Digital Commons Network^™

Dynamic Clamp: Alteration Of Response Properties And Creation Of Virtual Realities In Neurophysiology., Economo Mn, Fernandez Fr, White Ja

Faculty Publications

No abstract provided.

Latitudinal Differences In The Hibernation Characteristics Of Woodchucks (Marmota Monax), Stam M. Zervanos, Christine R. Maher Phd, Jerry A. Waldvogel, Gregory L. Florant

Faculty Publications

There is little information on the phenotypic flexibility of hibernation characteristics within species. To address this issue, we observed differences in hibernation characteristics of three free-ranging populations of woodchucks (Marmota monax) distributed along a latitudinal gradient from Maine to South Carolina. Data from free-ranging animals exhibited a direct relationship between latitude and length of the hibernation season. As expected, woodchucks in the northern latitudes hibernated longer than those in the southern latitudes. Also, the length of interbout arousals decreased with increase in latitude, whereas the length of torpor bouts and the number of arousals increased. Thus, we observed phenotypic plasticity …

Six Rna Viruses And Forty-One Hosts: Viral Small Rnas And Modulation Of Small Rna Repertoires In Vertebrate And Invertebrate Systems, Poornima Parameswaran, Ella Sklan, Courtney Wilkins, Trever Burgon, Melanie A. Samuel, Rui Lu, K. Mark Ansel, Vigo Heissmeyer, Shirit Einav, William Jackson, Tammy Doukas, Suman Paranjape, Charlotta Polacek, Flavia Barreto Dos Santos, Roxana Jalili, Farbod Babrzadeh, Baback Gharizadeh, Dirk Grimm, Mark Kay, Satoshi Koike, Peter Sarnow, Mostafa Ronaghi, Shou Wei Ding, Eva Harris, Marie Chow, Michael S. Diamond, Karla Kirkegaard, Jeffrey S. Glenn, Andrew Z. Fire

Faculty Publications

We have used multiplexed high-throughput sequencing to characterize changes in small RNA populations that occur during viral infection in animal cells. Small RNA-based mechanisms such as RNA interference (RNAi) have been shown in plant and invertebrate systems to play a key role in host responses to viral infection. Although homologs of the key RNAi effector pathways are present in mammalian cells, and can launch an RNAi-mediated degradation of experimentally targeted mRNAs, any role for such responses in mammalian host-virus interactions remains to be characterized. Six different viruses were examined in 41 experimentally susceptible and resistant host systems. We identified virus-derived …

Kaposi's Sarcoma-Associated Herpesvirus Glycoproteins B And K8.1 Regulate Virion Egress And Synthesis Of Vascular Endothelial Growth Factor And Viral Interleukin-6 In Bcbl-1 Cells, R. Subramanian, I. Sehgal, O. D'Auvergne, K. G. Kousoulas

Faculty Publications

Kaposi's sarcoma-associated herpesvirus (KSHV) viral glycoproteins play important roles in the infectious life cycle and have been implicated in KSHV-associated endothelial cell transformation, angiogenesis, and KS-induced malignancies. KSHV-associated primary effusion lymphomas (PELs) secrete high levels of vascular endothelial growth factor (VEGF) and viral interleukin-6 (vIL-6) in vitro and VEGF, vIL-6, and basic-fibroblast growth factor (b-FGF) in mouse xenografts. KSHV-encoded glycoproteins B (gB) and K8.1 stimulate VEGF secretion, most likely mediated by direct or indirect binding to cell surface receptors, including the gB-specific αVβ3 and α3β1 integrins. In this study, the short interfering RNA (siRNA)-mediated inhibition of either gB or K8.1 …

The Combined Effects Of Rivers And Refugia Generate Extreme Cryptic Fragmentation Within The Common Ground Skink (Scincella Lateralis), Nathan D. Jackson, Christopher C. Austin

