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University of Nebraska - Lincoln

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Articles 871 - 900 of 1371

Full-Text Articles in Bioresource and Agricultural Engineering

Sop For Pathway Inference In Integrated Microbial Genomes (Img), Iain Anderson, Amy Chen, Victor Markowitz, Nikos Kyrpides, Natalia Ivanova Jan 2011

Sop For Pathway Inference In Integrated Microbial Genomes (Img), Iain Anderson, Amy Chen, Victor Markowitz, Nikos Kyrpides, Natalia Ivanova

United States Department of Energy: Publications

One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG terms, which are organized into IMG pathways. Based on manual and automatic assignment of IMG terms, the presence or absence of IMG pathways is automatically inferred. The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown. In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding …

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Complete Genome Sequence Of The Cellulolytic Thermophile Clostridium Thermocellum Dsm1313, Lawrence Feinberg, Justine Foden, Trisha Barrett, Karen Walston Davenport, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Alla Lapidus, Susan Lucas, Jan-Fang Cheng, Samuel Pitluck, Tanja Woyke, Natalia Ivanova, Natalia Mikhailova, Miriam Land, Loren Hauser, D. Aaron Argyros, Lynne Goodwin, David Hogsett, Nicky Caiazza Jan 2011

Complete Genome Sequence Of The Cellulolytic Thermophile Clostridium Thermocellum Dsm1313, Lawrence Feinberg, Justine Foden, Trisha Barrett, Karen Walston Davenport, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Alla Lapidus, Susan Lucas, Jan-Fang Cheng, Samuel Pitluck, Tanja Woyke, Natalia Ivanova, Natalia Mikhailova, Miriam Land, Loren Hauser, D. Aaron Argyros, Lynne Goodwin, David Hogsett, Nicky Caiazza

United States Department of Energy: Publications

Clostridium thermocellum DSM1313 is a thermophilic, anaerobic bacterium with some of the highest rates of cellulose hydrolysis reported. The complete genome sequence reveals a suite of carbohydrate-active enzymes and demonstrates a level of diversity at the species level distinguishing it from the type strain ATCC 27405.

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Img/M: The Integrated Metagenome Data Management And Comparative Analysis System, Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides Jan 2011

Img/M: The Integrated Metagenome Data Management And Comparative Analysis System, Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides

United States Department of Energy: Publications

The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context. IMG/M integrates metagenome data sets with isolate microbial genomes from the IMG system. IMG/M’s data content and analytical capabilities have been extended through regular updates since its first release in 2007. IMG/M is available at http://img.jgi.doe.gov/m. A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER: http://img.jgi.doe.gov/mer).

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Complete Genome Sequence Of Lactobacillus Buchneri Nrrl B-30929, A Novel Strain From A Commercial Ethanol Plant, Siqing Liu, Timothy D. Leathers, Alex Copeland, Olga Chertkov, Lynne Goodwin, David A. Mills Jan 2011

Complete Genome Sequence Of Lactobacillus Buchneri Nrrl B-30929, A Novel Strain From A Commercial Ethanol Plant, Siqing Liu, Timothy D. Leathers, Alex Copeland, Olga Chertkov, Lynne Goodwin, David A. Mills

United States Department of Energy: Publications

Lactobacillus buchneri strain NRRL B-30929 was a contaminant obtained from a commercial ethanol fermentation. This facultative anaerobe is unique because of its rapid growth on xylose and simultaneous fermentation of xylose and glucose. The strain utilizes a broad range of carbohydrate substrates and possesses a high tolerance to ethanol and other stresses, making it an attractive candidate for bioconversion of biomass substrates to various bioproducts. The genome sequence of NRRL B-30929 will provide insight into the unique properties of this lactic acid bacterium.

