Digital Commons Network^™

Soybean Cultivars Resulted From More Recombination Events Than Unselected Lines In The Same Population, T. R. Stefaniak, D. L. Hyten Jr., V. R. Pantalone, A. Klarer, T. W. Pfeiffer

Department of Agronomy and Horticulture: Faculty Publications

The selection of superior adapted cultivars has contributed to the doubling of soybean [Glycine max (L.) Merr.] yields in the USA since 1930. Genetic variation was required for this selection to be effective. The objective of this study was to evaluate the importance of homologous chromosome meiotic recombination in the creation of soybean cultivars. A set of 10 adapted high-yielding cultivars selected from the cross ‘Williams’ × ‘Essex’ was com-pared with a set of 156 random recombinant inbred lines (RILs) from the same population. Crossover events were identified using 143 simple sequence repeat (SSR) markers span-ning all 20 soybean …

Circular Ultrasound Compounding By Designed Matrix Weighting, Gregory Bashford, Jonathan Morse

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Spatial compounding is an imaging technique that aims to improve image contrast by combining partially decorrelated images acquired at different angles or positions. In conventional spatial compounding, data sets are combined with equal weighting. Here, we describe an alternative method of reconstruction using algorithms which weight the data based on a “quality” matrix. The quality matrix is derived from beam-forming characteristics. For each data set, the reliability of the data is assumed to vary spatially. By compounding the data based on the quality matrix, a complete image is formed. Here, we describe the construction of a rotational translation stage and …

Variable Upper And Lower Crop Water Stress Index Baselines For Corn And Soybean, J. O. Payero, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Upper and lower crop water stress index (CWSI) baselines adaptable to different environments and times of day are needed to facilitate irrigation scheduling with infrared thermometers. The objective of this study was to develop dynamic upper and lower CWSI baselines for corn and soybean. Ten-minute averages of canopy temperatures from corn and soybean plots at four levels of soil water depletion were measured at North Platte, Nebraska, during the 2004 growing season. Other variables such as solar radiation (R_s), air temperature (T_a), relative humidity (RH), wind speed (u), and plant canopy height (h) were …

Use Of Time Domain Reflectometry For Continuous Monitoring Of Nitrate-Nitrogen In Soil And Water, J. O. Payero, David D. Tarkalson, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Nitrate-Nitrogen (NO₃-N) losses to ground and surface water are an environmental and agronomic concern in modern crop production systems in the Central Great Plains. Monitoring techniques for nitrogen use in agricultural production are needed to increase crop yield, optimize nitrogen use, and reduce NO₃-N leaching. Time domain reflectometry (TDR) could potentially be calibrated to continuously measure NO₃-N in soil and water. The objectives of this study were to: (1) evaluate the effect of different factors affecting the response of the bulk electrical conductivity (ECb) sensed by TDR, (2) compare the sensitivity and differences between …

Nonintrusive Mapping Of Near-Surface Preferential Flow, R. S. Freeland, Lameck O. Odhiambo, J. S. Tyner, J. T. Ammons, W. C. Wright

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A unique survey protocol has been developed that maps near-subsurface preferential flow using integrated ground-penetrating radar (GPR) and a differential geographical positioning system (DGPS). The survey protocol consists of a mobile GPR system that spirals outward along a prescribed course, continuously gathering subsurface data for an extended period. Metered water is applied to a centrally located water-ponding ring, after first capturing the initial dry-state pattern signatures. The water radiates outward beneath the surface as it follows preferential flow pathways, which the GPR instrumentation spiraling above highlights. After data are collected, pre- and post-water time-elapsed images profiles are segmented by pattern …

Interference Effects In The Memory For Serially Presented Locations In Clark’S Nutcrackers, Nucifraga Columbiana, Jody L. Lewis, Alan C. Kamil

Papers in Behavior in Biological Sciences

The authors tested the spatial memory of serially presented locations in Clark’s nutcrackers (Nucifraga columbiana). Birds were serially presented with locations in an open room. The authors buried a seed in a sand-filled cup at each location and then tested nutcrackers for their memory for each location in the list by using the cluster method. For each item in the list, the authors opened a cluster of 6 holes. Accuracy was measured by how many tries were required for the bird to find the correct location within each cluster. In Experiments 1 and 2, the authors presented 2 …

