Digital Commons Network^™

Natural Variants Of Photosystem Ii Subunit D1 Tune Photochemical Fitness To Solar Intensity, David J. Vinyard, Javier Gimpel, Gennady M. Ananyev, Mario A. Cornejo, Susan S. Golden, Stephen P. Mayfield, G. Charles Dismukes

Faculty Publications

Background: Cyanobacteria use multiple PSII-D1 isoforms to adapt to environmental conditions. Results: D1:2 achieves higher quantum efficiency of water oxidation and biomass accumulation rate at high light versus D1:1; the latter is more efficient at low light due to less charge recombination. Conclusion: A functional advantage for D1:1 is revealed for the first time. Significance: Improved photochemical efficiency at low light suggests an evolutionary advantage to retain D1:1. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.

Comparison Of Risk Of Radiogenic Second Cancer Following Photon And Proton Craniospinal Irradiation For A Pediatric Medulloblastoma Patient, Rui Zhang, Rebecca M. Howell, Annelise Giebeler, Phillip J. Taddei, Anita Mahajan, Wayne D. Newhauser

Faculty Publications

Pediatric patients who received radiation therapy are at risk of developing side effects such as radiogenic second cancer. We compared proton and photon therapies in terms of the predicted risk of second cancers for a 4 year old medulloblastoma patient receiving craniospinal irradiation (CSI). Two CSI treatment plans with 23.4 Gy or Gy (RBE) prescribed dose were computed: a three-field 6 MV photon therapy plan and a four-field proton therapy plan. The primary doses for both plans were determined using a commercial treatment planning system. Stray radiation doses for proton therapy were determined from Monte Carlo simulations, and stray radiation …

An Extract Of Artemisia Dracunculus L. Inhibits Ubiquitin-Proteasome Activity And Preserves Skeletal Muscle Mass In A Murine Model Of Diabetes, Heather Kirk-Ballard, Zhong Q. Wang, Priyanka Acharya, Xian H. Zhang, Yongmei Yu, Gail Kilroy, David Ribnicky, William T. Cefalu, Z. Elizabeth Floyd

Faculty Publications

Impaired insulin signaling is a key feature of type 2 diabetes and is associated with increased ubiquitin-proteasome-dependent protein degradation in skeletal muscle. An extract of Artemisia dracunculus L. (termed PMI5011) improves insulin action by increasing insulin signaling in skeletal muscle. We sought to determine if the effect of PMI5011 on insulin signaling extends to regulation of the ubiquitin-proteasome system. C2C12 myotubes and the KK-Ay murine model of type 2 diabetes were used to evaluate the effect of PMI5011 on steady-state levels of ubiquitylation, proteasome activity and expression of Atrogin-1 and MuRF-1, muscle-specific ubiquitin ligases that are upregulated with impaired insulin …

Marr Family Transcription Factors, Anne Grove

Faculty Publications

No abstract provided.

Variation In Sodium Current Amplitude Between Vasopressin And Oxytocin Hypothalamic Supraoptic Neurons, Reese Scroggs, Lie Wang, Ryoichi Teruyama, William E. Armstrong

Faculty Publications

Biophysical characteristics of tetrodotoxin-sensitive sodium (Na+) currents were studied in vasopressin (VP) and oxytocin (OT) supraoptic neurons acutely isolated from rat hypothalamus. Na+ current density (pA/pF) was significantly greater in VP neurons than in OT neurons. No significant difference between VP and OT neurons was detected regarding the voltage dependence of activation and steady-state inactivation, or rate of recovery from inactivation of Na+ currents. In both VP and OT neurons, the macroscopic inactivation of the Na+ currents was best fitted with a double-exponential expression suggesting two rates of inactivation. Also in both types, the time course of recovery from inactivation …

Genomic Reconstruction Of Transcriptional Regulatory Networks In Lactic Acid Bacteria, Dmitri A. Ravcheev, Aaron A. Best, Natalia V. Sernova, Marat D. Kazanov, Pavel S. Novichkov, Dmitri A. Rodionov

Faculty Publications

Background

Genome scale annotation of regulatory interactions and reconstruction of regulatory networks are the crucial problems in bacterial genomics. The Lactobacillales order of bacteria collates various microorganisms having a large economic impact, including both human and animal pathogens and strains used in the food industry. Nonetheless, no systematic genome-wide analysis of transcriptional regulation has been previously made for this taxonomic group.

