Digital Commons Network^™

Phytochrome-Mediated Development In Land Plants: Red Light Sensing Evolves To Meet The Challenges Of Changing Light Environments, Sarah Mathews

Faculty Publications

Phytochromes are photoreceptors that provide plants with circadian, seasonal, and positional information critical for the control of germination, seedling development, shade avoidance, reproduction, dormancy, and sleep movements. Phytochromes are unique among photoreceptors in their capacity to interconvert between a red-absorbing form (absorption maximum of ∼660 nm) and a far-red absorbing form (absorption maximum of ∼730 nm), which occur in a dynamic equilibrium within plant cells, corresponding to the proportions of red and far-red energy in ambient light. Because pigments in stems and leaves absorb wavelengths below about 700 nm, this provides plants with an elegant system for detecting their position …

Thermal Stability Landscape For Klenow Dna Polymerase As A Function Of Ph And Salt Concentration, Allison J. Richard, Chin Chi Liu, Alexandra L. Klinger, Matthew J. Todd, Tara M. Mezzasalma, Vince J. Licata

Faculty Publications

The thermal denaturation of Klenow DNA polymerase has been characterized over a wide variety of solution conditions to obtain a relative stability landscape for the protein. Measurements were conducted utilizing a miniaturized fluorescence assay that measures Tm based on the increase in the fluorescence of 1,8-anilinonaphthalene sulfonate (ANS) when the protein denatures. The melting temperature (Tm) for Klenow increases as the salt concentration is increased and as the pH is decreased. Klenow's Tm spans a range of over 20 °C, from 40 to 62 °C, depending upon the solution conditions. The landscape reconciles and extends previously measured Tm values for …

Integrin Structures And Conformational Signaling, Bing Hao Luo, Timothy A. Springer

Faculty Publications

Integrins are cell adhesion molecules that play critical roles in development, wound healing, hemostasis, immunity and cancer. Advances in the past two years have shed light on the structural basis for integrin regulation and signaling, especially on how global conformational changes between bent and extended conformations relate to the inter-domain and intra-domain shape shifting that regulates affinity for ligand. The downward movements of the C-terminal helices of the α I and β I domains and the swing-out of the hybrid domain play pivotal roles in integrin conformational signaling. Experiments have also shown that integrins transmit bidirectional signals across the plasma …

Effects Of Long-Term Hypoxia On Enzymes Of Carbohydrate Metabolism In The Gulf Killifish, Fundulus Grandis, Mery L. Mártinez, Christie Landry, Ryan Boehm, Steve Manning, Bernard B. Rees

Faculty Publications

The goal of the current study was to generate a comprehensive, multi-tissue perspective of the effects of chronic hypoxic exposure on carbohydrate metabolism in the Gulf killifish Fundulus grandis. Fish were held at approximately 1.3 mg l(-1) dissolved oxygen (similar to 3.6 kPa) for 4 weeks, after which maximal activities were measured for all glycolytic enzymes in four tissues (white skeletal muscle, liver, heart and brain), as well as for enzymes of glycogen metabolism (in muscle and liver) and gluconeogenesis (in liver). The specific activities of enzymes of glycolysis and glycogen metabolism were strongly suppressed by hypoxia in white skeletal …

Open Source, Openness, And Higher Education, David Wiley

Faculty Publications

With the growth of open source software and other related trends, a culture of openness is advancing from the edges of society to the core of academic culture. In this article I provide an overview of how the expansion of open source software in culture at large has affected the world of education, describe how the greater use of open source software in education has unfolded hand-in-hand with the development of open course content and open access research, and argue that this more comprehensive shift towards "openness" in academic practice is not only a positive trend, but a necessary one …

Pharmacogenomics: Analyzing Snps In The Cyp2d6 Gene Using Amino Acid Properties, Wesley A. Beckstead, Mark J. Clement, Mark Ebbert, David Mcclellan, Timothy O'Connor

Faculty Publications

Each year people suffer from complications of adverse drug reactions, but with pharmacogenomics there is hope to prevent thousands of these people from suffering or dying needlessly. The CYP2D6 gene is responsible for metabolizing a large portion of these drugs. Because of the gene’s importance, various approaches have been taken to analyze CYP2D6 and single nucleotide polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyze the effects of SNPs on encoded protein complexes by focusing on the biochemical properties of each nonsynonymous substitution using the program TreeSAAP. We apply this technique to SNPs found in the …

Palazzolo, The Public Trust, And The Property Owner's Reasonable Expectations: Takings And The South Carolina Marsh Island Bridge Debate, Erin Ryan

Faculty Publications

No abstract provided.

