Digital Commons Network^™

Dynamic Modeling Of Nitrogen Losses In River Networks Unravels The Coupled Effects Of Hydrological And Biogeochemical Processes, Richard B. Alexander, John Karl Bohlke, Elizabeth W. Boyer, Mark B. David, Judson W. Harvey, Patrick J. Mulholland, Sybil P. Seitzinger, Craig R. Tobias, Christina Tonitto, Wilfred M. Wollheim

Faculty Publications

The importance of lotic systems as sinks for nitrogen inputs is well recognized. A fraction of nitrogen in streamflow is removed to the atmosphere via denitrification with the remainder exported in streamflow as nitrogen loads. At the watershed scale, there is a keen interest in understanding the factors that control the fate of nitrogen throughout the stream channel network, with particular attention to the processes that deliver large nitrogen loads to sensitive coastal ecosystems. We use a dynamic stream transport model to assess biogeochemical (nitrate loadings, concentration, temperature) and hydrological (discharge, depth, velocity) effects on reach-scale denitrification and nitrate removal …

Historical Account Of The Two Family-Group Names In Use For The Single Accepted Family Comprising The "Fish Blood Flukes", Stephen A. Bullard, Kirsten Jensen, Robin M. Overstreet

Faculty Publications

The family-group name for the "fish blood flukes" is unstable, with both "Aporocotylidae Odhner, 1912" and "Sanguinicolidae von Graff, 1907 "in use for the single family. Although "Sanguinicolidae von Graff, 1907" (or "Graff, 1907") has been a widely-accepted family-group name for the fish blood flukes subsequent to Yamaguti's 1954 and 1958 synoptical publications ("Systema Helminthum"), a critical examination of the relevant literature, much of it published in German during 1900 through 1926, reveals that "Aporocotylidae Odhner, 1912" is the earliest available family-group name for these flukes. The name Aporocotylidae, moreover, was in wide usage by alpha taxonomists before 1954 and …

Argument Structure Effects In Action Verb Naming In Static And Dynamic Conditions, Dirk B. Den Ouden, Steve Fix, Todd B. Parrish, Cynthia K. Thompson

Faculty Publications

Argument structure, as in the participant roles entailed within the lexical representation of verbs, affects verb processing. Recent neuroimaging studies show that when verbs are heard or read, the posterior temporoparietal region shows increased activation for verbs with greater versus lesser argument structure complexity, usually bilaterally. In addition, patients with agrammatic aphasia show verb production deficits, graded based on argument structure complexity. In the present study, we used fMRI to examine the neural correlates of verb production in overt action naming conditions. In addition, we tested the differential effects of naming when verbs were presented dynamically in video segments versus …

From Cells To Coastlines: How Can We Use Physiology To Forecast The Impacts Of Climate Change?, Brian Helmuth

Faculty Publications

The interdisciplinary fields of conservation physiology, macrophysiology, and mechanistic ecological forecasting have recently emerged as means of integrating detailed physiological responses to the broader questions of ecological and evolutionary responses to global climate change. Bridging the gap between large-scale records of weather and climate (as measured by remote sensing platforms, buoys and ground-based weather stations) and the physical world as experienced by organisms (niche-level measurements) requires a mechanistic understanding of how ‘environmental signals’ (parameters such as air, surface and water temperature, food availability, water flow) are translated into signals at the scale of the organism or cell (e.g. body temperature, …

A Dynamic Attribute-Based Data Filtering And Recovery Scheme For Web Information Processing, Amit Ahuja, Yiu-Kai D. Ng

Faculty Publications

Web data being transmitted over a network channel on the Internet with excessive amount of data causes data processing problems, which include selectively choosing useful information to be retained for various data applications. In this paper, we present an approach for filtering less-informative attribute data from a source Website. A scheme for filtering attributes, instead of tuples (records), from a Website becomes imperative, since filtering a complete tuple would lead to filtering some informative, as well as less-informative, attribute data in the tuple. Since filtered data at the source Website may be of interest to the user at the destination …

Effects Of The Strong Start Curriculum On Students' Social And Emotional Competence, Kalli Kronmiller, Paul Caldarella, Lynnette Christensen, Thomas J. Kramer

Faculty Publications

Research questions: Do children in Grade 2 who participate in Strong Start show an increase in prosocial behaviors? Do children show a decrease in internalizing and externalizing behaviors? Do children at greater risk show greater changes? Do participating students and teachers find the Strong Start curriculum to be socially valid?