Results

A comparative genomics approach was used for reconstruction of transcriptional regulatory networks in 30 selected genomes of lactic acid bacteria. The inferred networks comprise regulons for 102 orthologous transcription factors (TFs), including 47 novel regulons for previously uncharacterized …

Control Of Flower Size, Beth A. Krizek, Jill T. Anderson

Faculty Publications

Flowers exhibit amazing morphological diversity in many traits, including their size. In addition to interspecific flower size differences, many species maintain significant variation in flower size within and among populations. Flower size variation can contribute to reproductive isolation of species and thus has clear evolutionary consequences. In this review we integrate information on flower size variation from both evolutionary and developmental biology perspectives. We examine the role of flower size in the context of mating system evolution. In addition, we describe what is currently known about the genetic basis of flower size based on quantitative trait locus (QTL) mapping in …

Standardized Treatment Planning Methodology For Passively Scattered Proton Craniospinal Irradiation, Annelise Giebeler, Wayne D. Newhauser, Richard A. Amos, Anita Mahajan, Kenneth Homann, Rebecca M. Howell

Faculty Publications

Background: As the number of proton therapy centers increases, so does the need for studies which compare proton treatments between institutions and with photon therapy. However, results of such studies are highly dependent on target volume definition and treatment planning techniques. Thus, standardized methods of treatment planning are needed, particularly for proton treatment planning, in which special consideration is paid to the depth and sharp distal fall-off of the proton distribution. This study presents and evaluates a standardized method of proton treatment planning for craniospinal irradiation (CSI).Methods: We applied our institution's planning methodology for proton CSI, at the time of …

Visual Homing With A Pan-Tilt Based Stereo Camera, Paramesh Nirmal, Damian M. Lyons

Faculty Publications

Visual homing is a navigation method based on comparing a stored image of the goal location and the current image (current view) to determine how to navigate to the goal location. It is theorized that insects, such as ants and bees, employ visual homing methods to return to their nest [1]. Visual homing has been applied to autonomous robot platforms using two main approaches: holistic and feature-based. Both methods aim at determining distance and direction to the goal location. Navigational algorithms using Scale Invariant Feature Transforms (SIFT) have gained great popularity in the recent years due to the robustness of …

Crowdsourcing With Arcgis Online For Natural Resources Management, Yanli Zhang, Matthew W. Mcbroom, Jason Grogan, Paul R. Blackwell

Faculty Publications

No abstract provided.

Radical-Containing Ultrafine Particulate Matter Initiates Epithelial-To-Mesenchymal Transitions In Airway Epithelial Cells, Paul T. Thevenot, Jordy Saravia, Nili Jin, Joseph D. Giaimo, Regina E. Chustz, Sarah Mahne, Matthew A. Kelley, Valeria Y. Hebert, Barry Dellinger, Tammy R. Dugas, Francesco J. Demayo, Stephania A. Cormier

Faculty Publications

Environmentally persistent free radicals (EPFRs) in combustion generated particulate matter (PM) are capable of inducing pulmonary pathologies and contributing to the development of environmental asthma. In vivo exposure of infant rats to EPFRs demonstrates their ability to induce airway hyperresponsiveness to methacholine, a hallmark of asthma. However, the mechanisms by which combustion-derived EPFRs elicit in vivo responses remain elusive. In this study, we used a chemically defined EPFR consisting of approximately 0.2 μm amorphrous silica containing 3% cupric oxide with the organic pollutant 1,2-dichlorobenzene (DCB-230). DCB-230 possesses similar radical content to urban-collected EPFRs but offers several advantages, including lack of …

