Digital Commons Network^™

Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan, Peter Revesz

School of Computing: Faculty Publications

Evolutionary studies usually assume that the genetic mutations are independent of each other. However, that does not imply that the observed mutations are independent of each other because it is possible that when a nucleotide is mutated, then it may be biologically beneficial if an adjacent nucleotide mutates too. With a number of decoded genes currently available in various genome libraries and online databases, it is now possible to have a large-scale computer-based study to test whether the independence assumption holds for pairs of adjacent amino acids. Hence the independence question also arises for pairs of adjacent amino acids within …

Physiological Evidence For Isopotential Tunneling In The Electron Transport Chain Of Methane-Producing Archaea, Nikolas Duszenko, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli. We found the quantity of MPh per …

Clearing Muddied Waters: Capture Of Environmental Dna From Turbid Waters, Kelly E. Williams, Kathryn P. Huyvaert, Antoinette J. Piaggio

United States Department of Agriculture Wildlife Services: Staff Publications

Understanding the differences in efficiencies of various methods to concentrate, extract, and amplify environmental DNA (eDNA) is vital for best performance of eDNA detection. Aquatic systems vary in characteristics such as turbidity, eDNA concentration, and inhibitor load, thus affecting eDNA capture efficiency. Application of eDNA techniques to the detection of terrestrial invasive or endangered species may require sampling at intermittent water sources that are used for drinking and cooling; these water bodies may often be stagnant and turbid. We present our best practices technique for the detection of wild pig eDNA in water samples, a protocol that will have wide …

Linguistics And Lis: A Research Agenda, Mary K. Bolin

University of Nebraska-Lincoln Libraries: Faculty Publications

No abstract provided.

Ectoparasitic Mites Of The Genus Gigantolaelaps (Acari: Mesostigmata: Laelapidae) Associated With Small Mammals Of The Genus Nephelomys (Rodentia: Sigmodontinae), Including Two New Species From Peru, Donald D. Gettinger, Scott Lyell Gardner

Scott L. Gardner Publications

An extensive survey of small mammals and ectoparasites along an altitudinal transect in the Manu Biodiversity Reserve in Peru found the sigmodontine rodent genus Nephelomys infested by mites of the genus Gigantolaelaps Fonseca, 1939. Two distinct species co-occurred exclusively in the pelage of Nephelomys keaysi, G. inca Fonseca and G. minima n. sp. Nephelomys levipes, which replaces N. keaysi at higher elevations, was infested exclusively with a single new species, G. nebulosa n. sp. In this paper, we formally describe these new mite species, and provide more information on the morphology of G. inca.

Nuclear Weapons In A Changing Climate: Probability, Increasing Risks, And Perception, Adam Liska, Tyler R. White, Eric Holley, Robert J. Oglesby

Adam Liska Papers

Many people tend to think that the outcome of any nuclear weapons use today will result in an escalatory situation with apocalyptic outcomes for the countries involved. Yet many factors are increasing the probability of the limited use of nuclear weapons (e.g., 1 to 20 warheads) in a range of conflict scenarios. Previous atmospheric model simulations of regional nuclear conflicts employing many relatively small bombs have been estimated to cause a global “nuclear autumn,” with great reductions in agricultural productivity, stratospheric ozone loss, and spread of hazardous radioactive fallout. The totality of these effects would result in widespread damage …

Center For Grassland Studies, Volume 23, Issue 2, Summer 2017

Center for Grassland Studies: Newsletters

2017 Nebraska Grazing Conference

Grazing Livestock Systems Internship

2017 Fall Seminar Series & Leu Lecture

PGA Golf Management Club Officers Selected for 2017-2018

Workshop … The Changing Face of Engagement: Reaching the 21st Century Forest and Rangeland Client

Congratulations, Graduates!

CGS Alumni Updates

2017 Nike Golf Camp

Kudos to PGAM Faculty and Staff

Frank L. and Mary Bruning Honored with First Annual Nebraska Grazing Lands Coalition Lifetime Achievement Award

Roadside Vegetation in Nebraska

Katie Cumming—Grazing Livestock Systems Graduate Research Assistant

An Update on Prairies in the Sky: Green Roofs

Spring Creek Prairie’s Outdoor Dinner Fundraiser

UNL Alum Qualifies for 99th …

Droughtscape, Summer 2017, National Drought Mitigation Center

DroughtScape: Quarterly Newsletter of the National Drought Mitigation Center (2007–2023)

