Digital Commons Network^™

Fluorescent Chemosensors For Toxic Organophosphorus Pesticides: A Review, Sherine O. Obare, Chandrima De, Wen Guo, Tajay L. Haywood, Tova A. Samuels, Clara P. Adams, Noah O. Masika, Desmond H. Murray, Ginger A. Anderson, Keith Campbell, Kenneth Fletcher

Faculty Publications

Many organophosphorus (OP) based compounds are highly toxic and powerful inhibitors of cholinesterases that generate serious environmental and human health concerns. Organothiophosphates with a thiophosphoryl (P=S) functional group constitute a broad class of these widely used pesticides. They are related to the more reactive phosphoryl (P=O) organophosphates, which include very lethal nerve agents and chemical warfare agents, such as, VX, Soman and Sarin. Unfortunately, widespread and frequent commercial use of OP-based compounds in agricultural lands has resulted in their presence as residues in crops, livestock, and poultry products and also led to their migration into aquifers. Thus, the design of …

Search For Pair Production Of Supersymmetric Top Quarks In Dilepton Events From Pp̄ Collisions At √S=1.96tev, T. Aaltonen, J. Adelman, T. Akimoto, B. Álvarez González, S. Amerio, D. Amidei, A. Anastassov, A. Annovi, J. Antos, G. Apollinari, A. Apresyan, T. Arisawa, A. Artikov, W. Ashmanskas, A. Attal, A. Aurisano, F. Azfar, W. Badgett, A. Barbaro-Galtieri, V. E. Barnes, B. A. Barnett, P. Barria, V. Bartsch, G. Bauer, P. H. Beauchemin, F. Bedeschi, D. Beecher, S. Behari

Faculty Publications

We present the results of a search for pair production of the supersymmetric partner of the top quark (the top squark t̃1) decaying to a b quark and a chargino χ̃1± with a subsequent χ̃1± decay into a neutralino χ̃10, lepton ℓ, and neutrino ν. Using a data sample corresponding to 2.7fb-1 of integrated luminosity of pp̄ collisions at √s=1.96TeV collected by the CDF II detector, we reconstruct the mass of top squark candidate events and fit the observed mass spectrum to a combination of standard model processes and t̃1t̃̄1 signal. We find no evidence for t̃1t̃̄1 production and set …

Surface And Hyporheic Transient Storage Dynamics Throughout A Coastal Stream Network, Martin A. Briggs, Michael N. Gooseff, Bruce J. Peterson, Kate Morkeski, Wilfred M. Wollheim, Charles S. Hopkinson

Faculty Publications

Transient storage of stream water and associated solutes is expected to vary along stream networks in response to related changes in stream hydraulic conditions and morphologic gradients. These spatial changes are relevant to a wide variety of processes (e.g., biogeochemical cycling), yet data regarding these dynamics are limited and almost exclusively confined to the general storage terms of transient storage models with a single‐storage zone (1‐SZ). We used a transient storage model with two‐storage zones (2‐SZ) to simulate field data from conservative solute injections conducted in a coastal stream network in Massachusetts to separately quantify surface transient storage (STS) and …

Synthesis And Characterization Of Free-Base, Copper, And Nickel Isocorroles, Giuseppe Pomarico, Xiao Xiao, Sara Nardis, Roberto Paolesse, Frank R. Fronczek, Kevin M. Smith, Yuanyuan Fang, Zhongping Ou, Karl M. Kadish

Faculty Publications

A series of free-base and metalated isocorroles represented as (TT-n-iso-Cor)H2 and (TT-n-iso-Cor)MII, where n = 5 or 10 and M = Ni or Cu, were synthesized and characterized by electrochemistry and spectroelectrochemistry in CH2Cl2 containing 0.1 M tetra-n-butylammonium perchlorate. The metalation of the free-base macrocycles with CoII, MnIII, or ZnII was also attempted but was unsuccessful. Six isocorroles were isolated and shown to undergo two stepwise oxidations to give π-cation radicals and dications in CH 2Cl2, with the most stable products being obtained in the case of the 10-substituted derivatives. The same isocorroles could also be reduced by one or …