Social Opportunity Causes Rapid Transcriptional Changes In The Social Behaviour Network Of The Brain In An African Cichlid Fish, K. P. Maruska, A. Zhang, A. Neboori, R. D. Fernald

Faculty Publications

Animals constantly integrate external stimuli with their own internal physiological state to make appropriate behavioural decisions. Little is known, however, about where in the brain the salience of these signals is evaluated, or which neural and transcriptional mechanisms link this integration to adaptive behaviours. We used an African cichlid fish Astatotilapia burtoni to test the hypothesis that a new social opportunity activates the conserved 'social behaviour network' (SBN), a collection of brain nuclei known to regulate social behaviours across vertebrates. We measured mRNA levels of immediate early genes (IEGs) in microdissected brain regions as a proxy for neuronal activation, and …

Effects Of Chlorantraniliprole And Thiamethoxam Rice Seed Treatments On Egg Numbers And First Instar Survival Of Lissorhoptrus Oryzophilus (Coleoptera: Curculionidae), S. K. Lanka, J. A. Ottea, J. M. Beuzelin, M. J. Stout

Faculty Publications

Effects of treatment of rice seeds with an anthranilic diamide, chlorantraniliprole, and a neonicotinoid, thiamethoxam, on egg laying and first instar survival in rice water weevil, Lissorhoptrus oryzophilus Kuschel, were examined under greenhouse conditions. Exposure of adult weevils to rice (6-7 leaf stage) grown from seeds treated with chlorantraniliprole and thiamethoxam resulted in reduction in numbers of eggs and first instars. The low egg numbers by adults exposed to chlorantraniliprole-treated plants was confirmed as a sublethal effect on adults: adult survival was not impacted after 4 d of feeding on foliage from chlorantraniliprole-treated plants but the number of eggs laid …

The Kaposi's Sarcoma-Associated Herpesvirus Orf34 Protein Binds To Hif-1Α And Causes Its Degradation Via The Proteasome Pathway, Muzammel Haque, Konstantin G. Kousoulas

Faculty Publications

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent for Kaposi's sarcoma (KS) and two other lymphoproliferative disorders, primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). Kaposi's sarcoma is a highly vascular tumor, and recently both hypoxia-inducible factor 1α (HIF-1α) and HIF-2α were detected in KS samples, indicating a role of HIFs in the KSHV life cycle. Previously, we showed that ORF34, a lytic gene of unassigned function, was activated by hypoxia and that ORF34 transcription was upregulated by both HIFs (M. Haque, D. A. Davis, V. Wang, I. Widmer, and R. Yarchoan, J Virol. 77:6761- 6768, 2003). In the …

Serum Γ-Glutamyltransferase And The Risk Of Heart Failure In Men And Women In Finland, Yujie Wang, Jaakko Tuomilehto, Pekka Jousilahti, Veikko Salomaa, Bin Li, Riitta Antikainen, Markku Mähönen, Peter T. Katzmarzyk, Gang Hu

Faculty Publications

Objectives: To evaluate the association of serum γ- glutamyltransferase (GGT) levels with heart failure (HF) risk in the Finnish population. Design: Prospective population-based cohort study. Setting: The present study, which is a part of FINRISK study, was carried out in Finland. Subject study cohorts included 18 353 Finnish men and 19 726 women who were 25-74 years of age and free of HF at baseline. Main outcome measures HF (636 men and 445 women) during a mean follow-up of 14.5 years. Results: Baseline measurement of different levels of serum GGT was used to predict incident HF. The multivariable-adjusted (age, sex, …

The Relative And Unique Contributions Of Emotion Dysregulation And Impulsivity To Posttraumatic Stress Disorder Among Substance Dependent Inpatients, Nicole H. Weiss, Matthew T. Tull, Michael D. Anestis, Kim L. Gratz