Contents

Drought policy write shops conclude in Caribbean

Drought encroaches on Northern Plains in second quarter

Impact tool racks up submissions in second quarter

Maps on new website highlight drought effects on ag industry

Centers release new flash drought tool: QuickDRI

NDMC contributes to EU report on disaster risk management

Groups earn Climate Adaptation award for work with tribes

NDMC, ICPAC director talk collaboration on drought in Greater Horn of Africa

Up next in MENA: Drought vulnerability assessments

Telling Fire’S Story Through Narrative And Art, Stephen W. Barrett

Joint Fire Science Program Digests

Modern works by highly skilled narrative authors and artists have become increasingly useful for telling the story of wildland fire in the United States. Using unconventional means—and with partial funding by the Joint Fire Science Program—creative individuals have spawned some colorful and heartfelt messages that convey insightful information about wildland fire, climate, and other elements of nature to an increasingly receptive public. Recent narrative works by well-known authors, such as Stephen J. Pyne, and creative art pieces by well-established and emerging artists have helped depict fire in a new light to audiences that scientists may rarely reach. This issue of …

Fish & Wildlife News: Summer 2017, Matt Trott

Fish and Wildlife News

No abstract provided.

Behavioral And Pharmacological Validation Of An Integrated Fear-Potentiated Startle And Prepulse Inhibition Paradigm, Mengjiao Zhang, Ming Li

Department of Psychology: Faculty Publications

Fear-potentiated startle (FPS) and prepulse inhibition (PPI) of acoustic startle are two widely used paradigms specifically designed to capture the impact of negative emotion (e.g. fear) and preattentive function on startle response. Currently, there is no single paradigm that incorporates both FPS and PPI, making it impossible to examine the potential interactions between fear and attention in the regulation of startle response. In this study, we developed an integrated FPS and PPI test protocol and validated it with psychoactive drugs. In Experiment 1, male Sprague-Dawley rats were randomly assigned to one of five groups, receiving either Light -Shock conditioning trials, …

American Society Of Parasitologists Newsletter, Volume 39, Number 1, Summer 2017, Scott Lyell Gardner

American Society of Parasitologists: Newsletter

Summer 2017 issue of the ASP newsletter.

Nebline, July 2017

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: The Road to Great (and Safe!) Grilling

Food & Health

Farm & Acreage

Pests & Wildlife

Horticulture

Early Childhood

4-H & Youth

and other extension news and events

Bat Community Composition And Monitoring For White-Nose Syndrome At First State National Historical Park, Delaware And Pennsylvania, Juliet Nagel, J. Edward Gates

United States National Park Service: Publications

Abstract

In recent years, bats have faced increasingly deadly threats on multiple fronts. Cave-dwelling bats have been decimated by the emergence of a disease, white-nose syndrome (WNS), caused by a fungal pathogen, Pseudogymnoascus destructans; and tree bats are dying in large numbers at wind power facilities. First State National Historical Park (FRST) is a new national park unit located in northern Delaware and Pennsylvania. Prior to this study, little information was available on bat species and their activity and distribution within FRST. To fill this knowledge gap, we conducted an inventory of bat species present at FRST. We used …

Cross Reactivity Of Immune Responses To Porcine Reproductive And Respiratory Syndrome Virus Infection, Ignacio Correas, Fernando A. Osorio, David Steffen, Asit K. Pattnaik, Hiep L. X. Vu

School of Veterinary and Biomedical Sciences: Faculty Publications

Because porcine reproductive and respiratory syndrome virus (PRRSV) exhibits extensive genetic variation among field isolates, characterizing the extent of cross reactivity of immune responses, and most importantly cell-mediated immunity (CMI), could help in the development of broadly cross-protective vaccines. We infected 12 PRRSV-naïve pigs with PRRSV strain FL12 and determined the number of interferon (IFN)-γ secreting cells (SC) by ELISpot assay using ten type 2 and one type 1 PRRSV isolates as recall antigens. The number of IFN-γ SC was extremely variable among animals, and with exceptions, late to appear. Cross reactivity of IFN-γ SC among type 2 isolates was …

Water Current, Volume 49, No. 3, Summer 2017

Water Current Newsletter

New University competition is “Testing Ag Performance Solutions”

Summer brings research work, students, tours and farm shows

Benchmarking The Energy Intensity Of Small Nebraska Wastewater Treatment Plants, Steven M. Hanna

Department of Environmental Engineering: Theses and Other Student Research

To help small communities improve the energy efficiency of their wastewater treatment plants, this study created energy benchmarking models for small wastewater plants serving populations of 10,000 or less and having average flows less than 1.5 million gallons per day (MGD). The purpose of these models is to allow comparisons among plants of similar type and size, identify what factors most significantly impact energy usage, and predict potential savings from changes in key plant characteristics.