Multiracial Identity And Affirmative Action, Nancy Leong

Faculty Publications

No abstract provided.

Fabrication And Characterization Of Poly(Propylene Fumarate) Scaffolds With Controlled Pore Structures Using 3-Dimensional Printing And Injection Molding, Kee-Won Lee, Shanfeng Wang, Lichun Lu, Esmaiel Jabbari, Bradford L. Currier, Michael J. Yaszemski

Faculty Publications

Poly(propylene fumarate) (PPF) is an injectable, biodegradable polymer that has been used for fabricating preformed scaffolds in tissue engineering applications because of in situ crosslinking characteristics. Aiming for understanding the effects of pore structure parameters on bone tissue ingrowth, 3-dimensional (3D) PPF scaffolds with controlled pore architecture have been produced in this study from computer-aided design (CAD) models. We have created original scaffold models with 3 pore sizes (300, 600, and 900 µm) and randomly closed 0%, 10%, 20%, or 30% of total pores from the original models in 3 planes. PPF scaffolds were fabricated by a series steps involving …

Reckoning With Rapanos: Revisiting "Waters Of The United States" And The Limits Of Federal Wetland Regulation, Jonathan H. Adler

Faculty Publications

Rapanos v. United States is the latest episode in the serial effort to identify the precise meaning of "waters of the United States." Federal courts have struggled to define the scope of federal regulatory jurisdiction under the Clean Water Act ("CWA") since the law was adopted.

Although no single opinion in Rapanos commanded a majority of the Court, the Court delivered a discernible holding. Specifically, the Court held that CWA jurisdiction over private lands is limited...and reaffirmed that federal regulatory authority only extends to those wetlands that have a "significant nexus" to navigable waters of the United States. Nonetheless, the …

Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell

Faculty Publications

Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the gap open and gap extension penalties for three nuclear ribosomal data sets. Particular attention is given to optimal phylogeny scores for 200 alignments of a range of gap open and gap extension penalties and their respective …

Large Grain Size Stochastic Optimization Alignment, Hyrum Carroll, Mark J. Clement, Perry Ridge, Dan Sneddon, Quinn O. Snell

Faculty Publications

DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima problem, where suboptimal guide trees produce incorrect gap insertions. The optimization alignment approach, has been shown to be effective in combining alignment and phylogenetic search in order to avoid the problems associated with poor guide trees. The optimization alignment algorithm operates at a small grain size, aligning each tree found, wasting time producing multiple sequence alignments for suboptimal trees. This research develops and analyzes a large grain size algorithm for optimization alignment that …

Lower Incisors Of Prairie Dogs (Cynomys) As Biorecorders Of Hibernation And Season Of Death, H. Thomas Goodwin, Eva M. Ryckman

Faculty Publications

Incremental dentin and associated enamel, features visible at the surface of lower incisors of rodents, may chronicle important life-history information. This study investigated surface features of lower incisors representing 4 taxa of prairie dogs (Cynomys) in relation to hibernation and season of year. A set of abnormalities in dentin and enamel, observed on 20 of 138 incisors, always chronicled an event ending in late winter or early spring and was interpreted as a hibernation mark. Hibernation was recorded in the incisors of obligate hibernators, C. leucurus and C. gunnisoni, as well as in 20% of specimens of the facultative heterotherm, …

A Fourier Transformation Based Method To Mine Peptide Space For Antimicrobial Activity, Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O. Elasri, Youping Deng

Faculty Publications

Background

Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is possible to discover new candidate peptides using the available genomic and proteomic data. High throughput computational techniques could also be used to virtually scan the entire peptide space for discovering out new candidate antimicrobial peptides.

