Digital Commons Network^™

Identification Of Repeat Structure In Large Genomes Using Repeat Probability Clouds, Wanjun Gu, Todd A. Castoe, Dale J. Hedges, Mark A. Batzer, David D. Pollock

Faculty Publications

The identification of repeat structure in eukaryotic genomes can be time-consuming and difficult because of the large amount of information (∼3 × 109 bp) that needs to be processed and compared. We introduce a new approach based on exact word counts to evaluate, de novo, the repeat structure present within large eukaryotic genomes. This approach avoids sequence alignment and similarity search, two of the most time-consuming components of traditional methods for repeat identification. Algorithms were implemented to efficiently calculate exact counts for any length oligonucleotide in large genomes. Based on these oligonucleotide counts, oligonucleotide excess probability clouds, or "P-clouds," were …

Phylogenetic Reconstruction From Transpositions, Feng Yue, Meng Zhang, Jijun Tang

Faculty Publications

Background
Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangement of these entities through computational means. As a result, genome rearrangement data has attracted increasing attentions from both biologists and computer scientists as a new type of data for phylogenetic analysis. The main events of genome rearrangements include inversions, transpositions and transversions. To date, GRAPPA and MGR are the most accurate …

An Evaluation Of An Upper-Division, General Education Information Literacy Program, Elizabeth S. Hopkins, Suzanne Julian

Faculty Publications

The Advanced Writing library instruction program at Brigham Young University's Harold B. Lee Library (HBLL) is intended to teach junior-level students advanced information literacy and research skills. The university general education curriculum requires students to participate in the program as part of their Advanced Writing course. When anecdotal feedback from librarians and students identified problems with the program, the authors conducted a qualitative evaluation of the program in order to identify problems and possible solutions. The evaluation included a student survey and focus groups with students, librarians, and English faculty. This paper describes the HBLL Advanced Writing instruction program, identifies …

Ultracompact Awg Using Air-Trench Bends With Perfluorocyclobutyl Polymer Waveguides, Seunghyun Kim, Gregory P. Nordin, John Ballato, Yongbin Lin, Nazli Rahmanian, Dennis W. Smith, Chris Topping

Faculty Publications

Using air-trench bends, an ultracompact 8 8 arrayed waveguide grating (AWG) demultiplexer (200-GHz channel spacing) for wavelength-division multiplexing (WDM) has been designed and fabricated with perfluorocyclobutyl (PFCB) core and clad co-polymers on a polyimide substrate. Compared to a conventional AWG in the same material system, the air-trench bend AWG shrinks the required chip area by a factor of 20. The decreased size is a factor in reducing the measured thermal shift to -0.012 nm/ C and decreasing the polarization-dependent wavelength shift to 1.3 nm.

Diagnoses For Leiognathus Lacepède 1802, Equula Cuvier 1815, Equulites Fowler 1904, Eubleekeria Fowler 1904, And A New Ponyfish Genus (Teleostei: Leiognathidae), Prosanta Chakrabarty, John S. Sparks

Faculty Publications

Recent phylogenetic work on ponyfishes has delimited and revealed the interrelationships of major leiognathid clades. To begin to recognize a monophyletic taxonomy for Leiognathidae we diagnose, delimit, and describe a number of ponyfish genera to reflect our current knowledge of their phylogenetic history. Equula Cuvier, 1815, is resurrected from synonymy with Leiognathus Lacepède, 1802, and comprises E. fasciata and E longispinis. Members of Equula, the sister group to all other members of Leiognathidae, are large-bodied ponyfishes characterized by conspicuous round yellow blotches on the flank. The genus Leiognathus Lacepède, 1802, the sister group to the remaining members of Leiognathidae less …

Precipitation Rates And Atmospheric Heat Transport During The Cenomanian Greenhouse Warming In North America: Estimates From A Stable Isotope Mass-Balance Model, David F. Ufnar, Greg A. Ludvigson, Luis González, Darren R. Gröcke