Thermodynamics Of The Dna Structural Selectivity Of The Pol I Dna Polymerases From Escherichia Coli And Thermus Aquaticus, Andy J. Wowor, Kausiki Datta, Hiromi S. Brown, Gregory S. Thompson, Sreerupa Ray, Anne Grove, Vince J. Licata

Faculty Publications

Understanding the thermodynamics of substrate selection by DNA polymerase I is important for characterizing the balance between replication and repair for this enzyme in vivo. Due to their sequence and structural similarities, Klenow and Klentaq, the large fragments of the Pol I DNA polymerases from Escherichia coll and Thermus aquaticus, are considered functional homologs. Klentaq, however, does not have a functional proofreading site. Examination of the DNA binding thermodynamics of Klenow and Klentaq to different DNA structures: single-stranded DNA (ss-DNA), primer-template DNA (pt-DNA), and blunt-end double-stranded DNA (ds-DNA) show that the binding selectivity pattern is similar when examined across a …

Proactive Parenting Practices During Early Adolescence: A Cluster Approach, Laura M. Padilla-Walker, Katherine J. Christensen, Randal D. Day

Faculty Publications

The purpose of the current study was to explore clusters of proactive parenting practices, and how they might vary as a function of parental demographics, the quality of the parent– child relationship, and the traits and behaviors of the adolescent child. Data were taken from the Flourishing Families Project, which includes 500 families with an early adolescent child (M age ¼ 11.49). Findings suggested that there were four clusters of parents, and patterns were similar for mothers and fathers. Findings also suggested that proactive clusters varied primarily as a function of demographics of the parent (e.g., religiosity, ethnicity, education) and …

On The Use Of Cartographic Projections In Visualizing Phylogenetic Treespace, Mark J. Clement, Quinn O. Snell, Kenneth Sundberg

Faculty Publications

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable …

Tobacco Mosaic Virus Based Thin Film Sensor For Detection Of Volatile Organic Compounds, Michael A. Bruckman, Jie Liu, Goutam Koley, Yu Li, Brian C. Benicewicz, Zhongwei Niu, Qian Wang

Faculty Publications

A thin film sensor for the detection of volatile organic compounds (VOC) was fabricated by deposition of oligo-aniline grafted tobacco mosaic virus (TMV) onto a glass substrate. The oligo-aniline motifs were conjugated onto the TMV surface by a traditional diazonium coupling reaction to tyrosine residues followed by Cu(I) catalyzed alkyne-azide cycloaddition (CuAAC) reaction. The modified TMV was easily fabricated into a thin film by directly drop coating onto a glass substrate. Upon integration of the glass substrate into a prototypical device, the virus-based thin film exhibited good sensitivity and selectivity toward ethanol and methanol vapour.

Abundance And Ecological Significance Of The Clam Rangia Cuneata (Sowerby, 1831) In The Upper Barataria Estuary (Louisiana, Usa), Wai Hing Wong, Nancy N. Rabalais, R. Eugene Turner

Faculty Publications

We proposed that Rangia cuneata (Sowerby, 1831) is an important estuarine bivalve with ecological significance in three coastal lakes in Barataria Bay, Gulf of Mexico—Lake Cataouatche, Lake Salvador and Lac des Allemands. Our goals were to determine the abundance and distribution of Rangia in these lakes and to measure clearance times to elucidate its potential impacts on phytoplankton communities. The estimated average densities of R. cuneata in Lake Cataouatche, Lake Salvador, and Lac des Allemands were 63, 157, and 107 individuals m−2, respectively, which is 30% lower than that observed in nearby Lake Pontchartrain. The size of clams in Lake …

Biogeographic Anomaly Or Human Introduction: A Cryptogenic Population Of Tree Skink (Reptilia: Squamata) From The Cook Islands, Oceania, Alison M. Hamilton, George R. Zug, Christopher C. Austin