Faculty Publications

Rivers can act as both islands of mesic refugia for terrestrial organisms during times of aridification and barriers to gene flow, though evidence for long-term isolation by rivers is mixed. Understanding the extent to which riverine barrier effects can be heightened for populations trapped in mesic refugia can help explain maintenance and generation of diversity in the face of Pleistocene climate change. Herein, we implement phylogenetic and population genetic approaches to investigate the phylogeographic structure and history of the ground skink, Scincella lateralis, using mtDNA and eight nuclear loci. We then test several predictions of a river-refugia model of diversification. …

Intracellular Consequences Of Sos1 Deficiency During Salt Stress, Dong Ha Oh, Sang Yeol Lee, Ray A. Bressan, Dae Jin Yun, Hans J. Bohnert

Faculty Publications

A mutation of AtSOS1 (Salt Overly Sensitive 1), a plasma membrane Na +/H+-antiporter in Arabidopsis thaliana, leads to a salt-sensitive phenotype accompanied by the death of root cells under salt stress. Intracellular events and changes in gene expression were compared during a non-lethal salt stress between the wild type and a representative SOS1 mutant, atsos1-1, by confocal microscopy using ion-specific fluorophores and by quantitative RT-PCR. In addition to the higher accumulation of sodium ions, atsos1-1 showed inhibition of endocytosis, abnormalities in vacuolar shape and function, and changes in intracellular pH compared to the wild type in root tip cells under …

A Systems Model Of Vesicle Trafficking In Arabidopsis Pollen Tubes, Naohiro Kato, Hongyu He, Alexander P. Steger

Faculty Publications

A systems model that describes vesicle trafficking during pollen tube growth in Arabidopsis (Arabidopsis thaliana) was constructed. The model is composed of ordinary differential equations that connect the molecular functions of genes expressed in pollen. The current model requires soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors (SNAREs) and small GTPases, Arf or Rab, to reasonably predict tube growth as a function of time. Tube growth depends on vesicle trafficking that transports phospholipid and pectin to the tube tip. The vesicle trafficking genes identified by analyzing publicly available transcriptome data comprised 328 genes. Fourteen of them are up-regulated by the gibberellin …

Effects Of Transgenic Rice Expressing Bacillus Thuringiensis Cry1ab Protein On Ground-Dwelling Collembolan Community In Postharvest Seasons, Y. Y. Bai, R. H. Yan, G. Y. Ye, F. N. Huang, J. A. Cheng

Faculty Publications

During 20052008, field studies were conducted at two locations in Chongqing, China, to assess the potential effects of transgenic rice expressing Bacillus thuringiensis (Bt) Cry1Ab protein on the nontarget ground-dwelling collembolan community in three postharvest seasons. Collembolans in non-Bt and Bt rice fields were sampled with pitfall traps during each of two postharvest seasons of 2005/2006 and 2006/2007 and litterbag traps during each of three postharvest seasons of 2005/2006, 2006/2007, and 2007/2008. Ground-dwelling collembolans in rice fields during the postharvest seasons were abundant, whereas community densities varied considerably between the two locations and among the three seasons. A total of …

Inefficient Tat-Dependent Export Of Periplasmic Amidases In An Escherichia Coli Strain With Mutations In Two Deda Family Genes, Rakesh Sikdar, William T. Doerrler

Faculty Publications

The DedA family genes are found in most bacterial genomes. Two of these proteins are Escherichia coli YqjA and YghB, predicted inner membrane proteins of unknown function sharing 61% amino acid identity. The E. coli single deletion mutants are largely without phenotype, but the double mutant (BC202; ΔyqjA::Tetr ΔyghB::Kanr) is characterized by incomplete cell division, temperature sensitivity, and altered phospholipid levels (K. Thompkins et al., J. Bacteriol. 190:4489-4500, 2008). In this report, we have better characterized the cell division chaining defect of BC202. Fluorescence recovery after photobleaching indicates that 58% of the cells in chains are compartmentalized by at least …

Greenhouse Gas Regulation Under The Clean Air Act: Structure, Effects, And Implications Of A Knowable Pathway, Nathan D. Richardson, Arthur G. Fraas, Dallas Butraw