Result

We have identified a unique indexing method based on biologically distinct characteristic features of known antimicrobial peptides. Analysis of the entries in the antimicrobial peptide databases, based on our indexing method, using Fourier transformation …

Interplay Of Isca And Iscu In Biogenesis Of Iron-Sulfur Clusters, Juanjuan Yang, Jacob P. Bitoun, Huangen Ding

Faculty Publications

Increasing evidence suggests that sulfur in ubiquitous iron-sulfur clusters is derived from L-cysteine via cysteine desulfurases. In Escherichia coli, the major cysteine desulfurase activity for biogenesis of iron-sulfur clusters has been attributed to IscS. The gene that encodes IscS is a member of an operon isc-SUA, which also encodes two highly conserved proteins: IscU and IscA. Previous studies suggested that both IscU and IscA may act as the iron-sulfur cluster assembly scaffold proteins. However, recent evidence indicated that IscA is an iron-binding protein that can provide iron for the iron-sulfur cluster assembly in IscU (Ding, H., Harrison, K., and Lu, …

Effects Of Rice Panicle Age On Quantitative And Qualitative Injury By The Rice Stink Bug (Hemiptera: Pentatomidae), Dilipkumar T. Patel, Michael J. Stout, James R. Fuxa

Faculty Publications

Greenhouse experiments were conducted to evaluate the effects of panicle age on quantitative and qualitative injury caused by rice stink bug, Oebalus pugnax pugnax (Fab.), infestations on rice, Oryza sativa L. The effects were measured at two infestation levels (one and two bugs per panicle) and compared with an undamaged control. Percentage of empty grains and average weight of filled grains (quantitative injury) and percentage of pecky rice (qualitative injury) were evaluated at grain maturity. Regardless of infestation level, insect feeding during anthesis and the early milk stage of grain development (first 8 d after anthesis) caused substantially higher numbers …

Adult Phyllophaga Ephilida Host Plant Feeding Preference, Aboubacar Diagne, Richard N. Story, Abner M. Hammond

Faculty Publications

Limited biological information about Phyllophaga ephilida, a major sweet potato pest in Louisiana, is available. In 2001 and 2002, a study was conducted in the laboratory to investigate the feeding preference of adult Phyllophaga ephilida (Say) (Coleoptera: Scarabaeidae) for the foliage of eight woody plant species: water oak (Quercus nigra L.), live oak (Quercus virginiana Mill.), red maple (Acer rubrum L.), slash pine (Pinus caribaea Morelet), pecan (Carya illinoensis (Wangenh) K. Koch), sweetgum (Liquidambar styraciflua L.), southern magnolia (Magnolia grandiflora L.), and American elm (Ulmus americana L.). Beetles were placed in an arena with the eight host plants and allowed …

Low-Frequency Ultrasound Increases Outer Membrane Permeability Of Pseudomonas Aeruginosa, Christopher M. Runyan, John C. Carmen, Benjamin L. Beckstead, Jared L. Nelson, Richard A. Robison, William G. Pitt

Faculty Publications

Low-frequency ultrasound has been investigated as an adjuvant to antimicrobial therapy, targeted at both planktonic and biofilm (sessile) organisms. Our previous work showed that ultrasound (US) effectively enhances the bactericidal activity of certain antibiotics against planktonic cultures (Pitt et al., 1994; Rediske et al., 1999) and in vitro biofilms (Johnson et al., 1998; Qian et al., 1999) and in vivo biofilms (Carmen et al., 2004b, 2005; Rediske et al., 2000) of gram-positive and gram-negative bacteria. Ultrasound was shown to increase the transport of antibiotics through biofilms (Carmen et al., 2004a) which could account for some (or all) of the enhanced …

Mesostructured Silica Chemically Doped With RuIi As A Superior Optical Oxygen Sensor, Bingfu Lei, Bin Li, Haoran Zhang, Shaozhe Lu, Zhuhong Zheng, Wenlian Li, Yue Wang

Faculty Publications

Novel oxygen sensors consisting of a [Ru(bpy)2phen]2+ (bpy: 2,2′-bipyridyl, phen: phenathroline) portion covalently grafted to a mesostructured silica-based network are prepared in situ via a sol-gel approach with the help of cetyltrimethylammonium-bromide (CTAB) surfactant. 1,10-Phenanthroline covalently grafted to 3-(triethoxysilyl)propyl isocyanate is used as not only the sol-gel precursor but also as the second ligand of the Ru(bpy)2d2 · 2H2O complex to prepare the sol-gel-derived mesostructured silicates for an oxygen sensor. For comparison purposes, the oxygen sensors in which [Ru(bpy)2phen]Q2 is conventionally physically incorporated into the matrix are also prepared. Elemental analysis, NMR, Fourier transform IR, UV-vis electronic absorption, luminescence-intensity quenching …

Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu

Faculty Publications

Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specificity of the computational predictions of TFBSs has been attributed to ubiquity of the motifs and the relaxed sequence requirements for binding. We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model. Results: Using the TFBS for the estrogen receptor (ER)alpha (estrogen response element [ERE]) as a model system, we extracted EREs from multiple molecular and genomic platforms …

The Psbq Protein Is Required In Arabidopsis For Photosystem Ii Assembly/Stability And Photoautotrophy Under Low Light Conditions, Xiaoping Yi, Stefan R. Hargett, Laurie K. Frankel, Terry M. Bricker

Faculty Publications

RNA interference was used to simultaneously suppress the expression of the two genes that encode the PsbQ proteins of Photosystem II (PS II) in Arabidopsis thaliana, psbQ-1 (At4g21280) and psbQ-2 (At4g05180). Two independent PsbQ-deficient plant lines were examined. These plant lines produced little detectable PsbQ protein. Under normal growth light conditions, the wild type and mutant plants were visually indistinguishable. Additionally, analysis of steady state oxygen evolution rates and chlorophyll fluorescence characteristics indicated little alteration of photosynthetic capacity in the mutant plants. No loss of other PS II proteins was evident. Interestingly, flash oxygen yield analysis performed on thylakoid membranes …

Post-Thaw Amendment Of Cryopreserved Sperm For Use In Artificial Insemination Of A Viviparous Fish, The Green Swordtail Xiphophorus Helleri, Qiaoxiang Dong, Changjiang Huang, Terrence R. Tiersch

Faculty Publications

Sperm cryopreservation protocols have been developed for live-bearers such as the green swordtail Xiphophorus helleri and the platyfish Xiphophorus couchianus. Despite the high post-thaw motility (∼ 75%) obtained in both species, the requirements of sperm storage within the female reproductive tract coupled with the process of internal fertilization place functional demands upon cryopreserved sperm samples far beyond those of oviparous species. The purpose of this study was to facilitate the artificial insemination process with cryopreserved sperm of X. helleri through evaluation of parameters related to sperm quality after thawing. Specifically, this study evaluated the effects on motility for fresh and …

Two Glucose-Sensing Pathways Converge On Rgt1 To Regulate Expression Of Glucose Transporter Genes In Saccharomyces Cerevisiae, Jeong-Ho Kim, Mark Johnston

Faculty Publications

The yeast Saccharomyces cerevisiae deploys two different types of glucose sensors on its cell surface that operate in distinct glucose signaling pathways: the glucose transporter-like Snf3 and Rgt2 proteins and the Gpr1 receptor that is coupled to Gpa2, a G-protein α subunit. The ultimate target of the Snf3/Rgt2 pathway is Rgt1, a transcription factor that regulates expression of HXT genes encoding glucose transporters. We have found that the cAMP-dependent protein kinase A (PKA), which is activated by the Gpr1/Gpa2 glucose-sensing pathway and by a glucose-sensing pathway that works through Ras1 and Ras2, catalyzes phosphorylation of Rgt1 and regulates its function. …

Proteomic And Genetic Approaches To Identifying Defence-Related Proteins In Rice Challenged With The Fungal Pathogen Rhizoctonia Solani, Joohyun Lee, Terry M. Bricker, Michael Lefevre, Shannon R.M. Pinson, James H. Oard

Faculty Publications

Sheath blight, caused by the fungus Rhizoctonia solani, is a major disease of rice world-wide, but little is known about the host response to infection. The objective of this study was to identify proteins and DNA markers in resistant and susceptible rice associated with response to infection by R. solani. Replicated two-dimensional polyacrylamide gel electrophoresis experiments were conducted to detect proteins differentially expressed under inoculated and non-inoculated conditions. Tandem mass spectra analysis using electrospray ionization quadrupole-time of flight mass spectrometry (ESI Q-TOF MS) was carried out for protein identification with the NCBI non-redundant protein database. Seven proteins were increased after …