Network Security Using Self Organized Multi-Agent Swarms, Eric M. Holloway, Gary B. Lamont, Gilbert L. Peterson

Faculty Publications

Computer network cyber-security is a very serious concern in many commercial, industrial, and military environments. This paper proposes a new computer network security approach defined by self organized agent swarms (SOMAS) which provides a novel computer network security management framework based upon desired overall system behaviors. The SOMAS structure evolves based upon the partially observable Markov decision process (POMDP) formal model and the more complex interactive-POMDP and decentralized-POMDP models. Example swarm specific and network based behaviors are formalized and simulated. This paper illustrates through various statistical testing techniques, the significance of this proposed SOMAS architecture.

Redox Control Of The Dna Damage-Inducible Protein Ding Helicase Activity Via Its Iron-Sulfur Cluster, Binbin Ren, Xuewu Duan, Huangen Ding

Faculty Publications

The Escherichia coli DNA damage-inducible protein DinG, a member of the superfamily 2 DNA helicases, has been implicated in the nucleotide excision repair and recombinational DNA repair pathways. Combining UV-visible absorption, EPR, and enzyme activity measurements, we demonstrate here that E. coli DinG contains a redox-active [4Fe-4S] cluster with a mid-point redox potential (Em) of -390 ± 23 mV (pH 8.0) and that reduction of the [4Fe-4S] cluster reversibly switches off the DinG helicase activity. Unlike the [4Fe-4S] cluster in E. coli dihydroxyacid dehydratase, the DinG [4Fe-4S] cluster is stable, and the enzyme remains fully active after exposure to 100-fold …

Rapid Headward Erosion Of Marsh Creeks In Response To Relative Sea Level Rise, Zoe J. Hughes, Duncan M. Fitzgerald, Carol A. Wilson, Steve C. Pennings, Kazimierz Wiçski, Amala Mahadevan

Faculty Publications

Tidal creeks in Cape Romain, South Carolina, are extending rapidly onto the established marsh platform producing an unusual morphology, which remains selfsimilar in time. A time-series of aerial photographs establishes that these channels are headward eroding at an approximate rate of 1.9 m/yr. The rapid rate of headward erosion suggests that the marsh platform is in disequilibrium and unable to keep pace with high local relative sea level rise (RSLR 〉3.2mm/yr) through accretionary processes. Biological feedbacks play a strong role in the morphological development of the creeks. Dieback of vegetation coupled with intense burrowing by crabs produces a bare and …

Quantitative And Fingerprint Analyses Of Chinese Sweet Tea Plant (Rubus Suavissimus S. Lee), Guixin Chou, Shun Jun Xu, Dong Liu, Yee Koh Gar, Jian Zhang, Zhijun Liu

Faculty Publications

The quality of botanical food is increasingly assessed by the content of multiple bioactive compounds. This study reports, for the first time, an HPLC fingerprinting method for the quality evaluation of Rubus suavissimus leaves possessing multiple bioactivities. Five constituents, gallic acid, rutin, ellagic acid, rubusoside, and steviol monoside, were quantified and used in developing qualitative chromatographic fingerprints. The limits of detection and quantification ranged from 0.29 to 37.86 μg/mL. The relative standard deviations (RSDs) of intra- and interday precisions were no more than 3.14 and 3.01%, respectively. The average recoveries were between 93.1 and 97.5%. The developed method was validated …

Survival Analysis With High-Dimensional Covariates: An Application In Microarray Studies, David Engler, Yi Li

Faculty Publications

Use of microarray technology often leads to high-dimensional and low-sample size (HDLSS) data settings. A variety of approaches have been proposed for variable selection in this context. However, only a small number of these have been adapted for time-to-event data where censoring is present. Among standard variable selection methods shown both to have good predictive accuracy and to be computationally efficient is the elastic net penalization approach. In this paper, adaptations of the elastic net approach are presented for variable selection both under the Cox proportional hazards model and under an accelerated failure time (AFT) model. Assessment of the two …

