Digital Commons Network^™

Endogenous And Exogenous Control Of Ecosystem Function: N Cycling In Headwater Streams, H. M. Valett, S. A. Thomas, P. J. Mulholland, J. R. Webster, C. N. Dahm, C. S. Fellows, C. L. Crenshaw, C. G. Peterson

School of Biological Sciences: Faculty Publications

Allochthonous inputs act as resource subsidies to many ecosystems, where they exert strong influences on metabolism and material cycling. At the same time, metabolic theory proposes endogenous thermal control independent of resource supply. To address the relative importance of exogenous and endogenous influences, we quantified spatial and temporal variation in ecosystem metabolism and nitrogen (N) uptake using seasonal releases of ¹⁵N as nitrate in six streams differing in riparian–stream interaction and metabolic character. Nitrate removal was quantified using a nutrient spiraling approach based on measurements of downstream decline in ¹⁵N flux. Respiration (R) and gross primary production (GPP) …

Nutrient Transport As Affected By Rate Of Overland Flow, John E. Gilley, W. F. Sabatka, B. Eghball, David B. Marx

Department of Biological Systems Engineering: Papers and Publications

Little information is currently available concerning the effects of varying flow rate on nutrient transport by overland flow. The objective of this study was to measure the effects of overland flow rate on nutrient transport following the application of beef cattle or swine manure to plots containing 0, 2, 4, or 8 Mg ha^-1 of corn residue. After addition of residue materials to 0.75 m wide by 2.0 m long plots, beef cattle or swine manure was added and the plots were then either disked or maintained in a no-till condition. Three 30 min simulated rainfall events, separated by …

Comparison Of Lipid Extraction Methods Of Food-Grade Sorghum (Sorghum Bicolor) Using Hexane, K. L. Christiansen, Curtis L. Weller, V. L. Schlegel, I. M. Dweikat

Department of Biological Systems Engineering: Papers and Publications

Much has been reported concerning sorghum phytochemicals, such as policosanols, but little literature exists on how various extraction methods might be used to optimize the recovery of such phytochemicals. The purpose of this study was to compare three extraction methods for recovery of different sorghum lipids. Lipids were extracted from whole kernel and ground Macia, a food-grade sorghum hybrid, with hexane by a Soxtec method, a refluxing method (RB), and a bench-scale recirculated solvent (RC) method. Comparisons of total lipid yield and lipid class yields extracted from the grain by each method were made. Total lipid yield for the three …

A Novel Ecological Role Of The Firmicutes Identified In Thermophilic Microbial Fuel Cells, Kelly C. Wrighton, Peter Agbo, Falk Warnecke, Karrie A. Weber, Eoin L. Brodie, Todd Z. Desantis, Philip Hugenholtz, Gary L. Andersen, John D. Coates

School of Biological Sciences: Faculty Publications

Significant effort is currently focused on microbial fuel cells (MFCs) as a source of renewable energy. Most studies concentrate on operation at mesophilic temperatures. However, anaerobic digestion studies have reported on the superiority of thermophilic operation and demonstrated a net energy gain in terms of methane yield. As such, our studies focused on MFC operation and microbiology at 55 °C. Over a 100-day operation, these MFCs were stable and achieved a power density of 37mW m^–2 with a coulombic efficiency of 89%. To infer activity and taxonomic identity of dominant members of the electricity-producing community, we performed phylogenetic microarray …

Bovine Herpesvirus Type 1 Induces Cell Death By A Cell Type Dependent Fashion, Vicki Geiser, Suzanne Rose, Clinton J. Jones

School of Veterinary and Biomedical Sciences: Faculty Publications

Bovine herpesvirus 1 (BHV-1), a member of the alpha-herpesvirinae subfamily, causes significant losses to the cattle industry. BHV-1 establishes latency in trigeminal ganglionic sensory neurons, but periodically reactivates from latency. Previous studies suggested that infection with BHV-1 induced novel morphological changes in rabbit skin cells (RS) versus bovine kidney cells (MDBK). Consequently, we hypothesized that viral infection led to a novel form of cell death in RS cells compared to MDBK cells. To test this hypothesis, we examined the levels of apoptosis in these cell types following infection with BHV-1. Infection of RS, but not MDBK, cells leads to high …

A Review Of The Biology Of Bovine Herpesvirus Type 1 (Bhv-I), Its Role As A Cofactor In The Bovine Respiratory Disease Complex And Development Of Improved Vaccines, Clinton J. Jones, Shafiqul Chowdhury

