Digital Commons Network^™

Monte Carlo Calculations And Measurements Of Absorbed Dose Per Monitor Unit For The Treatment Of Uveal Melanoma With Proton Therapy, Nicholas Koch, Wayne D. Newhauser, Uwe Titt, Dan Gombos, Kevin Coombes, George Starkschall

Faculty Publications

The treatment of uveal melanoma with proton radiotherapy has provided excellent clinical outcomes. However, contemporary treatment planning systems use simplistic dose algorithms that limit the accuracy of relative dose distributions. Further, absolute predictions of absorbed dose per monitor unit are not yet available in these systems. The purpose of this study was to determine if Monte Carlo methods could predict dose per monitor unit (D/MU) value at the center of a proton spread-out Bragg peak (SOBP) to within 1% on measured values for a variety of treatment fields relevant to ocular proton therapy. The MCNPX Monte Carlo transport code, in …

Gene Rearrangement Analysis And Ancestral Order Inference From Chloroplast Genomes With Inverted Repeat, Feng Yue, Liying Cui, Claude W. Depamphilis, Bernard M.E. Moret, Jijun Tang

Faculty Publications

Background
Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction.

Results
We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR …

Comment On “Contact Conditions For The Charge In The Theory Of The Electrical Double Layer”, Douglas Henderson, L. B. Bhuiyan

Faculty Publications

Exact results in any field, including statistical mechanics, are both aesthetically pleasing and very valuable in assessing theoretical approximations.

Synthesis And In Vitro Properties Of Trimethylamine- And Phosphonate-Substituted Carboranylporphyrins For Application In Bnct, Michael W. Easson, Frank R. Fronczek, Timothy J. Jensen, M. Graça H. Vicente

Faculty Publications

A series of carboranylporphyrins containing either amine or phosphonic acid functionalities and two to six closo-carborane clusters have been synthesized via a [2 + 2] condensation of a dimethylamino- or diethylphosphonate-substituted dipyrromethane with a dicarboranylmethyl-benzaldehyde. The X-ray structures of four key reaction intermediates (1, 2, 3, and 4a) and of two target porphyrins, the diphosphonate ester- and the diamino-tetracarboranylporphyrins 5b and 6a, are presented and discussed. In vitro studies using human carcinoma HEp2 and human glioblastoma T98G cells show that these porphyrins are non-toxic in the dark up to 100 μM concentrations, and that a tetracarboranylporphyrin bearing two quaternary ammonium …

Molecular Dynamics Simulations Of Biotin Carboxylase, Sten O.Nilsson Lili, Jiali Gao, Grover L. Waldrop

Faculty Publications

Biotin carboxylase catalyzes the ATP-dependent carboxylation of biotin and is one component of the multienzyme complex acetyl-CoA carboxylase that catalyzes the first committed step in fatty acid synthesis in all organisms. Biotin carboxylase from Escherichia coli, whose crystal structures with and without ATP bound have been determined, has served as a model system for this component of the acetyl-CoA carboxylase complex. The two crystal structures revealed a large conformational change of one domain relative to the other domains when ATP is bound. Unfortunately, the crystal structure with ATP bound was obtained with an inactive site-directed mutant of the enzyme. As …

The Innate Immune Database (Iidb), Martin Korb, G. R. Aistair, Vesteinn Thorsson, Christophe Battail, Bin Li, Daehee Hwang, Kathleen A. Kennedy, Jared C. Roach, Carrie M. Rosenberger, Mark Gilchrist, Daniel Zak, Carrie Johnson, Bruz Marzolf, Alan Aderem, Ilya Shmulevich, Hamid Bolouri

Faculty Publications

Background: As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site http://www.innateImmunity-systemsbiology.org. Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the …

Double-Stranded Rna-Activated Protein Kinase Pkr Of Fishes And Amphibians: Varying The Number Of Double-Stranded Rna Binding Domains And Lineage-Specific Duplications, Loubna Tazi, Stefan Rothenburg, Nikolaus Deigendesch, Madhusudan Dey, Thomas E. Dever

Faculty Publications

Double-stranded (ds) RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2alpha leading to the general inhibition of protein synthesis. Although PKR-like activity has been described in fish cells, the responsible enzymes eluded molecular characterization until the recent discovery of goldfish and zebrafish PKZ, which contain Z-DNA-binding domains instead of dsRNA-binding domains (dsRBDs). Fish and amphibian PKR genes have not been described so far. Results- Here we report the cloning and identification of 13 PKR genes from 8 teleost fish and amphibian species, including zebrafish, demonstrating the coexistence of …

