Digital Commons Network^™

Orientational Order Of A Ferroelectric Liquid Crystal With Small Layer Contraction, Rafal Korlacki, Vitaly P. Panov, Atsuo Fukuda, Jagdish K. Vij, Christopher M. Spillmann, Jawad Naciri

Department of Physics and Astronomy: Faculty Publications

We present spectroscopic and optical studies of a non-layer-shrinkage ferroelectric liquid crystal DSiKN65. The orientational order parameters S, measured with respect to the smectic layer normal using IR spectroscopy on a sample aligned homeotropically, does not exhibit any significant variation between the smectic-A* and smectic-C* phases. In contrast the birefringence of a planar homogenous sample abruptly increases at the smectic-A* to smectic-C* transition. This suggests a general increase in the orientational order, which can be described by the orientational order parameters S' defined with respect to the director. Simultaneous increase of S' and the director …

Entropy Localization In Magnetic Compounds And Thin-Film Nanostructures, Ralph Skomski, Christian Binek, Steven A. Michalski, Tathagata Mukherjee, Axel Enders, David J. Sellmyer

Ralph Skomski Publications

The effect of nanostructuring on the magnetic entropy of materials for room-temperature magnetic cooling is investigated by model calculations. The materials are structurally inhomogeneous with a large number of nonequivalent crystallographic sites. In the mean-field Heisenberg model, the entropy density is a unique function of the local magnetization so that the coupled set of nonlinear mean-field equations yields not only the magnetization but also the entropy density. Since most of the entropy is localized near grain boundaries, nanomagnetic cooling requires small feature sizes. Magnetic anisotropy is a substantial complication, even on a mean-field level, but the corresponding corrections are often …

Adsorption-Controlled Growth Of Bimno3 Films By Molecular-Beam Epitaxy, J. H. Lee, X. Ke, R. Misra, J. F. Ihlefeld, X. S. Xu, Z. G. Mei, T. Heeg, M. Roeckerath, J. Schubert, Z. K. Liu, J. L. Musfeldt, P. Schiffer, D. G. Schlom

Xiaoshan Xu Papers

We have developed the means to grow BiMnO₃ thin films with unparalleled structural perfection by reactive molecular-beam epitaxy and determined its band gap. Film growth occurs in an adsorption-controlled growth regime. Within this growth window bounded by oxygen pressure and substrate temperature at a fixed bismuth overpressure, single-phase films of the metastable perovskite BiMnO₃ may be grown by epitaxial stabilization. X-ray diffraction reveals phase-pure and epitaxial films with w rocking curve full width at half maximum values as narrow as 11 arc sec (0.003°). Optical absorption measurements reveal that BiMnO₃ has a direct band gap of 1.1±0.1 …

Interlayer Exchange Coupling Across A Ferroelectric Barrier, M. Ye. Zhuravlev, A. V. Vedyayev, Evgeny Y. Tsymbal

Evgeny Tsymbal Publications

A new magnetoelectric effect is predicted originating from the interlayer exchange coupling between two ferromagnetic layers separated by an ultrathin ferroelectric barrier. It is demonstrated that ferroelectric polarization switching driven by an external electric field leads to a sizable change in the interlayer exchange coupling. The effect occurs in asymmetric ferromagnet/ferroelectric/ferromagnet junctions due to a change in the electrostatic potential profile across the junction affecting the interlayer coupling. The predicted phenomenon indicates the possibility of switching the magnetic configuration by reversing the polarization of the ferroelectric barrier layer.

Heating Performance Assessment Of Domestic Microwave Ovens, Krishnamoorthy Pitchai, Sohan Birla, Jeyamkondan Subbiah, David D. Jones

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Due to inherent nature of standing wave patterns of microwaves inside a cavity and dielectric properties of different components in a food, microwave heating leaves non-uniform distribution of energy inside the food volumetrically. Achieving heating uniformity plays critical role in improving the safety of microwave heated products. In this paper, we present a method for assessing heating uniformity within domestic microwave ovens. A custom designed container
was used to assess heating uniformity of a range of microwave ovens using IR camera. The study suggested that the best place to place food in a microwave oven is not at center but …