Faculty Publications

Background: Despite elevated rates of posttraumatic stress disorder (PTSD) among substance use disorder (SUD) patients, as well as the clinical relevance of this co-occurrence, few studies have examined psychological factors associated with a PTSD–SUD diagnosis. Two factors worth investigating are emotion dysregulation and impulsivity, both of which are associated with PTSD and SUDs. Therefore, this study examined associations between PTSD and facets of emotion dysregulation and impulsivity within a sample of trauma-exposed SUD inpatients.

Methods: Participants were an ethnically diverse sample of 205 SUD patients in residential substance abuse treatment. Patients were administered diagnostic interviews and completed a …

High-Throughput Two-Dimensional Root System Phenotyping Platform Facilitates Genetic Analysis Of Root Growth And Development, Randy T. Clark, Adam N. Famoso, Keyan Zhao, Jon E. Shaff, Eric J. Craft, Carlos D. Bustamante, Susan R. Mccouch, Daniel J. Aneshansley, Leon V. Kochian

Faculty Publications

High-throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyse these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to, rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user-guided and …

Attachment And 'Hikikomori': A Psychosocial Developmental Model, Alexander Krieg, Jane R. Dickie

Faculty Publications

Background: Hikikomori (acute social withdrawal) is a social issue in Japan that affects both the society and the lives of the individual sufferers.

Aims: This study aims to connect attachment theory and hikikomori by using a culturally sensitive psychosocial developmental model that outlines the various stages of attachment throughout the developmental years.

Method: Twenty–four hikikomori sufferers and 60 comparison group participants were given questionnaires assessing parent and peer relationships, temperament and school experiences.

Results: We found the hikikomori participants had a higher incidence of ambivalent attachment, reported more parental and peer rejection and bullying, and expressed greater temperamental shyness. Path …

Covariance Localization With The Diffusion-Based Correlation Models, Max Yaremchuk, Dmitry A. Nechaev

Faculty Publications

Improving the performance of ensemble filters applied to models with many state variables requires regularization of the covariance estimates by localizing the impact of observations on state variables. A covariance localization technique based on modeling of the sample covariance with polynomial functions of the diffusion operator (DL method) is presented. Performance of the technique is compared with the non-adaptive (NAL) and adaptive (AL) ensemble localization schemes in the framework of numerical experiments with synthetic covariance matrices in a realistically inhomogeneous setting. It is shown that the DL approach is comparable in accuracy with the AL method when the ensemble size …

The Intestinal Microbiota In Aged Mice Is Modulated By Dietary Resistant Starch And Correlated With Improvements In Host Responses, Sybille Tachon, June Zhou, Michael Keenan, Roy Martin, Maria L. Marco

Faculty Publications

Dietary interventions might prevent or reverse age-related declines in health through modification of the activity and composition of the intestinal microbiota. As a first step toward more comprehensive evaluations of single dietary components on healthy aging, 16S rRNA gene amplicon sequencing was applied to determine the structure of the bacterial communities in the ceca of 20-month-old healthy mice fed energy-controlled diets containing 0, 18, or 36% type 2 resistant starch (RS) from high-amylose maize (HAM-RS2). The cecal microbiota of mice fed a diet depleted in RS and containing the readily digestible carbohydrate amylopectin were dominated by bacteria in the Firmicutes …

The Schrödinger Equation With Friction From The Quantum Trajectory Perspective, Sophya V. Garashchuk, Vaibhav Dixit, Bing Gu, James Mazzuca

Faculty Publications

Similarity of equations of motion for the classical and quantum trajectories is used to introduce afriction term dependent on the wavefunction phase into the time-dependent Schrödingerequation. The term describes irreversible energy loss by the quantum system. The force offriction is proportional to the velocity of a quantum trajectory. The resulting Schrödinger equationis nonlinear, conserves wavefunction normalization, and evolves an arbitrary wavefunction into the ground state of the system (of appropriate symmetry if applicable). Decrease in energy is proportional to the average kinetic energy of the quantum trajectory ensemble. Dynamics in the high friction regime is suitable for simple models of …

