Digital Commons Network^™

Decadal Variability Of Circulation In The Arctic Ocean Retrieved From Climatological Data By A Variational Method, Dmitri A. Nechaev, Max Yaremchuk, Motoyoshi Ikeda

Faculty Publications

[1] An inverse 3D finite-element ocean circulation model has been designed and used to study variability of the Arctic Ocean circulation in the last 4 decades. We obtained stationary model solutions with the temperature and salinity fields close to the ones given by the Environmental Working Group (EWG) [1998] atlas. Transports at the open boundaries, wind forcing and hydrographic fields are treated as unknowns, which are varied to minimize a quadratic cost function subject to model constraints. The inverse problem is solved for 10 gridded hydrographic data sets that were obtained as winter and summer averages of EWG data over …

Coastal Wetland Subsidence Arising From Local Hydrologic Manipulations, R. Eugene Turner

Faculty Publications

Twenty-three estimates of soil subsidence rates arising under the influence of local hydrologic changes from flap-gates, weirs, dikes, and culverts in tidal wetlands were compared to 75 examples of subsidence in drained agricultural wetlands. The induced subsidence rates from these hydrologic modifications in tidal wetlands can continue for more than 100 years, and range between 1.67 to 0.10 cm yr−1 within 1 to 155 years after the hydrologic modifications commence. These subsidence rates are lower than in freshwater wetlands drained for agricultural purposes, decline with age, and are significant in comparison to the rates of global sea level rise or …

Conserving Slow-Growing, Long-Lived Tree Species: Input From The Demography Of A Rare Understory Conifer, Taxus Floridana, Charles Kwit, Carol C. Horvitz, William J. Platt

Faculty Publications

Although land preservation and promotion of successful regeneration are important conservation actions, their ability to increase population growth rates of slow-growing, long-lived trees is limited. We investigated the demography of Taxus floridana Nutt., a rare understory conifer, in three populations in different ravine forests spanning its entire geographic range along the Apalachicola River Bluffs in northern Florida (U.S.A.). We examined spatial and temporal patterns in demographic parameters and projected population growth rates by using four years of data on the recruitment and survival of seedlings and established stems, and on diameter growth from cross-sections of dead stems. All populations experienced …

Brain Metastases In Melanoma: Roles Of Neurotrophins, Yvonne Denkins, Jane Reiland, Madhuchhanda Roy, Neeta Sinnappah-Kang, Jennifer Galjour, Brian P. Murry, Jason Blust, Rebecca Aucoin, Dario Marchetti

Faculty Publications

Brain metastasis, which occurs in 20% to 40% of all cancer patients, is an important cause of neoplastic morbidity and mortality. Successful invasion into the brain by tumor cells must include attachment to microvessel endothelial cells, penetration through the blood-brain barrier, and, of relevance, a response to brain survival and growth factors. Neurotrophins (NTs) are important in brain-invasive steps. Human melanoma cell lines express low-affinity NT receptor p75NTR in relation to their brain-metastatic propensity with their invasive properties being regulated by NGF, or nerve growth factor, the prototypic NT. They also express functional TrkC, the putative receptor for the invasion-promoting …

Conformational Subspace In Simulation Of Early-Stage Protein Folding, Wiktor Jurkowski, Michał Brylinski, Leszek Konieczny, Zdzisław Wiíniowski, Irena Roterman

Faculty Publications

A probability calculus was used to simulate the early stages of protein folding in ab initio structure prediction. The probabilities of particular φ and ψ angles for each of 20 amino acids as they occur in crystal forms of proteins were used to calculate the amount of information necessary for the occurrence of given φ and ψ angles to be predicted. It was found that the amount of information needed to predict φ and ψ angles with 5° precision is much higher than the amount of information actually carried by individual amino acids in the polypeptide chain. To handle this …

Analysis Of Facultative Lithotroph Distribution And Diversity On Volcanic Deposits By Use Of The Large Subunit Of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase, K. Nanba, G. M. King, K. Dunfield

Faculty Publications

A 492- to 495-bp fragment of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) (rbcL) was amplified by PCR from facultatively lithotrophic aerobic CO-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic DNA extracts from tephra and ash deposits from Kilauea volcano, for which atmospheric CO and hydrogen have been previously documented as important substrates. PCR products from the mats and volcanic sites were used to construct rbcL clone libraries. Phylogenetic analyses showed that the rbcL sequences from all isolates clustered with form IC rbcL sequences derived from facultative lithotrophs. In contrast, …