Selective Attention, Priming, And Foraging Behavior, Alan Kamil, Alan B. Bond

Papers in Behavior in Biological Sciences

Animals selectively filter and transform their sensory input, increasing the accuracy with which some stimuli are detected and effectively ignoring others. This filtering process, collectively referred to as “selective attention,” takes place at a variety of different levels in the nervous system. It was described in considerable detail by William James over a century ago (James, 1890/1950) and has been a principal focus of research in cognitive psychology for nearly 50 years (Parasuraman & Davies, 1984; Pashler, 1998; Richards, 1998). Investigations of selective attention have also been central to the study of animal cognition, where the process of attention has …

S-Adenosylmethionine Stabilizes Cystathionine Β-Synthase And Modulates Redox Capacity, Anna Prudova, Zachary Bauman, Aaron Braun, Victor Vitvitsky, Shelly C. Lu, Ruma Banerjee

Department of Biochemistry: Faculty Publications

The transsulfuration pathway converts homocysteine to cysteine and represents the metabolic link between antioxidant and methylation metabolism. The first and committing step in this pathway is catalyzed by cystathionine β-synthase (CBS), which is subject to complex regulation, including allosteric activation by the methyl donor, S-adenosylmethionine (AdoMet). In this study, we demonstrate that methionine restriction leads to a >10-fold decrease in CBS protein levels, and pulse proteolysis studies reveal that binding of AdoMet stabilizes the protein against degradation by ≈12 kcal/mol. These observations predict that under pathological conditions where AdoMet levels are diminished, CBS, and therefore glutathione levels, will be reduced. …

Purification And Initial Biochemical Characterization Of Atp:Cob(I)Alamin Adenosyltransferase (Eutt) Enzyme Of Salmonella Enterica, Nicole R. Baun, Jorge C. Escalante-Semerena

Department of Biochemistry: Faculty Publications

ATP:cob(I)alamin adenosyltransferase (EutT) of Salmonella

enterica was overproduced and enriched to ~70% homogeneity,

and its basic kinetic parameters were determined. Abundant

amounts of EutT protein were produced, but all of it remained

insoluble. Soluble active EutT protein (~70% homogeneous) was

obtained after treatment with detergent. Under conditions in which

cobalamin (Cbl) was saturating, _Km(ATP) = 10 µM, k_cat = 0.03 s^-1,

and V_max = 54.5 nM min^-1. Similarly, under conditions in which

MgATPwas saturating,K_m(Cbl) = 4.1µM, k_cat = 0.06 s^-1, andV_max= …

Sex-Specific Expression Of Alternative Transcripts In Drosophila, Lauren Mcintyre, Lisa Bono, Anne Genissel, Rick Westerman, Damion Junk, Marina Telonis-Scott, Lawrence G. Harshman, Marta Wayne, Artyom Kopp, Sergey V. Nuzhdin

School of Biological Sciences: Faculty Publications

Background: Many genes produce multiple transcripts due to alternative splicing or utilization of alternative transcription initiation/termination sites. This 'transcriptome expansion' is thought to increase phenotypic complexity by allowing a single locus to produce several functionally distinct proteins. However, sex, genetic and developmental variation in the representation of alternative transcripts has never been examined systematically. Here, we describe a genome-wide analysis of sex-specific expression of alternative transcripts in Drosophila melanogaster.

Results: We compared transcript profiles in males and females from eight Drosophila lines (OregonR and 2b, and 6 RIL) using a newly designed 60-mer oligonucleotide microarray that allows us …

Phylogenetic Analysis Of The Cardini Group Of Drosophila With Respect To Changes In Pigmentation, Jennifer A. Brisson, Jason Wilder, Hope Hollocher

School of Biological Sciences: Faculty Publications

Phenotypic variability is the engine that drives future diversification with the expectation that polymorphic ancestors give rise to descendants harboring a subset of the ancestral variation. Here we examine evolutionary transitions from polymorphism to monomorphism in a visually striking New World radiation of fruit flies, the Drosophila cardini group. This group is distributed across the Americas and the Caribbean islands and exhibits a wide spectrum of abdominal pigmentation variation. Specifically, the D. dunni subgroup consists of Caribbean island endemics, each of which is monomorphic for its pigmentation pattern, with an interspecific cline of pigmentation across the islands. The D. cardini …