Faculty Publications

It appears inevitable, absent legislative intervention, that regulation under the Clean Air Act (CAA) will move beyond mobile sources to the industrial and power facilities that emit most U.S. greenhouse gas (GHG) emissions. We analyze the mechanisms available to the EPA for regulating such sources, and identify one, New Source Performance Standards (NSPS) as the most predictable, likely, and practical, i.e. knowable, pathway. Based on the legal structure of the NSPS and the EPA’s traditional approach, we analyze a hypothetical GHG NSPS for one sector, coal electricity generation. This analysis indicates that efficiency improvements and perhaps biomass cofiring could be …

Dangers In Prescription Drugs: Filling A Private Law Gap In The Healthcare Debate, David G. Owen

Faculty Publications

No abstract provided.

A Lanthanide-Based Chemosensor For Bioavailable Fe3+ Using A Fluorescent Siderophore: An Assay Displacement Approach, Karen M. Orcutt, William Scott Jones, Andrea Mcdonald, David Schrock, Karl J. Wallace

Faculty Publications

The measurement of trace analytes in aqueous systems has become increasingly important for understanding ocean primary productivity. In oceanography, iron (Fe) is a key element in regulating ocean productivity, microplankton assemblages and has been identified as a causative element in the development of some harmful algal blooms. The chemosenor developed in this study is based on an indicator displacement approach that utilizes time-resolved fluorescence and fluorescence resonance energy transfer as the sensing mechanism to achieve detection of Fe3+ ions as low as 5 nM. This novel approach holds promise for the development of photoactive chemosensors for ocean deployment.

Carboxysomal Carbonic Anhydrases: Structure And Role In Microbial Co2 Fixation, Gordon C. Cannon, Sabine Heinhorst, Cheryl A. Kerfeld

Faculty Publications

Cyanobacteria and some chemoautotrophic bacteria are able to grow in environments with limiting CO₂ concentrations by employing a CO₂-concentrating mechanism (CCM) that allows them to accumulate inorganic carbon in their cytoplasm to concentrations several orders of magnitude higher than that on the outside. The final step of this process takes place in polyhedral protein microcompartments known as carboxysomes, which contain the majority of the CO₂-fixing enzyme, RubisCO. The efficiency of CO₂ fixation by the sequestered RubisCO is enhanced by co-localization with a specialized carbonic anhydrase that catalyzes dehydration of the …

Effects Of Metal Compounds With Distinct Physicochemical Properties On Iron Homeostasis And Antibacterial Activity In The Lungs: Chromium And Vanadium, Mitchell D. Cohen, Maureen Sisco, Colleen Prophete, Kotaro Yoshida, Lung-Chi Chen, Judith T. Zelikoff, Jason Smee, Alvin A. Holder, Jacqueline Stormhuerner, Debbie C. Crans, Andrew J. Ghio

Faculty Publications

In situ reactions of metal ions or their compounds are important mechanisms by which particles alter lung immune responses. The authors hypothesized that major determinants of the immunomodulatory effect of any metal include its redox behavior/properties, oxidation state, and/or solubility, and that the toxicities arising from differences in physicochemical parameters are manifest, in part, via differential shifts in lung iron (Fe) homeostasis. To test the hypotheses, immunomodulatory potentials for both pentavalent vanadium (V(V); as soluble metavanadate or insoluble vanadium pentoxide) and hexavalent chromium (Cr(VI); as soluble sodium chromate or insoluble calcium chromate) were quantified in rats after inhalation (5 h/day …

Redundant Journal Access: Why Pay More Than Once?, Jared L. Howland

Faculty Publications

PDF of Powerpoint Presentation on journal access. This presentation was given at the Electronic Resources and Libraries 2010 Conference in Austin, Texas.