Error As Means To Discovery, Kevin C. Elliott

Faculty Publications

This paper argues, first, that recent studies of experimentation, most notably by Deborah Mayo, provide the conceptual resources to describe scientific discovery’s early stages as error-probing processes. Second, it shows that this description yields greater understanding of those early stages, including the challenges that they pose, the research strategies associated with them, and their influence on the rest of the discovery process. Throughout, the paper examines the phenomenon of ‘‘chemical hormesis’’ (i.e., anomalous low-dose effects from toxic chemicals) as a case study that is important not only for the biological sciences but also for contemporary public policy. The resulting analysis …

Translocation As A Strategy To Rehabilitate The Queen Conch (Strombus Gigas) Population In The Florida Keys, Gabriel A. Delgado, Claudine T. Bartels, Robert A. Glazer, Nancy J. Brown-Peterson, Kevin J. Mccarthy

Faculty Publications

Queen conch (Strombus gigas) stocks in the Florida Keys once supported commercial and recreational fisheries, but overharvesting has decimated this once abundant snail. Despite a ban on harvesting this species since 1985, the local conch population has not recovered. In addition, previous work has reported that conch located in nearshore Keys waters are incapable of spawning because of poor gonadal condition, although reproduction does occur offshore. Queen conch in other areas undergo ontogenetic migrations from shallow, nearshore sites to offshore habitats, but conch in the Florida Keys are prevented from doing so by Hawk Channel. The present study was initiated …

A New Method For Estimation Of The Sensible Heat Flux Under Unstable Conditions Using Satellite Vector Winds, Jiayi Pan, Xiao-Hai Yan, Young-Heon Jo, Quanan Zheng, W. Timothy Liu

Faculty Publications

It has been difficult to estimate the sensible heat flux at the air - sea interface using satellite data because of the difficulty in remotely observing the sea level air temperature. In this study, a new method is developed for estimating the sensible heat flux using satellite observations under unstable conditions. The basic idea of the method is that the air - sea temperature difference is related to the atmospheric convergence. Employed data include the wind convergence, sea level humidity, and sea surface temperature. These parameters can be derived from the satellite wind vectors, Special Sensor Microwave Imager (SSM/I) precipitable …

Mistaking Marriage For Social Policy, Vivian E. Hamilton

Faculty Publications

This Article examines the role of marriage in society, focusing on the state's use of marriage as a proxy for desirable outcomes in social policy. Its analytical point of departure is the normative vision of modern marriage embraced by many of its proponents. From there, the idealized marriage is analyzed, not as a monolithic, opaque institution, but as one whose functional components may be identified and examined. The Article identifies the following as the primary functions of the normative marital family: expression; companionship; sex/procreation; caretaking; and economic support or redistribution. Analyzing the roles in society of each of these functions, …

Evolution, Theology, And Method - Part 3: Evolution And Adventist Theology, Fernando L. Canale

Faculty Publications

No abstract provided.

Church Planting As Growth Strategy: Is It Effective?, Skip Bell, Rod Davis

Faculty Publications

No abstract provided.

Particle Removal Rates By The Mud Shrimp Upogebia Pugettensis, Its Burrow, And A Commensal Clam: Effects On Estuarine Phytoplankton Abundance, Blaine D. Griffen, Theodore H. Dewitt, Chris Langdon

Faculty Publications

The burrowing shrimp Upogebia pugettensis is an abundant intertidal invertebrate of Pacific Northwest, USA bays and estuaries where it lives commensally with the bivalve Cryptomya californica. Suspension-feeding activities by the shrimp and by its commensal clam, as well as particle settlement within the burrow, represent 3 different components that could remove phytoplankton from water drawn into shrimp burrows. These 3 components together comprise what we call the ‘U. pugettensis shrimp-burrow complex’. In laboratory experiments, we measured particle removal by each of these components. Our results indicated that U. pugettensis itself is responsible for filtering the majority of phytoplankton removed …

Locking The Β3 Integrin I-Like Domain Into High And Low Affinity Conformations With Disulfides, Bing Hao Luo, Junichi Takagi, Timothy A. Springer