Faculty Publications

Stable isotope mass-balance modeling results of meteoric δ¹⁸O values from the Cenomanian Stage of the Cretaceous Western Interior Basin (KWIB) suggest that precipitation and evaporation fluxes were greater than that of the present and significantly different from simulations of Albian KWIB paleohydrology. Sphaerosiderite meteoric δ¹⁸O values have been compiled from the Lower Tuscaloosa Formation of southwestern Mississippi (25°N paleolatitude), The Dakota Formation Rose Creek Pit, Fairbury Nebraska (35°N) and the Dunvegan Formation of eastern British Columbia (55°N paleolatitude). These paleosol siderite δ¹⁸O values define a paleolatitudinal gradient ranging from − 4.2‰ VPDB at 25°N …

Assessment Of The Accuracy Of An Mcnpx-Based Monte Carlo Simulation Model For Predicting Three-Dimensional Absorbed Dose Distributions, U. Titt, N. Sahoo, X. Ding, Y. Zheng, W. D. Newhauser, X. R. Zhu, J. C. Polf, M. T. Gillin, R. Mohan

Faculty Publications

In recent years, the Monte Carlo method has been used in a large number of research studies in radiation therapy. For applications such as treatment planning, it is essential to validate the dosimetric accuracy of the Monte Carlo simulations in heterogeneous media. The AAPM Report no 105 addresses issues concerning clinical implementation of Monte Carlo based treatment planning for photon and electron beams, however for proton-therapy planning, such guidance is not yet available. Here we present the results of our validation of the Monte Carlo model of the double scattering system used at our Proton Therapy Center in Houston. In …

Neuropoietin Attenuates Adipogenesis And Induces Insulin Resistance In Adipocytes, Ursula A. White, William C. Stewart, Randall L. Mynatt, Jacqueline M. Stephens

Faculty Publications

Recent findings have implicated gp130 receptor ligands, particularly ciliary neurotrophic factor (CNTF), as potential antiobesity therapeutics. Neuropoietin (NP) is a recently discovered cytokine in the gp130 family that shares functional and structural features with CNTF and signals via the CNTF receptor tripartite complex comprised of CNTFRα, LIF receptor, and gp130. NP plays a role in the development of the nervous system, but the effects of NP on adipocytes have not been previously examined. Because CNTF exerts anti-obesogenic effects in adipocytes and NP shares the same receptor complex, we investigated the effects of NP on adipocyte development and insulin action. Using …

Remote Sensing Observatory Validation Of Surface Soil Moisture Using Advanced Microwave Scanning Radiometer E, Common Land Model, And Ground Based Data: Case Study In Smex03 Little River Region, Georgia, U.S., Minha Choi, Jennifer M. Jacobs, David D. Bosch

Faculty Publications

Optimal soil moisture estimation may be characterized by intercomparisons among remotely sensed measurements, ground‐based measurements, and land surface models. In this study, we compared soil moisture from Advanced Microwave Scanning Radiometer E (AMSR‐E), ground‐based measurements, and a Soil‐Vegetation‐Atmosphere Transfer (SVAT) model for the Soil Moisture Experiments in 2003 (SMEX03) Little River region, Georgia. The Common Land Model (CLM) reasonably replicated soil moisture patterns in dry down and wetting after rainfall though it had modest wet biases (0.001–0.054 m3/m3) as compared to AMSR‐E and ground data. While the AMSR‐E average soil moisture agreed well with the other data sources, it had …

Structure Of The Thioredoxin-Like Domain Of Yeast Glutaredoxin 3, Lydia M. Gibson, Nin N. Dingra, Caryn E. Outten, Lukasz Lebioda

Faculty Publications

Yeast glutaredoxin 3 (Grx3) is a cytosolic protein that regulates the activity of the iron-responsive transcriptional activator Aft1. This member of the monothiol glutaredoxin family contains a thioredoxin-like domain and a glutaredoxin-like domain, which both possess a monothiol active site. The crystal structure of the thioredoxin-like domain has been determined at 1.5 Å resolution and represents the first published structure of this domain for the monothiol glutaredoxin family. The loop containing the signature motif WAxxC is partially disordered, indicating a greater degree of flexibility in this region compared with classical dithiol thioredoxins with a WCGPC active-site motif.

