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Simultaneous Measurement Of Deep Tissue Blood Flow And Oxygenation Using Noncontact Diffuse Correlation Spectroscopy Flow-Oximeter, Ting Li, Yu Lin, Yu Shang, Lian He, Chong Huang, Margaret M. Szabunio, Guoqiang Yu

Biomedical Engineering Faculty Publications

We report a novel noncontact diffuse correlation spectroscopy flow-oximeter for simultaneous quantification of relative changes in tissue blood flow (rBF) and oxygenation (Δ[oxygenation]). The noncontact probe was compared against a contact probe in tissue-like phantoms and forearm muscles (n = 10), and the dynamic trends in both rBF and Δ[oxygenation] were found to be highly correlated. However, the magnitudes of Δ[oxygenation] measured by the two probes were significantly different. Monte Carlo simulations and phantom experiments revealed that the arm curvature resulted in a significant underestimation (~-20%) for the noncontact measurements in Δ[ …

Plant-Symbiotic Fungi As Chemical Engineers: Multi-Genome Analysis Of The Clavicipitaceae Reveals Dynamics Of Alkaloid Loci, Christopher L. Schardl, Carolyn A. Young, Uljana Hesse, Stefan G. Amyotte, Kalina Andreeva, Patrick J. Calie, Damien J. Fleetwood, David C. Haws, Neil Moore, Birgitt Oeser, Daniel G. Panaccione, Kathryn K. Schweri, Christine R. Voisey, Mark L. Farman, Jerzy W. Jaromczyk, Bruce A. Roe, Donal M. O'Sullivan, Barry Scott, Paul Tudzynski, Zhiqiang An, Elissaveta G. Arnaoudova, Charles T. Bullock, Nikki D. Charlton, Li Chen, Murray Cox, Randy D. Dinkins, Simona Florea, Anthony E. Glenn, Anna Gordon, Ulrich Güldener, Daniel R. Harris, Walter Hollin, Jolanta Jaromczyk, Richard D. Johnson, Anar K. Khan, Eckhard Leistner, Adrian Leuchtmann, Chunjie Li, Jinge Liu, Jinze Liu, Miao Liu, Wade Mace, Caroline Machado, Padmaja Nagabhyru, Juan Pan, Jan Schmid, Koya Sugawara, Ulrike Steiner, Johanna E. Takach, Eiji Tanaka, Jennifer S. Webb, Ella V. Wilson, Jennifer L. Wiseman, Ruriko Yoshida, Zheng Zeng

Plant Pathology Faculty Publications

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic …

Low Concentrations Of Silver Nanoparticles In Biosolids Cause Adverse Ecosystem Responses Under Realistic Field Scenario, Benjamin P. Colman, Christina L. Arnaout, Sarah Anciaux, Claudia K. Gunsch, Michael F. Hochella Jr., Bojeong Kim, Gregory V. Lowry, Bonnie M. Mcgill, Brian C. Reinsch, Curtis J. Richardson, Jason M. Unrine, Justin P. Wright, Liyan Yin, Emily S. Bernhardt

Plant and Soil Sciences Faculty Publications

A large fraction of engineered nanomaterials in consumer and commercial products will reach natural ecosystems. To date, research on the biological impacts of environmental nanomaterial exposures has largely focused on high-concentration exposures in mechanistic lab studies with single strains of model organisms. These results are difficult to extrapolate to ecosystems, where exposures will likely be at low-concentrations and which are inhabited by a diversity of organisms. Here we show adverse responses of plants and microorganisms in a replicated long-term terrestrial mesocosm field experiment following a single low dose of silver nanoparticles (0.14 mg Ag kg⁻¹ soil) applied via a …

Plants And Plant Products Useful For Biofuel Manufacture And Feedstock, And Methods Of Producing Same, Seth Debolt, Darby Harris, Jozsef Stork