Biosynthesis Of The Caenorhabditis Elegans Dauer Pheromone, Rebecca A. Butcher, Justin R. Ragains, Weiqing Li, Gary Ruvkun, Jon Clardy, Yi Mak Ho

Faculty Publications

To sense its population density and to trigger entry into the stress-resistant dauer larval stage, Caenorhabditis elegans uses the dauer pheromone, which consists of ascaroside derivatives with short, fatty acid-like side chains. Although the dauer pheromone has been studied for 25 years, its biosynthesis is completely uncharacterized. The daf-22 mutant is the only known mutant defective in dauer pheromone production. Here, we show that daf-22 encodes a homolog of human sterol carrier protein SCPx, which catalyzes the final step in peroxisomal fatty acid β-oxidation. We also show that dhs-28, which encodes a homolog of the human D-bifunctional protein that acts …

Desiccation Survival In An Antarctic Nematode: Molecular Analysis Using Expressed Sequenced Tags, Byron J. Adams, Bishwo N. Adhikari, Diana H. Wall

Faculty Publications

Background: Nematodes are the dominant soil animals in Antarctic Dry Valleys and are capable of surviving desiccation and freezing in an anhydrobiotic state. Genes induced by desiccation stress have been successfully enumerated in nematodes; however we have little knowledge of gene regulation by Antarctic nematodes which can survive multiple environmental stresses. To address this problem we investigated the genetic responses of a nematode species, Plectus murrayi, that is capable of tolerating Antarctic environmental extremes, in particular desiccation and freezing. In this study, we provide the first insight into the desiccation induced transcriptome of an Antarctic nematode through cDNA library construction …

Rationally Designed Integrin Β3 Mutants Stabilized In The High Affinity Conformation, Bing Hao Luo, John Karanicolas, Laura D. Harmacek, David Baker, Timothy A. Springer

Faculty Publications

Integrins are important cell surface receptors that transmit bidirectional signals across the membrane. It has been shown that a conformational change of the integrin β-subunit headpiece (i.e. the β I domain and the hybrid domain) plays a critical role in regulating integrin ligand binding affinity and function. Previous studies have used coarse methods (a glycan wedge, mutations in transmembrane contacts) to force the β-subunit into either the open or closed conformation. Here, we demonstrate a detailed understanding of this conformational change by applying computational design techniques to select five amino acid side chains that play an important role in the …

Mycobacterium Smegmatis Histone-Like Protein Hlp Is Nucleoid Associated: Research Letter, Anirban Mukherjee, Patrick J. Dimario, Anne Grove

Faculty Publications

Eubacteria encode proteins that are required for nucleoid organization and for regulation of DNA-dependent processes. Of these histone-like proteins (Hlps), Escherichia coli HU has been shown to associate with the nucleoid and to regulate processes such as DNA repair and recombination. In contrast, the divergent HU homologs encoded by mycobacteria have been variously identified as involved in the physiology of dormancy, in the response to cold shock, or as laminin-binding proteins associated with the cell envelope. We show here, contrary to previous reports that the HU-related Hlp from Mycobacterium smegmatis associates with the nucleoid in vivo. Using indirect fluorescent antibody …

Reactivity Of Nitric Oxide With The [4fe-4s] Cluster Of Dihydroxyacid Dehydratase From Escherichia Coli, Xuewu Duan, Juanjuan Yang, Binbin Ren, Guoqiang Tan, Huangen Ding

Faculty Publications

Although the NO (nitric oxide)-mediated modification of iron-sulfur proteins has been well-documented in bacteria and mammalian cells, specific reactivity of NO with iron-sulfur proteins still remains elusive. In the present study, we report the first kinetic characterization of the reaction between NO and iron-sulfur clusters in protein using the Escherichia coli IlvD (dihydroxyacid dehydratase) [4Fe-4S] cluster as an example. Combining a sensitive NO electrode with EPR (electron paramagnetic resonance) spectroscopy and an enzyme activity assay, we demonstrate that NO is rapidly consumed by the IlvD [4Fe-4S] cluster with the concomitant formation of the IlvD-bound DNIC (dinitrosyl-iron complex) and inactivation of …