Novel Implementation Of Conditional Co-Regulation By Graph Theory To Derive Co-Expressed Genes From Microarray Data, Arun Rawat, Georg J. Seifert, Youping Deng

Faculty Publications

Background

Most existing transcriptional databases like Comprehensive Systems-Biology Database (CSB.DB) and Arabidopsis Microarray Database and Analysis Toolbox (GENEVESTIGATOR) help to seek a shared biological role (similar pathways and biosynthetic cycles) based on correlation. These utilize conventional methods like Pearson correlation and Spearman rank correlation to calculate correlation among genes. However, not all are genes expressed in all the conditions and this leads to their exclusion in these transcriptional databases that consist of experiments performed in varied conditions. This leads to incomplete studies of co-regulation among groups of genes that might be linked to the same or related biosynthetic pathway.

Results …

In-Plane Photonic Transduction Of Silicon-On-Insulator Microcantilevers, Ryan Anderson, Seunghyun Kim, Gregory P. Nordin, Jong Wook Noh, Jaime Cardenas

Faculty Publications

We demonstrate an in-plane photonic transduction method for microcantilevers, which have been widely investigated for sensor applications. In our approach the microcantilever is etched to form a single mode rib waveguide. Light propagates down the microcantilever and crosses a small gap at the free end of the microcantilever, some of which is captured by an asymmetrical multimode waveguide that terminates in a Y-branch. The Y-branch outputs are used to form a differential signal that is monotonically dependent on microcantilever deflection. The measured differential signal matches simulation when microcantilever rotation is properly accounted for. The measured differential signal sensitivity is 1.4 …

Intro To The Digital World -- For Nlu Academic Cabinet, August 2008, Kathleen A. Walsh

Faculty Publications

Designed as a "beginner's intro" to online life and online learning; themed around 3 questions: what's going on in the digital world?, what's wrong with these kids today (Gen M)?, and what could all of this mean for online teaching and learning at NLU?

Genome-Wide Transposon Tagging Reveals Location-Dependent Effects On Transcription And Chromatin Organization In Arabidopsis, Faye M. Rosin, Naohide Watanabe, Jean Luc Cacas, Naohiro Kato, Juana M. Arroyo, Yuda Fang, Bruce May, Matthew Vaughn, Joseph Simorowski, Umamaheswari Ramu, Richard W. Mccombie, David L. Spector, Robert A. Martienssen, Eric Lam

Faculty Publications

The interphase nucleus exists as a highly dynamic system, the physical properties of which have functional importance in gene regulation. Not only can gene expression be influenced by the local sequence context, but also by the architecture of the nucleus in three-dimensions (3D), and by the interactions between these levels via chromatin modifications. A challenging task is to resolve the complex interplay between sequence- and genome structure-based control mechanisms. Here, we created a collection of 277 Arabidopsis lines that allow the visual tracking of individual loci in living plants while comparing gene expression potential at these locations, via an identical …

Estimating Species Trees Using Multiple-Allele Dna Sequence Data, Liang Liu, Dennis K. Pearl, Robb T. Brumfield, Scott V. Edwards

Faculty Publications

Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it becomes more challenging to estimate relationships at the level of species, either because concatenation becomes inappropriate due to conflicts among individual gene trees, or because the species from which multiple alleles have been sampled may not form monophyletic groups in the estimated tree. We propose a Bayesian hierarchical model to reconstruct species trees from multiple-allele, multilocus sequence data, building on a recently proposed method for estimating …

Telomeres And Race: What Can We Learn About Human Biology From Health Differentials?, Jay S. Kaufman, Richard S. Cooper

Faculty Publications

The advent of molecular technology that can be applied across large population samples has added - rather than reduced - complexity in the analysis of the intertwined effects of social history and heritable factors on health outcomes. The report by Hunt et al. in this issue of Aging Cell provides an example of the promises and dilemmas associated with this increased complexity. © 2008 The Authors Journal compilation © Blackwell Publishing Ltd/The Anatomical Society of Great Britain and Ireland 2008.