Gratiana Boliviana (Coleoptera: Chrysomelidae) Does Not Feed On Jamaican Nightshade Solanum Jamaicense (Solanaceae), W. A. Overholt, R. Diaz, L. Markle, J. Medal

Faculty Publications

Jamaican nightshade has been in Florida for at least 77 years, but is considered rare and only found in 4 counties in the central peninsula. However, there are many examples of long lag periods between the time an exotic plant arrives at a new location, and the time it spreads and becomes highly invasive (Sakai et al. 2001). Locally dense populations of Jamaican nightshade in hammock areas in Saint Lucie and Osceola counties suggest that the plant is adapted to at least some habitats in Florida, and could eventually spread to similar habitats and become a serious exotic invader. The …

Determination Of Enantiomeric Compositions Of Analytes Using Novel Fluorescent Chiral Molecular Micelles And Steady State Fluorescence Measurements, Alicia A. Williams, Sayo O. Fakayode, Onur Alptürk, Christina M. Jones, Mark Lowry, Robert M. Strongin, Isiah M. Warner

Faculty Publications

Novel fluorescent chiral molecular micelles (FCMMs) were synthesized, characterized, and employed as chiral selectors for enantiomeric recognition of non-fluorescent chiral molecules using steady state fluorescence spectroscopy. The sensitivity of the fluorescence technique allowed for investigation of low concentrations of chiral selector (3.0∈×∈10 -5 M) and analyte (5.0∈×∈10 -6 M) to be used in these studies. The chiral interactions of glucose, tartaric acid, and serine in the presence of FCMMs poly(sodium N-undecanoyl-l-tryptophanate) [poly-l-SUW], poly(sodium N-undecanoyl-l-tyrosinate) [poly-l-SUY], and poly(sodium N-undecanoyl-l- phenylalininate) [poly-SUF] were based on diastereomeric complex formation. Poly-l-SUW had a significant fluorescence emission spectral difference as compared to poly-l-SUY and poly-l-SUF …

Afm-Based Lithography For Nanoscale Protein Assays, Johnpeter Ngunjiri, Jayne C. Garno

Faculty Publications

No abstract provided.

Achieving Precision And Reproducibility For Writing Patterns Of N-Alkanethiol Self-Assembled Monolayers With Automated Nanografting, Johnpeter N. Ngunjiri, Algernon T. Kelley, Zorabel M. Lejeune, Jie Ren Li, Brian R. Lewandowski, Wilson K. Serem, Stephanie L. Daniels, Kathie L. Lusker, Jayne C. Garno

Faculty Publications

Nanografting is a high-precision approach for scanning probe lithography, which provides unique advantages and capabilities for rapidly writing arrays of nanopatterns of thiol self-assembled monolayers (SAMs). Nanografting is accomplished by force-induced displacement of molecules of a matrix SAM, followed immediately by the self-assembly of n-alkanethiol ink molecules from solution. The feedback loop used to control the atomic force microscope tip position and displacement enables exquisite control of forces applied to the surface, ranging from pico to nanonewtons. To achieve high-resolution writing at the nanoscale, the writing speed, direction, and applied force need to be optimized. There are strategies for programing …

Collpas: Activity Hotspots For Frugivorous Bats (Phyllostomidae) In The Peruvian Amazon, Adriana Bravo, Kyle E. Harms, Richard D. Stevens, Louise H. Emmons

Faculty Publications

In the SE Peruvian Amazon, large numbers of frugivorous bats regularly visit natural forest clearings known locally as collpas (which are also referred to as clay licks or mineral licks). Bats arrive at collpas to drink water that has accumulated in depressions created by larger geophagous mammals that consume exposed soil. Although collpa visitation is common, little is known about its causes and its ecological implications for the bat community. We compared patterns of use of collpas and non-collpa forest sites by bats in SE Peru. We mist netted bats at collpas and non-collpa sites during the dry season and …

Laboratory And Field Evaluations Of Silwet L-77 And Kinetic Alone And In Combination With Imidacloprid And Abamectin For The Management Of The Asian Citrus Psyllid, Diaphorina Citri (Hemiptera: Psyllidae), Rajagopalbabu Srinivasan, Marjorie A. Hoy, Raghuwinder Singh, Michael E. Rogers

Faculty Publications

Silwet L-77, an organosilicone adjuvant, was used to enhance coverage of an entomopathogenic fungus in field trials conducted in a central Florida citrus research grove. The results indicated that Silwet L-77, by itself, was toxic to nymphs of the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae). Laboratory bioassays were conducted to confirm the toxicity of the adjuvant to eggs, nymphs, and adults of D. citri. Silwet L-77 at 0.05% (500 ppm) killed all nymphs, but was not as effective against eggs and adults. However, Silwet L-77, when combined with a reduced rate (one-tenth the lowest label rate = LLR) …