Generating ‘As-Applied’ Pesticide Distribution Maps From A Self-Propelled Agricultural Sprayer Based On Nozzle Pressure Data, Joe D. Luck, Ajay Sharda, Santosh Pitla, John P. Fulton, Scott A. Shearer

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

The application of pre-emergence, post-emergence, and burn-down herbicides (i.e., glyphosate) continues to increase as producers attempt to reduce both negative environmental impacts from tillage and input costs from labor, machinery and materials. The use of precision agriculture technologies such as automatic boom section control allows producers to reduce offtarget application when applying herbicides. While automatic boom section control provides benefits, pressure differences across the spray boom resulting from boom section actuation can lead to offrate application errors. Off-rate errors may also result from spray rate controller compensation for ground speed changes and velocity variation across the spray boom during turning …

Testing Fuel Efficiency Of A Tractor With A Continuously Variable Transmission, Bart A. Coffman, Michael F. Kocher, Viacheslav I. Adamchuk, Roger M. Hoy, Erin E. Blankenship

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A John Deere 8530 IVT tractor (Waterloo, Iowa) with a continuously variable transmission (CVT) that could be operated in automatic (CVT) or manual (fixed gear ratio) mode was tested for fuel consumption at a setpoint travel speed of 9 km·h^‐1 with 17 different drawbar loads. Linear regression analysis results showed that with the throttle set to maximum in both transmission modes, operating the tractor with the transmission in the automatic mode was more fuel efficient than operating with the transmission in the manual mode when the drawbar power was approximately 78%, or less, of maximum power. When load transition …

Testing Of Rtk-Level Satellite-Based Tractor Auto-Guidance Using A Visual Sensor System, Dwight Easterly, Viacheslav I. Adamchuk, Roger M. Hoy, Michael F. Kocher

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The use of satellite-based positioning has advanced considerably in the world of agriculture, providing a range of technical solutions that include the automated steering of tractors and self-propelled machinery. With the development of auto-guidance systems comes the need to evaluate their performance. Given that current precision and accuracy claims are relatively small in magnitude, it is imperative there be a testing system capable of detecting errors with ten times greater accuracy-- possibly as little as a few millimeters. A visual sensor was adopted to achieve this level of measurement resolution. The sensor was used to determine the cross-track error estimates …

Using A Vision Sensor System For Performance Testing Of Satellite-Based Tractor Auto-Guidance, Dwight Easterly, Viacheslav I. Adamchuk, Michael F. Kocher, Roger M. Hoy

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A vision sensing system for the measurement of auto-guidance pass-to-pass and long-term errors was implemented to test the steering performance of tractors equipped with auto-guidance systems. The developed test system consisted of an optical machine vision sensor rigidly mounted on the rear of the tested tractor. The center of the drawbar hitch pin point was used as the reference from which to measure the deviation of the tractor’s actual travel path from its desired path. The system was built and calibrated to a measurement accuracy of better than 2 mm. To evaluate the sensor, two auto-guidance systems equipped with RTK-level …

Ultrasound-Assisted Osmotic Dehydration Of Strawberries: Effect Of Pretreatment Time And Ultrasonic Frequency, Juan Garcia-Noguera, Francisca I. P. Oliveira, Maria Izabel Gallão, Curtis L. Weller, Sueli Rodrigues, Fabiano A. N. Fernandes

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Pretreatment of fruits prior to drying has shown success in reducing drying time and costs. In this work, ultrasound-assisted osmotic dehydration has been implemented as a method to increase water diffusivity and reduce drying time in strawberries. Strawberry halves were immersed in distilled water and in two different concentrations of sucrose solutions while pretreatment time and ultrasonic frequency levels were varied to determine their effect on drying time, water loss, and soluble solids gain. A microscopic analysis was carried out to evaluate the formation of microchannels and other changes to the fruit tissue structure. Greater sucrose concentration used in ultrasound- …

Numerically Predicting Seepage Gradient Forces And Erosion: Sensitivity To Soil Hydraulic Properties, Garey A. Fox, Derek M. Heeren, Glenn V. Wilson, E. J. Langendoen, Amanda K. Fox, Maria L. Chu-Agor