Lake Macrophyte Nutrient Index Of Standing Waters In Serbia (Limnis), Dušanka Laketić, Snežana Radulović, Milica Živković, Tamara Jurca, Mac H. Alford

Faculty Publications

The aim of this study was to derive a Macrophyte Nutrient Index for standing waters in Serbia, based on the LEAFPACS method and to correlate it against existing Lake Typology.

A single data matrix of 46 species and 1463 sample quadrats was compiled from two datasets: a revised phytocenological database given according to Braun-Blanquet Cover Abundance Scale and a database of sample quadrats collected during the summer months of 2009, 2010 and 2011 at 31 lakes in Serbia. The nutrient indices (MSI) for 46 lake hydrophytes were calculated using the Reprediction Algorithm on N-Ellenberg's values. A Macrophyte …

Confronting Myths About Household Food Insecurity And Excess Weight, Edward A. Frongillo Jr.

Faculty Publications

No abstract provided.

A Phylogeny Of Birds Based On Over 1,500 Loci Collected By Target Enrichment And High-Throughput Sequencing, John E. Mccormack, Michael G. Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn, Robb T. Brumfield

Faculty Publications

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny …

Indicators Of Family Care For Development For Use In Multicountry Surveys, Patricia Kariger, Edward A. Frongillo Jr., Patrice Engle, Pia M. Rebello Britto, Sara M. Sywulka, Purnima Menon

Faculty Publications

Indicators of family care for development are essential for ascertaining whether families are providing their children with an environment that leads to positive developmental outcomes. This project aimed to develop indicators from a set of items, measuring family care practices and resources important for caregiving, for use in epidemiologic surveys in developing countries. A mixed method (quantitative and qualitative) design was used for item selection and evaluation. Qualitative and quantitative analyses were conducted to examine the validity of candidate items in several country samples. Qualitative methods included the use of global expert panels to identify and evaluate the performance of …

Effects Of Rare And Common Blood Pressure Gene Variants On Essential Hypertension: Results From The Family Blood Pressure Program, Clue, And Atherosclerosis Risk In Communities Studies, Khanh Dung H. Nguyen, Vasyl Pihur, Santhi K. Ganesh, Ankit Rakha, Richard S. Cooper, Steven C. Hunt, Barry I. Freedman, Joe Coresh, W. H.Linda Kao, Alanna C. Morrison, Eric Boerwinkle, Georg B. Ehret, Aravinda Chakravarti

Faculty Publications

Rationale: Hypertension affects ≈30% of adults in industrialized countries and is the major risk factor for cardiovascular disease. Objective: We sought to study the genetic effect of coding and conserved noncoding variants in syndromic hypertension genes on systolic blood pressure (BP) and diastolic BP to assess their overall impact on essential hypertension. Methods and Results: We resequenced 11 genes (AGT, CYP11B1, CYP17A1, HSD11B2, NR3C1, NR3C2, SCNN1A, SCNN1B, SCNN1G, WNK1, and WNK4) in 560 European American (EA) and African American ancestry GenNet participants with extreme systolic BP. We investigated genetic associations of 2535 variants with BP in 19997 EAs and in …

Biogenic Nitrogen Gas Production At The Oxic–Anoxic Interface In The Cariaco Basin, Venezuela, E. Montes, M. A. Altabet, F. E. Muller-Karger, M. I. Scranton, R. C. Thunell, Claudia R. Benitez-Nelson, L. Lorenzoni, Y. M. Astor