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Vista Region Viewer (Rviewer)—A Computational System For Prioritizing Genomic Intervals For Biomedical Studies, Igor Lukashin, Pavel Novichkov, Dario Boffelli, Alex R. Paciorkowski, Simon Minovitsky, Song Yang, Inna Dubchak Jan 2011

Vista Region Viewer (Rviewer)—A Computational System For Prioritizing Genomic Intervals For Biomedical Studies, Igor Lukashin, Pavel Novichkov, Dario Boffelli, Alex R. Paciorkowski, Simon Minovitsky, Song Yang, Inna Dubchak

United States Department of Energy: Publications

Summary:
Current genome browsers are designed for linear browsing of individual genomic regions, but the high-throughput nature of experiments aiming to elucidate the genetic component of human disease makes it very important to develop user-friendly tools for comparing several genomic regions in parallel and prioritizing them based on their functional content. We introduce VISTA Region Viewer (RViewer), an interactive online tool that allows for efficient screening and prioritization of regions of the human genome for follow-up studies. The tool takes as input genetic variation data from different biomedical studies, determines a number of various functional parameters for both coding …

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Complete Genome Sequence Of The Plant Growth-Promoting Endophyte Burkholderia Phytofirmans Strain Psjn, Alexandra Weilharter, Birgit Mitter, Maria V. Shin, Patrick S. G. Chain, Jerzy Nowak, Angela Sessitsch Jan 2011

Complete Genome Sequence Of The Plant Growth-Promoting Endophyte Burkholderia Phytofirmans Strain Psjn, Alexandra Weilharter, Birgit Mitter, Maria V. Shin, Patrick S. G. Chain, Jerzy Nowak, Angela Sessitsch

United States Department of Energy: Publications

Burkholderia phytofirmans PsJNT is able to efficiently colonize the rhizosphere, root, and above-ground plant tissues of a wide variety of genetically unrelated plants, such as potatoes, canola, maize, and grapevines. Strain PsJN shows strong plant growth-promoting effects and was reported to enhance plant vigor and resistance to biotic and abiotic stresses. Here, we report the genome sequence of this strain, which indicates the presence of multiple traits relevant for endophytic colonization and plant growth promotion.

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Characterization Of The Intragranular Water Regime Within Subsurface Sediments: Pore Volume, Surface Area, And Mass Transfer Limitations, Michael B. Hay, Deborah L. Stoliker, James A. Davis, John M. Zachara Jan 2011

Characterization Of The Intragranular Water Regime Within Subsurface Sediments: Pore Volume, Surface Area, And Mass Transfer Limitations, Michael B. Hay, Deborah L. Stoliker, James A. Davis, John M. Zachara

United States Department of Energy: Publications

Although ‘‘intragranular’’ pore space within grain aggregates, grain fractures, and mineral surface coatings may contain a relatively small fraction of the total porosity within a porous medium, it often contains a significant fraction of the reactive surface area, and can thus strongly affect the transport of sorbing solutes. In this work, we demonstrate a batch experiment procedure using tritiated water as a high-resolution diffusive tracer to characterize the intragranular pore space. The method was tested using uranium contaminated sediments from the vadose and capillary fringe zones beneath the former 300A process ponds at the Hanford site (Washington). Sediments were contacted …

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Multispecies Diffusion Models: A Study Of Uranyl Species Diffusion, Chongxuan Liu, Jianying Shang, John M. Zachara Jan 2011

Multispecies Diffusion Models: A Study Of Uranyl Species Diffusion, Chongxuan Liu, Jianying Shang, John M. Zachara

United States Department of Energy: Publications

Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found …

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Transient Groundwater Chemistry Near A River: Effects On U(Vi) Transport In Laboratory Column Experiments, Jun Yin, Roy Haggerty, Deborah L. Stoliker, Douglas B. Kent, Jonathan D. Istok, Janek Greskowiak, John M. Zachara Jan 2011

Transient Groundwater Chemistry Near A River: Effects On U(Vi) Transport In Laboratory Column Experiments, Jun Yin, Roy Haggerty, Deborah L. Stoliker, Douglas B. Kent, Jonathan D. Istok, Janek Greskowiak, John M. Zachara