Helping Child Welfare Workers Improve Cultural Competence By Utilizing Spiritual Genograms With Native American Families And Children, Gordon E. Limb, David R. Hodge

Faculty Publications

This study represents an initial step at giving child welfare workers an important assessment tool as they seek to provide culturally and spiritually competent services to Native American families and children. In order to determine the relevancy and consistency of utilizing a modified spiritual genogram assessment tool with Native Americans, 50 Native American experts reviewed, rated, and gave feedback on its use. Results showed that while there were limitations in utilizing spiritual genograms, this assessment tool could help child welfare workers become more culturally competent as they develop interventions with Native American families and children.

Virus Discovery By Deep Sequencing And Assembly Of Virus-Derived Small Silencing Rnas, Qingfa Wu, Yingjun Luo, Rui Lu, Nelson Lau, Eric C. Lai, Wan Xiang Li, Shou Wei Ding

Faculty Publications

In response to infection, invertebrates process replicating viral RNA genomes into siRNAs of discrete sizes to guide virus clearance by RNA interference. Here, we show that viral siRNAs sequenced from fruit fly, mosquito, and nematode cells were all overlapping in sequence, suggesting a possibility of using siRNAs for viral genome assembly and virus discovery. To test this idea, we examined contigs assembled from published small RNA libraries and discovered five previously undescribed viruses from cultured Drosophila cells and adult mosquitoes, including three with a positive-strand RNA genome and two with a dsRNA genome. Notably, four of the identified viruses exhibited …

Construction, Figures Of Merit And Testing Of A Single-Cell Fluorescence Excitation Spectroscopy System, Laura S. Hill, Tammi L. Richardson, Louisa T.M. Profeta, Timothy J. Shaw, Christopher J. Hintz, Benjamin S. Twining, Evelyn Lawrenz, Micheal L. Myrick

Faculty Publications

Characterization of phytoplankton community composition is critical to understanding the ecology and biogeochemistry of the oceans. One approach to taxonomic characterization takes advantage of differing pigmentation between algal taxa and thus differences in fluorescence excitation spectra. Analyses of bulk water samples, however, may be confounded by interference from chromophoric dissolved organic matter or suspended particulate matter. Here, we describe an instrument that uses a laser trap based on a Nikon TE2000-U microscope to position individual phytoplankton cells for confocal fluorescence excitation spectroscopy, thus avoiding interference from the surrounding medium. Quantitative measurements of optical power give data in the form of …

Structural Basis For The Photoconversion Of A Phytochrome To The Activated Pfr Form, Andrew T. Ulijasz, Gabriel Cornilescu, Claudia C. Cornilescu, Junrui Zhang, Mario Rivera, John L. Markley, Richard D. Vierstra

Faculty Publications

Phytochromes are a collection of bilin-containing photoreceptors that regulate numerous photoresponses in plants and microorganisms through their ability to photointerconvert between a red-light-absorbing, ground state (Pr) and a far-red-light-absorbing, photoactivated state (Pfr). Although the structures of several phytochromes as Pr have been determined, little is known about the structure of Pfr and how it initiates signalling. Here we describe the three-dimensional solution structure of the bilin-binding domain as Pfr, using the cyanobacterial phytochrome from Synechococcus OSB′. Contrary to predictions, light-induced rotation of the A pyrrole ring but not the Dring is the primary motion of the chromophore during photoconversion. Subsequent …

Psifr: An Integrated Resource For Prediction Of Protein Structure And Function, Shashi B. Pandit, Michal Brylinski, Hongyi Zhou, Mu Gao, Adrian K. Arakaki, Jeffrey Skolnick

Faculty Publications

In the post-genomic era, the annotation of protein function facilitates the understanding of various biological processes. To extend the range of function annotation methods to the twilight zone of sequence identity, we have developed approaches that exploit both protein tertiary structure and/or protein sequence evolutionary relationships. To serve the scientific community, we have integrated the structure prediction tools, TASSER, TASSER-Lite and METATASSER, and the functional inference tools, FINDSITE, a structure-based algorithm for binding site prediction, Gene Ontology molecular function inference and ligand screening, EFICAz2, a sequence-based approach to enzyme function inference and DBD-hunter, an algorithm for predicting DNA-binding proteins and …