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Research has suggested that streambank seepage can be an important mechanism of bank instability; however, limited information is available on the level of soil characterization necessary to accurately predict seepage gradient forces and erosion. The objective of this research was to quantify the expected range of predicted seepage gradients for various degrees of site characterization. Uncertainty analysis on seepage gradient predictions was performed relative to variability in soil hydraulic properties. A two-dimensional unsaturated/saturated groundwater flow model was used to simulate a homogeneous soil layer for sand and loamy sand soils packed at various bulk densities, ρ_b. A pedotransfer …

Regulation Of Sealing Ring Formation By L-Plastin And Cortactin In Osteoclasts, Tao Ma, Kavitha Sadashivalah, Nandakumar Madayiputhiya, Meenakshi A. Chellaia

Department of Biochemistry: Faculty Publications

The aim of this study is to identify the exact mechanism(s) by which cytoskeletal structures are modulated during bone resorption. In this study, we have shown the possible role of different actin-binding and signaling proteins in the regulation of sealing ring formation. Our analyses have demonstrated a significant increase in cortactin and a corresponding decrease in L-plastin protein levels in osteoclasts subjected to bone resorption for 18 h in the presence of RANKL, M-CSF, and native bone particles. Time-dependent changes in the localization of L-plastin (in actin aggregates) and cortactin (in the sealing ring) suggest that these proteins may be …

Formation Of The Redox Cofactor Centers During Cox1 Maturation In Yeast Cytochrome Oxidase, Oleh Khalimonchuk, Megan Bestwick, Brigitte Meunier, Talina C. Watts, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The biogenesis of cytochrome c oxidase initiates with synthesis and maturation of the mitochondrionencoded Cox1 subunit prior to the addition of other subunits. Cox1 contains redox cofactors, including the low-spin heme a center and the heterobimetallic heme a₃:Cu_B center. We sought to identify the step in the maturation of Cox1 in which the redox cofactor centers are assembled. Newly synthesized Cox1 is incorporated within one early assembly intermediate containing Mss51 in Saccharomyces cerevisiae. Subsequent Cox1 maturation involves the progression to downstream assembly intermediates involving Coa1 and Shy1. We show that the two heme a cofactor sites …

Dynamic Changes In Genome-Wide Histone H3 Changes Lysine 4 Methylation Patterns In Response To Dehydration Stress In Arabidopsis Thaliana, Karin V. Van Dijk, Yong Ding, Sridar Achary Malkaram, Jean-Jack Riethoven, Rong Liu, Jingyi Yang, Peter Laczko, Han Chen, Yuannan Xia, Istvan Ladunga, Zoya V. Avramova, Michael E. Fromm

School of Biological Sciences: Faculty Publications

Background: The molecular mechanisms of genome reprogramming during transcriptional responses to stress are associated with specific chromatin modifications. Available data, however, describe histone modifications only at individual plant genes induced by stress. We have no knowledge of chromatin modifications taking place at genes whose transcription has been down-regulated or on the genome-wide chromatin modification patterns that occur during the plant’s response to dehydration stress. Results: Using chromatin immunoprecipitation and deep sequencing (ChIP-Seq) we established the wholegenome distribution patterns of histone H3 lysine 4 mono-, di- and tri-methylation (H3K4me1, H3K4me2, and H3K4me3, respectively) in Arabidopsis thaliana during watered and dehydration stress …

Phosphatidylinositol 5-Phosphate Links Dehydration Stress To The Activity Of Arabidopsis Trithorax-Like Factor Atx1, Ivan Ndamukong, David R. Jones, Hanna Lapko, Nullin Divecha, Zoya V. Avramova

School of Biological Sciences: Faculty Publications

Background: Changes in gene expression enable organisms to respond to environmental stress. Levels of cellular lipid second messengers, such as the phosphoinositide PtdIns5P, change in response to a variety of stresses and can modulate the localization, conformation and activity of a number of intracellular proteins. The plant trithorax factor (ATX1) trimethylates the lysine 4 residue of histone H3 (H3K4me3) at gene coding sequences, which positively correlates with gene transcription. Microarray analysis has identified a target gene (WRKY70) that is regulated by both ATX1 and by the exogenous addition of PtdIns5P in Arabidopsis. Interestingly, ATX1 …