Viability And Fertilizing Capacity Of Cryopreserved Sperm From Three North American Acipenseriform Species: A Retrospective Study, Á Horváth, W. R. Wayman, J. C. Dean, B. Urbányi, T. R. Tiersch, S. D. Mims, D. Johnson, J. A. Jenkins

Faculty Publications

Populations of sturgeon across the globe are threatened due to unregulated harvest and habitat loss, and the status varies among species across North America. Ready access to viable and functional sperm would contribute to recovery programmes for these species. In this study, we examined the motility, viability (cell membrane integrity) of cryopreserved sperm from three North American acipenseriform species and fertilizing capacity. Milt samples were collected from captive shortnose sturgeon (Acipenser brevirostrum), wild paddlefish (Polyodon spathula) and pallid sturgeon (Scaphirhynchus albus) and cryopreserved using combinations of Modified Tsvetkova's (MT) extender, Original Tsvetkova's extender, and modified Hanks' balanced salt solution, along …

Effective Single-Particle Order-N Scheme For The Dynamics Of Open Noninteracting Many-Body Systems, Yuriy V. Pershin Dr, Y. Dubi, M. Di Ventra

Faculty Publications

Quantum master equations are common tools to describe the dynamics of many-body systems open to an environment. Due to the interaction with the latter, even for the case of noninteracting electrons, the computational cost to solve these equations increases exponentially with the partical number. We propose a simple scheme, which allows to study the dynamics of N noninteracting electrons taking into account both dissipation effects and Fermi statistics, with a computational cost that scales linearly with N. Our method is based on a mapping of the many-body system to a specific set of effective single-particle systems. We provide detailed …

Decline In A Dominant Invertebrate Species Contributes To Altered Carbon Cycling In A Low-Diversity Soil Ecosystem, Byron J. Adams, J. E. Barrett, Ross A. Virginia, Diana H. Wall

Faculty Publications

Low-diversity ecosystems cover large portions of the Earth's land surface, yet studies of climate change on ecosystem functioning typically focus on temperate ecosystems, where diversity is high and the effects of individual species on ecosystem functioning are difficult to determine. We show that a climate-induced decline of an invertebrate species in a low-diversity ecosystem could contribute to significant changes in carbon © cycling. Recent climate variability in the McMurdo Dry Valleys of Antarctica is associated with changes in hydrology, biological productivity, and community composition of terrestrial and aquatic ecosystems. One of the greatest changes documented in the dry valleys is …

Prevalence And Infection Load Dynamics Of Rickettsia Felis In Actively Feeding Cat Fleas, Kathryn E. Reif, Rhett W. Stout, Gretchen C. Henry, Lane D. Foil, Kevin R. Macaluso

Faculty Publications

Background: Rickettsia felis is a flea-associated rickettsial pathogen recurrently identified in both colonized and wild-caught cat fleas, Ctenocephalides felis. We hypothesized that within colonized fleas, the intimate relationship between R. felis and C. felis allows for the coordination of rickettsial replication and metabolically active periods during flea bloodmeal acquisition and oogenesis. Methodology/Principal Findings: a quantitative real-time PCR assay was developed to quantify R. felis in actively feeding R. felis-infected fleas. In three separate trials, fleas were allowed to feed on cats, and a mean of 3.9 × 106 R. felis 17-kDa gene copies was detected for each flea. A distinct …

Q-Dock: Low-Resolution Flexible Ligand Docking With Pocket-Specific Threading Restraints, Michal Brylinski, Jeffrey Skolnick

Faculty Publications

The rapidly growing number of theoretically predicted protein structures requires robust methods that can utilize low-quality receptor structures as targets for ligand docking. Typically, docking accuracy falls off dramatically when apo or modeled receptors are used in docking experiments. Low-resolution ligand docking techniques have been developed to deal with structural inaccuracies in predicted receptor models. In this spirit, we describe the development and optimization of a knowledge-based potential implemented in Q-Dock, a low-resolution flexible ligand docking approach. Self-docking experiments using crystal structures reveals satisfactory accuracy, comparable with all-atom docking. All-atom models reconstructed from Q-Dock's low-resolution models can be further refined …

Size And Heterozygosity Influence Partner Selection In The Formosan Subterranean Termite, Claudia Husseneder, Dawn M. Simms