United States Department of Energy: Publications

In the 300 Area of a U(VI)-contaminated aquifer at Hanford, Washington, USA, inorganic carbon and major cations, which have large impacts on U(VI) transport, change on an hourly and seasonal basis near the Columbia River. Batch and column experiments were conducted to investigate the factors controlling U(VI) adsorption/desorption by changing chemical conditions over time. Low alkalinity and low Ca concentrations (Columbia River water) enhanced adsorption and reduced aqueous concentrations. Conversely, high alkalinity and high Ca concentrations (Hanford groundwater) reduced adsorption and increased aqueous concentrations of U(VI). An equilibrium surface complexation model calibrated using laboratory batch experiments accounted for the decrease …

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Simulating Adsorption Of U(Vi) Under Transient Groundwater Flow And Hydrochemistry: Physical Versus Chemical Nonequilibrium Model, Janek Greskowiak, Michael Hay, Henning Prommer, Chongxuan Liu, Vincent Post, Rui Ma, James Davis, Chunmiao Zheng, John M. Zachara Jan 2011

Simulating Adsorption Of U(Vi) Under Transient Groundwater Flow And Hydrochemistry: Physical Versus Chemical Nonequilibrium Model, Janek Greskowiak, Michael Hay, Henning Prommer, Chongxuan Liu, Vincent Post, Rui Ma, James Davis, Chunmiao Zheng, John M. Zachara

United States Department of Energy: Publications

Coupled intragrain diffusional mass transfer and nonlinear surface complexation processes play an important role in the transport behavior of U(VI) in contaminated aquifers. Two alternative model approaches for simulating these coupled processes were analyzed and compared: (1) the physical nonequilibrium approach that explicitly accounts for aqueous speciation and instantaneous surface complexation reactions in the intragrain regions and approximates the diffusive mass exchange between the immobile intragrain pore water and the advective pore water as multirate first-order mass transfer and (2) the chemical nonequilibrium approach that approximates the diffusion-limited intragrain surface complexation reactions by a set of multiple first-order surface complexation …

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Transition Of Cellulose Crystalline Structure And Surface Morphology Of Biomass As A Function Of Ionic Liquid Pretreatment And Its Relation To Enzymatic Hydrolysis, Gang Cheng, Patanjali Varanasi, Chenlin Li, Hanbin Liu, Yuri B. Melnichenko, Blake A. Simmons, Michael S. Kent, Seema Singh Jan 2011

Transition Of Cellulose Crystalline Structure And Surface Morphology Of Biomass As A Function Of Ionic Liquid Pretreatment And Its Relation To Enzymatic Hydrolysis, Gang Cheng, Patanjali Varanasi, Chenlin Li, Hanbin Liu, Yuri B. Melnichenko, Blake A. Simmons, Michael S. Kent, Seema Singh

United States Department of Energy: Publications

Cellulose is inherently resistant to breakdown, and the native crystalline structure (cellulose I) of cellulose is considered to be one of themajor factors limiting its potential in terms of cost-competitive lignocellulosic biofuel production. Here we report the impact of ionic liquid pretreatment on the cellulose crystalline structure in different feedstocks, including microcrystalline cellulose (Avicel), switchgrass (Panicum virgatum), pine (Pinus radiata), and eucalyptus (Eucalyptus globulus), and its influence on cellulose hydrolysis kinetics of the resultant biomass. These feedstocks were pretreated using 1-ethyl-3-methyl imidazolium acetate ([C2mim][OAc]) at 120 and 160°C for 1, 3, 6, and 12 …

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Absolute High-Resolution Se+ Photoionization Cross-Section Measurements With Rydberg-Series Analysis, D. A. Esteves, R. C. Bilodeau, N. C. Sterling, R. A. Phaneuf, A. L. D. Kilcoyne, E. C. Red, A. Aguilar Jan 2011

