Digital Commons Network^™

Developmental Changes In The Organization Of Functional Connections Between The Basal Ganglia And Cerebral Cortex, Deanna J. Greene, Timothy O. Laumann, Joseph W. Dubis, S. Katie Ihnen, Maital Neta, Jonathan D. Power, John R. Pruett Jr., Kevin J. Black, Bradley L. Schlaggar

Department of Psychology: Faculty Publications

The basal ganglia (BG) comprise a set of subcortical nuclei with sensorimotor, cognitive, and limbic subdivisions, indicative of functional organization. BG dysfunction in several developmental disorders suggests the importance of the healthy maturation of these structures. However, few studies have investigated the development of BG functional organization. Using resting-state functional connectivity MRI (rs-fcMRI), we compared human child and adult functional connectivity of the BG with rs-fcMRI-defined cortical systems. Because children move more than adults, customized preprocessing, including volume censoring, was used to minimize motion-induced rsfcMRI artifact. Our results demonstrated functional organization in the adult BG consistent with subdivisions previously identified …

Iterative Assembly Of Two Separate Polyketide Chains By The Same Single-Module Bacterial Polyketide Synthase In The Biosynthesis Of Hsaf, Yaoyao Li, Haotong Chen, Yanjiao Ding, Yunxuan Xie, Haoxin Wang, Ronald Cerny, Yuemao Shen, Liangcheng Du

Ronald Cerny Publications

HSAF (1) was isolated from the biocontrol agent Lysobacter enzymogenes (Figure 1).^[1-4]

This bacterial metabolite belongs to polycyclic tetramate macrolactams (PTM) that are

emerging as a new class of natural products with distinct structural features. ^{[5, 6]} HSAF

exhibits a potent antifungal activity and shows a novel mode of action.^[1-4] The HSAF

biosynthetic gene cluster contains only a single-module hybrid polyketide synthasenonribosomal

peptide synthetase (PKS-NRPS), although the PTM scaffold is apparently

derived from two separate hexaketide chains and an ornithine residue.^[1-4] This suggests that

the same PKS module would act not only iteratively, but also …

Phosphatase-Inert Glucosamine 6‑Phosphate Mimics Serve As Actuators Of The Glms Riboswitch, Xiang Fei, Thomas Holmes, Julianna Diddle, Lauren Hintz, Dan Delaney, Alex Stock, Danielle Renner, Molly Mcdevitt, David B. Berkowitz, Juliane K. Soukup

David Berkowitz Publications

The glmS riboswitch is unique among generegulating riboswitches and catalytic RNAs. This is because its own metabolite, glucosamine-6-phosphate (GlcN6P), binds to the riboswitch and catalytically participates in the RNA selfcleavage reaction, thereby providing a novel negative feedback mechanism. Given that a number of pathogens harbor the glmS riboswitch, artificial actuators of this potential RNA target are of great interest. Structural/kinetic studies point to the 2- amino and 6-phosphate ester functionalities in GlcN6P as being crucial for this actuation. As a first step toward developing artificial actuators, we have synthesized a series of nine GlcN6P analogs bearing phosphatase-inert surrogates in place …

Energy-Resolved Collision-Induced Dissociation Pathways Of Model N-Linked Glycopeptides: Implications For Capturing Glycan Connectivity And Peptide Sequence In A Single Experiment, Venkata Kolli, Eric D. Dodds

Department of Chemistry: Faculty Publications

Tandem mass spectrometry (MS/MS) of glycopeptides stands among the principal analytical approaches for assessing protein glycosylation in a site-specific manner. The aims of such experiments are often to determine the monosaccharide connectivity of the glycan, the amino acid sequence of the peptide, and the site of glycan attachment. This level of detail is often difficult to achieve using any single ion dissociation method; however, precedent does exist for use of collision-induced dissociation (CID) to establish either the connectivity of the oligosaccharide or the sequence of the polypeptide depending upon the applied collision energy. Unfortunately, the relative energy requirements for glycan …