Horticulture Faculty Patents

A method of processing plant cellulose includes providing plant cellulose that is from a plant expressing a CESA polypeptide variant having at least one amino acid mutation in its carboxy-terminal transmembrane region; and saccharifying the plant cellulose to produce fermentable sugars. The method can also include fermenting the fermentable sugars to produce alcohol. A method of producing a plant having beneficial saccharification properties includes introducing into a plant a polynucleotide encoding a CESA polypeptide variant having at least one amino acid mutation in its carboxy-terminal transmembrane region; and expressing in the plant the CESA polypeptide variant, wherein plant cellulose of …

Sequencing Of The Sea Lamprey (Petromyzon Marinus) Genome Provides Insights Into Vertebrate Evolution, Jeramiah J. Smith, Shigehiro Kuraku, Carson Holt, Tatjana Sauka-Spengler, Ning Jiang, Michael S. Campbell, Mark D. Yandell, Tereza Manousaki, Axel Meyer, Ona E. Bloom, Jennifer R. Morgan, Joseph D. Buxbaum, Ravi Sachidanandam, Carrie Sims, Alexander S. Garruss, Malcolm Cook, Robb Krumlauf, Leanne M. Wiedemann, Stacia A. Sower, Wayne A. Decatur, Jeffrey A. Hall, Chris T. Amemiya, Nil R. Saha, Katherine M. Buckley, Jonathan P. Rast, Sabyasachi Das, Masayuki Hirano, Nathanael Mccurley, Peng Guo, Nicolas Rohner, Clifford J. Tabin, Paul Piccinelli, Greg Elgar, Magali Ruffier, Bronwen L. Aken, Stephen M.J. Searle, Matthieu Muffato, Miguel Pignatelli, Javier Herrero, Matthew Jones, C. Titus Brown, Yu-Wen Chung-Davidson, Kaben G. Nanlohy, Scot V. Libants, Chu-Yin Yeh, David W. Mccauley, James A. Langeland, Zeev Pancer, Bernd Fritzsch, Pieter J. De Jong, Baoli Zhu, Lucinda L Fulton, Brenda Theising, Paul Flicek, Marianne E. Bronner, Wesley C. Warren, Sandra W. Clifton, Richard K. Wilson, Weiming Li

Biology Faculty Publications

Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred …

Pyrvinium Pamoate Changes Alternative Splicing Of The Serotonin Receptor 2c By Influencing Its Rna Structure, Manli Shen, Stanislav Bellaousov, Michael Hiller, Pierre De La Grange, Trevor O. Creamer, Orit Malina, Ruth Sperling, David H. Mathews, Peter Stoilov, Stefan Stamm

Molecular and Cellular Biochemistry Faculty Publications

The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2'-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5'-splice site forms intramolecular base pairs that …

Regional Contingencies In The Relationship Between Aboveground Biomass And Litter In The World’S Grasslands, Lydia R. O'Halloran, Elizabeth T. Borer, Eric W. Seabloom, Sarah Hobbie, Andrew S. Macdougall, Elsa E. Cleland, Rebecca L. Mcculley, W. Stan Harpole, Kirsten S. Hofmockel, Wei Li, Nicole M. Decrappeo, Chengjin Chu, Guozhen Du, Jonathan D. Bakker, Kendi F. Davies, Brett A. Melbourne, Jennifer Firn, Nicole Hagenah, Johannes M. H. Knops, John W. Morgan, John L. Orrock, Suzanne M. Prober, Carly J. Stevens

Plant and Soil Sciences Faculty Publications

Based on regional-scale studies, aboveground production and litter decomposition are thought to positively covary, because they are driven by shared biotic and climatic factors. Until now we have been unable to test whether production and decomposition are generally coupled across climatically dissimilar regions, because we lacked replicated data collected within a single vegetation type across multiple regions, obfuscating the drivers and generality of the association between production and decomposition. Furthermore, our understanding of the relationships between production and decomposition rests heavily on separate meta-analyses of each response, because no studies have simultaneously measured production and the accumulation or decomposition of …

Berry Preparation And Extracts, Russell J. Mumper, Jin Dai, Vincent S. Gallicchio

Pharmaceutical Sciences Faculty Patents

Compositions having antioxidant and anti-inflammatory activity, and methods for providing such compositions, are disclosed. In one aspect, the compositions are derived by exposing a berry to an acidic solvent composition, adding a cryoprotectant, and recovering a berry extract having a stabilized anthocyanin content. Compositions comprising the stabilized anthocyanin-containing berry extract, formulated for oral and/or topical administration, are provided also.