Absolute High-Resolution Se+ Photoionization Cross-Section Measurements With Rydberg-Series Analysis, D. A. Esteves, R. C. Bilodeau, N. C. Sterling, R. A. Phaneuf, A. L. D. Kilcoyne, E. C. Red, A. Aguilar

United States Department of Energy: Publications

Absolute single photoionization cross-section measurements for Se+ ions were performed at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory using the photo-ion merged-beams technique. Measurements were made at a photon energy resolution of 5.5 meV from 17.75 to 21.85 eV spanning the 4s24p34So3/2 ground-state ionization threshold and the 2Po3/2,2Po1/2,2Do5/2, and2Do3/2 metastable state thresholds. Extensive analysis of the complex resonant structure in this region identified numerous Rydberg series of resonances and …

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Photoionization Measurements For The Iron Isonuclear Sequence Fe3+, Fe5+, And Fe7+, M. F. Gharaibeh, A. Aguilar, A. M. Covington, E. D. Emmons, S. W. J. Scully, R. A. Phaneuf, A. Muller, J. D. Bozek, A. L. D. Kilcoyne, A. S. Schlachter, I. Alvarez, C. Cisneros, G. Hinojosa Jan 2011

Photoionization Measurements For The Iron Isonuclear Sequence Fe3+, Fe5+, And Fe7+, M. F. Gharaibeh, A. Aguilar, A. M. Covington, E. D. Emmons, S. W. J. Scully, R. A. Phaneuf, A. Muller, J. D. Bozek, A. L. D. Kilcoyne, A. S. Schlachter, I. Alvarez, C. Cisneros, G. Hinojosa

United States Department of Energy: Publications

Cross sections for single photoionization of Fe3+, Fe5+, and Fe7+ ions were measured at spectral resolutions of 0.04, 0.15, and 0.13 eV, respectively, by merging mass- and charge-selected ion beams with a beam of monochromatized synchrotron undulator radiation. The measurements span photon energy ranges beginning at the ionization thresholds and extending several tens of electron volts to include the most important resonant contributions due to 3p–nd transitions to autoionizing states. The photoion yield spectra are characterized by narrow resonances and also broad features in Fe3+ and Fe5+ that are believed to result …

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An Approach To Crystallizing Proteins By Metal-Mediated Synthetic Symmetrization, Arthur Laganowsky, Minglei Zhao, Angela B. Soriaga, Michael R. Sawaya, Duilio Cascio, Todd O. Yeates Jan 2011

An Approach To Crystallizing Proteins By Metal-Mediated Synthetic Symmetrization, Arthur Laganowsky, Minglei Zhao, Angela B. Soriaga, Michael R. Sawaya, Duilio Cascio, Todd O. Yeates

United States Department of Energy: Publications

Combining the concepts of synthetic symmetrization with the approach of engineering metal-binding sites, we have developed a new crystallization methodology termed metal-mediated synthetic symmetrization. In this method, pairs of histidine or cysteine mutations are introduced on the surface of target proteins, generating crystal lattice contacts or oligomeric assemblies upon coordination with metal. Metal-mediated synthetic symmetrization greatly expands the packing and oligomeric assembly possibilities of target proteins, thereby increasing the chances of growing diffraction-quality crystals. To demonstrate this method, we designed various T4 lysozyme (T4L) and maltose-binding protein (MBP) mutants and cocrystallized them with one of three metal ions: copper (Cu …

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Modification Of Native Grasses For Biofuel Production May Increase Virus Susceptibility, Abbie C. Schrotenboer, Michael S. Allen, Carolyn M. Malmstrom Jan 2011

Modification Of Native Grasses For Biofuel Production May Increase Virus Susceptibility, Abbie C. Schrotenboer, Michael S. Allen, Carolyn M. Malmstrom

United States Department of Energy: Publications

Bioenergy production is driving modifications to native plant species for use as novel biofuel crops. Key aims are to increase crop growth rates and to enhance conversion efficiency by reducing biomass recalcitrance to digestion. However, selection for these biofuel-valuable traits has potential to compromise plant defenses and alter interactions with pests and pathogens. Insect-vectored plant viruses are of particular concern because perennial crops have potential to serve as virus reservoirs that influence regional disease dynamics. In this study, we examined relationships between growth rates and biomass recalcitrance in five switchgrass (Panicum virgatum) populations, ranging from near wild type …