Highly Selective Gas Sensor Arrays Based On Thermally Reduced Graphene Oxide, Alexey Lipatov, Alexey Varezhnikov, Peter Wilson, Victor Sysoev, Andrei Kolmakov, Alexander Sinitskii

Department of Chemistry: Faculty Publications

The electrical properties of reduced graphene oxide (rGO) have been previously shown to be very sensitive to surface adsorbates, thus making rGO a very promising platform for highly sensitive gas sensors. However, poor selectivity of rGO-based gas sensors remains a major problem for their practical use. In this paper, we address the selectivity problem by employing an array of rGO-based integrated sensors instead of focusing on the performance of a single sensing element. Each rGO-based device in such an array has a unique sensor response due to the irregular structure of rGO films at different levels of organization, ranging from …

Structure And Function Of Preq1 Riboswitches, Catherine D. Eichhorn, Mijeong Kang, Juli Feigon

Department of Chemistry: Faculty Publications

PreQ₁ riboswitches help regulate the biosynthesis and transport of PreQ₁ (7-aminomethyl-7- deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of PreQ₁ riboswitches have been identified (PreQ₁-I and PreQ₁-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon PreQ₁ binding, each of which has distinct unusual features and modes …

Analogues Of (-)-Picropodophyllin, Synthesis And Uses Thereof, David B. Berkowitz, Sylvain Broussy

Department of Chemistry: Faculty Publications

Analogs of (-)-Picropodophyllin, synthesis thereof, and uses in pharmaceuticals as inhibitors of IGF1RK.

Analysis Of Biomolecular Interactions Using Affinity Microcolumns: A Review, Xiwei Zheng, Zhao Li, Sandya Beeram, Maria Podariu, Ryan Matsuda, Erika L. Pfaunmiller, Christopher J. White Ii, Natasha Carter, David S. Hage

David Hage Publications

Affinity chromatography has become an important tool for characterizing biomolecular interactions. The use of affinity microcolumns, which contain immobilized binding agents and have volumes in the mid-to-low microliter range, has received particular attention in recent years. Potential advantages of affinity microcolumns include the many analysis and detection formats that can be used with these columns, as well as the need for only small amounts of supports and immobilized binding agents. This review examines how affinity microcolumns have been used to examine biomolecular interactions. Both capillary-based microcolumns and short microcolumns are considered. The use of affinity microcolumns with zonal elution and …

The Temperature Independence Of Interaction Strength In A Sit-And-Wait Predator, Rachel A. Novich, Emma K. Erickson, Ryan M. Kalinoski, John Delong

School of Biological Sciences: Faculty Publications

The strength of interactions between consumers and their resources has important implications for the overall structure and function of food webs. These interactions can change with warming, depending on the foraging mode of the predator. Theory predicts that warming increases foraging velocity in ectotherms, but in a sit-and-wait predator that has zero velocity when foraging, the interaction strength should be temperature independent. Using the protist Urocentrum turbo and the sit-and- wait copepod Orthocyclops modestus, we tested this prediction by measuring dynamic interaction strengths (effect of a predator on prey population growth rate) and by estimating the parameters of a …

Urban Ecology: Advancing Science And Society, Colby J. Tanner, Frederick R. Adler, Nancy B. Grimm, Peter M. Groffman, Simon A. Levin, Jason Munshi-South, Diane E. Pataki, Mitchell Pavao-Zuckerman, William G. Wilson

School of Biological Sciences: Faculty Publications

Urban ecology has quickly become established as a central part of ecological thinking. As cities continue to grow in size and number, two questions serve to unify this broad and multidisciplinary research landscape: (1) how can urban ecology contribute to the science of ecology, and (2) how can urban ecology be applied to make cities more livable and sustainable? In spite of the advances made thus far, there are many unexplored ways of integrating the science and application of urban ecology. Although scientists assess and make predictions regarding the connections between environmental and socioeconomic processes, practitioners involved in real-world application …

Glycosyl Rotation And Distortion By Key Residues In Endocellulase Cel6a From Theromobifida Fusca, Tao Lu, Zuoming Zhang, Chi Zhang

School of Biological Sciences: Faculty Publications

Endocellulases are one kind of the important biodegrading cellulose enzymes. Experimental results show that a rotated and distorted preactivated structure exists before the substrate entering the transition state. The molecular dynamic simulation of endocellulase Cel6A models revealed a correlation between the rotation and distortion of pyranoside ring in −1 glycosyl unit of the substrate. The two key residues, Tyr73 and Ser189, in Cal6A cooperate to rotate and distort the pyranoside ring in the cellulose hydrolysis.