The Human Intermediate Filament Database: Comprehensive Information On A Gene Family Involved In Many Human Diseases, Ildiko Szeverenyi, Andrew J. Cassidy, Wang Chung Cheuk, Bernett T.K. Lee, John E.A. Common, Stephen C. Ogg, Huijia Chen, Yin Sim Shu, Walter L.P. Goh, Woei Ng Kee, John A. Simpson, Lian Chee Li, Hui Eng Goi, Bin Li, Declan P. Lunny, Danny Chuon, Aparna Venkatesh, Hoe Khoo Kian, W. H.Irwin Mclean, Ping Lim Yun, E. Birgitte Lane

Faculty Publications

We describe a revised and expanded database on human intermediate filament proteins, a major component of the eukaryotic cytoskeleton. The family of 70 intermediate filament genes (including those encoding keratins, desmins, and lamins) is now known to be associated with a wide range of diverse diseases, at least 72 distinct human pathologies, including skin blistering, muscular dystrophy, cardiomyopathy, premature aging syndromes, neurodegenerative disorders, and cataract. To date, the database catalogs 1,274 manually-curated pathogenic sequence variants and 170 allelic variants in intermediate filament genes from over 459 peer-reviewed research articles. Unrelated cases were collected from all of the six sequence homology …

Seasonal Variability Of The Observed Barrier Layer In The Arabian Sea, Pankajakshan Thadathil, Prasad Thoppil, R.R. Pao, P.M. Muraleedharan, Y.K. Somayajulu, V.V. Gopalakrishna, Raghu Murtugudde, G.V. Reddy, C. Revichandran

Faculty Publications

The formation mechanisms of the barrier layer ( BL) and its seasonal variability in the Arabian Sea ( AS) are studied using a comprehensive dataset of temperature and salinity profiles from Argo and other archives for the AS. Relatively thick BL of 20-60 m with large spatial extent is found in the central-southwestern AS ( CSWAS), the convergence zone of the monsoon wind, during the peak summer monsoon ( July-August) and in the southeastern AS ( SEAS) and northeastern AS ( NEAS) during the winter ( January-February). Although the BL in the SEAS has been reported before, the observed thick …

Gender-Role Orientation As Determinant Of Entrepreneurial Self-Efficacy, Mary Conway Dato-On, Stephen L. Mueller

Faculty Publications

Entrepreneurial self-efficacy (ESE) is often included in entrepreneurial intentions models to explain why some individuals are more likely than others to become entrepreneurs. An unsettled question among researchers is whether ESE differs between men and women. While early studies seem to suggest that men have higher ESE than women, more recent studies are inconclusive. Lacking empirical support for gender differences in ESE compels researchers to look for other factors to explain variation in entrepreneurial self-efficacy. The present study confirms two recent studies finding no significant difference in ESE between men and women in a representative sample of MBA students. This …

Peer Review In An Undergraduate Biology Curriculum: Effects On Students’ Scientific Reasoning, Writing And Attitudes, Briana Eileen Timmerman

Faculty Publications

Scientific reasoning and writing skills are ubiquitous processes in science and therefore common goals of science curricula, particularly in higher education. Providing the individualized feedback necessary for the development of these skills is often costly in terms of faculty time, particularly in large science courses common at research universities. Past educational research literature suggests that the use of peer review may accelerate students’ scientific reasoning skills without a concurrent demand on faculty time per student. Peer review contains many elements of effective pedagogy such as peer-peer collaboration, repeated practice at evaluation and critical thinking, formative feedback, multiple contrasting examples, and …

Money Or Nothing: The Adverse Environmental Consequences Of Uncompensated Land Use Controls, Jonathan H. Adler

Faculty Publications

The conventional wisdom holds that requiring compensation for environmental land use controls would severely limit environmental protection efforts. There are increasing reasons to question this assumption. Both economic theory and recent empirical research--focused primarily on the Endangered Species Act but potentially applicable to other environmental regulations that create similar incentives--demonstrate that failing to compensate private landowners for the costs of regulation discourages voluntary conservation efforts and can encourage the destruction of environmental resources. The lack of a compensation requirement also means that land use regulation is "underpriced" as compared to other environmental protection measures for which government agencies must pay. …

Systems Biology Approaches Identify Atf3 As A Negative Regulator Of Toll-Like Receptor 4 (Nature (2006) 441, (173-178)), Mark Gilchrist, Vesteinn Thorsson, Bin Li, Alistair G. Rust, Martin Korb, Jared C. Roach, Kathleen Kennedy, Tsonwin Hai, Hamid Bolouri, Alan Aderem

Faculty Publications

No abstract provided.

