Digital Commons Network^™

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 …

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 …

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 …

Mosquito Soldiers: Malaria, Yellow Fever, And The Course Of The American Civil War, Frank R. Freemon

Civil War Book Review

Examining the Role of Disease and the Civil War

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 …

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 …

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, …

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 …

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 …

Interaction Of Francisella Asiatica With Tilapia (Oreochromis Niloticus) Innate Immunity, Esteban Soto, Denise Fernandez, Ronald Thune, John P. Hawke

Faculty Publications

Members of the genus Francisella are facultative intracellular bacteria that cause important diseases in a wide variety of animals worldwide, including humans and fish. Several genes that are important for intramacrophage survival have been identified, including the iglC gene, which is found in the iglABCD operon in the Francisella sp. pathogenicity island (FPI). In the present study, we examined the interaction of wild-type Francisella asiatica and a ΔiglC mutant strain with fish serum and head kidney-derived macrophages (HKDM). Both the wild-type and the mutant strains were resistant to killing by normal and heat-inactivated sera. The wild-type F. asiatica is able …

Siamese Cooperates With The Cdh1-Like Protein Ccs52a1 To Establish Endoreplication In Arabidopsis Thaliana Trichomes, Remmy Kasili, Jason D. Walker, L. Alice Simmons, Jing Zhou, Lieven De Veylder, John C. Larkin

Faculty Publications

Endoreplication, also known as endoreduplication, is a phyogenetically widespread modified version of the cell cycle in which DNA replication is not followed by cell division. The SIAMESE (SIM) gene of Arabidopsis thaliana encodes the founding member of a novel class of plant-specific cyclin-dependent kinase (CDK) inhibitors and is a key regulator of endoreplication during the development of trichomes (shoot epidermal hairs). Here, we have identified mutations in the CCS52A1 gene as genetic modifiers of the multicellular trichome phenotype of sim mutants. Loss-of-function ccs52A1 mutations dramatically enhance the multicellularity of sim mutants trichomes in double mutants, whereas overexpression of CCS52A1 completely …

Effects Of Dietary Fat On Resistant Starch Fermentation In Mice, Diana Badkoobeh

Honors Capstones

No abstract provided.

Identification Of Yeasts From The Gut Of Cotinis Nitida Using Its And Lsu Rrna D1/D2 Gene Sequences, Kevin Campbell

Honors Capstones

No abstract provided.

The Cytotoxicity Of Nitrite And Nitrate In E. Coli, Aaron P. Landry

Honors Capstones

No abstract provided.

Inheritance Of Traits Associated With Phosphorus Utilization Efficiency In Maize, Roberto Fritsche-Neto, Glauco Vieira Miranda, Rodrigo Oliveira Delima, Leandro Vagno De Souza, Jaeveson Da Silva

Faculty Publications

The objective of this work was to determine the genetic effects that control the inheritance of characters associated with the phosphorus utilization efficiency (PUE) in maize, and to determine the relationship among them. A diallel between six maize cultivars was performed and 15 hybrid combinations were obtained from it. These cultivars were evaluated in high and low phosphorus availability in the greenhouse and field. Plant response to nutrient availability (RU) and traits associated to utilization and translocation efficiency were measured. There were significant interactions between hybrid combinations and phosphorus availability for plant dry matter mass (MSP), P concentration in plants …

Effects Of Dietary Fat On Resistant Starch Fermentation In Mice, Diana Badkoobeh

Honors Capstones

No abstract provided.

The Young Adult Speaks For Herself: My Reading Of Modern Criticism And The Twilight Saga, Elizabeth Spence

Honors Capstones

No abstract provided.

Steroid Receptor Expression In The Fish Inner Earvaries With Sex, Social Status, And Reproductive State, Karen P. Maruska, Russell D. Fernald

Faculty Publications

Background: Gonadal and stress-related steroid hormones are known to influence auditory function across vertebrates but the cellular and molecular mechanisms responsible for steroid-mediated auditory plasticity at the level of the inner ear remain unknown. The presence of steroid receptors in the ear suggests a direct pathway for hormones to act on the peripheral auditory system, but little is known about which receptors are expressed in the ear or whether their expression levels change with internal physiological state or external social cues. We used qRT-PCR to measure mRNA expression levels of multiple steroid receptor subtypes (estrogen receptors: ERα, ERβa, ERβb; androgen …

Transcriptional Factors That Promote Formation Of White Adipose Tissue, Ursula A. White, Jacqueline M. Stephens