Includes supplementary material.

Integrating Evolutionary And Functional Tests Of Adaptive Hypotheses: A Case Study Of Altitudinal Differentiation In Hemoglobin Function In An Andean Sparrow, Zonotrichia Capensis, Zachary A. Cheviron, Chandrasekhar Natarajan, Joana Projecto-Garcia, Douglas K. Eddy, Jennifer Jones, Matthew D. Carling, Christopher C. Witt, Hideaki Moriyama, Roy E. Weber, Angela Fago, Jay F. Storz

School of Biological Sciences: Faculty Publications

In air-breathing vertebrates, the physiologically optimal blood-O_² affinity is jointly determined by the prevailing partial pressure of atmospheric O₂, the efficacy of pulmonary O₂ transfer, and internal metabolic demands. Consequently, genetic variation in the oxygenation properties of hemoglobin (Hb) may be subject to spatially varying selection in species with broad elevational distributions. Here we report the results of a combined functional and evolutionary analysis of Hb polymorphism in the rufouscollared sparrow (Zonotrichia capensis), a species that is continuously distributed across a steep elevational gradient on the Pacific slope of the Peruvian Andes. We integrated …

Comparison Of The Wing Polyphenic Response Of Pea Aphids (Acyrthosiphon Pisum) To Crowding And Predator Cues, Swapna R. Purandare, Brigitte Tenhumberg, Jennifer A. Brisson

School of Biological Sciences: Faculty Publications

1. Pea aphids (Acyrthosiphon pisum Harris; Hemiptera: Aphididae) exhibit transgenerational wing polyphenism, in which unwinged females produce genetically identical winged offspring in response to environmental cues such as overcrowding and predation risk that indicate poor habitat quality.

2. Laboratory experiments were carried out to explore the intensity of the wing polyphenic response of pea aphids exposed to cues from ladybird predators and crowding, and their response was compared to pea aphids that were not exposed to any cues (control).

3. The study used cues from two different ladybird species: Coccinella septempunctata L. (Coleoptera: Coccinellidae) and Hippodamia convergens Guérin-Méneville (Coleoptera: …

Physiological And Transcriptional Memory In Guard Cells During Repetitive Dehydration Stress, Laetitia Virlouvet, Michael E. Fromm

Nebraska Center for Biotechnology: Faculty and Staff Publications

Arabidopsis plants subjected to a daily dehydration stress and watered recovery cycle display physiological and transcriptional stress memory. Previously stressed plants have stomatal apertures that remain partially closed during a watered recovery period, facilitating reduced transpiration during a subsequent dehydration stress. Guard cells (GCs) display transcriptional memory that is similar to that in leaf tissues for some genes, but display GC-specific transcriptional memory for other genes. The rate-limiting abscisic acid (ABA) biosynthetic genes NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) and ALDEHYDE OXIDASE 3 (AAO3) are expressed at much higher levels in GCs, particularly during the watered recovery interval, relative to their low …

The Pseudomonas Syringae Type Iii Effector Hopd1 Suppresses Effector-Triggered Immunity, Localizes To The Endoplasmic Reticulum, And Targets The Arabidopsis Transcription Factor Ntl9, Anna Block, Tania Y. Toruno, Christian G. Elowsky, Chi Zhang, Jens Steinbrenner, Jim Beynon, James R. Alfano