School of Veterinary and Biomedical Sciences: Faculty Publications

Infection of cattle by bovine herpesvirus type 1 (BHV-1) can lead to upper respiratory tract disorders, conjunctivitis, genital disorders and immune suppression. BHV-1-induced immune suppression initiates bovine respiratory disease complex (BRDC), which costs the US cattle industry approximately 3 billion dollars annually. BHV-1 encodes at least three proteins that can inhibit specific arms of the immune system: (i) bICPO inhibits interferon-dependent transcription, (ii) the UL41.5 protein inhibits CD8⁺ T-cell recognition of infected cells by preventing trafficking of viral peptides to the surface of the cells and (iii) glycoprotein G is a chemokine-binding protein that prevents homing of lymphocytes to …

How Does Age Affect Baseline Screening Mammography Performance Measures? A Decision Model, James Keen, John D. Keen

School of Veterinary and Biomedical Sciences: Faculty Publications

Background: In order to promote consumer-oriented informed medical decision-making regarding screening mammography, we created a decision model to predict the age dependence of the cancer detection rate, the recall rate and the secondary performance measures (positive predictive values, total intervention rate, and positive biopsy fraction) for a baseline mammogram.
Methods: We constructed a decision tree to model the possible outcomes of a baseline screening mammogram in women ages 35 to 65. We compared the single baseline screening mammogram decision with the no screening alternative. We used the Surveillance Epidemiology and End Results national cancer database as the primary input to …

Arabidopsis Drb4, Ago1, Ago7, And Rdr6 Participate In A Dcl4-Initiated Antiviral Rna Silencing Pathway Negatively Regulated By Dcl1, Feng Qu, Xiaohong Ye, Thomas Jack Morris

School of Biological Sciences: Faculty Publications

Plant RNA silencing machinery enlists four primary classes of proteins to achieve sequence-specific regulation of gene expression and mount an antiviral defense. These include Dicer-like ribonucleases (DCLs), Argonaute proteins (AGOs), dsRNA-binding proteins (DRBs), and RNA-dependent RNA polymerases (RDRs). Although at least four distinct endogenous RNA silencing pathways have been thoroughly characterized, a detailed understanding of the antiviral RNA silencing pathway is just emerging. In this report, we have examined the role of four DCLs, two AGOs, one DRB, and one RDR in controlling viral RNA accumulation in infected Arabidopsis plants by using a mutant virus lacking its silencing suppressor. Our …

Analysis Of Wnt Signaling During Caenorhabditis Elegans Postembryonic Development, Samantha Van Hoffelen, Michael A. Herman

School of Biological Sciences: Faculty Publications

Wnts play a central role in the development of many cells and tissue types in all species studied to date. Like many other extracellular signaling pathways, secreted Wnt proteins are involved in many different processes; in C. elegans these include cell proliferation, differentiation, cell migration, control of cell polarity, axon outgrowth, and control of the stem cell niche. Perturbations in Wnt signaling are also key factors in cancer formation, and therefore of interest to oncobiologists. Wnts are secreted glycoproteins, which bind to Frizzled transmembrane receptors and signal either through, or independently of β-catenin. Both β-catenin-dependent (Wnt/β-catenin) and -independent pathways function …

Chemical And Sensory Properties Of Beef Of Known Source And Finished On Wet Distillers Grains Diets Containing Varying Types And Levels Of Roughage, B. E. Jenschke, Joshua R. Benton, Chris R. Calkins, Timothy P. Carr, Kent M. Eskridge, Terry Klopfenstein, Galen E. Erickson

Department of Animal Science: Faculty Publications

Beef knuckles (n = 160) were obtained from source-verified cattle finished on 30% wet distillers grains plus solubles enriched with varying levels of alfalfa hay (4 or 8%), corn silage (6 or 12%), or corn stalks (3 or 6%) based on NDF. Proximate analysis, pH, oxidation-reduction potential, fatty acid composition, and sensory analysis were conducted on the rectus femoris muscle to determine if roughage inclusion, in conjunction with wet distillers grains plus solubles and cattle source, affects beef flavor with particular interest in liver-like off-flavor. Proximate analysis, fat content, and oxidation-reduction potential were unaffected (P ≥ 0.129) by diet or …

Primary Neuron/Astrocyte Co-Culture On Polyelectrolyte Multilayer Films: A Template For Studying Astrocyte-Mediated Oxidative Stress In Neurons, Srivatsan Kidambi, Ilsoon Lee, Christina Chan

Department of Chemical and Biomolecular Engineering: Faculty Publications

We engineered patterned co-cultures of primary neurons and astrocytes on polyelectrolyte multilayer (PEM) films without the aid of adhesive proteins/ligands to study the oxidative stress mediated by astrocytes on neuronal cells. A number of studies have explored engineering co-culture of neurons and astrocytes predominantly using cell lines rather than primary cells owing to the difficulties involved in attaching primary cells onto synthetic surfaces. To our knowledge this is the first demonstration of patterned co-culture of primary neurons and astrocytes for studying neuronal metabolism. In our study, we used synthetic polymers, namely poly(diallyldimethylammoniumchloride) (PDAC) and sulfonated poly(styrene) (SPS) as the polycation …