Phylogenetics Of The Florally Diverse Andean Clade Iochrominae (Solanaceae), Stacey Dewitt Smith, David A. Baum

School of Biological Sciences: Faculty Publications

Recent molecular phylogenetic studies of Solanaceae have identified many well-supported clades within the family and have permitted the creation of a phylogenetic system of classification. Here we estimate the phylogeny for Iochrominae, a clade of Physaleae sensu Olmstead et al. (1999), which contains 34 Andean species encompassing an immense diversity of floral forms and colors. Using three nuclear regions, ITS, the second intron of LEAFY, and exons 2 to 9 of the granule-bound starch synthase gene (waxy), we evaluated the monophyly of the traditional genera comprising Iochrominae and assessed the extent of interspecific hybridization within the clade. …

Anaerobic Nitrate-Dependent Iron(Ii) Bio-Oxidation By A Novel Lithoautotrophic Betaproteobacterium, Strain 2002, Karrie A. Weber, Jarrod Pollock, Kimberly A. Cole, Susan M. O'Connor, Laurie A. Achenbach, John D. Coates

School of Biological Sciences: Faculty Publications

Microbial nitrate-dependent Fe(II) oxidation is known to contribute to iron biogeochemical cycling; however, the microorganisms responsible are virtually unknown. In an effort to elucidate this microbial metabolic process in the context of an environmental system, a 14-cm sediment core was collected from a freshwater lake and geochemically characterized concurrently with the enumeration of the nitrate-dependent Fe(II)-oxidizing microbial community and subsequent isolation of a nitrate-dependent Fe(II)-oxidizing microorganism. Throughout the sediment core, ambient concentrations of Fe(II) and nitrate were observed to coexist. Concomitant most probable number enumeration revealed the presence of an abundant nitrate-dependent Fe(II)- oxidizing microbial community (2.4 × 10^{3 …}

Protein Binding Site Prediction Using An Empirical Scoring Function, Shide Liang, Chi Zhang, Song Liu, Yaoqi Zhou

School of Biological Sciences: Faculty Publications

Most biological processes are mediated by interactions between proteins and their interacting partners including proteins, nucleic acids and small molecules. This work establishes a method called PINUP for binding site prediction of monomeric proteins. With only two weight parameters to optimize, PINUP produces not only 42.2% coverage of actual interfaces (percentage of correctly predicted interface residues in actual interface residues) but also 44.5% accuracy in predicted interfaces (percentage of correctly predicted interface residues in the predicted interface residues) in a cross validation using a 57-protein dataset. By comparison, the expected accuracy via random prediction (percentage of actual interface residues in …

Incorporating Animal Behavior Into Seed Dispersal Models: Implications For Seed Shadows, Sabrina E. Russo, Stephen Portnoy, Carol K. Augspurger

School of Biological Sciences: Faculty Publications

Seed dispersal fundamentally influences plant population and community dynamics but is difficult to quantify directly. Consequently, models are frequently used to describe the seed shadow (the seed deposition pattern of a plant population). For vertebrate dispersed plants, animal behavior is known to influence seed shadows but is poorly integrated in seed dispersal models. Here, we illustrate a modeling approach that incorporates animal behavior and develop a stochastic, spatially explicit simulation model that predicts the seed shadow for a primate-dispersed tree species (Virola calophylla, Myristicaceae) at the forest stand scale. The model was parameterized from field-collected data on …

Spatial Associations Of Humus, Nutrients And Soils In Mixed Dipterocarp Forest At Lambir, Sarawak, Malaysian Borneo, I. C. Baillie, P.S. Ashton, S.P. Chin, S.J. Davies, P.A. Palmiotto, Sabrina E. Russo, S. Tan

School of Biological Sciences: Faculty Publications

Discrete humus layers are common on podzols under temperate coniferous and tropical heath forests, and patchy layers also occur under some temperate broadleaved forests on non-podzolic soils. We used multiple data sets to test the reported association of humus with oligotrophic but non-podzolic soils under non-heath dipterocarp forest at Lambir, Sarawak. We examined the distribution, morphology and nutrient dynamics of necromass on soils derived from sandstone and shale. Concentrations of the main mineral nutrients were lower in fresh litter on the very oligotrophic sandstone soils than on shale. The rates of litterfall were similar, so that annual litterfall fluxes of …