Nebraska Center for Biotechnology: Faculty and Staff Publications

Pseudomonas syringae type III effectors are known to suppress plant immunity to promote bacterial virulence. However, the activities and targets of these effectors are not well understood. We used genetic, molecular, and cell biology methods to characterize the activities, localization, and target of the HopD1 type III effector in Arabidopsis. HopD1 contributes to P. syringae virulence in Arabidopsis and reduces effector-triggered immunity (ETI) responses but not pathogen-associated molecular pattern-triggered immunity (PTI) responses. Plants expressing HopD1 supported increased growth of ETI-inducing P. syringae strains compared with wild-type Arabidopsis. We show that HopD1 interacts with the membrane-tethered Arabidopsis transcription factor NTL9 and …

Landscape Evaluation And Restoration Planning, Paul F. Hessburg, R. Brion Salter, Keith M. Reynolds, James D. Dickinson, William L. Gaines, Ricky J. Harrod

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Contemporary land managers are beginning to understand that landscapes of the early 20th century exhibited complex patterns of compositional and structural conditions at several different scales, and that there was interplay between patterns and processes within and across scales. Further, they understand that restoring integrity of these conditions has broad implications for the future sustainability of native species, ecosystem services, and ecological processes. Many too are hungry for methods to restore more natural landscape patterns of habitats and more naturally functioning disturbance regimes; all in the context of a warming climate. Attention is turning to evaluating whole landscapes at local …

Tree-Ring Stable Isotopes Record The Impact Of A Foliar Fungal Pathogen On Co2 Assimilation And Growth In Douglas-Fir, Brandy J. Saffell, Frederick C. Meinzer, Steven L. Voelker, David C. Shaw, J. Renée Brooks, Barbara Lachenbruch, Jennifer Mckay

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Swiss needle cast (SNC) is a fungal disease of Douglas-fir (Pseudotsuga menziesii) that has recently become prevalent in coastal areas of the Pacific Northwest. We used growth measurements and stable isotopes of carbon and oxygen in tree-rings of Douglas-fir and a non-susceptible reference species (western hemlock, Tsuga heterophylla) to evaluate their use as proxies for variation in past SNC infection, particularly in relation to potential explanatory climate factors. We sampled trees from an Oregon site where a fungicide trial took place from 1996 to 2000, which enabled the comparison of stable isotope values between trees with and …

Recovery Of Wolverines In The Western United States: Recent Extirpation And Recolonization Or Range Retraction And Expansion?, Kevin S. Mckelvey, Keith B. Aubry, Neil J. Anderson, Anthony P. Clevenger, Jeffrey P. Copeland, Kimberley S. Heinemeyer, Robert M. Iman, John R. Squires, John S. Waller, Kristine L. Pilgrim, Michael K. Schwartz

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Wolverines were greatly reduced in number and possibly extirpated from the contiguous United States (U.S.) by the early 1900s. Wolverines currently occupy much of their historical range in Washington, Idaho, Montana, and Wyoming, but are absent from Utah and only single individuals are known to occur in California and Colorado. In response, the translocation of wolverines to California and Colorado is being considered. If wolverines are to be reintroduced, managers must identify appropriate source populations based on the genetic affinities of historical and modern wolverine populations. We amplified the mitochondrial control region of 13 museum specimens dating from the late …

Housing Development Erodes Avian Community Structure In U.S. Protected Areas, Eric M. Wood, Anna M. Pidgeon, Volker C. Radeloff, David Helmers, Patrick D. Culbert, Nicholas S. Keuler, Curtis H. Flather

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Protected areas are a cornerstone for biodiversity conservation, but they also provide amenities that attract housing development on inholdings and adjacent private lands. We explored how this development affects biodiversity within and near protected areas among six ecological regions throughout the United States. We quantified the effect of housing density within, at the boundary, and outside protected areas, and natural land cover within protected areas, on the proportional abundance and proportional richness of three avian guilds within protected areas. We developed three guilds from the North American Breeding Bird Survey, which included Species of Greatest Conservation Need, land cover affiliates …

Performance Of Species Richness Estimators Across Assemblage Types And Survey Parameters, Gordon C. Reese, Kenneth R. Wilson, Curtis H. Flather

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Aim A raw count of the species encountered across surveys usually underestimates species richness. Statistical estimators are often less biased. Nonparametric estimators of species richness are widely considered the least biased, but no particular estimator has consistently performed best. This is partly a function of estimators responding differently to assemblage-level factors and survey design parameters. Our objective was to evaluate the performance of raw counts and nonparametric estimators of species richness across various assemblages and with different survey designs.