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2011 Nebraska Water Monitoring Programs Report, Marty Link Jan 2011

2011 Nebraska Water Monitoring Programs Report, Marty Link

Nebraska Department of Environmental Quality: Reports

The Nebraska Department of Environmental Quality (NDEQ) is charged with monitoring, assessing, and to the extent possible, managing the state’s water resources. The purpose of this work is to protect and maintain good quality water and encourage or execute activities to improve poor water quality. Monitoring is done on the over 18,000 miles of flowing rivers and streams, our greater than 280,000 acres of surface water in lakes and reservoirs, and the vast storage of groundwater in Nebraska’s aquifers.

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Charge And Fluence Lifetime Measurements Of A Dc High Voltage Gaas Photogun At High Average Current, J. Grames, R. Suleiman, P. A. Adderley, J. Clark, J. Hansknecht, D. Machie, M. Poelker, M. L. Stutzman Jan 2011

Charge And Fluence Lifetime Measurements Of A Dc High Voltage Gaas Photogun At High Average Current, J. Grames, R. Suleiman, P. A. Adderley, J. Clark, J. Hansknecht, D. Machie, M. Poelker, M. L. Stutzman

United States Department of Energy: Publications

GaAs-based dc high voltage photoguns used at accelerators with extensive user programs must exhibit long photocathode operating lifetime. Achieving this goal represents a significant challenge for proposed high average current facilities that must operate at tens of milliamperes or more. This paper describes techniques to maintain good vacuum while delivering beam, and techniques that minimize the ill effects of ion bombardment, the dominant mechanism that reduces photocathode yield of a GaAs-based dc high voltage photogun. Experimental results presented here demonstrate enhanced lifetime at high beam currents by: (a) operating with the drive laser beam positioned away from the electrostatic center …

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Glypican-3 Targeting Of Liver Cancer Cells Using Multifunctional Nanoparticles, James O. Park, Zachary Stephen, Conory Sun, Omid Veiseh, Forrest M. Kievit, Chen Fang, Matthew Leung, Hyejung Mok, Miqin Zhang Jan 2011

Glypican-3 Targeting Of Liver Cancer Cells Using Multifunctional Nanoparticles, James O. Park, Zachary Stephen, Conory Sun, Omid Veiseh, Forrest M. Kievit, Chen Fang, Matthew Leung, Hyejung Mok, Miqin Zhang

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Imaging is essential in accurately detecting, staging, and treating primary liver cancer (hepatocellular carcinoma [HCC]), one of the most prevalent and lethal malignancies. We developed a novel multifunctional nanoparticle (NP) specifically targeting glypican-3 (GPC3), a proteoglycan implicated in promotion of cell growth that is overexpressed in most HCCs. Quantitative real-time polymerase chain reaction was performed to confirm the differential GPC3 expression in two human HCC cells, Hep G2 (high) and HLF (negligible). These cells were treated with biotin-conjugated GPC3 monoclonal antibody (aGPC3) and subsequently targeted using superparamagnetic iron oxide NPs conjugated to streptavidin and Alexa Fluor 647. Flow cytometry demonstrated …

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Magnetite Nanoparticles For Medical Mr Imaging, Zachary R. Stephen, Forrest M. Kievit, Miqin Zhang Jan 2011

Magnetite Nanoparticles For Medical Mr Imaging, Zachary R. Stephen, Forrest M. Kievit, Miqin Zhang

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Magnetic resonance imaging (MRI) has become one of the most widely used and powerful tools for non-invasive clinical diagnosis due to its high soft tissue contrast, spatial resolution, and penetration depth1. In addition, images are acquired without the use of ionizing radiation or radiotracers that would cause unwanted harmful side-effects. A considerable amount of research in medical MR imaging is focused on the development of contrast agents that can provide better delineation between healthy and diseased tissue. Magnetic nanoparticles (MNPs) are a major class of nanoscale material currently under extensive development for improved diagnosis of a wide range of diseases, …