Yy1'S Longer Dna-Binding Motifs, Jeong Do Kim, Joomyeong Kim

Faculty Publications

The DNA-binding sites of YY1 located within two newly identified downstream genes of YY1, Peg3 (GGCGCCATnTT) and Xist (CCGCCATnTT), are longer than the known motif of YY1 (CGCCATnTT). Gel shift assays indicated that these DNA-binding sites are previously unnoticed, longer motifs of YY1. Independent DNA-binding motif studies further confirmed that YY1 recognizes a longer sequence (GCCGCCATTTTG) as its consensus motif. This longer motif exhibited higher affinity to the YY1 protein than the known motif. Another DNA-binding motif study was also performed using a protein containing three amino acid substitutions in the first zinc finger unit of YY1, mimicking the zinc …

Puma: Bayesian Analysis Of Partitioned (And Unpartitioned) Model Adequacy, Jeremy M. Brown, Robert Eldabaje

Faculty Publications

The accuracy of Bayesian phylogenetic inference using molecular data depends on the use of proper models of sequence evolution. Although choosing the best model available from a pool of alternatives has become standard practice in statistical phylogenetics, assessment of the chosen model's adequacy is rare. Programs for Bayesian phylogenetic inference have recently begun to implement models of sequence evolution that account for heterogeneity across sites beyond variation in rates of evolution, yet no program exists to assess the adequacy of these models. PuMA implements a posterior predictive simulation approach to assessing the adequacy of partitioned, unpartitioned and mixture models of …

An Rig-I-Like Rna Helicase Mediates Antiviral Rnai Downstream Of Viral Sirna Biogenesis In Caenorhabditis Elegans, Rui Lu, Erbay Yigit, Wan Xiang Li, Shou Wei Ding

Faculty Publications

Dicer ribonucleases of plants and invertebrate animals including Caenorhabditis elegans recognize and process a viral RNA trigger into virus-derived small interfering RNAs (siRNAs) to guide specific viral immunity by Argonaute-dependent RNA interference (RNAi). C. elegans also encodes three Dicer-related helicase (drh) genes closely related to the RIG-I-like RNA helicase receptors which initiate broad-spectrum innate immunity against RNA viruses in mammals. Here we developed a transgenic C. elegans strain that expressed intense green fluorescence from a chromosomally integrated flock house virus replicon only after knockdown or knockout of a gene required for antiviral RNAi. Use of the reporter nematode strain in …

Association Of Regions On Chromosomes 6 And 7 With Blood Pressure In Nigerian Families, Bamidele O. Tayo, Amy Luke, Xiaofeng Zhu, Adebowale Adeyemo, Richard S. Cooper

Faculty Publications

Background: Elevated blood pressure (BP) shares a level of heritability similar to many other traits related to cardiovascular risk; however, specific susceptibility loci have been difficult to localize. We conducted a multistage study of BP as a continuous trait in a low-risk West African population in which it was anticipated that environmental exposures would be reduced in complexity and intensity. In our earlier genome-wide linkage study for BP in this population, strong linkage evidence was noted on chromosomes 6 and 7. Methods and Results: We subsequently genotyped a total of 3431 tag single-nucleotide polymorphisms (SNPs) in 3 regions (viz, 152.68 …

Response Of Melittia Oedipus (Lepidoptera: Sesiidae) To Visual Cues Is Increased By The Presence Of Food Source, G. V.P. Reddy, Z. T. Cruz, N. Braganza, R. Muniappan

Faculty Publications

Visual and olfactory cues were shown to mediate short-distance orientation to different colors in the presence and in the absence of food in Melittia oedipus Oberthür (Lepidoptera: Sesiidae), a biological control agent of Coccinia grandis (L.) Voigt (Violales: Cucurbitaceae). Yellow was the color most preferred by M. oedipus, and adults landed significantly more on yellow paper moistened with honey-water. The next preferred colors were gray and white with the identical food source. Colors such as red, blue, green, brown, and black were least preferred by M. oedipus and attracted the adults on par with each other. The M. oedipus landings …