Faculty Publications

In monogamous species that exhibit extensive biparental investment, such as termites, both sexes are predicted to be selective when choosing a mate. Size-related traits are expected to be important in partner selection because the fat reserves of the colony founders sustain the incipient colony. Partner relatedness and heterozygosity determine the degree of inbreeding and genetic diversity within the colony and may thus also influence partner selection. To test these predictions, we investigated whether phenotypic and genetic traits influence mate choice and/or competitive advantage during pair formation of Formosan subterranean termites, Coptotermes formosanus (Isoptera: Rhinotermitidae). Pair formation in termites normally occurs …

Replication Of The Wellcome Trust Genome-Wide Association Study Of Essential Hypertension: The Family Blood Pressure Program, Georg B. Ehret, Alanna C. Morrison, Ashley A. O'Connor, Megan L. Grove, Lisa Baird, Karen Schwander, Alan Weder, Richard S. Cooper, D. C. Rao, Steven C. Hunt, Eric Boerwinkle, Aravinda Chakravarti

Faculty Publications

Essential hypertension is a principal cardiovascular risk factor whose origin remains unknown. Classical genetic studies have shown that blood pressure is at least partially heritable, opening a window to understanding the pathophysiology of essential hypertension in the human using modern genetic tools. The Wellcome Trust Case Control Consortium has recently published the results of screening the genomes of 2000 essential hypertension cases and 3000 controls using 500000 genome-wide single nucleotide polymorphisms (SNPs). None of the variants proved to be genome-wide significant after correction for multiple tests but the most significantly associated SNPs (P<10-5) constitute a priority list that warrant follow-up in other studies. We describe here replication studies of the top six SNPs in subjects from the US National Heart, Lung, and Blood Institute funded Family Blood Pressure Program comprising 11433 individuals recruited by hypertensive families. The results suggest that only one of the six SNPs might be associated with essential hypertension in Americans of European origin. This SNP shows a significant but opposite effect in Americans of Hispanic origin and no association in African Americans. The significance of the opposing effect estimates is unclear. No replication could be shown for hypertension status, but there are differences in study design. This attempted replication highlights that essential hypertension studies will require more comprehensive and larger genetic screens.

Leaf Area Index Simulation In Soybean Grown Under Near-Optimal Conditions, T. D. Setiyono, A. Weiss, J. E. Specht, K. G. Cassman, A. Dobermann

Faculty Publications

Different approaches have been used to simulate leaf area index (LAI) in soybean (Glycine max L. Merr). Many of these approaches require genotype-specific calibration procedures. Studies modeling LAI dynamics under optimal growth conditions with yields close to the yield potential of soybean have remained scarce. A sink-driven approach was developed and evaluated for LAI simulation in soybean under near-optimal environments. The rate of change in expanding leaf area was simulated using the first derivative of a logistic function accounting for plant population density, air temperature, and water deficit. The rate of change in senescing leaf area was also simulated using …

Highly Efficient Circulating Tumor Cell Isolation From Whole Blood And Label-Free Enumeration Using Polymer-Based Microfluidics With An Integrated Conductivity Sensor, André A. Adams, Paul I. Okagbare, Juan Feng, Matuesz L. Hupert, Don Patterson, Jost Götten, Robin L. Mccarley, Dimitris Nikitopoulos, Michael C. Murphy, Steven A. Soper

Faculty Publications

A novel microfluidic device that can selectively and specifically isolate exceedingly small numbers of circulating tumor cells (CTCs) through a monoclonal antibody (mAB) mediated process by sampling large input volumes (≥1 mL) of whole blood directly in short time periods (<37 >min) was demonstrated. The CTCs were concentrated into small volumes (190 nL), and the number of cells captured was read without labeling using an integrated conductivity sensor following release from the capture surface. The microfluidic device contained a series (51) of high-aspect ratio microchannels (35 μm width x 150 μm depth) that were replicated in poly(methyl methacrylate), PMMA, from …

Tnfα Sirna Reduces Brain Tnf And Eeg Delta Wave Activity In Rats, Ping Taishi, Lynn Churchill, Mingxiang Wang, Daniel Kay, Christopher J. Davis, Xin Guan, Alok De, Tadanobu Yasuda, Fan Liao, James M. Krueger