Wolbachia Association With The Tsetse Fly, Glossina Fuscipes Fuscipes, Reveals High Levels Of Genetic Diversity And Complex Evolutionary Dynamics, Rebecca E. Symula, Uzma Alam, Corey L. Brelsfoard, Yineng Wu, Richard Echodu, Loyce M. Okedi, Serap Aksoy, Adalgisa Caccone

Entomology Faculty Publications

BACKGROUND: Wolbachia pipientis, a diverse group of α-proteobacteria, can alter arthropod host reproduction and confer a reproductive advantage to Wolbachia-infected females (cytoplasmic incompatibility (CI)). This advantage can alter host population genetics because Wolbachia-infected females produce more offspring with their own mitochondrial DNA (mtDNA) haplotypes than uninfected females. Thus, these host haplotypes become common or fixed (selective sweep). Although simulations suggest that for a CI-mediated sweep to occur, there must be a transient phase with repeated initial infections of multiple individual hosts by different Wolbachia strains, this has not been observed empirically. Wolbachia has been found in the tsetse fly, Glossina …

Striatal Glutamate Release In L-Dopa-Induced Dyskinetic Animals, Nina Nevalainen, Martin Lundblad, Greg A. Gerhardt, Ingrid Strömberg

Neuroscience Faculty Publications

L-DOPA-induced dyskinesia is a common side effect developed after chronic treatment with 3,4-dihydroxyphenyl-l-alanine (l-DOPA) in Parkinson's disease. The biological mechanisms behind this side effect are not fully comprehended although involvement of dopaminergic, serotonergic, and glutamatergic systems has been suggested. The present study utilizes in vivo amperometry to investigate the impact from unilateral 6-hydroxydopamine lesions and l-DOPA (4 mg/kg, including benserazide 15 mg/kg) -induced dyskinetic behavior on striatal basal extracellular glutamate concentration and potassium-evoked glutamate release in urethane-anesthetized rats. Recordings were performed before and after local L-DOPA application in the striatum. In addition, effects from the 5-HT_1A receptor agonist (2R)-(+)-8-hydroxy-2-(di-n-propylamino)tetralin …

Block Copolymer Cross-Linked Nanoassemblies Improve Particle Stability And Biocompatibility Of Superparamagnetic Iron Oxide Nanoparticles, Mo Dan, Daniel F. Scott, Peter A. Hardy, Robert J. Wydra, J. Zach Hilt, Robert A. Yokel, Younsoo Bae

Pharmaceutical Sciences Faculty Publications

PURPOSE: To develop cross-linked nanoassemblies (CNAs) as carriers for superparamagnetic iron oxide nanoparticles (IONPs).

METHODS: Ferric and ferrous ions were co-precipitated inside core-shell type nanoparticles prepared by cross-linking poly(ethylene glycol)-poly(aspartate) block copolymers to prepare CNAs entrapping Fe(3)O(4) IONPs (CNA-IONPs). Particle stability and biocompatibility of CNA-IONPs were characterized in comparison to citrate-coated Fe(3)O(4) IONPs (Citrate-IONPs).