Faculty Publications

Archaeological and molecular data have revealed that the present day faunas of many island groups in Melanesia, Polynesia, and Micronesia are not representative of the biodiversity generated within this region on an evolutionary timescale. Erroneous inferences regarding the mechanisms of speciation and the significance of long distance dispersal in shaping the present diversity of these island systems have resulted from this incomplete diversity and distributional data. The lizard fauna east of Samoa has been suggested to derive entirely from human-mediated introductions, a distribution congruent with biogeographic patterns for other Pacific species. Distinguishing between introduced populations and those that result from …

Host Specificity Tests Of Gratiana Graminea (Coleoptera: Chrysomelidae), A Potential Biological Control Agent Of Tropical Soda Apple, Solanum Viarum (Solanaceae), J. Medal, N. Bustamante, M. Vitorino, L. Beal, W. Overholt, R. Diaz, J. Cuda

Faculty Publications

Multiple-choice and no-choice tests were conducted at the Department of Agriculture, Division of Plant Industry Quarantine facility in Gainesville, FL to determine the specificity of the Brazilian leaf-beetle Gratiana graminea Klug, a candidate for biological control of Solanum viarum, tropical soda apple. One hundred fifteen plant species in 32 families were included in the feeding-oviposition multiple-choice tests including the target weed and the 5 major cultivated Solanaceae Capsicum annuum L., Lycopersicon sculentum Mill., Nicotiana tabacum L., Solanum melongena L., and Solanum tuberosum L. Eight to 12 plant species, including always the main target weed, growing in 1-gallon pots were simultaneously …

Historical Divergence And Gene Flow: Coalescent Analyses Of Mitochondrial, Autosomal And Sex-Linked Loci In Passerina Buntings, Matthew D. Carling, Irby J. Lovette, Robb T. Brumfield

Faculty Publications

Quantifying the role of gene flow during the divergence of closely related species is crucial to understanding the process of speciation. We collected DNA sequence data from 20 loci (one mitochondrial, 13 autosomal, and six sex-linked) for population samples of Lazuli Buntings (Passerina amoena) and Indigo Buntings (Passerina cyanea) (Aves: Cardinalidae) to test explicitly between a strict allopatric speciation model and a model in which divergence occurred despite postdivergence gene flow. Likelihood ratio tests of coalescent-based population genetic parameter estimates indicated a strong signal of postdivergence gene flow and a strict allopatric speciation model was rejected. Analyses of partitioned datasets …

Spatial And Temporal Variability In Host Use By Helicoverpa Zea As Measured By Analyses Of Stable Carbon Isotope Ratios And Gossypol Residues, Graham Head, Ryan E. Jackson, John Adamczyk, Julius R. Bradley, John Van Duyn, Jeff Gore, Dick D. Hardee, B. Rogers Leonard, Randall Luttrell, John Ruberson, J. Walt Mullins, Robert G. Orth, Sakuntala Sivasupramaniam, Richard Voth

Faculty Publications

A high dose/refuge strategy has been adopted in the USA to manage the risk of Bacillus thuringiensis (Bt) resistance in target pests such as the cotton bollworm (CBW), Helicoverpa zea (Boddie) in transgenic Bt cotton Gossypium hirsutum L. Structured refuges, consisting of non-Bt cotton, have been a mandated part of this strategy to produce non-selected insects that are temporally and spatially synchronous with insects from the Bt crop, diluting Bt resistance alleles through mating. However, the bollworm is highly polyphagous and exploits a large number of crop and weedy hosts concurrently with Bt cotton. A study was carried out in …

Determination Of Sperm Concentration For Small-Bodied Biomedical Model Fishes By Use Of Microspectrophotometry, Ereene Tan, Huiping Yang, Terrence R. Tiersch

Faculty Publications

The goal of this study was to establish an efficient method for determination of sperm concentration requiring only 1-2 μL of sample by use of microspectrophotometry. The objectives were (1) determination of wavelengths with absorbance profiles appropriate for analysis of sperm suspensions from zebrafish Danio rerio, green swordtail Xiphophorus helleri, and medaka Oryzias latipes collected by crushing of dissected testis or by stripping of live males; (2) generation of standard curves and equations between sperm sample absorbance and sperm concentration estimated by hemocytometer counts; (3) accuracy verification of equations for estimating concentration by microspectrophotometry; and (4) analysis of the precision …