Functional Genomics Tool: Gene Silencing In Ixodes Scapularis Eggs And Nymphs By Electroporated Dsrna, Shahid Karim, Emily Troiano, Thomas N. Mather

Faculty Publications

Background

Ticks are blood-sucking arthropods responsible for transmitting a wide variety of disease-causing agents, and constitute important public health threats globally. Ixodes scapularis is the primary vector of the Lyme disease agent in the eastern and central U.S. RNAi is a mechanism by which gene-specific double-stranded RNA (dsRNA) triggers degradation of homologous mRNA transcripts. Here, we describe an optimized protocol for effectively suppressing gene expression in the egg and nymphal stages of I. scapularis by electroporation.

Results

The genes encoding the putative Phospholipase A₂ (PLA₂), cytoplasmic Cystatin, Syntaxin-5, β-Actin and Calreticulin were targeted by delivering the dsRNA …

Pyritization Of Trace Metals In Estuarine Sediments And The Controlling Factors: A Case In Jiaojiang Estuary Of Zhejiang Province, China, Siyuan Ye, Edward A. Laws, Qiang Wu, Shaojun Zhong, Xigui Ding, Guangming Zhao, Shaojun Gong

Faculty Publications

Three undisturbed sediment samples were collected from the intertidal zone of the Jiaojiang Estuary of Zhejiang Province, China. The sediments were found to contain remarkably low concentrations of organic carbon (< 0.6%) and acid volatile sulfide (AVS) (< 30 μmol g^-1). The availability of these two substrates likely constrained sulfate reduction and pyritization of several trace metals, respectively. This was especially true at one station where AVS concentrations in the upper 20 cm averaged less than 0.05 μmol g^-1. Although the depth dependence of the degree of trace metal pyritization was generally consistent with expectations based on redox conditions, depth profiles of reactive-metal and pyrite-metal concentrations …

Functional Characterization Of The Chlamydomonas Reinhardtii Erg3 Ortholog, A Gene Involved In The Biosynthesis Of Ergosterol, Kristy M. Brumfield, James V. Moroney, Thomas S. Moore, Tiffany A. Simms, David Donze

Faculty Publications

Background: The predominant sterol in the membranes of the alga Chlamydomonas reinhardtii is ergosterol, which is commonly found in the membranes of fungi, but is rarely found in higher plants. Higher plants and fungi synthesize sterols by different pathways, with plants producing cycloartenol as a precursor to end-product sterols, while nonphotosynthesizing organisms like yeast and humans produce lanosterol as a precursor. Analysis of the C. reinhardtii genome sequence reveals that this algae is also likely to synthesize sterols using a pathway resembling the higher plant pathway, indicating that its sterols are synthesized somewhat differently than in fungi. The work presented …

Albedo Estimates For Land Surface Models And Support For A New Paradigm Based On Foliage Nitrogen Concentration, D. Y. Hollinger, Scott V. Ollinger, Andrew D. Richardson, T. P. Meyers, D. B. Dail, M. E. Martin, N. A. Scott, T. J. Arkebauer, D. D. Baldocchi, K. L. Clark, P. S. Curtis, K. J. Davis, A. R. Desai, D. Dragoni, M. L. Goulden, L. Gu, G. G. Katul, S. G. Pallardy, K. T. Paw, H. P. Schmid, P. C. Stoy, A. E. Suyker, S. B. Verma

Faculty Publications

Vegetation albedo is a critical component of the Earth's climate system, yet efforts to evaluate and improve albedo parameterizations in climate models have lagged relative to other aspects of model development. Here, we calculated growing season albedos for deciduous and evergreen forests, crops, and grasslands based on over 40 site‐years of data from the AmeriFlux network and compared them with estimates presently used in the land surface formulations of a variety of climate models. Generally, the albedo estimates used in land surface models agreed well with this data compilation. However, a variety of models using fixed seasonal estimates of albedo …