RESULTS: CNA-IONPs, approximately 30 nm in diameter, showed no precipitation in water, PBS, or a cell culture medium after 3 or 30 h, at 22, 37, and 43°C, and 1, 2.5, and 5 mg/mL, whereas Citrate-IONPs agglomerated rapidly (> 400 nm) in all …

Changes In Bacterial Growth Rate Govern Expression Of The Borrelia Burgdorferi Ospc And Erp Infection-Associated Surface Proteins, Brandon L. Jutras, Alicia M. Chenail, Brian Stevenson

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The Lyme disease spirochete controls production of its OspC and Erp outer surface proteins, repressing protein synthesis during colonization of vector ticks but increasing expression when those ticks feed on vertebrate hosts. Early studies found that the synthesis of OspC and Erps can be stimulated in culture by shifting the temperature from 23°C to 34°C, leading to a hypothesis that Borrelia burgdorferi senses environmental temperature to determine its location in the tick-mammal infectious cycle. However, borreliae cultured at 34°C divide several times faster than do those cultured at 23°C. We developed methods that disassociate bacterial growth rate and temperature, allowing …

Imatinib Reverses Doxorubicin Resistance By Affecting Activation Of Stat3-Dependent Nf-Κb And Hsp27/P38/Akt Pathways And By Inhibiting Abcb1, Jonathan T. Sims, Sourik S. Ganguly, Holly Bennett, J. Woodrow Friend, Jessica Tepe, Rina Plattner

Pharmacology and Nutritional Sciences Faculty Publications

Despite advances in cancer detection and prevention, a diagnosis of metastatic disease remains a death sentence due to the fact that many cancers are either resistant to chemotherapy (conventional or targeted) or develop resistance during treatment, and residual chemoresistant cells are highly metastatic. Metastatic cancer cells resist the effects of chemotherapeutic agents by upregulating drug transporters, which efflux the drugs, and by activating proliferation and survival signaling pathways. Previously, we found that c-Abl and Arg non-receptor tyrosine kinases are activated in breast cancer, melanoma, and glioblastoma cells, and promote cancer progression. In this report, we demonstrate that the c-Abl/Arg inhibitor, …

Genetic Diversity In The Modern Horse Illustrated From Genome-Wide Snp Data, Jessica L. Petersen, James R. Mickelson, E. Gus Cothran, Lisa S. Andersson, Jeanette Axelsson, Ernie Bailey, Danika Bannasch, Matthew M. Binns, Alexandre S. Borges, Pieter Brama, Artur Da Câmara Machado, Ottmar Distl, Michela Felicetti, Laura Fox-Clipsham, Kathryn T. Graves, Gérard Guérin, Bianca Haase, Telhisa Hasegawa, Karin Hemmann, Emmeline W. Hill, Tosso Leeb, Gabriella Lindgren, Hannes Lohi, Maria Susana Lopes, Beatrice A. Mcgivney, Sofia Mikko, Nicholas Orr, M. Cecilia T. Penedo, Richard J. Piercy, Marja Raekallio, Stefan Rieder, Knut H. Røed, Maurizio Silvestrelli, June Swinburne, Teruaki Tozaki, Mark Vaudin, Claire M. Wade, Molly E. Mccue

Veterinary Science Faculty Publications

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect …

Nanotubes As Mitochondrial Uncouplers, Patrick G. Sullivan

Neuroscience Faculty Patents

A method of uncoupling mitochondria in a subject including administering nanotubes to the subject in a therapeutically effective amount, wherein the nanotubes are self-rectifying is provided. A method of decreasing reactive oxygen species and decreasing detrimental loading of Ca²⁺ into mitochondria is provided, including administering a pharmaceutically effective amount of nanotubes into the subject. A method of reducing weight, treating cancer, reducing the effects of traumatic brain injury, or reducing the effects of ageing, in a subject including administering a pharmaceutically effective amount of nanotubes into the subject is also provided.

Nanotubes As Mitochondrial Uncouplers, Patrick G. Sullivan

Neuroscience Faculty Patents

A method of uncoupling mitochondria in a subject including administering nanotubes to the subject in a therapeutically effective amount, wherein the nanotubes are self-rectifying is provided. A method of decreasing reactive oxygen species and decreasing detrimental loading of Ca²⁺ into mitochondria is provided, including administering a pharmaceutically effective amount of nanotubes into the subject. A method of reducing weight, treating cancer, reducing the effects of traumatic brain injury, or reducing the effects of ageing, in a subject including administering a pharmaceutically effective amount of nanotubes into the subject is also provided.