Tc-99m Pyrophosphate Imaging Of Poloxamer-Treated Electroporated Skeletal Muscle In An In Vivo Rat Model, Kenneth L. Matthews, John N. Aarsvold, Robert A. Mintzer, Chin Tu Chen, Raphael C. Lee

Faculty Publications

Objective: This study investigates whether 99mTc pyrophosphate (PYP) imaging provides a quantitative non-invasive assessment of the extent of electroporation injury, and of the effect of poloxamer in vivo on electroporated skeletal muscle. Methods: High-voltage electrical shock was used to produce electroporation injury in an anesthetized rat's hind limb. In each experiment, the injured limb was treated intravenously by either poloxamer-188, dextran, or saline, and subsequently imaged with 99mTc PYP. The radiotracer's temporal behavior among the experimental groups was compared using curve fitting of time-activity curves from the dynamic image data. Results: The washout kinetics of 99mTc PYP changed in proportion …

Tc-99m Pyrophosphate Imaging Of Poloxamer-Treated Electroporated Skeletal Muscle In An In Vivo Rat Model, Kenneth L. Matthews, John N. Aarsvold, Robert A. Mintzer, Chin Tu Chen, Raphael C. Lee

Faculty Publications

Objective: This study investigates whether 99mTc pyrophosphate (PYP) imaging provides a quantitative non-invasive assessment of the extent of electroporation injury, and of the effect of poloxamer in vivo on electroporated skeletal muscle. Methods: High-voltage electrical shock was used to produce electroporation injury in an anesthetized rat's hind limb. In each experiment, the injured limb was treated intravenously by either poloxamer-188, dextran, or saline, and subsequently imaged with 99mTc PYP. The radiotracer's temporal behavior among the experimental groups was compared using curve fitting of time-activity curves from the dynamic image data. Results: The washout kinetics of 99mTc PYP changed in proportion …

An Improved Cloning Strategy For Chromatin-Immunoprecipitation-Derived Dna Fragments, Jennifer M. Huang, Jeong Do Kim, Hana Kim, Joomyeong Kim

Faculty Publications

No abstract provided.

Promoting Physical Activity In Children And Youth: A Leadership Role For Schools: A Scientific Statement From The American Heart Association Council On Nutrition, Physical Activity, And Metabolism (Physical Activity Committee) In Collaboration With The Councils On Cardiovascular Disease In The Young And Cardiovascular Nursing, Russell R. Pate, Michael G. Davis, Thomas N. Robinson, Elaine J. Stone, Thomas L. Mckenzie, Judith C. Young

Faculty Publications

No abstract provided.

Introduction: Self-Organization In Nonequilibrium Chemical Systems, Irving R. Epstein, John A. Pojman, Oliver Steinbock

Faculty Publications

The field of self-organization in nonequilibrium chemical systems comprises the study of dynamical phenomena in chemically reacting systems far from equilibrium. Systematic exploration of this area began with investigations of the temporal behavior of the Belousov-Zhabotinsky oscillating reaction, discovered accidentally in the former Soviet Union in the 1950s. The field soon advanced into chemical waves in excitable media and propagating fronts. With the systematic design of oscillating reactions in the 1980s and the discovery of Turing patterns in the 1990s, the scope of these studies expanded dramatically. The articles in this Focus Issue provide an overview of the development and …

Examining The Cdcynergy Event Assessment Tool: An Investigation Of The Anthrax Crisis In Boca Raton, Florida, J. J. Mcintyre, Steven J. Venette

Faculty Publications

This paper examines the dependability of the Event Assessment Tool over time. The latter is part of a CD-ROM-Emergency Risk Communication CDCynergy-distributed primarily to public information officers in the United States by the Centers for Disease Control and Prevention. The Event Assessment Tool is designed to aid emergency professionals in identifying the magnitude of a crisis event and to suggest appropriate actions to confront such a situation. Applied twice during the 2001 anthrax bioterrorism crisis in Boca Raton, Florida, the tool functioned in a binary manner by first indicating a moderate crisis level (on 4 October) and then four days …