Energy usage and plant data from 83 small, mechanical wastewater plants in Nebraska were collected and used to create energy benchmarking models. Data obtained from …

Querying And Visualization Of Moving Objects Using Constraint Databases, Semere M. Woldemariam

School of Computing: Dissertations, Theses, and Student Research

Good querying and visualization of moving objects and their trajectories is still an open problem. This thesis investigates three types of moving objects. First, projectiles, whose parabolic motion is difficult to represent. Second, moving objects that slide down a slope. The representation of these objects is challenging because of their accelerating motion. Third, the motion of migrating animals. The motion of migrating animals is challenging because it also involves some spatio-temporal interpolation. The thesis shows a solution to these problems using ideas from physics and an implementation in the MLPQ constraint databases system. The MLPQ implementation enables several complex spatio-temporal …

Induction And Suppression Of Antiviral Rna Silencing By Tomato Spotted Wilt Virus, Sergio M. Gabriel Peralta

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

Tomato spotted wilt virus (TSWV) is an emerging pathogen with wide host range and one of the most important viruses of plants. Information regarding processing of negative single stranded RNA viruses such as TSWV in the RNA silencing pathway remains limited. In nature TSWV is only transmitted by thrips as vectors and since infection occurs in both thrips and plants, an experimental system to transmit using thrips and the detection of TSWV were established. In order to understand the processing of TSWV in the RNA silencing pathway, Arabidopsis thaliana as a model plant was used in the genetic analysis against …

Recreational Angler Site Choice And Behavior Within Midwestern Reservoirs, Brian S. Harmon

School of Natural Resources: Dissertations, Theses, and Student Research

Anglers are the dominant predator in most inland fisheries. Although anglers make decisions across multiple scales, most research targets larger spatial and temporal scales of angler behavior, and thus little is known regarding angler behavior within a fishing trip. Outcomes of within-trip behavior affect larger spatial and temporal scales and are thus important to the management of recreational fisheries. Bank angler site choice was recorded at four reservoirs in the Salt Valley system across the open-water season of 2016. Previous research indicated that angler distribution did not match the distribution of fish, so another approach was taken. Counts of anglers …

Trophic Dynamics Of Flathead Catfish In The Missouri River Bordering Nebraska, Dylan R. Turner

School of Natural Resources: Dissertations, Theses, and Student Research

Understanding the trophic dynamics of large, riverine ecosystems is complex and requires knowledge from several inputs and outputs of the ecosystem. Most riverine ecosystems have been altered in some way whether through damming, channelizing, or diverting water. The Missouri River is not immune to these anthropogenic alterations. The river has dams throughout its middle portion and is channelized from Sioux City, Iowa to its confluence with the Mississippi River. Flathead Catfish pylodictus olivarius are one of the most ecologically harmful introduced species but little research has looked at the influence native populations of Flathead Catfish have on native prey populations …

Middle Miocene Paleoenvironmental Reconstruction Of The Central Great Plains From Stable Carbon Isotopes In Large Mammals, Willow H. Nguy

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

Middle Miocene (18-12 Mya) mammalian faunas of the North American Great Plains contained a much higher diversity of apparent browsers than any modern biome. This has been attributed to greater primary productivity, which may have supported greater browser diversity that commonly corresponds with densely vegetated habitats. However, several lines of proxy evidence suggest that open woodlands or savannas dominated middle Miocene biomes; neither of which support many browsers today. Stable carbon isotopes in mammalian herbivore tooth enamel were used to reconstruct vegetation structure of middle Miocene biomes.

Stable carbon isotopes in C₃ dominated environments reflect vegetation density and herbivores …

Attenuating The Side Effects Of Caloric Restriction Through Exercise And Increased Protein Intake, Jay A. Petersen

Department of Nutrition and Health Sciences: Dissertations, Theses, and Student Research

The effects of caloric restriction (CR) on weight loss and health outcomes are documented, but few controlled studies have addressed its effect on performance. Fat free mass (FFM) is reduced during CR, which may impair performance. The purpose of this thesis was to explore the capacity of these strategies to attenuate the side-effects of calorie-restricted weight loss: Exercise, which preserves FFM during CR, may be employed to maintain performance in an energy-deficient state, and a high protein intake may work in combination with exercise to further protect FFM and performance. Two studies were utilized to address this purpose. In study …

Dissecting The Genetic Basis Of Salt Tolerance In Rice (Oryza Sativa), Malachy Thomas Campbell

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

Excessive salt is a major factor limiting crop productivity. Rice is an important food crop worldwide, and provides a major source of calories for billions of people in tropical and subtropical developing countries. In many regions throughout Southeast Asia, rice is grown in low-lying coastal regions, which are prone to ingress by seawater. Rice is highly sensitive to salt stress, with mild salinity resulting in large reductions in yield. Improving salt tolerance in rice is essential for ensuring food security for many individuals throughput the developing world.