Bilitrienones From The Chemical Oxidation Of Dodecasubstituted Porphyrins, Owendi Ongayi, M. Graça H. Vicente, Brahma Ghosh, Frank R. Fronczek, Kevin M. Smith

Faculty Publications

The structure of the ring-opened product from direct oxidation of meso-tetra-arylporphyrins has been controversial for three decades. Herein we show that bilitrienones 2 are obtained from oxidation of metal-free dodecasubstituted porphyrins 1 in the presence of sodium nitrite, trifluoroacetic acid, and air oxygen. The presence of the para-nonyl groups in 1b stabilized the corresponding bilitrienone 2b, which was characterized by X-ray crystallography. In the absence of the para-nonyl groups bilitrienone 2a undergoes a rapid hydration reaction, giving biladienone 3a as the major isolated product. The molecular structures of 2b and 3a, and the photochemical isomerization of 3a are discussed. © …

Science And Religion In Western History: Models And Relationships, Alan Padgett

Faculty Publications

No abstract provided.

Using Video Feedback To Measure Self-Efficacy, Linda Bobo, Amanda Andrews

Faculty Publications

When a student has a high sense of self-efficacy, foreseeing success and providing positive guides and supports for performing the skill will usually occur. A low self-efficacy tends to predict failure and anticipation of what could go wrong. Videotape feedback provided to students has reported favorable outcomes. Self-efficacy could alter performance in learning a psychomotor competency skill (PCS). The purpose of this study was a) to assess the self-efficacy of athletic training students in learning to perform a PCS; and b) to measure the impact on self-efficacy by implementing an educational intervention of video feedback in learning to perform a …

Methane Emission From A Tropical Wetland In Ka'au Crater, O'Ahu, Hawai'i, Maxime Grand, Eric Gaidos

Faculty Publications

Natural tropical wetlands constitute an important but still poorly studied source of atmospheric methane, a powerful greenhouse gas. We measured net methane emission, soil profiles of methane generation and oxidation, and related environmental parameters in a tropical wetland occupying the Ka'au extinct volcanic crater on the Hawaiian island of O'ahu. The wetland has a fluctuating water table with dynamics that can be reproduced using precipitation data and a simple model. Median net methane flux was 117 mg m-2 day-1 and is consistent with measurements at other tropical sites. Net methane flux in the Commelina diffusa—dominated vegetation pattern (honohono) was significantly …

The Carboxyl-Terminal Segment Of Apolipoprotein A-V Undergoes A Lipid-Induced Conformational Change, Kasuen Mauldin, B. L. Lee, M. Oleszczuk, B. D. Sykes, R. O. Ryan

Faculty Publications

Apolipoprotein (apo) A-V is a 343-residue, multidomain protein that plays an important role in regulation of plasma triglyceride homeostasis. Primary sequence analysis revealed a unique tetraproline sequence (Pro293-Pro296) near the carboxyl terminus of the protein. A peptide corresponding to the 48-residue segment beyond the tetraproline motif was generated from a recombinant apoA-V precursor wherein Pro295 was replaced by Met. Cyanogen bromide cleavage of the precursor protein, followed by negative affinity chromatography, yielded a purified peptide. Nondenaturing polyacrylamide gel electrophoresis verified that apoA-V(296-343) solubilizes phospholipid vesicles, forming a relatively heterogeneous population of reconstituted high-density lipoprotein with Stokes’ diameters>17 nm. At …

The Effect Of Service- Learning On Interdisciplinary Learning And Curriculum Reinforcement, And Its Application To Public School Environments, Madeline Kovarik

Faculty Publications

This qualitative research project focused on the impact of service-learning experiences on an interdisciplinary college freshman course. The research included the impact on academic learning, the application of concepts into a public school educational environment, and the perceptions regarding the contribution to the school being served. Participants were college freshmen students who received pre and post surveys and participated in both verbal and written reflections. Analysis of the survey responses and reflection data indicated the service-learning experiences enhanced student learning. Analysis of data also indicated a disconnect between recognized community needs and college student involvement toward fulfilling the needs.