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Biological Approaches For Addressing The Grand Challenge Of Providing Access To Clean Drinking Water, Mark R. Riley, Charles P. Gerba, Menachem Elimelech Jan 2011

Biological Approaches For Addressing The Grand Challenge Of Providing Access To Clean Drinking Water, Mark R. Riley, Charles P. Gerba, Menachem Elimelech

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The U.S. National Academy of Engineering (NAE) recently published a document presenting “Grand Challenges for Engineering”. This list was proposed by leading engineers and scientists from around the world at the request of the U.S. National Science Foundation (NSF). Fourteen topics were selected for these grand challenges, and at least seven can be addressed using the tools and methods of biological engineering. Here we describe how biological engineers can address the challenge of providing access to clean drinking water. This issue must be addressed in part by removing or inactivating microbial and chemical contaminants in order to properly deliver water …

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Detection And Quantification Of Poliovirus Infection Using Ftir Spectroscopy And Cell Culture, Felipe T. Lee-Montiel, Kelly A. Reynolds, Mark R. Riley Jan 2011

Detection And Quantification Of Poliovirus Infection Using Ftir Spectroscopy And Cell Culture, Felipe T. Lee-Montiel, Kelly A. Reynolds, Mark R. Riley

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Background: In a globalized word, prevention of infectious diseases is a major challenge. Rapid detection of viable virus particles in water and other environmental samples is essential to public health risk assessment, homeland security and environmental protection. Current virus detection methods, especially assessing viral infectivity, are complex and time-consuming, making point-of-care detection a challenge. Faster, more sensitive, highly specific methods are needed to quantify potentially hazardous viral pathogens and to determine if suspected materials contain viable viral particles. Fourier transform infrared (FTIR) spectroscopy combined with cellular-based sensing, may offer a precise way to detect specific viruses. This approach utilizes infrared …

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Development Of An Angular Scanning System For Sensing Vertical Profiles Of Soil Electrical Conductivity, Viacheslav Adamchuk, Ahmad S. Mat Su, Roger A. Eigenberg, Richard B. Ferguson Jan 2011

Development Of An Angular Scanning System For Sensing Vertical Profiles Of Soil Electrical Conductivity, Viacheslav Adamchuk, Ahmad S. Mat Su, Roger A. Eigenberg, Richard B. Ferguson

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Apparent soil electrical conductivity (ECa) is typically mapped to define soil spatial variability within an agricultural field. Knowledge of the vertical variability of ECa is desired to define the site‐specific behavior of the soil profile. A pneumatic angular scanning system (PASS) was developed to sense horizontal and vertical changes of ECa on‐the‐go with an electromagnetic induction (EMI) instrument using an angular scanning method. This sensor system consists of a sled with a rotating mechanism, an EMI sensor, an inclinometer, and a pneumatic actuator. The system was evaluated at the University of Nebraska‐Lincoln Agricultural Research and Development …

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Identification Of Holocarboxylase Synthetase Chromatin Binding Sites In Human Mammary Cell Lines Using The Damid Technology, Dipika Singh, Angela K. Pannier, Janos Zempleni Jan 2011

Identification Of Holocarboxylase Synthetase Chromatin Binding Sites In Human Mammary Cell Lines Using The Damid Technology, Dipika Singh, Angela K. Pannier, Janos Zempleni

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Holocarboxylase synthetase (HCS) is a chromatin protein that is essential for mediating the covalent binding of biotin to histones. Biotinylation of histones plays crucial roles in the repression of genes and repeats in the human genome. We tested the feasibility of DNA adenine methyltransferase identification (DamID) technology to map HCS binding sites in human mammary cell lines. Full-length HCS was fused to Dam for subsequent transfection into breast cancer (MCF-7) and normal breast (MCF-10A) cells. HCS docking sites in chromatin were identified by using the unique adenine methylation sites established by Dam in the fusion construct; docking sites were unambiguously …