Faculty Publications

Although integrin α subunit I domains exist in multiple conformations, it is controversial whether integrin β subunit I-like domains undergo structurally analogous movements of the α7-helix that are linked to affinity for ligand. Disulfide bonds were introduced into the β3 integrin I-like domain to lock its β6-α7 loop and α7-helix in two distinct conformations. Soluble ligand binding, ligand mimetic mAb binding and cell adhesion studies showed that disulfide-bonded receptor αIIbβ3T329C/A347C was locked in a low affinity state, and dithiothreitol treatment restored the capability of being activated to high affinity binding; by contrast, disulfide-bonded αIIbβ3V332C/M335C was locked in a high affinity …

Extreme Free Energy Stabilization Of Taq Dna Polymerase, Allyn J. Schoeffler, Allison M. Joubert, Fenggang Peng, Farheen Khan, Chin Chi Liu, Vince J. Licata

Faculty Publications

We have examined the chemical denaturations of the Klentaq and Klenow large-fragment domains of the Type 1 DNA polymerases from Thermus aquaticus (Klentaq) and Escherichia coli (Klenow) under identical solution conditions in order to directly compare the stabilization energetics of the two proteins. The high temperature stability of Taq DNA polymerase is common knowledge, and is the basis of its use in the polymerase chain reaction. This study, however, is aimed at understanding the thermodynamic basis for this high-temperature stability. Chemical denaturations with guanidine hydrochloride report a folding free energy (ΔG) for Klentaq that is over 20 kcal/mol more favorable …

Nmr Difference Spectroscopy With A Dual Saddle-Coil Difference Probe, Megan A. Macnaughtan, Aaron P. Smith, Peter B. Goldsbrough, Robert E. Santini, Daniel Raftery

Faculty Publications

A new difference probe for nuclear magnetic resonance (NMR) spectroscopy is presented. The difference probe uses two saddle-shaped coils to excite and detect two samples simultaneously. The samples are held in a specially modified 3-mm NMR tube with an Ultem plastic disk to separate the samples. The probe's resonant circuit contains two crossed diodes that passively switch the relative phase of each coil during the NMR experiment. The result is a difference spectrum from the two samples. The degree of cancellation of common signals was determined to be approximately 90%, and the application of the probe to relaxation-edited difference spectroscopy …

Seasonal Use Of Bridges By Rafinesque's Big-Eared Bat, Corynorhinus Rafinesquii, In Southern Mississippi, Austin W. Trousdale, David C. Beckett

Faculty Publications

We conducted surveys of concrete bridges in southern Mississippi from 2000–2002 to determine the phenological pattern of use by Rafinesque's big-eared bat, Corynorhinus rafinesquii. The earliest dates on which we located maternity colonies were 9 March 2000, 20 April 2001, and 15 May 2002. Maternity colonies increased in size and abundance as spring progressed. Pups were born in mid- to late May (first observed 12 May 2000, 15 May 2001, 27 May 2002) and nursed through midsummer (lactating females last captured 14 July 2000, 25 July 2001, 16 July 2002). Colony size and percentage of bridges occupied by bats declined …

An Assessment Of Hiv/Aids Risk In Higher Education Students In Yerevan, Armenia, Talin Babikian, Mary Catherin Freier, Gary L. Hopkins, Ralph Diclemente, Duane C. Mcbride, Matt Riggs

Faculty Publications

Armenia's current sociopolitical and economic instability and the alarming HIV incidence rates in neighboring countries amplify its risk for a national epidemic. The goals of this study were to assess HIV/AIDS knowledge and risk behaviors among higher education students in Yerevan. Knowledge of HIV transmission through sexual intercourse was markedly higher than that on intravenous transmission and prevailing myths; however, HIV/AIDS knowledge was not related to risk behaviors. Tobacco and alcohol prevalence was relatively high. Students reported risky sexual behaviors, including inconsistent condom use, casual sex, and multiple partners. In addition to descriptive statistics delineating gender differences across the target …

Heparanase Degrades Syndecan-1 And Perlecan Heparan Sulfate: Functional Implications For Tumor Cell Invasion, Jane Reiland, Ralph D. Sanderson, Marian Waguespack, Steven A. Barker, Robert Long, Daniel D. Carson, Dario Marchetti

Faculty Publications

Heparanase (HPSE-1) is involved in the degradation of both cell-surface and extracellular matrix (ECM) heparan sulfate (HS) in normal and neoplastic tissues. Degradation of heparan sulfate proteoglycans (HSPG) in mammalian cells is dependent upon the enzymatic activity of HPSE-1, an endo-β -D-glucuronidase, which cleaves HS using a specific endoglycosidic hydrolysis rather than an eliminase type of action. Elevated HPSE-1 levels are associated with metastatic cancers, directly implicating HPSE-1 in tumor progression. The mechanism of HPSE-1 action to promote tumor progression may involve multiple substrates because HS is present on both cell-surface and ECM proteoglycans. However, the specific targets of HPSE-1 …

Human Glutaminyl Cyclase And Bacterial Zinc Aminopeptidase Share A Common Fold And Active Site, Rachell E. Booth, Simon C. Lovell, Stephanie A. Misquitta, Robert C. Bateman Jr.