Two Chloride Sources In Soils Of The Mcmurdo Dry Valleys, Antarctica, Huiming Bao, Jaime D. Barnes, Zachary D. Sharp, David R. Marchant

Faculty Publications

Sulfate, nitrate, and chloride are major water-soluble anions in soils of the McMurdo Dry Valleys (MDV), Antarctica. We measured the chloride stable isotope composition of 40 soil samples from 16 different soil profiles. The soil profiles come from three different microclimate zones in the MDV: a coastal thaw zone, which fosters a seasonally saturated active layer; a stable upland zone, in which air and soil temperatures are too cold to foster active layers and/or significant snowmelt; and an intermediate, inland mixed zone. Results show that the total water-soluble chloride content is low in both the coastal and the upland zones, …

Two Chloride Sources In Soils Of The Mcmurdo Dry Valleys, Antarctica, Huiming Bao, Jaime D. Barnes, Zachary D. Sharp, David R. Marchant

Faculty Publications

Sulfate, nitrate, and chloride are major water-soluble anions in soils of the McMurdo Dry Valleys (MDV), Antarctica. We measured the chloride stable isotope composition of 40 soil samples from 16 different soil profiles. The soil profiles come from three different microclimate zones in the MDV: a coastal thaw zone, which fosters a seasonally saturated active layer; a stable upland zone, in which air and soil temperatures are too cold to foster active layers and/or significant snowmelt; and an intermediate, inland mixed zone. Results show that the total water-soluble chloride content is low in both the coastal and the upland zones, …

Imprinting Of An Evolutionarily Conserved Antisense Transcript Gene Apeg3, Jung Ha Choo, Jeong Do Kim, Joomyeong Kim

Faculty Publications

APeg3 is an antisense transcript gene of Peg3, which has been recently identified from rat brain. Careful analyses of EST databases indicated that a homologous transcript also exists in other mammalian species, including mouse, cow and human. 5′-and 3′-RACE experiments have subsequently identified a 900-bp cDNA sequence of APeg3 from mouse brain. Mouse APeg3 is localized in the 3′UTR of Peg3 with an intronless genomic structure. The expression of mouse APeg3 is derived mainly from the paternal allele, indicating the imprinting of this antisense transcript gene in brain. Strand-specific RNA analyses also revealed the expression of both human and cow …

The Psb27 Protein Facilitates Manganese Cluster Assembly In Photosystem Ii, Johnna L. Roose, Himadri B. Pakrasi

Faculty Publications

Photosystem II (PSII) is a large membrane protein complex that uses light energy to convert water to molecular oxygen. This enzyme undergoes an intricate assembly process to ensure accurate and efficient positioning of its many components. It has been proposed that the Psb27 protein, a lumenal extrinsic subunit, serves as a PSII assembly factor. Using a psb27 genetic deletion strain (Δpsb27) of the cyanobacterium Synechocystis sp. PCC 6803, we have defined the role of the Psb27 protein in PSII biogenesis. While the Psb27 protein was not essential for photosynthetic activity, various PSII assembly assays revealed that the Δpsb27 mutant was …

Origin Of The Eastern Brownsnake, Pseudonaja Textilis (Duméril, Bibron And Duméril) (Serpentes: Elapidae: Hydrophiinae) In New Guinea: Evidence Of Multiple Dispersals From Australia, And Comments On The Status Of Pseudonaja Textilis Pughi Hoser 2003, David J. Williams, Mark O'Shea, Roland L. Daguerre, Catharine E. Pook, Wolfgang Wüster, Christopher J. Hayden, John D. Mcvay, Owen Paiva, Teatu Lohi Matainaho, Kenneth D. Winkel, Christopher C. Austin

Faculty Publications

Pseudonaja textilis is a widespread and common snake in eastern parts of Australia, but its distribution in New Guinea is poorly understood, and the origin of the New Guinea populations and its timing have been the subject of much speculation. Phylogenetic analysis of mitochondrial DNA sequences from three New Guinea populations of P. textilis indicates that New Guinea was colonised from two independent eastern and western migration routes most likely in the Pleistocene. One dispersal event from northern Queensland led to the populations in eastern New Guinea (Milne Bay, Oro and Central Provinces, Papua New Guinea), whereas another, from Arnhem …

Comment On "How Accurate Are (234)Th Measurements In Seawater Based On The Mno(2)-Impregnated Cartridge Technique?'' By Pinghe Cai Et Al., Chin-Chang Hung, S. Bradley Moran, J. Kirk Cochran, Laodong Guo, Laodong Guo, Peter H. Santschi

Faculty Publications

No abstract provided.