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Cellular Arrays For Large-Scale Analysis Of Transcription Factor Activity, Abigail D. Bellis, Beatriz Peňalver-Bernabé, Michael S. Weiss, Michael E. Yarrington, Maria V. Barbolina, Angela K. Pannier, Jacqueline S. Jeruss, Linda J. Broadbelt, Lonnie D. Shea Jan 2011

Cellular Arrays For Large-Scale Analysis Of Transcription Factor Activity, Abigail D. Bellis, Beatriz Peňalver-Bernabé, Michael S. Weiss, Michael E. Yarrington, Maria V. Barbolina, Angela K. Pannier, Jacqueline S. Jeruss, Linda J. Broadbelt, Lonnie D. Shea

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Identifying molecular mechanisms or therapeutic targets is typically based on large-scale cellular analysis that measures the abundance of mRNA or protein; however, abundance does not necessarily correlate with activity. We report a method for direct large-scale quantification of active pathways that employs a cellular array with parallel gene delivery of constructs that report pathway activity. The reporter constructs encode luciferase, whose expression is influenced by binding of transcription factors (TFs), which are the downstream targets of signaling pathways. Luciferase levels are quantified by bioluminescence imaging (BLI), which allows for rapid, noninvasive measurements. Activity profiles by BLI of 32 TFs were …

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Microarray Analysis Of Gene Expression Profiles In Cells Transfected With Nonviral Vectors, Sarah A. Plautz, Gina Boanca, Jean-Jack M. Riethoven, Angela K. Pannier Jan 2011

Microarray Analysis Of Gene Expression Profiles In Cells Transfected With Nonviral Vectors, Sarah A. Plautz, Gina Boanca, Jean-Jack M. Riethoven, Angela K. Pannier

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Inefficient gene delivery is a critical factor limiting the use of nonviral methods in therapeutic applications including gene therapy and tissue engineering. There have been few efforts to understand or engineer the molecular signaling pathways that dictate the efficacy of gene transfer. Microarray analysis was used to determine endogenous gene expression profiles modulated during nonviral gene transfer. Nonviral DNA lipoplexes were delivered to HEK 293T cells. Flow cytometry was used to isolate a population of transfected cells. Expression patterns were compared between transfected and nontransfected samples, which revealed three genes that were significantly upregulated in transfected cells, including RAP1A, …

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Flocculation Of Wall-Deficient Cells Of Chlamydomonas Reinhardtii Mutant Cw15 By Calcium And Methanol, Matt Scholz, Takanori Hoshino, Mark R. Riley, Joel Cuello Jan 2011

Flocculation Of Wall-Deficient Cells Of Chlamydomonas Reinhardtii Mutant Cw15 By Calcium And Methanol, Matt Scholz, Takanori Hoshino, Mark R. Riley, Joel Cuello

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Flocculation is a common and inexpensive method for harvesting algae from solution. After nitrogen starvation, it was shown that 83 + 3% of the wall-deficient cells of the cw 15 mutant of Chlamydomonas reinhardtii flocculated from 12 mL samples within 15 min after the addition of 15 mM calcium chloride at pH 8.4. Only 24 2% of the wildtype strain flocculated under these conditions, thus demonstrating how a simple mutation might facilitate process design. The data suggested that algae grown in waters with similar calcium concentrations (e.g. certain wastewaters) might be harvested through simple pH adjustment. It was also discovered …

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Performance Of Extended Shuttleworth‐Wallace Model For Estimating And Partitioning Of Evapotranspiration In A Partial Residue‐Covered Subsurface Drip‐Irrigated Soybean Field, Lameck O. Odhiambo, Suat Irmak Jan 2011