Structural And Stratigraphic Control On The Migration Of A Contaminant Plume At The P Reactor Area, Savannah River Site, South Carolina, Antonio E. Cameron González, Camelia C. Knapp, Michael G. Waddell, Adrian Addison, John M. Shafer

Faculty Publications

Geophysical methods, including a shallow seismic reflection (SSR) survey, surface and borehole ground-penetrating radar (GPR) data, and electrical resistivity imaging (ERI), were conducted at the Savannah River site (SRS), South Carolina, to investigate the shallow stratigraphy, hydrogeophysical zonation, and the applicability and performance of these geophysical techniques for hydrogeological characterization in contaminant areas. The study site is the P Reactor area located within the upper Atlantic coastal plain, with clastic sediments ranging from Late Cretaceous to Miocene in age. The target of this research was the delineation and prediction of migration pathways of a trichloroethylene (TCE) contaminant plume that originates …

Six Cases In Search Of A Decision: The Story Of In Re Marriage Cases, Jean C. Love, Patricia A. Cain

Faculty Publications

This chapter will appear in the book, Women and the Law Stories, to be published by Foundation Press (Elizabeth Schneider and Stephanie Wildman, eds.) in fall 2010. The chapter provides historical context for the groundbreaking decision in In re Marriage Cases, which, for a time at least, provided marriage equality for same-sex couples in the State of California. The authors discuss the development of the state constitution, the extension of its equality provisions to protect women, the California Supreme Court’s historic ruling in 1948 that extended marriage equality to interracial couples, and the state’s unique history in the advancement of …

Evaluating Ecosystem Response To Oyster Restoration And Nutrient Load Reduction With A Multispecies Bioenergetics Model, Richard S. Fulford, Denise L. Breitburg, Mark Luckenbach, Roger I.E. Newell

Faculty Publications

Many of the world's coastal ecosystems are impacted by multiple stressors each of which may be subject to different management strategies that may have overlapping or even conflicting objectives. Consequently, management results may be indirect and difficult to predict or observe. We developed a network simulation model intended specifically to examine ecosystem-level responses to management and applied this model to a comparison of nutrient load reduction and restoration of highly reduced stocks of bivalve suspension feeders (eastern oyster, Crassostrea virginica) in an estuarine ecosystem (Chesapeake Bay, USA). Model results suggest that a 50% reduction in nutrient inputs from the watershed …

Chemical Inhibition Of Caax Protease Activity Disrupts Yeast Ras Localization, Surya P. Mandahar, Emily R. Hildebrandt, William H. Jacobsen, George M. Santangelo, Walter K. Schmidt

Faculty Publications

Proteins possessing a C-terminal CaaX motif, such as the Ras GTPases, undergo extensive post-translational modification that includes attachment of an isoprenoid lipid, proteolytic processing and carboxylmethylation. Inhibition of the enzymes involved in these processes is considered a cancer-therapeutic strategy. We previously identified nine in vitro inhibitors of the yeast CaaX protease Rce1p in a chemical library screen (Manandhar et al., 2007). Here, we demonstrate that these agents disrupt the normal plasma membrane distribution of yeast GFP-Ras reporters in a manner that pharmacologically phenocopies effects observed upon genetic loss of CaaX protease function. Consistent with Rce1p being the in vivo target …

I/O-Efficient Compressed Text Indexes: From Theory To Practice, Sheng Yuan Chiu, Wing Kai Hon, Rahul Shah, Jeffrey Scott Vitter

Faculty Publications

Pattern matching on text data has been a fundamental field of Computer Science for nearly 40 years. Databases supporting full-text indexing functionality on text data are now widely used by biologists. In the theoretical literature, the most popular internal-memory index structures are the suffix trees and the suffix arrays, and the most popular external-memory index structure is the string B-tree. However, the practical applicability of these indexes has been limited mainly because of their space consumption and I/O issues. These structures use a lot more space (almost 20 to 50 times more) than the original text data and are often …