Determination Of Mrna Half-Lives In Candida Albicans Using Thiolutin As A Transcription Inhibitor, Bessie W. Kebaara, Lindsey E. Nielsen, Kenneth Nickerson, Audrey L. Atkin

Kenneth Nickerson Papers

A method for determining mRNA half-lives in the polymorphic fungus Candida albicans is described. It employs growth in a defined medium, the inhibition of transcription with thiolutin (10–20 μg/mL), and quantitative Northern blotting. The method is effective for the A72, SC5314, and CAI-4 strains of C. albicans, and for mRNAs that have a wide variety of decay rates and steady-state abundances. The range of half-lives detected (from 4–168 min) shows that this method is effective for mRNAs with widely varying half-lives. The mRNA decay rates obtained are compared with those for orthologous mRNAs from Saccharomyces cerevisiae. This procedure …

Hen1 Recognizes 21–24 Nt Small Rna Duplexes And Deposits A Methyl Group Onto The 2' Oh Of The 3' Terminal Nucleotide, Zhiyong Yang, Yon W. Ebright, Bin Yu, Xuemei Chen

Bin Yu Publications

microRNAs (miRNAs) and small interfering RNAs (siRNAs) in plants bear a methyl group on the ribose of the 3' terminal nucleotide. We showed previously that the methylation of miRNAs and siRNAs requires the protein HEN1 in vivo and that purified HEN1 protein methylates miRNA/miRNA* duplexes in vitro. In this study, we show that HEN1 methylates both miRNA/miRNA* and siRNA/siRNA* duplexes in vitro with a preference for 21–24 nt RNA duplexes with 2 nt overhangs. We also demonstrate that HEN1 deposits the methyl group on to the 2' OH of the 3' terminal nucleotide. Among various modifications thatcanoccuronthe ribose of …

Erratum: Dynamics Of Filament Formation In A Kerr Medium [Phys Rev. A 71, 063811 (2005)], Martin Centurion, Ye Pu, Mankei Tsang, Demetri Psaltis

Martin Centurion Publications

We have found an error in this paper -- [Phys Rev. A 71, 063811 (2005)]. In our calculation of the intensity threshold for breakdown in CS₂ we erroneously used the ionization energy of molecular CS₂ (10.08 eV). The correct value should be 3.3 eV, the band gap energy of liquid CS₂ . Using the band gap energy, nonlinear absorption will be a three-photon process, and the calculated breakdown threshold becomes 8.5 × 10¹¹ W/cm² (as opposed to the value of 2×10¹³ W/cm² reported previously). Multiphoton absorption and plasma defocusing could then become significant …

Liberty, Gender, And The Family, Jennifer Mckitrick

Department of Philosophy: Faculty Publications

DISCUSSIONS OF JUSTICE within the classical liberal, libertarian tradition have been universalist. They have aspired to apply to any human community, whatever the makeup of its membership. Certainly some feminists have taken issue with this, arguing that the classical liberal, libertarian understanding of justice fails to address the concerns of women, indeed, does women an injustice. Among these we find Susan Moller Okin, and it will be my task in this essay to explore whether Okin's criticism is well founded. Susan Moller Okin's justice, Gender, and the Family is a landmark feminist discussion of distributive justice that raises issues no …

Stochastic Algorithm For Improved Operations At Isolated High Speed Intersections, Anuj Sharma, Darcy M. Bullock, Srinivas Peeta

Department of Civil and Environmental Engineering: Faculty Publications

The current practice of specifying simultaneous gap out logic at isolated high speed signalized intersections places constraints on the signal controller logic that cannot be satisfied under high congestion level. Further, it often results in degraded signal efficiency and dilemma zone protection. A stochastic approach is proposed in this paper with the objective of increasing safety and efficiency at these intersections.