Biophysics Of Zebrafish (Danio Rerio) Sperm, M. Hagedorn, J. Ricker, M. Mccarthy, S. A. Meyers, T. R. Tiersch, Z. M. Varga, F. W. Kleinhans

Faculty Publications

In the past two decades, laboratories around the world have produced thousands of mutant, transgenic, and wild-type zebrafish lines for biomedical research. Although slow-freezing cryopreservation of zebrafish sperm has been available for 30 years, current protocols lack standardization and yield inconsistent post-thaw fertilization rates. Cell cryopreservation cannot be improved without basic physiological knowledge, which was lacking for zebrafish sperm. The first goal was to define basic cryobiological values for wild-type zebrafish sperm and to evaluate how modern physiological methods could aid in developing improved cryopreservation protocols. Coulter counting methods measured an osmotically inactive water fraction (Vb) of 0.37 ± 0.02 …

Line Edge Detection And Characterization In Sem Images Using Wavelets, Wei Sun, Jose A. Romagnoli, Joseph W. Tringe, Sonia E. Létant, Pieter Stroeve, Ahmet Palazoglu

Faculty Publications

Edge characterization has become increasingly important in nanotechnology due to the growing demand for precise nanoscale structure fabrication and assembly. Edge detection is often performed by thresholding the spatial information of a top-down image obtained by scanning electron microscopy or other surface characterization techniques. Results are highly dependent on an arbitrary threshold value, which makes it difficult to reveal the nature of the real surface and to compare results among images. In this paper, we present an alternative edge boundary detection technique based on the wavelet framework. Our results indicate that the method facilitates nanoscale edge detection and characterization by …

Correlating Threshold Power With Free-Space Bandwidth For Low-Directivity Antennas, Abu T.M. Sayem, Mark G. Douglas, Gernot Schmidt, Ben Petric, Mohammod Ali

Faculty Publications

This paper develops a threshold power rationale that can be used to demonstrate inherent compliance for portable wireless devices with specific absorption rate (SAR) limits over the 300-6000-MHz frequency range. This is achieved first by understanding the relationship between basic antenna parameters (bandwidth, operating frequency, and distance to the body) and SAR. From this, an upper limit is determined for the power transmitted by a portable wireless device such that the SAR will not exceed the compliance limit. Based on the presented computational and measured data, an empirical formula is developed for the threshold power as a function of the …

A Structural Interpretation Of The Effect Of Gc-Content On Efficiency Of Rna Interference, Chi Yu Chan, C Steven Carmack, Dang D. Long, Anil Maliyekkel, Yu Shao, Igor Roninson, Ye Ding

Faculty Publications

BACKGROUND: RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful technique for eukaryotic gene knockdown. siRNA GC-content negatively correlates with RNAi efficiency, and it is of interest to have a convincing mechanistic interpretation of this observation. We here examine this issue by considering the secondary structures for both the target messenger RNA (mRNA) and the siRNA guide strand. RESULTS: By analyzing a unique homogeneous data set of 101 shRNAs targeted to 100 endogenous human genes, we find that: 1) target site accessibility is more important than GC-content for efficient RNAi; 2) …

Dietary Resistant Starch Increases Hypothalamic Pomc Expression In Rats, Li Shen, Michael J. Keenan, Roy J. Martin, Richard T. Tulley, Anne M. Raggio, Kathleen L. Mccutcheon, Jun Zhou

Faculty Publications

Resistant starch (RS) is fermentable dietary fiber. Inclusion of RS in the diet causes decreased body fat accumulation and altered gut hormone profile. This study investigates the effect of feeding RS on the neuropeptide messenger RNA (mRNA) expressions in the arcuate nucleus (ARC) of the hypothalamus and whether vagal afferent nerves are involved. The rats were injected intraperitoneally with capsaicin to destroy unmyelinated small vagal afferent nerve fibers. The cholecystokinin (CCK) food suppression test was performed to validate the effectiveness of the capsaicin treatment. Then, capsaicin-treated rats and vehicle-treated rats were subdivided into a control diet or a RS diet …