Natural Selection On Testosterone Production In A Wild Songbird Population, Joel W. Mcglothlin, Danielle J. Whittaker, Sara E. Schrock, Nicole M. Gerlach, Jodie M. Jawor, Eric A. Snajdr, Ellen D. Ketterson

Faculty Publications

Because of their role in mediating life-history trade-offs, hormones are expected to be strongly associated with components of fitness; however, few studies have examined how natural selection acts on hormonal variation in the wild. In a songbird, the dark-eyed junco (Junco hyemalis), field experiments have shown that exogenous testosterone alters individuals' resolution of the survival-reproduction trade-off, enhancing reproduction at the expense of survival. Here we used standardized injections of gonadotropin-releasing hormone (GnRH) to assay variation in the testosterone production of males. Using measurements of annual survival and reproduction, we found evidence of strong natural selection acting on GnRH-induced …

A Novel Gene Network Inference Algorithm Using Predictive Minimum Description Length Approach, Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng, Chaoyang Zhang

Faculty Publications

Background: Reverse engineering of gene regulatory networks using information theory models has received much attention due to its simplicity, low computational cost, and capability of inferring large networks. One of the major problems with information theory models is to determine the threshold which defines the regulatory relationships between genes. The minimum description length (MDL) principle has been implemented to overcome this problem. The description length of the MDL principle is the sum of model length and data encoding length. A user-specified fine tuning parameter is used as control mechanism between model and data encoding, but it is difficult to …

High Amino Acid Diversity And Positive Selection At A Putative Coral Immunity Gene (Tachylectin-2), Marshall L. Hayes, Ron I. Eytan, Michael E. Hellberg

Faculty Publications

Background. Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef. Here, we examine variation in and selection on a putative innate immunity gene from Oculina, …

Genomic Organization And Molecular Phylogenies Of The Beta (Β) Keratin Multigene Family In The Chicken (Gallus Gallus) And Zebra Finch (Taeniopygia Guttata): Implications For Feather Evolution, Matthew J. Greenwold, Roger H. Sawyer

Faculty Publications

Background: The epidermal appendages of reptiles and birds are constructed of beta (β) keratins. The molecularphylogeny of these keratins is important to understanding the evolutionary origin of these appendages, especially feathers. Knowing that the crocodilian β-keratin genes are closely related to those of birds, the published genomes ofthe chicken and zebra finch provide an opportunity not only to compare the genomic organization of their β- keratins,but to study their molecular evolution in archosaurians.

Results: The subfamilies (claw, feather, feather-like, and scale) of β-keratin genes are clustered in the same 5' to 3' orderon microchromosome 25 in chicken and zebra finch, …

Iron-Binding Activity Of Human Iron-Sulfur Cluster Assembly Protein Hisca1, Jianxin Lu, Jacob P. Bitoun, Guoqiang Tan, Wu Wang, Wenguang Min, Huangen Ding

Faculty Publications

A human homologue of the iron-sulfur cluster assembly protein IscA (hIscA1) has been cloned and expressed in Escherichia coli cells. The UV-visible absorption and EPR (electron paramagnetic resonance) measurements reveal that hIscA1 purified from E. coli cells contains a mononuclear iron centre and that the iron binding in hIscA1 expressed in E. coli cells can be furthermodulated by the iron content in the cell growth medium. Additional studies show that purified hIscA1 binds iron with an iron association constant of approx. 2×1019 M-1, and that the iron-bound hIscA1 is able to provide the iron for the iron-sulfur cluster assembly in …

Lysine-Based Zwitterionic Molecular Micelle For Simultaneous Separation Of Acidic And Basic Proteins Using Open Tubular Capillary Electrochromatography, Leonard Moore, Zorabel M. Lejeune, Candace A. Luces, Arther T. Gates, Min Li, Bilal El-Zahab, Jayne C. Garno, Isiah M. Warner

Faculty Publications

In this work, a zwitterionic molecular micelle, poly-ε-sodium- undecanoyl lysinate (poly-ε-SUK), was synthesized and employed as a coating in open tubular capillary electrochromatography (OT-CEC) for protein separation. The zwitterionic poly-ε-SUK containing both carboxylic acid and amine groups can be either protonated or deprotonated depending on the pH of the background electrolyte; therefore, either an overall positively or negatively charged coating can be achieved. This zwitterionic coating allows protein separations in either normal or reverse polarity mode depending on the pH of the background electrolyte. The protein mixtures contained four basic proteins (lysozyme, cytochrome c, α-chymotrypsinogen A, and ribonuclease A) and …