Revisiting The Relationship Between Regenerative Ability And Aging, Ashley W. Seifert, S. Randal Voss

Biology Faculty Publications

Contrary to the longstanding view that newts (Notophthalamus viridescens), but not axolotls (Ambystoma mexicanum), can regenerate a lens, a recent report in BMC Biology by Panagiotis Tsonis and colleagues shows axolotls indeed possess this ability during early larval stages. In contrast, they show that zebrafish never posses this ability, even as embryos. This underscores the importance of comparing regenerative ability across species and reinforces the need to consider organ regeneration in the context of evolution, development, and aging.

Activation Of Thromboxane A2 Receptor (Tp) Increases The Expression Of Monocyte Chemoattractant Protein -1 (Mcp-1)/Chemokine (C-C Motif) Ligand 2 (Ccl2) And Recruits Macrophages To Promote Invasion Of Lung Cancer Cells, Xiuling Li, Hsin-Hsiung Tai

Pharmaceutical Sciences Faculty Publications

Thromboxane synthase (TXAS) and thromboxane A₂ receptor (TP), two critical components for thromboxane A₂ (TXA₂) signaling, have been suggested to be involved in cancer invasion and metastasis. However, the mechanisms by which TXA₂ promotes these processes are still unclear. Here we show that TXA₂ mimetic, I-BOP, induced monocyte chemoattractant protein -1(MCP-1)/chemokine (C-C motif) ligand 2 (CCL2) expression at both mRNA and protein levels in human lung adenocarcinoma A549 cells stably over-expressing TP receptor α isoform (A549-TPα). The induction of MCP-1 was also found in other lung cancer cells H157 and H460 that express relatively …

Genome-Wide Analysis Reveals Selection For Important Traits In Domestic Horse Breeds, Jessica L. Petersen, James R. Mickelson, Aaron K. Rendahl, Stephanie J. Valberg, Lisa S. Andersson, Jeanette Axelsson, Ernie Bailey, Danika Bannasch, Matthew M. Binns, Alexandre S. Borges, Pieter Brama, Artur Da Câmara Machado, Stefano Capomaccio, Katia Cappelli, E. Gus Cothran, Ottmar Distl, Laura Fox-Clipsham, Kathryn T. Graves, Gérard Guérin, Bianca Haase, Telhisa Hasegawa, Karin Hemmann, Emmeline W. Hill, Tosso Leeb, Gabriella Lindgren, Hannes Lohi, Maria Susana Lopes, Beatrice A. Mcgivney, Sofia Mikko, Nicholas Orr, M. Cecilia T. Penedo, Richard J. Piercy, Marja Raekallio, Stefan Rieder, Knut H Røed, June Swinburne, Teruaki Tozaki, Mark Vaudin, Claire M. Wade, Molly E. Mccue

Veterinary Science Faculty Publications

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with …

Chimeric Isoprenoid Synthases And Uses Thereof, Joe Chappell, Kyoungwhan Back

Plant and Soil Sciences Faculty Patents

Provided is a chimeric isoprenoid synthase polypeptide including a first domain from a first isoprenoid synthase joined to a second domain from a second, heterologous, isoprenoid synthase, whereby the chimeric isoprenoid synthase is capable of catalyzing the production of isoprenoid reaction products that are not produced in the absence of the second domain of the second, heterologous, isoprenoid synthase. Also provided is a chimeric isoprenoid synthase polypeptide including an asymmetrically positioned heterologous domain, whereby the chimeric isoprenoid synthase is capable of catalyzing the production of isoprenoid reaction products that are not produced when the domain is positioned at its naturally-occurring …