Faculty Publications

Background: Glutaminyl cyclase (QC) forms the pyroglutamyl residue at the amino terminus of numerous secretory peptides and proteins. We previously proposed the mammalian QC has some features in common with zinc aminopeptidases. We now have generated a structural model for human QC based on the aminopeptidase fold (pdb code 1AMP) and mutated the apparent active site residues to assess their role in QC catalysis.

Results: The structural model proposed here for human QC, deposited in the protein databank as 1MOI, is supported by a variety of fold prediction programs, by the circular dichroism spectrum, and by the presence …

Interferon Antagonist Proteins Of Influenza And Vaccinia Viruses Are Suppressors Of Rna Silencing, Wan Xiang Li, Hongwei Li, Rui Lu, Feng Li, Monica Dus, Peter Atkinson, Edward W.A. Brydon, Kyle L. Johnson, Adolfo García-Sastre, L. Andrew Ball, Peter Palese, Shou Wei Ding

Faculty Publications

Homology-dependent RNA silencing occurs in many eukaryotic cells. We reported recently that nodaviral infection triggers an RNA silencing-based antiviral response (RSAR) in Drosophila, which is capable of a rapid virus clearance in the absence of expression of a virus-encoded suppressor. Here, we present further evidence to show that the Drosophila RSAR is mediated by the RNA interference (RNAi) pathway, as the viral suppressor of RSAR inhibits experimental RNAi initiated by exogenous double-stranded RNA and RSAR requires the RNAi machinery. We demonstrate that RNAi also functions as a natural antiviral immunity in mosquito cells. We further show that vaccinia virus and …

Resolution Of Mixed Human Dna Samples Using Mitochondrial Dna Sequence Variants, Jerilyn A. Walker, Randall K. Garber, Dale J. Hedges, Gail E. Kilroy, Jinchuan Xing, Mark A. Batzer

Faculty Publications

No abstract provided.

Four Novel Genes Required For Optimal Photoautotrophic Growth Of The Cyanobacterium Synechocystis Sp. Strain Pcc 6803 Identified By In Vitro Transposon Mutagenesis, Shulu Zhang, Susan M. Laborde, Laurie K. Frankel, Terry M. Bricker

Faculty Publications

Four novel Synechocystis sp. strain PCC 6803 genes (sll1495, sll0804, slr11306, and slr1125) which encode hypothetical proteins were determined by transposon mutagenesis to be required for optimal photoautotrophic growth. Mutations were also recovered in ccmK4, a carboxysome coat protein homologue, and me, the decarboxylating NADP+-dependent malic enzyme. This is the first report that these known genes are required for optimal photoautotrophy.

Studies Of The Role Of The Drosophila Scs And Scs′ Insulators In Defining Boundaries Of A Chromosome Puff, Emily J. Kuhn, Craig M. Hart, Pamela K. Geyer

Faculty Publications

Insulators are DNA elements that establish independent transcriptional domains within eukaryotic genomes. The Drosophila scs and scs′ insulators localize near the borders of a structural domain in the polytene chromosomes, known as a puff, produced by transcription of the 87A heat shock protein (hsp) genes. It has been suggested that scs and scs′ are boundary elements that delimit this decondensed chromatin domain, reflecting the mechanism by which these sequences act to constrain regulatory interactions. This model was tested using transposons that carried a yellow gene to assess enhancer blocking and an hsp70-lacZ gene to examine the structure of a heat …

Seawater Acclimation Causes Independent Alterations In Na +/Tk+- And H+-Atpase Activity In Isolated Mitochondria-Rich Cell Subtypes Of The Rainbow Trout Gill, Guy S. Hawkings, Fernando Galvez, Greg G. Goss