Solid-State Memcapacitive System With Negative And Diverging Capacitance, J. Martinez-Rincon, M. Di Ventra, Yuriy V. Pershin Dr

Faculty Publications

We suggest a possible realization of a solid-state memory capacitive (memcapacitive) system. Our approach relies on the slow polarization rate of a medium between plates of a regular capacitor. To achieve this goal, we consider a multilayer structure embedded in a capacitor. The multilayer structure is formed by metallic layers separated by an insulator so that nonlinear electronic transport (tunneling) between the layers can occur. The suggested memcapacitor shows hysteretic charge-voltage and capacitance-voltage curves, and both negative and diverging capacitance within certain ranges of the field. This proposal can be easily realized experimentally and indicates the possibility of information storage …

Advancing The Future Of Physical Activity Guidelines In Canada: An Independent Expert Panel Interpretation Of The Evidence, Antero Kesäniemi, Chris J. Riddoch, Bruce Reeder, Steven N. Blair, Thorkild I. A. Sørensen

Faculty Publications

The Canadian Society for Exercise Physiology, in partnership with the Public Health Agency of Canada, has initiated a review of their physical activity guidelines to promote healthy active living for Canadian children, youth, adults and older adults; previous guidelines were released in 2002, 2002, 1998 and 1999 respectively. Several background papers from this project were published recently and provide foundation evidence upon which to base new guidelines. Furthermore, comprehensive systematic reviews were completed to ensure a rigorous evaluation of evidence informing the revision of physical activity guidelines for asymptomatic populations. The overall guideline development process is being guided and assessed …

Could Light Harvesting Complexes Exhibit Non-Classical Effects At Room Temperature?, Mark M. Wilde, James M. Mccracken, Ari Mizel

Faculty Publications

Mounting experimental and theoretical evidence suggest that coherent quantum effects play a role in the efficient transfer of an excitation from a chlorosome antenna to a reaction centre in the Fenna-Matthews-Olson protein complex. However, it is conceivable that a satisfying alternate interpretation of the results is possible in terms of a classical theory. To address this possibility, we consider a class of classical theories satisfying the minimal postulates of macrorealism and frame Leggett-Garg-type tests that could rule them out. Our numerical simulations indicate that even in the presence of decoherence, several tests could exhibit the required violations of the Leggett-Garg …

Assessing The Efficacy Of Modis Satellite-Derived Start Of Growing Season For Jurisdictional Determination Of East Texas Bottomland Hardwood Wetlands, Karen Malone, Hans Michael Williams, I-Kuai Hung, Daniel Unger

Faculty Publications

Introduction: Crucial to the determination of a jurisdictional wetland is the definition of “growing season”. Satellite imagery is being utilized in other ecological applications, but is lagging in wetland growing season determination. Both cost and temporal limitations historically have restrained use of satellite imagery in assessing the start up of the growing season. Multiple commercial satellites are available that provide high resolution imagery, but the cost are prohibitive for most studies. The National Aeronautics and Space Administration (NASA) and the U.S. Geological Survey (USGS) jointly manage the Landsat and the Moderate-resolution Imaging Spectroradiometer (MODIS) satellite programs. Landsat Enhanced Thematic Mapper …

Detection And Filtering Of Landmark Occlusions Using Terrain Spatiograms, Damian M. Lyons

Faculty Publications

A team of robots cooperating to quickly produce a map needs to share landmark information between members so that the local maps can be accurately merged. However, the appearance of landmarks as seen by members of the team can change dramatically due to the phenomenon of occlusion.

We have previously presented an approach to landmark representation using Terrain Spatiograms – an extension to image spatiograms in which the spatial information relates to the scene rather than the image. Because this representation preserves depth structure, it is possible to identify and filter potential occlusions.

We present an approach to identifying and …