Soluble Human Epidermal Growth Factor Receptor 2 (Sher2) As A Potential Risk Assessment, Screening, And Diagnostic Biomarker Of Lung Adenocarcinoma, Abby L. Cosentino-Boehm, Jacqueline M. Lafky, Tammy M. Greenwood, Kimberly D. Kimbler, Marites C. Buenafe, Yuxia Wang, Adam J. Branscum, Ping Yang, Nita J. Maihle, Andre T. Baron

Obstetrics and Gynecology Faculty Publications

Lung cancer is the leading cause of cancer-related death in the United States. Here, we evaluated the potential clinical utility of soluble human epidermal growth factor receptor 2 (sHER2) for the risk assessment, screening, and diagnosis of non-small cell lung cancer (NSCLC) using an unmatched case-control study design. Serum sHER2 concentrations were measured by immunoassay in 244 primary NSCLC cases and 218 healthy controls. Wilcoxon rank-sum tests, logistic regression models, and receiver operating characteristic plots were used to assess whether sHER2 is associated with lung cancer. Median serum sHER2 concentrations are higher in patients with adenocarcinoma than squamous cell carcinoma …

"Beef: The Real Health Food", Peter Ballerstedt

Forage Symposium at the Kentucky Cattlemen’s Convention

The 2010 Dietary Guidelines for Americans recommends restricting our intake of saturated fat to less than 7 percent of calories, and our cholesterol intake to less than 300 mg per day (less than two eggs). They promote the use of low-fat milk and lean meat, and the use of “meat substitutes” in school lunches. These recommendations are consistent with the official dietary policy that began in 1977 with the release of the first Dietary Goals for the United States by the United States Senate Select Committee on Nutrition and Human Needs. These guidelines were not justified by the then-available science. …

Assembly Of The Type Ii Secretion System Such As Found In Vibrio Cholerae Depends On The Novel Pilotin Asps, Rhys A. Dunstan, Eva Heinz, Lakshmi C. Wijeyewickrema, Robert N. Pike, Anthony W. Purcell, Timothy J. Evans, Judyta Praszkier, Roy M. Robins-Browne, Richard A. Strugnell, Konstantin V. Korotkov, Trevor Lithgow

Molecular and Cellular Biochemistry Faculty Publications

The Type II Secretion System (T2SS) is a molecular machine that drives the secretion of fully-folded protein substrates across the bacterial outer membrane. A key element in the machinery is the secretin: an integral, multimeric outer membrane protein that forms the secretion pore. We show that three distinct forms of T2SSs can be distinguished based on the sequence characteristics of their secretin pores. Detailed comparative analysis of two of these, the Klebsiella-type and Vibrio-type, showed them to be further distinguished by the pilotin that mediates their transport and assembly into the outer membrane. We have determined the crystal structure of …

Reference Gene Selection For Qrt-Pcr Analysis In The Sweetpotato Whitefly, Bemisia Tabaci (Hemiptera: Aleyrodidae), Rumei Li, Wen Xie, Shaoli Wang, Qingjun Wu, Nina Yang, Xin Yang, Huipeng Pan, Xiaomao Zhou, Lianyang Bai, Baoyun Xu, Xuguo Zhou, Youjun Zhang

Entomology Faculty Publications

BACKGROUND: Accurate evaluation of gene expression requires normalization relative to the expression of reliable reference genes. Expression levels of "classical" reference genes can differ, however, across experimental conditions. Although quantitative real-time PCR (qRT-PCR) has been used extensively to decipher gene function in the sweetpotato whitefly Bemisia tabaci, a world-wide pest in many agricultural systems, the stability of its reference genes has rarely been validated.