A Unified Association Analysis Approach For Family And Unrelated Samples Correcting For Stratification, Xiaofeng Zhu, Shengchao Li, Richard S. Cooper, Robert C. Elston

Faculty Publications

There are two common designs for association mapping of complex diseases: case-control and family-based designs. A case-control sample is more powerful to detect genetic effects than a family-based sample that contains the same numbers of affected and unaffected persons, although additional markers may be required to control for spurious association. When family and unrelated samples are available, statistical analyses are often performed in the family and unrelated samples separately, conditioning on parental information for the former, thus resulting in reduced power. In this report, we propose a unified approach that can incorporate both family and case-control samples and, provided the …

Quenching Of Highly Vibrationally Excited Pyrimidine By Collisions With Co4, Jeremy A. Johnson, Andrew M. Duffin, Brian J. Hom, Karl E. Jackson, Eric T. Sevy

Faculty Publications

Relaxation of highly vibrationally excited pyrimidine (C4N2H4) by collisions with carbon dioxide has been investigated using diode laser transient absorption spectroscopy. Vibrationally hot pyrimidine (E'=40,635 cm^-1) was prepared by 248-nm excimer laser excitation, followed by rapid radiationless relaxation to the ground electronic state. The nascent rotational population distribution (J=58–80) of the 0000 ground state of CO2 resulting from collisions with hot pyrimidine was probed at short times following the excimer laser pulse. Doppler spectroscopy was used to measure the CO2 recoil velocity distribution for J=58–80 of the 0000 state. Rate constants and probabilities for collisions populating these CO2 rotational states …

Ozone Exposure In A Mouse Model Induces Airway Hyperreactivity That Requires The Presence Of Natural Killer T Cells And Il-17, Paul B. Savage, Muriel Pichavant, Sho Goya, Everett H. Meyer, Richard A. Johnston, Hye Y. Kim, Ponpan Matangkasombut, Ming Zhu, Yoichiro Iwakura, Rosemarie H. Dekruyff, Stephanie A. Shore, Dale T. Umetsu

Faculty Publications

Exposure to ozone, which is a major component of air pollution, induces a form of asthma that occurs in the absence of adaptive immunity. Although ozone-induced asthma is characterized by airway neutrophilia, and not eosinophilia, it is nevertheless associated with airway hyperreactivity (AHR), which is a cardinal feature of asthma. Because AHR induced by allergens requires the presence of natural killer T (NKT) cells, we asked whether ozone-induced AHR had similar requirements. We found that repeated exposure of wild-type (WT) mice to ozone induced severe AHR associated with an increase in airway NKT cells, neutrophils, and macrophages. Surprisingly, NKT cell-deficient …

Novel Role Of Antioxidant-1 (Atox1) As A Copper-Dependent Transcription Factor Involved In Cell Proliferation, S. Itoh, H. W. Kim, O. Nakagawa, K. Ozumi, Susan M. Lessner, H. Aoki, K. Akram, R. D. Mckinney, M. Ushio-Fukai, T. Fukai

Faculty Publications

Copper plays a fundamental role in regulating cell growth. Many types of human cancer tissues have higher copper levels than normal tissues. Copper can also induce gene expression. However, transcription factors that mediate copper-induced cell proliferation have not been identified in mammals. Here we show that antioxidant-1 (Atox1), previously appreciated as a copper chaperone, represents a novel copper-dependent transcription factor that mediates copper-induced cell proliferation. Stimulation of mouse embryonic fibroblasts (MEFs) with copper markedly increased cell proliferation, cyclin D1 expression, and entry into S phase, which were completely abolished in Atox1^-/- MEFs. Promoter analysis and EMSA revealed that copper …

In Vivo Yy1 Knockdown Effects On Genomic Imprinting, Joomyeong Kim, Jeong Do Kim

Faculty Publications

The YY1 transcription factor is predicted to control several imprinted domains, including the Peg3, Gnas and Xist/Tsix regions. To test this possibility, we have used RNA interference strategies to generate transgenic mouse lines that express reduced levels of the cellular YY1 protein. As predicted, lowering YY1 levels resulted in global expression changes in these three imprinted domains. In neonatal brains, most imprinted genes of the Peg3 domain were up-regulated. In the Gnas domain, Nespas was down-regulated, whereas three other imprinted transcripts were up-regulated, including Nesp, Gnasxl and Exon1A. In the Xist/Tsix domain, no obvious change was detected in the expression …