Faculty Publications

Adipocytes are highly specialized cells that play a major role in energy homeostasis in vertebrate organisms. Excess adipocyte size or number is a hallmark of obesity, which is currently a global epidemic. Obesity is a major risk factor for the development of type II diabetes (T2DM), cardiovascular disease, and hypertension. Obesity and its related disorders result in dysregulation of the mechanisms that control the expression of metabolic and endocrine related genes in adipocytes. Therefore, understanding adipocyte differentiation is relevant not only for gaining insight into the pathogenesis of metabolic diseases, but also for identifying proteins or pathways which might be …

Fine Mapping Of The Association With Obesity At The Fto Locus In African-Derived Populations, Mohamed T. Hassanein, Helen N. Lyon, Thutrang T. Nguyen, Ermeg L. Akylbekova, Kevin Waters, Guillaume Lettre, Bamidele Tayo, Terrence Forrester, Daniel F. Sarpong, Dan O. Stram, Johannah L. Butler, Rainford Wilks, Jiankang Liu, Loic Le Marchand, Laurence N. Kolonel, Xiaofeng Zhu, Brian Henderson, Richard Cooper, Colin Mckenzie, Herman A. Taylor, Christopher A. Haiman, Joel N. Hirschhorn

Faculty Publications

Genome-wide association studies have identified many common genetic variants that are associated with polygenic traits, and have typically been performed with individuals of recent European ancestry. In these populations, many common variants are tightly correlated, with the perfect or near-perfect proxies for the functional or true variant showing equivalent evidence of association, considerably limiting the resolution of fine mapping. Populations with recent African ancestry often have less extensive and/or different patterns of linkage disequilibrium (LD), and have been proposed to be useful in fine-mapping studies. Here, we strongly replicate and fine map in populations of predominantly African ancestry the association …

Water Equivalent Thickness Values Of Materials Used In Beams Of Protons, Helium, Carbon And Iron Ions, Rui Zhang, Phillip J. Taddei, Markus M. Fitzek, Wayne D. Newhauser

Faculty Publications

Heavy charged particle beam radiotherapy for cancer is of increasing interest because it delivers a highly conformal radiation dose to the target volume. Accurate knowledge of the range of a heavy charged particle beam after it penetrates a patient's body or other materials in the beam line is very important and is usually stated in terms of the water equivalent thickness (WET). However, methods of calculating WET for heavy charged particle beams are lacking. Our objective was to test several simple analytical formulas previously developed for proton beams for their ability to calculate WET values for materials exposed to beams …

Q-DockLhm: Low-Resolution Refinement For Ligand Comparative Modeling, Michal Brylinski, Jeffrey Skolnick

Faculty Publications

The success of ligand docking calculations typically depends on the quality of the receptor structure. Given improvements in protein structure prediction approaches, approximate protein models now can be routinely obtained for the majority of gene products in a given proteome. Structure-based virtual screening of large combinatorial libraries of lead candidates against theoretically modeled receptor structures requires fast and reliable docking techniques capable of dealing with structural inaccuracies in protein models. Here, we present Q-DockLHM, a method for low-resolution refinement of binding poses provided by FINDSITELHM, a ligand homology modeling approach. We compare its performance to that of classical ligand docking …

Biogeographic Breaks In Vanuatu, A Nascent Oceanic Archipelago, Alison M. Hamilton, Elaine R. Klein, Christopher C. Austin

Faculty Publications

The study of distinct biogeographic demarcations has played a pivotal role in our understanding processes responsible for patterns of species distributions and, importantly, the role of geologic processes in promoting biotic diversification. Biogeographic barriers such as Wallace's line have been shown to be the result of old geologic processes shaping ancient faunal or floral diversification events. Based on distributions of birds, bats, reptiles, plants, and invertebrates we identify a distinct biogeographic disjunction in Vanuatu, a geologically nascent oceanic archipelago. We discuss mechanisms contributing to this concordant pattern across these disparate taxonomic groups in light of geologic history, ocean currents, vegetation, …

The Genome Of A Songbird, Wesley C. Warren, David F. Clayton, Hans Ellegren, Arthur P. Arnold, Ladeana W. Hillier, Axel Künstner, Steve Searle, Simon White, Albert J. Vilella, Susan Fairley, Andreas Heger, Lesheng Kong, Chris P. Ponting, Erich D. Jarvis, Claudio V. Mello, Pat Minx, Peter Lovell, Tarciso A.F. Velho, Margaret Ferris, Christopher N. Balakrishnan, Saurabh Sinha, Charles Blatti, Sarah E. London, Yun Li, Ya Chi Lin, Julia George, Jonathan Sweedler, Bruce Southey, Preethi Gunaratne, Michael Watson, Kiwoong Nam, Niclas Backström, Linnea Smeds, Benoit Nabholz

Faculty Publications

The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chickenthe only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they …