Fast-Nmr - Functional Annotation Screening Technology Using Nmr Spectroscopy, Kelly A. Mercier, Michael Baranski, Viswanathan Ramanathan, Peter Z. Revesz, Rong Xiao, Gaetano T. Montelione, Robert Powers

Robert Powers Publications

An abundance of protein structures emerging from structural genomics and the Protein Structure Initiative (PSI) are not amenable to ready functional assignment because of a lack of sequence and structural homology to proteins of known function. We describe a high-throughput NMR methodology (FAST-NMR) to annotate the biological function of novel proteins through the structural and sequence analysis of protein-ligand interactions. This is based on basic tenets of biochemistry where proteins with similar functions will have similar active sites and exhibit similar ligand binding interactions, despite global differences in sequence and structure. Protein-ligand interactions are determined through a tiered NMR screen …

Coupling Between Primary Terrestrial Succession And The Trophic Development Of Lakes At Glacier Bay, Alaska, D. R. Engstrom, Sherilyn C. Fritz

Department of Earth and Atmospheric Sciences: Faculty Publications

The natural eutrophication of lakes is still an accepted concept in limnology, arising as it does from the earliest efforts to classify lakes and place them in an evolutionary sequence. Recent studies of newly formed lakes at Glacier Bay, Alaska, only partially support this idea, and suggest more variable trends in lake trophic development which are under local (catchment-level) control. Here we use sediment cores from several lakes in Glacier Bay National Park to examine the relationship between successional changes in catchment vegetation and trends in water-column nitrogen (a limiting nutrient) and lake primary production. Terrestrial succession at Glacier Bay …

Isopiestic Measurement Of The Osmotic Coefficients Of Aqueous {Xh2So4 + (1−X)Fe2(So4)3} Solutions At 298.15 And 323.15 K, Mariano Velazquez-Rivera, Donald Palmer, Richard Kettler

Department of Earth and Atmospheric Sciences: Faculty Publications

This study measures the osmotic coefficients of {xH₂SO₄ +(1−x)Fe₂ (SO₄)₃}(aq) solutions at 298.15 and 323.15 K that have ionic strengths as great as 19.3 mol•kg^-1, using the isopiestic method. Experiments utilized both aqueous NaCl and H₂SO₄ as reference solutions. Equilibrium values of the osmotic coefficient obtained using the two different reference solutions were in satisfactory internal agreement. The solutions follow generally the Zdanovskii empirical linear relationship and yield values of a_w for the Fe₂ (SO₄)₃–H₂O binary system at 298.15 …

Spectrum Of General Surgical Problems In The Developmentally Disabled Adults, Kamran Khalid, Saleh M. Al-Salamah

Saudi Medical Journal

OBJECTIVE: This study highlights the spectrum of general surgical problems necessitating admission on intellectually disabled adult patients. Problems encountered in the management and the ways to overcome various difficulties are highlighted. METHODS: Prospective collection of data on 63 consecutive developmentally disabled adult patients admitted to the Department of General Surgery, Riyadh Medical Complex (RMC), Riyadh, Kingdom of Saudi Arabia for various indications from January 2000 through December 2004. Demographic details, clinical presentation, diagnostic modalities, associated physical and neurological disabilities, coexisting medical condition, treatment options, morbidity and mortality were analyzed. Various difficulties encountered during the management and mean to overcome these …

Prilocaine Induced Methemoglobinemia, Sahender G. Aygencel, Emine Akinci, Gul Pamukcu

Saudi Medical Journal

No abstract provided.

The Factors Of Arteriovenous Fistula Failure In Hemodialysis Patient, Abdolhassan Talaiezadeh, Faramarz Paziar

Saudi Medical Journal

No abstract provided.

Dark-Lumen Magnetic Resonance Colonography, Mathias Goyen, Waleed Ajaj, Thomas Lauenstein

Saudi Medical Journal

No abstract provided.

Diagnostic Value Of Mr Imaging In Meniscal Tears Of The Knee, Khalilollah Nazem, Khashayar Jabalameli, Farhad Iranpour

Saudi Medical Journal

No abstract provided.

Intramuscular Artemether In The Treat-Ment Of Uncomplicated Plasmodium Falciparum Malaria In Sudanese Patients, Ayda R. Mohammed-Ali, Musa M. Kheir, Ishag Adam

Saudi Medical Journal

No abstract provided.