Digital Commons Network^™

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′′ …

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 …

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 …

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 …

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 …

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

United States Department of Agriculture 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 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 …

Integrating Lidar Data And Multi-Temporal Aerial Imagery To Map Wetland Inundation Dynamics Using Google Earth Engine, Qiusheng Wu, Charles B. Lane, Xuecao Li, Kaiguang Zhao, Yuyu Zhou, Nicholas Clinton, Ben Devries, Heather E. Golden, Megan W. Lang

United States Environmental Protection Agency: Publications

The Prairie Pothole Region of North America is characterized by millions of depressional wetlands, which provide critical habitats for globally significant populations of migratory waterfowl and other wildlife species. Due to their relatively small size and shallow depth, these wetlands are highly sensitive to climate variability and anthropogenic changes, exhibiting inter- and intra-annual inundation dynamics. Moderate-resolution satellite imagery (e.g., Landsat, Sentinel) alone cannot be used to effectively delineate these small depressional wetlands. By integrating fine spatial resolution Light Detection and Ranging (LiDAR) data and multi-temporal (2009–2017) aerial images, we developed a fully automated approach to delineate wetland inundation extent at …

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 …

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 …

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 …

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 …

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 …

Optimal Allocation Of Energy Storage And Wind Generation In Power Distribution Systems, Carlos Mendoza

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

The advent of energy storage technologies applications for the electric power system gives new tools for planners to cope with the operation challenges that come from the integration of renewable generation in medium voltage networks. This work proposes and implements an optimization model for Battery Energy Storage System (BESS) and distributed generation allocation in radial distribution networks. The formulation aims to assist distribution system operators in the task of making decisions on energy storage investment, BESSs' operation, and distributed generation penetration's level to minimize electricity costs. The BESSs are required to participate in energy arbitrage and voltage control. In addition, …

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 …

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 …

Two New Species And Two New Combinations In Saphenista Walsingham, 1914 From Western North America (Lepidoptera: Tortricidae), John W. Brown

Insecta Mundi

Saphenista bartellae Brown, new species (TL: Colorado), and S. powelli Brown, new species (TL: California) (Lepidoptera: Tortricidae), are described and illustrated. Two other western North American species, S. latipunctana (Walsingham, 1879), new combination, and S. dilutana (Walsingham, 1879), new combination, are transferred to Saphenista based on morphology of the genitalia.

A New Species Of Allomallodon Santos-Silva And Galileo, 2010 From Bolivia (Coleoptera: Cerambycidae: Prioninae: Macrotomini), James E. Wappes, Antonio Santos-Silva

Insecta Mundi

A new species of Allomallodon Santos-Silva and Galileo, 2010, A. bolivianus Wappes and Santos-Silva (Coleoptera: Cerambycidae: Prioninae: Macrotomini), is described from Bolivia and a key is provided to separate the three species now assigned to the genus.

Thopeutica Petertaylori, A New Tiger Beetle Species (Coleoptera: Cicindelidae) From Mindanao, Philippines, Milton Norman D. Medina, Analyn A. Cabras, Jürgen Wiesner

Insecta Mundi

Thopeutica (Thopeutica) petertaylori Medina, Cabras and Wiesner (Coleoptera: Cicindelidae), new species, is described from the Cagan river, New Bataan, Mindanao. It is characterized by the metallic ground colour of the elytra, prominent middle tooth in the labrum, and bottle-shaped aedeagus with apical hook.

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 …

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.

Lepidoptera Pests Of Sapodilla (Manilkara Zapota (L.) Van Royen) In South Florida, With Some Comments On Life History And Natural Control, Jose I. Martinez, Jonathan H. Crane, Jeff Wasielewski, Jacqueline Y. Miller, Daniel Carrillo

Insecta Mundi

Sapodilla (Manilkara zapota (L.) van Royen) is originally from the Neotropics, and has become one of the most important tropical crops in the last few decades. The major producers include India, Mexico, Sri Lanka, the Philippines, Venezuela and Guatemala. It is also a minor crop in the United States, specifically South Florida. In 2015, it was reported that Florida growers suffered a loss of up to 80% of their production due to lepidopteran pests. We surveyed two sapodilla orchards weekly in South Florida for about six months. We collected 1,070 lepidopteran individuals (i.e., larvae, pupae and adults) belonging to seven …

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.

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 …

Modeling Elementary Students’ Ideas About Heredity: A Comparison Of Curricular Interventions, Cory Forbes, Dante Cisterna, Devarati Bhattacharya, Ranu Roy

School of Natural Resources: Faculty Publications

Learning about heredity is important across the K–12 continuum. However, these ideas may be challenging for students. We examined third-grade students’ ideas about heredity in the context of a new, six-week, model-based science unit that uses corn as a model organism to support students’ ideas about heredity. We analyzed data collected during implementation of the unit, including student artifacts and interviews. We compared these data to those from a pilot version of the curriculum – implemented in the prior year – that was focused on the same disciplinary concepts but was not designed around scientific modeling. Our findings illustrate levels …

Index To Volume 87

Nebraska Bird Review

14 pages: Akers, Danny 108 to Zeglen, Nancy 45