Evolution Of The Kdo2-Lipid A Biosynthesis In Bacteria, Stephen O. Opiyo, Rosevelt L. Pardy, Hideaki Moriyama, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Background: Lipid A is the highly immunoreactive endotoxic center of lipopolysaccharide (LPS). It anchors the LPS into the outer membrane of most Gram-negative bacteria. Lipid A can be recognized by animal cells, triggers defense-related responses, and causes Gram-negative sepsis. The biosynthesis of Kdo₂-lipid A, the LPS substructure, involves with nine enzymatic steps.

Results: In order to elucidate the evolutionary pathway of Kdo₂-lipid A biosynthesis, we examined the distribution of genes encoding the nine enzymes across bacteria. We found that not all Gram-negative bacteria have all nine enzymes. Some Gram-negative bacteria have no genes encoding …

Interspecific Relationships Among Growth, Mortality And Xylem Traits Of Woody Species From New Zealand, Sabrina E. Russo, Kerry L. Jenkins, Susan K. Wiser, Maria Uriarte, Richard P. Duncan, David A. Coomes

School of Biological Sciences: Faculty Publications

1. Wood density is considered a key functional trait influencing the growth and survival of woody plants and has been shown to be related to a slow-fast rate-of-living continuum. Wood density is, however, an emergent trait arising from several vascular properties of wood, including the diameter and frequency of xylem conduits.

2. We aimed to test the hypotheses that there is a set of inter-related trade-offs linked to the different functions of wood, that these trade-offs have direct consequences for tree growth and survival and that these trade-offs underlie the observed correlations between wood density and demographic rates. We evaluated …

Isolation And Characterization Of Bacteria Resistant To Metallic Copper Surfaces, Christophe Espírito Santo, Paula Vasconcelos Morais, Gregor Grass

School of Biological Sciences: Faculty Publications

Metallic copper alloys have recently attracted attention as a new antimicrobial weapon for areas where surface hygiene is paramount. Currently it is not understood on a molecular level how metallic copper kills microbes, but previous studies have demonstrated that a wide variety of bacteria, including Escherichia coli, Staphylococcus aureus, and Clostridium difficile, are inactivated within minutes or a few hours of exposure. In this study, we show that bacteria isolated from copper alloy coins comprise strains that are especially resistant against the toxic properties exerted by dry metallic copper surfaces. The most resistant of 294 isolates were …

Female Field Crickets Incur Increased Parasitism Risk When Near Preferred Song, Cassandra M. Martin, William E. Wagner Jr.

School of Biological Sciences: Faculty Publications

Female animals often prefer males with conspicuous traits because these males provide direct or indirect benefits. Conspicuous male traits, however, can attract predators. This not only increases the risk of predation for conspicuous males but also for the females that prefer them. In the variable field cricket, Gryllus lineaticeps, males that produce preferred song types provide females with greater material benefits, but they are also more likely to attract lethal parasitoid flies. First, we conducted a field experiment that tested the hypothesis that females have a greater risk of fly parasitism when in association with preferred high chirp rate …

Microevolution Of Intermediary Metabolism: Evolutionary Genetics Meets Metabolic Biochemistry, Anthony J. Zera

School of Biological Sciences: Faculty Publications

During the past decade, microevolution of intermediary metabolism has become an important new research focus at the interface between metabolic biochemistry and evolutionary genetics. Increasing recognition of the importance of integrative studies in evolutionary analysis, the rising interest in ‘evolutionary systems biology’, and the development of various ‘omics’ technologies have all contributed significantly to this developing interface. The present review primarily focuses on five prominent areas of recent research on pathway microevolution: lipid metabolism and life-history evolution; the electron transport system, hybrid breakdown and speciation; glycolysis, alcohol metabolism and population adaptation in Drosophila; chemostat selection in microorganisms; and anthocyanin …

Epsvr And Epmeta: Prediction Of Antigenic Epitopes Using Support Vector Regression And Multiple Server Results, Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang

School of Biological Sciences: Faculty Publications

Background: Accurate prediction of antigenic epitopes is important for immunologic research and medical applications, but it is still an open problem in bioinformatics. The case for discontinuous epitopes is even worse - currently there are only a few discontinuous epitope prediction servers available, though discontinuous peptides constitute the majority of all B-cell antigenic epitopes. The small number of structures for antigen-antibody complexes limits the development of reliable discontinuous epitope prediction methods and an unbiased benchmark to evaluate developed methods.