Location We used both simulated and published field data.

Methods We evaluated the bias, precision and accuracy of raw counts and …

A New Metric For Quantifying Burn Severity: The Relativized Burn Ratio, Sean A. Parks, Gregory K. Dillon, Carol Miller

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Satellite-inferred burn severity data have become increasingly popular over the last decade for management and research purposes. These data typically quantify spectral change between pre-and post-fire satellite images (usually Landsat). There is an active debate regarding which of the two main equations, the delta normalized burn ratio (dNBR) and its relativized form (RdNBR), is most suitable for quantifying burn severity; each has its critics. In this study, we propose and evaluate a new Landsat-based burn severity metric, the relativized burn ratio (RBR), that provides an alternative to dNBR and RdNBR. For 18 fires in the western US, we compared the …

Contribution Of Reactive And Proactive Control To Children’S Working Memory Performance: Insight From Item Recall Durations In Response Sequence Planning, Nicolas Chevalier, Tiffany D. James, Sandra A. Wiebe, Jennifer Mize Nelson, Kimberly Espy

Department of Psychology: Faculty Publications

The present study addressed whether developmental improvement in working memory span task performance relies upon a growing ability to proactively plan response sequences during childhood. Two hundred thirteen children completed a working memory span task in which they used a touchscreen to reproduce orally presented sequences of animal names. Children were assessed longitudinally at 7 time points between 3 and 10 years of age. Twenty-one young adults also completed the same task. Proactive response sequence planning was assessed by comparing recall durations for the 1st item (preparatory interval) and subsequent items. At preschool age, the preparatory interval was generally shorter …

The Longitudinal Impact Of Intimate Partner Aggression And Relationship Status On Women’S Physical Health And Depression Symptoms, Laura E. Watkins, Anna E. Jaffe, Lesa Hoffman, Kim L. Gratz, Terri L. Messman-Moore, David Dilillo

Department of Psychology: Faculty Publications

Intimate partner aggression (IPA) has many detrimental effects, particularly among young women. The present study examined the longitudinal effects of IPA victimization and relationship status on physical health and depression symptoms in a sample of 375 community women between the ages of 18 and 25 years. All variables were assessed at 4 occasions over a 12-month period (i.e., 1 assess-ment every 4 months). Multilevel modeling revealed that IPA victimization had both between- and within-person effects on women’s health outcomes, and relationship status had within-person effects when women did not report current IPA. Although IPA was generally related to greater physical …

Interoception And Learning: Import To Understanding And Treating Diseases And Psychopathologies, Rick A. Bevins, Joyce Besheer

Department of Psychology: Faculty Publications

Chemotherapeutic agents nauseate cancer patients. Some individuals with schizophrenia hear voices. Chronic pain can be reduced by analgesics. Nausea, voices, and pain are examples of internal (interoceptive) stimuli closely linked with a disease and/or its treatment. There is evidence that the perception and, hence, role of these internal stimuli can be modified by one’s learning history. There is also increased awareness by researchers and practitioners of the potential import of learning involving internal states to some diseases and psychopathologies. Unfortunately, the science, theory, and practice appear to be trailing behind awareness. In this mini-review, we describe two examples: smoking and …

The Effect Of Barium On Perceptions Of Taste Intensity And Palatability, Angela M. Dietsch, Nancy Pearl Solomon, Catriona M. Steele, Cathy A. Pelletier

Department of Special Education and Communication Disorders: Faculty Publications