Tunable Resistive M-Dpeg Acid Patterns On Polyelectrolyte Multilayers At Physiological Conditions: Template For Directed Deposition Of Biomacromolecules, Srivatsan Kidambi, Christina Chan, Ilsoon Lee

Department of Chemical and Biomolecular Engineering: Faculty Publications

This paper describes a new class of salt-responsive poly(ethylene glycol) (PEG) self-assembled monolayers (SAMs) on top of polyelectrolyte multilayer (PEMs) films. PEM surfaces with poly(diallyldimethylammonium chloride) as the topmost layer are chemically patterned by microcontact printing (μCP) oligomeric PEG molecules with an activated carboxylic acid terminal group (m-dPEG acid). The resistive m-d-poly(ethylene glycol) (m-dPEG) acid molecules on the PEMs films were subsequently removed from the PEM surface with salt treatment, thus converting the nonadhesive surfaces into adhesive surfaces. The resistive PEG patterns facilitate the directed deposition of various macromolecules such as polymers, dyes, colloidal particles, proteins, liposomes, and nucleic acids. …

Cell Adhesion On Surfaces Of Varying Topographies, Ilsoon Lee, Christina Chan, Srivatsan Kidambi

Department of Chemical and Biomolecular Engineering: Faculty Publications

Micro-topography of a surface influences cell adhesion and proliferation. To improve adhesion, polyelectrolyte multilayers (PEMs) are built on patterned support layers to increase surface wettability, thereby improving attachment and spreading of the cells. Physical parameters, such as pattern size and pitch, in part, regulate cell adhesion and proliferation. Varying the surface topography provides a method to influence cell attachment and proliferation for tissue engineering applications.

Evolution Of Set-Domain Protein Families In The Unicellular And Multicellular Ascomycota Fungi, Chendhore Veerappan, Zoya Avramova, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Background: The evolution of multicellularity is accompanied by the occurrence of differentiated tissues, of organismal developmental programs, and of mechanisms keeping the balance between proliferation and differentiation. Initially, the SET-domain proteins were associated exclusively with regulation of developmental genes in metazoa. However, finding of SET-domain genes in the unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that SET-domain proteins regulate a much broader variety of biological programs. Intuitively, it is expected that the numbers, types, and biochemical specificity of SET-domain proteins of multicellular versus unicellular forms would reflect the differences in their biology. However, comparisons across the unicellular and multicellular …

Optimal Data Partitioning And A Test Case For Ray-Finned Fishes (Actinopterygii) Based On Ten Nuclear Loci, Chenhong Li, Guoqing Lu, Guillermo Ortí

School of Biological Sciences: Faculty Publications

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative …

Interspecific Demographic Trade-Offs And Soil-Related Habitat Associations Of Tree Species Along Resource Gradients, Sabrina E. Russo, Patrick Brown, Sylvester Tan, Stuart J. Davies

School of Biological Sciences: Faculty Publications

Summary

1. Interspecific relationships between fundamental demographic rates, often called demographic trade-offs, emerge from constraints within individuals related to morphology, physiology and resource allocation. Plant species that grow fast in high light usually have high mortality in shade, and this well-established relationship in part defines a species’ successional niche. More generally, this relationship represents a trade-off between a species’ ability to grow quickly to exploit abundant resources vs. avoiding mortality when resources are less plentiful, but few studies have described this demographic trade-off with respect to environmental factors other than light.

2. Using demographic data from 960 tree species in …

Analysis Of The N-Glycans Of Recombinant Human Factor Ix Purified From Transgenic Pig Milk, Geun-Cheol Gil, William H. Velander, Kevin E. Van Cott

Department of Chemical and Biomolecular Engineering: Faculty Publications

Glycosylation of recombinant proteins is of particular

importance because it can play significant roles in the

clinical properties of the glycoprotein. In this work, the

N-glycan structures of recombinant human Factor IX (tg-

FIX) produced in the transgenic pig mammary gland were

determined. Themajority of theN-glycans of transgenic pigderived

Factor IX (tg-FIX) are complex, bi-antennary with

one or two terminal N-acetylneuraminic acid (Neu5Ac) moieties.