Results: In this work, we present two novel server applications for discontinuous epitope prediction: EPSVR and EPMeta, where EPMeta …

Ignoring Population Structure Can Lead To Erroneous Predictions Of Future Population Size, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Predictions of future population size often assume population structures are stable. Are we missing the boat if we ignore the occurrence of unstable or transient dynamics?

Agricultural crops are regularly infested with insect pests whose population size can reach outbreak densities in some years, causing considerable income loss to farmers. In general, the risk of pest outbreaks is highest when insects disperse to crop fields early in the growing season and the population growth rate is high. The population growth rate measures how much the population size (i.e., number of individuals of a species in a defined area) changes per …

Structured Population Dynamics: An Introduction To Integral Modeling, Joseph Briggs, Kathryn Dabbs, Michael Holm, Joan Lubben, Richard Rebarber, Brigitte Tenhumberg, Daniel Riser-Espinoza

School of Biological Sciences: Faculty Publications

In this article we illuminate the differences and similarities between matrix population models and integral population models for single-species stage structured populations. We illustrate the use of integral models with an application to Platte thistle, following Rose et al. [22], showing how the model is determined by basic life history functions. PPMs are ubiquitous in ecology, but for many purposes an IPM might be easier and/or more accurate to use. In TABLE 1 we summarize the similarities between PPMs and IPMs. In order to compare the predictions for PPMs and IPMs, enough data must be available to find the parameters …

Analysis Of Mirna Modifications, Bin Yu, Xuemei Chen

School of Biological Sciences: Faculty Publications

After transcription, a large number of cellular RNAs employ modifications to increase their diversity and functional potential. Modifications can occur on the base, ribose, or both, and are important steps in the maturation of many RNAs. Our lab recently showed that plant microRNAs (miRNAs) possess a 2′-O-methyl group on the ribose of the 3′ terminal nucleotide, and that this methyl group is added after miRNA/miRNA* formation. One function of this modification is to protect miRNAs from 3′ terminal uridylation by an unknown enzymatic activity. It is possible that uridylation of miRNAs triggers their degradation. Here we describe a …

Mate Choice And Learning, Eileen Hebets, Laura Sullivan-Beckers

Eileen Hebets Publications

While an individual’s genetic framework is a major contributor in determining its eventual mate choice, the role of the environment in further influencing mating decisions has long been recognized. Animals gather information from the environment throughout life, and in some cases, may apply this information to increase their odds of obtaining a high-quality mate. In short, these individuals learn. Moreover, such learning can have a social component. “Social learning” is a general term that describes any learning based on observing, interacting with, and/or imitating others in a social context. Social learning can transmit information vertically, generation to generation (e.g., parent …

Nm23-H1 Can Induce Cell Cycle Arrest And Apoptosis In B Cells, Tathagata Choudhuri, Masanao Murakami, Rajeev Kaul, Sushil K. Sahu, Suchitra Mohanty, Subhash C. Verma, Pankaj Kumar, Erle S. Robertson

School of Biological Sciences: Faculty Publications

Nm23-H1 is a well-known tumor metastasis suppressor, which functions as a nucleoside-diphosphate kinase converting nucleoside diphosphates to nucleoside triphosphates with an expense of ATP. It regulates a variety of cellular activities, including proliferation, development, migration and differentiation known to be modulated by a series of complex signaling pathway. Few studies have addressed the mechanistic action of Nm23-H1 in the context of these cellular processes. To determine the downstream pathways modulated by Nm23-H1, we expressed Nm23-H1 in a Burkitt lymphoma derived B-cell line BJAB and performed pathway specific microarray analysis. The genes with significant changes in expression patterns were clustered in …