Barium may affect the perception of taste intensity and palatability. Such differences are important considerations in the selection of dysphagia assessment strategies and interpretation of results. Eighty healthy women grouped by age (younger, older) and genetic taste status (supertaster, nontaster) rated intensity and palatability for seven tastants prepared in deionized water with and without 40 % w/v barium: noncarbonated and carbonated water, diluted ethanol, and high concentrations of citric acid (sour), sodium chloride (salty), caffeine (bitter), and sucrose (sweet). Mixed-model analyses explored the effects of barium, taster status, and age on perceived taste intensity and acceptability of stimuli. Barium was …

Characterization Of Sex-Based Differences In The Mechanical Properties Of Human Finger Glabrous Tissue Using A Fiberoptic Sensor, Lalit Venkatesan, Steven M. Barlow

Department of Special Education and Communication Disorders: Faculty Publications

TAC-Cell is a custom-built somatosensory stimulator that delivers pneumatic cutaneous tactile inputs to virtually any skin target on the body and by virtue of its non-ferrous materials is compatible with functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) brain scanners. In this study, we describe the method to measure apparent skin displacement induced by TAC-Cell stimulation of the glabrous surface of the distal phalanx of the index finger. Specifically, we studied the effect of four servo controller input voltages (0.4V to 1.0V) on resultant skin displacement among eighteen, neurotypical adult male and female participants. A fiberoptic displacement sensor, commonly used …

Qualities Of Romantic Relationships And Consistent Condom Use Among Dating Young Adults, Larry Gibbs, Wendy D. Manning, Monica A. Longmore, Peggy C. Giordano

Department of Sociology: Faculty Publications

Emerging adulthood is marked by significant changes in interpersonal and sexual relationships with delays in marriage meaning that young adults are facing increasingly longer periods of nonmarital sexual engagement (Arnett 2000). Understanding factors that influence contraceptive use is critical because young adults experience the highest rates of unintended pregnancy and sexually transmitted infections (STIs). Drawing on the Toledo Adolescent Relationship Study (TARS) (n = 437) we examine how variations in the qualities of dating relationship are associated with consistent condom use and consider the reasons for inconsistent condom use. We find that negative relationship dynamics, such as verbal abuse, intimate …

“Bomb Talk” And Erving Goffman’S Frame Analysis, Michael R. Hill

Department of Sociology: Faculty Publications

Erving Goffman’s Frame Analysis is introduced (together with several of Goffman’s basic concepts, including “strips”, “frames”, “keys”, “fabrications”, etc.) and applied to “bomb talk” (i.e., the different ways in which westerners discuss and/or refer to the reality of nuclear weapons). This analysis confirms (as Goffman predicts) that the manner in which everyday life is conceptualized and subsequently transformed is extraordinarily flexible. Goffman offers a coherent knowledge-producing system, one that is best carefully studied before applying his precisely-defined concepts to other aspects of our social world. Frame Analysis provides the means for analyzing the organization of everyday life and answering many …

Towards A Formal Understanding Of Bateson's Rule: Chromatic Symmetry In Cyclic Boolean Networks And Its Relationship To Organism Growth And Cell Differentiation, Yuri Cantor, Bilal Khan, Kirk Dombrowski

Department of Sociology: Faculty Publications

There has been considerable prior research on the biological processes of morphogenesis and cellular differentiation, and the manner by which these processes give rise to symmetries in biological structures. Here we extend our previous work on thermal robustness and attractor density in cyclic formal Boolean dynamical systems, introducing a new form of spectral analysis on digital organisms at the cellular level. We interpret the phenomena of radial and bilateral symmetry in terms of spatial periodicities in the color sequences, as manifested by an organism while it orbits in its attractors. We provide new results on the influence of various organism …

Teaching About Organized Racism, Kathleen Blee, Kelsy Burke

Department of Sociology: Faculty Publications

The challenges of teaching about organized racism are different than those found in teaching about other aspects of American race relations. On the one hand, it can be quite easy to engage students in the topic of organized racism, at least on a surface level, as the vile propaganda and violent actions of racist groups and movements are sensational and provocative. Students across racial lines, like the general public, for the most part have strong negative opinions about the Ku Klux Klan, neo-Nazis, and racist skinheads and are eager to share these (Nelson et al. 1997; Schuman et al. 1997). …