Performance Of Extended Shuttleworth‐Wallace Model For Estimating And Partitioning Of Evapotranspiration In A Partial Residue‐Covered Subsurface Drip‐Irrigated Soybean Field, Lameck O. Odhiambo, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Estimation of actual evapotranspiration (ET), especially its partitioning into plant transpiration (T) and soil evaporation (E), in agricultural fields is important for effective soil water management and conservation and for understanding the interactions between ET, T, and E with the management practices. Direct field measurements of ET, T, and E rates are difficult and costly; hence, mathematical models are used for estimating them. The objective of this study was to evaluate the practical applicability of the Shuttleworth‐Wallace (S‐W) model to estimate and partition ET in a subsurface drip‐irrigated soybean (Glycine max L. Merr.) field with partial residue cover. While its …

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Focused Ion Beam Patterned Fe Thin Films: A Study By Selective Area Stokes Polarimetry And Soft X-Ray Microscopy, P. J. Cook, T. H. Shen, P. J. Grundy, M.-Y. Im, P. Fischer, S. A. Morton, A. L. D. Kilcoyne Jan 2011

Focused Ion Beam Patterned Fe Thin Films: A Study By Selective Area Stokes Polarimetry And Soft X-Ray Microscopy, P. J. Cook, T. H. Shen, P. J. Grundy, M.-Y. Im, P. Fischer, S. A. Morton, A. L. D. Kilcoyne

United States Department of Energy: Publications

A combination of analytical techniques, with special emphasis on selective area Stokes polarimetry, has been used to explore the structural properties and magnetic behavior of focused ion beam patterned Fe thin films under controlled Ga+ ion irradiation. Ion irradiation at doses ranging from 7.7×1015 to 5.2×1016 Ga ions cm-2 did not noticeably alter the chemical properties of the Fe, but changes to the film structure and increased coercivity were observed even after the lowest doses. Magnetic transmission x-ray microscopy provided detailed information about the magnetization reversal process occurring within a patterned area of film comprising both …

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Error Analysis Of Large-Eddy Simulation Of The Turbulent Non-Premixed Sydney Bluff-Body Flame, A. M. Kempf, B. J. Geurts, J. C, Oefelein Jan 2011

Error Analysis Of Large-Eddy Simulation Of The Turbulent Non-Premixed Sydney Bluff-Body Flame, A. M. Kempf, B. J. Geurts, J. C, Oefelein

United States Department of Energy: Publications

A computational error analysis is applied to the large-eddy simulation of the turbulent non-premixed Sydney bluff-body flame, where the error is defined with respect to experimental data. The errorlandscape approach is extended to heterogeneous compressible turbulence, which is coupled to combustion as described by a flamelet model. The Smagorinsky model formulation is used to model the unknown turbulent stresses. We introduce several measures to quantify the total simulation error and observe a striking ‘valley-structure’ in the error that arises as function of the spatial resolution and the Smagorinsky length parameter. The optimal refinement strategy that can be extracted from this …

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Combining Power Plant Water Needs And Carbon Dioxide Storage Using Saline Formations: Implications For Carbon Dioxide And Water Management Policies, Peter Kobos, Malynda Cappelle, Jim Krumhansl, Thomas Dewers, Andrea Mcnemar, David Borns Jan 2011

Combining Power Plant Water Needs And Carbon Dioxide Storage Using Saline Formations: Implications For Carbon Dioxide And Water Management Policies, Peter Kobos, Malynda Cappelle, Jim Krumhansl, Thomas Dewers, Andrea Mcnemar, David Borns

United States Department of Energy: Publications

Research involving management of carbon dioxide has increased markedly over the last decade as it relates to concerns over climate change. Capturing and storing carbon dioxide (CO2) in geological formations is one of many proposed methods to manage, and likely reduce, CO2 emissions from burning fossil fuels in the electricity sector. Saline formations represent a vast storage resource, and the waters they contain could be managed for beneficial use. To address this issue, a methodology was developed to test the feasibility of linking coal-fired power plants, deep saline formations for CO2 storage, and extracting and treating …

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