RESULTS: In this study, 15 candidate reference genes from B. tabaci were evaluated using two Excel-based algorithms geNorm and Normfinder under a diverse set of biotic and abiotic conditions. At least two reference genes were …

Risk Score Modeling Of Multiple Gene To Gene Interactions Using Aggregated-Multifactor Dimensionality Reduction, Hongying Dai, Richard J. Charnigo, Mara L. Becker, J. Steven Leeder, Alison A. Motsinger-Reif

Statistics Faculty Publications

BACKGROUND: Multifactor Dimensionality Reduction (MDR) has been widely applied to detect gene-gene (GxG) interactions associated with complex diseases. Existing MDR methods summarize disease risk by a dichotomous predisposing model (high-risk/low-risk) from one optimal GxG interaction, which does not take the accumulated effects from multiple GxG interactions into account.

RESULTS: We propose an Aggregated-Multifactor Dimensionality Reduction (A-MDR) method that exhaustively searches for and detects significant GxG interactions to generate an epistasis enriched gene network. An aggregated epistasis enriched risk score, which takes into account multiple GxG interactions simultaneously, replaces the dichotomous predisposing risk variable and provides higher resolution in the quantification …

A Neural Network Model To Translate Brain Developmental Events Across Mammalian Species, Radhakrishnan Nagarajan, Jeffrey N. Jonkman

Biostatistics Faculty Publications

Translating the timing of brain developmental events across mammalian species using suitable models has provided unprecedented insights into neural development and evolution. More importantly, these models can prove to be useful abstractions and predict unknown events across species from known empirical event timing data retrieved from published literature. Such predictions can be especially useful since the distribution of the event timing data is skewed with a majority of events documented only across a few selected species. The present study investigates the choice of single hidden layer feed-forward neural networks (FFNN) for predicting the unknown events from the empirical data. A …

Gleevec, An Abl Family Inhibitor, Produces A Profound Change In Cell Shape And Migration, Zaozao Chen, Elizabeth Lessey, Matthew E. Berginski, Li Cao, Jonathan Li, Xavier Trepat, Michelle Itano, Shawn M. Gomez, Maryna Kapustina, Cai Huang, Keith Burridge, George Truskey, Ken Jacobson

Markey Cancer Center Faculty Publications

The issue of how contractility and adhesion are related to cell shape and migration pattern remains largely unresolved. In this paper we report that Gleevec (Imatinib), an Abl family kinase inhibitor, produces a profound change in the shape and migration of rat bladder tumor cells (NBTII) plated on collagen-coated substrates. Cells treated with Gleevec adopt a highly spread D-shape and migrate more rapidly with greater persistence. Accompanying this more spread state is an increase in integrin-mediated adhesion coupled with increases in the size and number of discrete adhesions. In addition, both total internal reflection fluorescence microscopy (TIRFM) and interference reflection …

Snap And Obesity, Craig Gundersen

University of Kentucky Center for Poverty Research Discussion Paper Series

No abstract.

Valuation Of Recreational Beach Quality And Water Quality Management Strategies In Oahu, Jerrod M. Penn

Theses and Dissertations--Agricultural Economics

Hawaii’s pristine ocean and tropical environment is a keystone of Hawaii tourism and the state economy. Water pollution from stormwater and development threatens the beach quality to both residents and tourists. In order to understand the lost nonmarket value, we assess changes in quality of beach characteristics including water and sand quality, swimming safety conditions, and congestion using a Discrete Choice Experiment of recreational beach users. Further, we study willingness to pay (WTP) for water management strategies in Hawaii using another discrete choice experiment, including structural and nonstructural Best Management Practices, testing, monitoring, and educational efforts.

Using a mixed logit …

Improving Farm Management Decisions By Analyzing Production Expenditure Allocations And Farm Performance Standing, William A. Osborne

Theses and Dissertations--Agricultural Economics

This study examines the potential effects of categorical increases in production expenditures on farm income performance according to farm standing. The objective of this study is to expose differences in anticipated net farm income return from production expenditure investments and the optimal expense allocation strategy for each performance level. Studying farm performance through segregation by utilizing a two-tier analysis and quantile regression acknowledges the possibility that managerial strategy can differ based on managerial ability. Study outcomes are useful to farm managers because they offer more prescription style results and interpretations than found in other farm performance studies. Study findings show …