Increased Dendrite Branching In Aβpp/Ps1 Mice And Elongation Of Dendrite Arbors By Fasudil Administration, Brian A. Couch, George J. Demarco, Shannon L. Gourley, Anthony J. Koleske

School of Biological Sciences: Faculty Publications

Amyloid-β (Aβ) overproduction and dendrite arbor atrophy are hallmarks of Alzheimer’s disease. The RhoA GTPase (Rho) signals through Rho kinase (ROCK) to control cytoskeletal dynamics and regulate neuron structure. Hyperactive Rho signaling destabilizes neurons leading to dendritic regression that can be rescued by genetic or pharmacological reduction of ROCK signaling. To understand what effect reduced ROCK signaling has on the dendrite arbors of mice that overproduce Aβ, we administered the ROCK inhibitor fasudil to AβPP/PS1 transgenic mice. We report that increased dendrite branching occurs in AβPP/PS1 mice and that fasudil promotes …

The Abl And Arg Non-Receptor Tyrosine Kinases Regulate Different Zones Of Stress Fiber, Focal Adhesion, And Contractile Network Localization In Spreading Fibroblasts, Justin G. Peacock, Brian A. Couch, Anthony J. Koleske

School of Biological Sciences: Faculty Publications

Directed cell migration requires precise spatial control of F-actin-based leading edge protrusion, focal adhesion (FA) dynamics, and actomyosin contractility. In spreading fibroblasts, the Abl family kinases, Abl and Arg, primarily localize to the nucleus and cell periphery, respectively. Here we provide evidence that Abl and Arg exert different spatial regulation on cellular contractile and adhesive structures. Loss of Abl function reduces FA, F-actin, and phosphorylated myosin light chain (pMLC) staining at the cell periphery, shifting the distribution of these elements more to the center of the cell than in wild-type (WT) and arg^—/— cells. Conversely, loss of Arg function …

Mitochondrial-Nuclear Epistasis Affects Fitness Within Species But Does Not Contribute To Fixed Incompatibilities Between Species Of Drosophila, Kristi L. Montooth, Colin D. Meiklejohn, Dawn N. Abt, David M. Rand

School of Biological Sciences: Faculty Publications

Efficient mitochondrial function requires physical interactions between the proteins encoded by the mitochondrial and nuclear genomes. Co-evolution between these genomes may result in the accumulation of incompatibilities between divergent lineages. We test whether mitochondrialnuclear incompatibilities have accumulated within the Drosophila melanogaster species subgroup by combining divergent mitochondrial and nuclear lineages and quantifying the effects on relative fitness. Precise placement of nine mtDNAs from D. melanogaster, D. simulans and D. mauritiana into two D. melanogaster nuclear genetic backgrounds reveals significant mitochondrial-nuclear epistasis affecting fitness in females. Combining the mitochondrial genomes with three different D. melanogaster X chromosomes reveals significant epistasis …

Synaptic Clustering Of Psd-95 Is Regulated By C-Abl Through Tyrosine Phosphorylation, Karen Perez De Arce, Lorena Varela-Nallar, Olivia Farias, Alejandra Cifuentes, Paulina Bull, Brian A. Couch, Anthony J. Koleske, Nibaldo C. Inestrosa, Alejandra R. Alvarez

School of Biological Sciences: Faculty Publications

The c-Abl tyrosine kinase is present in mouse brain synapses, but its precise synaptic function is unknown. We found that c-Abl levels in the rat hippocampus increase postnatally, with expression peaking at the first postnatal week. In 14 d in vitro hippocampal neuron cultures, c-Abl localizes primarily to the postsynaptic compartment, in which it colocalizes with the postsynaptic scaffold protein postsynaptic density protein-95 (PSD-95) in apposition to presynaptic markers. c-Abl associates with PSD-95, and chemical or genetic inhibition of c-Abl kinase activity reduces PSD-95 tyrosine phosphorylation, leading to reduced PSD-95 clustering and reduced synapses in treated neurons. c-Abl can phosphorylate …