Aggregation Of Montmorillonite And Organic Matter In Aqueous Media Containing Artificial Seawater, Yoko Furukawa, Janet L. Watkins, Jinwook Kim, Kenneth J. Curry, Richard H. Bennett

Faculty Publications

Background

The dispersion-aggregation behaviors of suspended colloids in rivers and estuaries are affected by the compositions of suspended materials (i.e., clay minerals vs. organic macromolecules) and salinity. Laboratory experiments were conducted to investigate the dispersion and aggregation mechanisms of suspended particles under simulated river and estuarine conditions. The average hydrodynamic diameters of suspended particles (representing degree of aggregation) and zeta potential (representing the electrokinetic properties of suspended colloids and aggregates) were determined for systems containing suspended montmorillonite, humic acid, and/or chitin at the circumneutral pH over a range of salinity (0 – 7.2 psu).

Results

The montmorillonite-only system increased the …

Ca2+ Extrusion By Ncx Is Compromised In Olfactory Sensory Neurons Of Omp-/- Mice, Hyun J. Kwon, Jae Hyung Koo, Frank Zufall, Trese Leinders-Zufall, Frank L. Margolis

Faculty Publications

Background: The role of olfactory marker protein (OMP), a hallmark of mature olfactory sensory neurons (OSNs), has been poorly understood since its discovery. The electrophysiological and behavioral phenotypes of OMP knockout mice indicated that OMP influences olfactory signal transduction. However, the mechanism by which this occurs remained unknown. Principal Findings: We used intact olfactory epithelium obtained from WT and OMP-/- mice to monitor the Ca2+ dynamics induced by the activation of cyclic nucleotide-gated channels, voltage-operated Ca2+ channels, or Ca2+ stores in single dendritic knobs of OSNs. Our data suggested that OMP could act to modulate the Ca2+-homeostasis in these neurons …

Race And Ancestry In Biomedical Research: Exploring The Challenges, Timothy Caulfield, Stephanie M. Fullerton, Sarah E. Ali-Khan, Laura Arbour, Esteban G. Burchard, Richard S. Cooper, Billie Jo Hardy, Simrat Harry, Robyn Hyde-Lay, Jonathan Kahn, Rick Kittles, Barbara A. Koenig, Sandra S.J. Lee, Michael Malinowski, Vardit Ravitsky, Pamela Sankar, Stephen W. Scherer, Béatrice Séguin, Darren Shickle, Guilherme Suarez-Kurtz, Abdallah S. Daar

Faculty Publications

The use of race in biomedical research has, for decades, been a source of social controversy. However, recent events, such as the adoption of racially targeted pharmaceuticals, have raised the profile of the race issue. In addition, we are entering an era in which genomic research is increasingly focused on the nature and extent of human genetic variation, often examined by population, which leads to heightened potential for misunderstandings or misuse of terms concerning genetic variation and race. Here, we draw together the perspectives of participants in a recent interdisciplinary workshop on ancestry and health in medicine in order to …

Structural Characterization Of The Hemophore Hasap From Pseudomonas Aeruginosa: Nmr Spectroscopy Reveals Protein-Protein Interactions Between Holo-Hasap And Hemoglobin, Aileen Y. Alontaga, Juan Carlos Rodriguez, Ernst Schönbrunn, Andreas Becker, Todd Funke, Erik T. Yukl, Takahiro Hayashi, Jordan Stobaugh, Pierre Moënne-Loccoz, Mario Rivera

Faculty Publications

Pseudomonas aeruginosa secretes a 205 residue long hemophore (full-length HasAp) that is subsequently cleaved at the C'-terminal domain to produce mainly a 184 residue long truncated HasAp that scavenges heme [Letoffé, S., Redeker, V., and Wandersman, C. (1998) Mol. Microbiol. 28, 1223-1234]. HasAp has been characterized by X-ray crystallography and in solution by NMR spectroscopy. The X-ray crystal structure of truncated HasAp revealed a polypeptide αβ fold and a ferriheme coordinated axially by His32 and Tyr75, with the side chain of His83 poised to accept a hydrogen bond from the Tyr75 phenolic acid group. NMR investigations conducted with full-length HasAp …