We also found that the N-glycan structures of tg-FIX

produced in the porcine mammary epithelial cells differed

with respect to N-glycans from glycoproteins produced in

other porcine tissues. tg-FIX contains …

Numerical Simulation Of A Novel Blast Wave Mitigation Device, Zhenbi Su, Wen Peng, Zhaoyan Zhang, George Gogos, Reed Skaggs, Bryan Cheeseman

Department of Mechanical and Materials Engineering: Faculty Publications

This paper proposes a novel blast wave mitigation device, consisting of a piston–cylinder assembly. A shock wave is induced inside the device when it is subject to a blast wave. The shock wave propagates inside the device and is reflected repeatedly. The physical processes within the blast wave mitigation device are simulated numerically. Numerical predictions are in excellent agreement with analytical solutions for special cases of the investigated problem that are available in the literature. The peak pressure on the base of the device caused by the blast wave is studied using a number of design parameters. The numerical simulation …

Fabrication Of High Aspect Ratio Metal Nanotips By Nanosecond Pulse Laser Melting, Bo Cui, Lin Wu, Stephen Y. Chou

Department of Mechanical and Materials Engineering: Faculty Publications

The authors have developed an approach to fabricate sharp and high aspect ratio metal tips using nanosecond pulse laser melting. A quartz wafer covered with a thin chromium (Cr) film was placed on top of a second wafer with a sub-micrometer gap between them and the Cr film facing the second wafer. Then an excimer laser pulse (308 nm wavelength, 20 ns pulse duration) was shone from the back of the quartz wafer and melted the Cr film momentarily (several hundred nanoseconds). It is found that the molten Cr films can self-form discrete metal pillars connecting the two wafers. After …

Conduction In Rectangular Plates With Boundary Temperatures Specified, James V. Beck, Neil T. Wright, A. Haji-Sheikh, Kevin D. Cole, Donald E. Amos

Department of Mechanical and Materials Engineering: Faculty Publications

Steady-state components of heat conduction solutions may have very slowly convergent series for temperatures and non-convergent heat fluxes for temperature boundary conditions. Previous papers have proposed methods to remove these convergence problems. However, even more effective procedures based on insights of Morse and Feshbach are given herein. In some cases it is possible to replace poorly-convergent or non-convergent series by closed-form algebraic solutions. Examples are given.

A Slip Model For Rarefied Gas Flows At Arbitrary Knudsen Number, Lin Wu

Department of Mechanical and Materials Engineering: Faculty Publications

A slip model for wall bounded rarefied gas flows is derived from kinetic theory. A corresponding modified Reynolds lubrication equation is obtained from the slip velocity boundary conditions at walls for high Knudsen number gas flows. The slip model in a simplest form has predictions very close to the numerical solutions of linearized Boltzmann equation in the whole Knudsen number range, and is preferable to the widely applied 1st order (Maxwell slip model), 2nd order, and 1.5 order slip models.

Control Of The Nanoscale Crystallinity And Phase Separation In Polymer Solar Cells, Chih-Wei Chu, Hoichang Yang, Wei-Jen Hou, Jinsong Huang, Gang Li, Yang Yang

Department of Mechanical and Materials Engineering: Faculty Publications

Grazing-incidence x-ray diffraction and atomic force microscopy were performed on bulk heterojunction regioregular poly(3-hexylthiophene) (RR-P3HT) [6,6]-phenyl-C₇₁-butyric acid methyl esters spin-cast films with different film processing conditions to correlate the crystalline nanostructure of P3HT with the corresponding solar cell performance. The increase in long wavelength absorption for solvent annealed films is related to highly conjugated crystal structure of RR-P3HT phase-separated in the active layer. Upon thermal annealing, the solvent annealed 50-nm-thick device shows high solar cell performance with fill factor up to 73% and power conversion efficiency of 3.80%.

Low Reproductive Success Of Mallards In A Grassland-Dominated Landscape In The Sandhills Of Nebraska, Larkin A. Powell, Johann Walker, Zach Cunningham, Mark P. Vrtiska, Scott Stephens

School of Natural Resources: Faculty Publications

The Sandhills of Nebraska comprise approximately 5,000,000 ha of native grassland interspersed with numerous groundwater-fed wetlands. A substantial population of the mallard (Anas platyrhynchos) nests in this region. Previous investigations of nest survival probability of ducks in the Sandhills have estimated surprisingly low rates of nest survival for a grassland-dominated landscape. These investigations were conducted on public lands and most nest searching took place near wetlands where activity of nest predators might be highest. We predicted that mallards would nest at varying distances from wetlands and that survival probability of a representative sample of duck nests would increase with distance …

Meso-Scale Weather And Climate Observations In Kentucky For Societal Benefit, Rezaul Mahmood

School of Natural Resources: Faculty Publications

No abstract provided.

A Coupled Mm5-Noah And Surface Model-Based Assessment Of Sensitivity Of Planetary Boundary Layer Variables To Anomalous Soil Moisture Conditions, Rezaul Mahmood

School of Natural Resources: Faculty Publications

No abstract provided.