Phytohormones regulate the mutualistic symbiotic interaction between legumes and rhizobia, nitrogen-fixing soil bacteria, notably by controlling the formation of the infection thread in the root hair (RH). At the cellular level, the formation of the infection thread is promoted by the translocation of plasma membrane microdomains at the tip of the RH. We hypothesize that phytohormones regulate the translocation of plasma membrane microdomains to regulate infection thread formation. Accordingly, we treated with hormone and hormone inhibitors transgenic soybean roots expressing fusions between the Green Fluorescent Protein (GFP) and GmFWL1 or GmFLOT2/4, two microdomain-associated proteins translocated at the tip of the …

Critical Time For Weed Removal In Corn (Zea Mays L.) As Influenced By Pre Herbicides, Ayse Nur Ulusoy

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

A weed control program that utilizes PRE herbicides and ensures a timely post-emergence weed removal could protect growth and yield of corn. The use of pre-emergence (PRE) herbicides for weed control could reduce the need for multiple POST applications of glyphosate in glyphosate-tolerant (GT) corn and provide an additional mode of action for combating glyphosate-resistant weeds. Thus, field studies were conducted in 2017 and 2018 at Concord, NE with the following objectives develop weed management recommendations that considers soil applied herbicides and determine proper timing of glyphosate based on the crop growth stage.

Therefore the material in this thesis is …

The Impact Of Veterans Treatment Courts On The Community, Daniela Mettos, Amanda Leingang

Cornhusker Economics

With the United States’ ongoing presence in the Middle East and the ever-present possibility of future conflict, the commitment to tend to the unique needs of veterans returning from combat is an essential one. The number of veterans suffering from mental health issues, substance abuse disorders, and physical trauma continues to rise. With this comes an increased risk of Intimate Partner Violence (IPV), drug and alcohol abuse, and repeating criminal behavior, all of which increase the likelihood that veterans will find themselves involved in the criminal justice system at some point following their combat service.

Utilizing effective, reliable, and focused …

Individual Based Model To Simulate The Evolution Of Insecticide Resistance, William B. Jamieson

Department of Mathematics: Dissertations, Theses, and Student Research

Insecticides play a critical role in agricultural productivity. However, insecticides impose selective pressures on insect populations, so the Darwinian principles of natural selection predict that resistance to the insecticide is likely to form in the insect populations. Insecticide resistance, in turn, severely reduces the utility of the insecticides being used. Thus there is a strong economic incentive to reduce the rate of resistance evolution. Moreover, resistance evolution represents an example of evolution under novel selective pressures, so its study contributes to the fundamental understanding of evolutionary theory.

Insecticide resistance often represents a complex interplay of multiple fitness trade-offs for individual …

High-Throughput Nano-Scale Characterization Of Membrane Proteins Using Fluorescence-Detection Size-Exclusion Chromatography, Alex J. Vecchio, Robert M. Stroud

Department of Biochemistry: Faculty Publications

Structural biology has revealed predicting heterologous expression levels, homogeneity, and stability of a protein from its primary structure are exceedingly difficult. Membrane proteins, in particular, present numerous challenges that make obtaining milligram quantities of quality samples problematic. For structural and functional investigation of these molecules, however, this is what is required. Fluorescence size-exclusion chromatography (F-SEC), a technique where a protein of biological interest is fused to green fluorescent protein (GFP) and monitored, circumvents many bottlenecks inherent to membrane protein structural biology. In vivo expression yields, as well as in vitro homogeneity and stability, can be rapidly evaluated utilizing nanogram quantities …

Ephemeroptera (Insecta) In Cuba, Carlos Naranjo L., Janice G. Peters, Pedro López Del Castillo

Insecta Mundi

Systematic, faunistic and ecological aspects of the six families and 34 species and subspecies in the order Ephemeroptera currently recorded from Cuba are reviewed based primarily on a reference collection located at the Universidad de Oriente (Santiago de Cuba), collections at the Institute of Ecology and Systematics (Havana) and historic literature. A key to nymphs is included with photographs of significant features of many species. An annotated list of species is presented with comments on type localities, species ecology and distribution. The morpho- ecological types of the nymphs are updated according to current taxonomic changes, and indicator species of organic …

Genus Olivensa Lane, 1965 In French Guiana, And Description Of A New Species (Coleoptera: Cerambycidae: Lamiinae), Pierre-Henri Dalens, Frédéric Robin

Insecta Mundi

Olivensa sonzognii Dalens and Robin, sp. nov. (Coleoptera: Cerambycidae: Lamiinae) is described from French Guiana and compared to other local species. A new key for the genus Olivensa Lane, 1965 is proposed.

Notes On The Natural History Of Plesioclytus Morrisi Wappes And Skelley, 2015 And Plesioclytus Relictus Giesbert, 1993 (Coleoptera: Cerambycidae), Kyle E. Schnepp

Insecta Mundi

The host plant and life history observations of Plesioclytus morrisi Wappes and Skelley and Plesioclytus relictus Giesbert (Coleoptera: Cerambycidae: Plesioclytini) are described for the first time. The host for both species is shown to be Polygonum polygamum Vent. (Polygonaceae). Observations also indicate that plants chosen for oviposition occur in open sand areas of scrub habitat.