Faculty Publications

Tumor necrosis factor alpha (TNFα) is a pleiotropic cytokine with several CNS physiological and pathophysiological actions including sleep, memory, thermal and appetite regulation. Short interfering RNAs (siRNA) targeting TNFα were incubated with cortical cell cultures and microinjected into the primary somatosensory cortex (SSctx) of rats. The TNFα siRNA treatment specifically reduced TNFα mRNA by 45% in vitro without affecting interleukin-6 or gluR1-4 mRNA levels. In vivo the TNFα siRNAα reduced TNFα mRNA, interleukin-6 mRNA and gluR1 mRNA levels compared to treatment with a scrambled control siRNA. After in vivo microinjection, the density of TNFα-immunoreactive cells in layer V of the …

Latitudinal Variation In Leaf And Tree Traits Of The Mangrove Avicennia Germinans (Avicenniaceae) In The Central Region Of The Gulf Of Mexico, Rodrigo Méndez-Alonzo, Jorge López-Portillo, Victor H. Rivera-Monroy

Faculty Publications

The variation in leaf mass per area, leaf nutrients (% carbon, nitrogen and phosphorus), and the allometric relation between tree height and diameter of the black mangrove, Avicennia germinans, were explored in nine mangrove forests in similar environments along a 50 latitudinal gradient in the central region of the Gulf of Mexico, as indicated by a southward increase in temperature and precipitation. There was no correlation between leaf nitrogen or phosphorus content and latitude. Leaf mass per area and leaf carbon content were positively correlated with latitude and negatively correlated with temperature and annual rainfall, whereas asymptotic tree height and …

Non-Beneficial Pediatric Research And The Best Interest Standard: A Reconciliation, Paul J. Litton

Faculty Publications

Federal efforts beginning in the 1990's have successfully increased pediatric research to improve medical care for all children. Since 1997, the FDA has requested 800 pediatric studies involving 45,000 children. Much of this research is "non-beneficial"; that is, it exposes pediatric subjects to risk even though these children will not benefit from participating in the research. Non-beneficial pediatric research (NBPR) seems, by definition, contrary to the best interests of pediatric subjects, which is why one state supreme court has essentially prohibited it. It also appears that the only plausible rationale for this research is utilitarian, as it risks some children …

Weak Competition Among Tropical Tree Seedlings: Implications For Species Coexistence, C. E.Timothy Paine, Kyle E. Harms, Stefan A. Schnitzer, Walter P. Carson

Faculty Publications

The intensity of competition among forest tree seedlings is poorly understood, but has important ramifications for their recruitment and for the maintenance of species diversity. Intense competition among seedlings could allow competitively dominant species to exclude subordinate species. Alternatively, the low density and small stature of forest tree seedlings could preclude intense interseedling competition. In this case, other processes, such as size-asymmetric competition with adults, interactions with consumers, or neutral dynamics would prevail as those structuring the forest understory. We tested the intensity of, and potential for, intraspecific competition among tree seedlings of three species (Brosimum alicastrum, Matisia cordata, and …

Cu/Zn Superoxide Dismutases In Developing Cotton Fibers: Evidence For An Extracellular Form, Hee Jin Kim, Naohiro Kato, Sunran Kim, Barbara Triplett

Faculty Publications

Hydrogen peroxide and other reactive oxygen species are important signaling molecules in diverse physiological processes. Previously, we discovered superoxide dismutase (SOD) activity in extracellular protein preparations from fiber-bearing cotton (Gossypium hirsutum L.) seeds. We show here, based on immunoreactivity, that the enzyme is a Cu/Zn-SOD (CSD). Immunogold localization shows that CSD localizes to secondary cell walls of developing cotton fibers. Five cotton CSD cDNAs were cloned from cotton fiber and classified into three subfamilies (Group 1: GhCSD1; Group 2: GhCSD2a and GhCSD2b; Group 3: GhCSD3 and GhCSD3s). Members of Group 1 and 2 are expressed throughout fiber development, but predominant …