Faculty Publications

Mitochondria-rich cells (MR cells) of the gills of rainbow trout undergo changes in relative distribution and biochemical function during acclimation to partial-strength (10‰) and full-strength (30‰) seawater. In isolated total gill cells, Na+/K+-ATPase activity increased fivefold and H+-ATPase activity decreased fourfold when trout were acclimated to either 10‰ or 30‰ seawater. When total MR gill cells were separated based on differential binding to peanut lectin agglutinin (PNA), the PNA subtypes underwent a change in relative distribution in seawater-acclimated fish. In freshwater, the ratio of PNA-: PNA+ was 65:35 while in seawater the distribution changed to 20:80 PNA-:PNA+. Additionally, differential changes …

Effects Of Aerobic Exercise On Anxiety Sensitivity, Joshua J. Broman-Fulks, Mitchell E. Berman, Brian A. Rabian, Michael J. Webster

Faculty Publications

Anxiety sensitivity is a known precursor to panic attacks and panic disorder, and involves the misinterpretation of anxiety-related sensations. Aerobic exercise has been shown to reduce generalized anxiety, and may also reduce anxiety sensitivity through exposure to feared physiological sensations. Accordingly, 54 participants with elevated anxiety sensitivity scores completed six 20-min treadmill exercise sessions at either a high-intensity aerobic (n = 29) or low-intensity (n = 25) level. Self-ratings of anxiety sensitivity, fear of physiological sensations associated with anxiety, and generalized anxiety were obtained at pretreatment, post-treatment, and one-week follow-up. Results indicated that both high- and low-intensity exercise reduced anxiety …

Laboratory Project In Wireless Fsk Receiver Design, Michael A. Jensen, Cynthia Fuse, Raymond Woodward

Faculty Publications

This paper describes a wireless local area network laboratory project that provides senior and first-year graduate students in microwave engineering courses the opportunity to design, build, and test several passive microstrip components and integrate them into a working system. Students design filters, couplers, amplifiers, diode detectors, quarter-wave transformers, antennas, and stub matching networks in weekly labs that parallel-lectures in a one-semester microwave engineering course. This paper also describes simple inexpensive prototyping and testing methods that have been used in this course. Laboratory materials and technical details of the design are provided on the web for students and educators.

Limited Conformational Space For Early-Stage Protein Folding Simulation, M. Bryliński, W. Jurkowski, L. Konieczny, I. Roterman

Faculty Publications

Motivation: The problem of early-stage protein folding is critical for protein structure prediction. The model presented introduces a common definition of protein structures which may be treated as the possible in silico early-stage form of the polypeptide chain. Limitation of the conformational space to the ellipse path on the Ramachandran map was tested as a possible sub-space to represent the early-stage structure for simulation of protein folding. The proposed conformational sub-space was developed on the basis of the backbone conformation, with side-chain interactions excluded. Results: The ellipse-path-limited conformation of BPTI was created using the criterion of shortest distance between Phi, …

Visual Detection Of Cysteine And Homocysteine, Oleksandr Rusin, Nadia N. St. Luce, Rezik A. Agbaria, Jorge O. Escobedo, Shan Jiang, Isiah M. Warner, Fareed B. Dawan, Kun Lian, Robert M. Strongin

Faculty Publications

The determination of cysteine and homocysteine levels is of great current interest for the monitoring of desease states. A new colorimetric method for the simultaneous detection of L-cysteine and L-homocysteine has been developed. A fluorescein derivative reacts with the above amino acids, producing their respective thiazolidines resulting in color changes. Interference from other amino acids and proteins is minimal. Copyright © 2004 American Chemical Society.

Androgen Receptor Expression In The Rat Prostate Is Down-Regulated By Dietary Phytoestrogens, Edwin D. Lephart, Trent D. Lund, Daniel J. Munson, Herman Aldercreutz, Robert J. Handa

Faculty Publications

Background- It is well established that the growth of the prostate gland is a hormone-dependent phenomenon involving both androgenic and estrogenic control. Proliferation of prostate cells is, at least in part, under control of estrogen receptor beta (ER-beta). Phytoestrogens bind ER-beta with high affinity and therefore may have antiproliferative effects in the prostate. Methods- The prostates of male Long-Evans rats fed a diet high in phytoestrogens (Phyto-600) or very low levels of phytoestrogens (Phyto-free) were analyzed to determine the impact of dietary phytoestrogens on prostate weight and androgen receptor (AR) expression in the prostate. Results- Dietary phytoestrogens significantly decreased post-pubertal …