Faculty Publications

Excess nitrogen gas (N2xs) was measured in samples collected at six locations in the eastern and western sub-basins of the Cariaco Basin, Venezuela, in September 2008 (non-upwelling conditions) and March 2009 (upwelling conditions). During both sampling periods, N2xs concentrations were below detection in surface waters, increasing to ~ 22 μmol N kg−1 at the oxic–anoxic interface ([O2] < ~ 4 μmol kg−1, ~ 250 m). Below the oxic–anoxic interface (300–400 m), the average concentration of N2xs was 24.7 ± 1.9 μmol N kg−1 in September 2008 and 27.5 ± 2.0 μmol N kg−1 in March 2009, i.e., N2xs concentrations within this depth interval were ~ 3 μmol N kg−1 higher (p < 0.001) during the upwelling season compared to the non-upwelling period. These results suggest that N-loss in the Cariaco Basin may vary seasonally in response to changes in the flux of sinking particulate organic matter. We attribute the increase in N2xs concentrations, or N-loss, observed during upwelling to: (1) higher availability of fixed nitrogen derived from suspended and sinking particles at the oxic–anoxic interface and/or (2) enhanced ventilation at the oxic–anoxic interface during upwelling.

Synthesis And Cellular Studies Of Polyamine Conjugates Of A Mercaptomethyl-Carboranylporphyrin, N. V.S.Dinesh K. Bhupathiraju, M. Graça H. Vicente

Faculty Publications

Seven polyamine conjugates of a tri(p-carboranylmethylthio) tetrafluorophenylporphyrin were prepared in high yields by sequential substitution of the p-phenyl fluoride of tetrakis(pentafluorophenyl)porphyrin (TPPF), and investigated as boron delivery agents for boron neutron capture therapy (BNCT). The polyamines used were derivatives of the natural-occurring spermine with different lengths of the carbon chains, terminal primary amine groups and, in two of the conjugates, additional aminoethyl moieties. A tri(polyethylene glycol) conjugate was also synthesized for comparison purposes. The polyamine conjugates showed low dark cytotoxicity (IC50 >400 μM) and low phototoxicity (IC50 >40 μM at 1.5 J/cm 2). All polyamine conjugates, with one exception, showed …

Synthesis And Structure-Activity Relationship Of Piperidine-Derived Non-Urea Soluble Epoxide Hydrolase Inhibitors, Stevan Pecic, Svetlana Pakhomova, Marcia E. Newcomer, Christophe Morisseau, Bruce D. Hammock, Zhengxiang Zhu, Alison Rinderspacher, Shi Xian Deng

Faculty Publications

A series of potent amide non-urea inhibitors of soluble epoxide hydrolase (sEH) is disclosed. The inhibition of soluble epoxide hydrolase leads to elevated levels of epoxyeicosatrienoic acids (EETs), and thus inhibitors of sEH represent one of a novel approach to the development of vasodilatory and anti-inflammatory drugs. Structure-activities studies guided optimization of a lead compound, identified through high-throughput screening, gave rise to sub-nanomolar inhibitors of human sEH with stability in human liver microsomal assay suitable for preclinical development. © 2012 Elsevier Ltd. All rights reserved.

Dna-Binding Motif And Target Genes Of The Imprinted Transcription Factor Peg3, Michelle M. Thiaville, Jennifer M. Huang, Hana Kim, Muhammad B. Ekram, Tae Young Roh, Joomyeong Kim

Faculty Publications

The Peg3 gene is expressed only from the paternally inherited allele located on proximal mouse chromosome 7. The PEG3 protein encoded by this imprinted gene is predicted to bind DNA based on its multiple zinc finger motifs and nuclear localization. In the current study, we demonstrated PEG3's DNA-binding ability by characterizing its binding motif and target genes. We successfully identified target regions bound by PEG3 from mouse brain extracts using chromatin immunoprecipitation analysis. PEG3 was demonstrated to bind these candidate regions through the consensus DNA-binding motif AGTnnCnnnTGGCT. In vitro promoter assays established that PEG3 controls the expression of a given …