In this work, the overall goals were to characterize a diverse collection of …

Abundance And Distribution Of Microbial Cells And Viruses In An Alluvial Aquifer, Donald Pan, Jason Nolan, Kenneth H. Williams, Karrie A. Weber

School of Biological Sciences: Faculty Publications

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Colorado …

How Question Types Reveal Student Thinking: An Experimental Comparison Of Multiple-True-False And Free-Response Formats, Joanna K. Hubbard, Macy A. Potts, Brian A. Couch

School of Biological Sciences: Faculty Publications

Assessments represent an important component of undergraduate courses because they affect how students interact with course content and gauge student achievement of course objectives. To make decisions on assessment design, instructors must understand the affordances and limitations of available question formats. Here, we use a crossover experimental design to identify differences in how multiple-true-false (MTF) and free-response (FR) exam questions reveal student thinking regarding specific conceptions. We report that correct response rates correlate across the two formats but that a higher percentage of students provide correct responses for MTF questions. We find that MTF questions reveal a high prevalence of …

Identification Of The Atpase Subunit Of The Primary Maltose Transporter In The Hyperthermophilic Anaerobe Thermotoga Maritima, Raghuveer Singh, Derrick White, Paul H. Blum

School of Biological Sciences: Faculty Publications

Thermotoga maritima is a hyperthermophilic anaerobic bacterium that produces molecular hydrogen (H₂) by fermentation. It catabolizes a broad range of carbohydrates through the action of diverse ABC transporters. However, in T. maritima and related species, highly similar genes with ambiguous annotation obscure a precise understanding of genome function. In T. maritima, three putative malK genes, all annotated as ATPase subunits, exhibited high identity to each other. To distinguish between these genes, malK disruption mutants were constructed by gene replacement, and the resulting mutant cell lines were characterized. Only a disruption of malK3 produced a defect in maltose …

Assessing Plant-Wax Markers As A Tool To Estimate Intake And Diet Composition In Beef Cattle, Emily J. Hilburger

Department of Animal Science: Dissertations, Theses, and Student Research

Estimating feed efficiency of ruminants in grazing environments is difficult due to challenges in measuring intake and diet composition of animals that are freely grazing. Plant-wax markers, especially n-alkanes (ALK), have been shown to be a potential tool to calculate intake and diet composition.

Two indoor experiments were conducted in successive years to assess ALK reliability to facilely estimate DMI (EDMI) and diet composition. Heifers were fed a ration of 69.8% corn silage and 30% ground alfalfa with a daily supplement containing a ALK marker (C₃₂). Using a pooled fecal sample increased the …

Aspect: A Survey To Assess Student Perspective Of Engagement In An Active-Learning Classroom, Benjamin L. Wiggins, Sarah L. Eddy, Leah Wener-Fligner, Karen Freisem, Daniel Z. Grunspan, Elli J. Theobald, Jerry Timbrook, Alison J. Crowe

Department of Sociology: Faculty Publications

The primary measure used to determine relative effectiveness of in-class activities has been student performance on pre/posttests. However, in today’s active-learning classrooms, learning is a social activity, requiring students to interact and learn from their peers. To develop effective active-learning exercises that engage students, it is important to gain a more holistic view of the student experience in an active-learning classroom. We have taken a mixed-methods approach to iteratively develop and validate a 16-item survey to measure multiple facets of the student experience during active-learning exercises. The instrument, which we call Assessing Student Perspective of Engagement in Class Tool (ASPECT), …

Studies In Directed Catalytic Asymmetric Hydroboration Of 1,2-Disubstituted Unsaturated Amide, Shuyang Zhang

Department of Chemistry: Dissertations, Theses, and Student Research

The Rh-catalyzed, substrate directed catalytic asymmetric hydroboration of γ,δ-unsaturated amides provides a direct route to enantioenriched acyclic secondary γ-borylated carbonyl derivatives with high regio- and enantioselectivity. The catalytic condition optimization and substrate scope study is discussed, including the effects in catalytical asymmetric hydroboration on pre-installed chiral γ,δ-unsaturated amides. A mechanistic study from kinetic approach by graphical manipulation (reaction progress kinetic analysis for substrate orders and normalized time analysis for catalyst order.) was discussed in this thesis

Advisor: Professor James M. Takacs