Engineering Commons^™

Raman Multiplexers For Alternative Gene Splicing, Lan Sun, Chenxu Yu, Joseph Irudayaraj

Chenxu Yu

Nonfluorescent labels were used for an array-format multiplex detection of alternative splice junctions of breast cancer susceptibility gene 1 (BRCA1) by surface-enhanced Raman scattering (SERS). A four-plex detection scheme using nonfluorescent labels was demonstrated for DNA sequences specific to four BRCA1 alternative splice variants:  Δ(11q) (the last 3309 nt deleted from exon 11), Δ(9, 10) (exon 9 and 10 deleted), Δ(5) (exon 5 deleted), and Δ(5q, 6) (the last 22 nt of exon 5 and the entire exon 6 is deleted). This is the first proof-of-concept study to apply SERS-based detection using nonfluorescent labels to investigate alternative gene splicing. Detection …

Aquatic Bacteria Removal Using Carbon Nanotubes, Suvish Melanta

Biological and Agricultural Engineering Undergraduate Honors Theses

The purpose of this project is to explore the functionality of carbon nanotubes as a bacterial removal method, specifically towards water-borne bacterial pathogens in wastewater by utilizing its unique magnetic and bacteria-binding properties. The general protocol set for this research follows five steps: 1) Preparation of wastewater media, 2) preparation of CNT culture, 3) preparation of reaction mixture with CNTs for bacterial binding, 4) magnetic separation of bacteria-bound-CNT clusters and, 5) assessment of supernatant. The CNTs effectively removed bacterial contaminants in the wastewater (10%, v/v) after the sand filtration process from the Paul R. Noland Wastewater Facility at Fayetteville, Arkansas. …

Genome Sequencing And Analysis Of The Biomass-Degrading Fungus Trichoderma Reesei (Syn. Hypocrea Jecorina), Diego Martinez, Randy M. Berka, Bernard Henrissat, Markku Saloheimo, Mikko Arvas, Scott E. Baker, Jarod Chapman, Olga Chertkov, Pedro M. Coutinho, Dan Cullen, Etienne G. J. Danchin, Igor V. Grigoriev, Paul Harris, Melissa Jackson, Christian P. Kubicek, Cliff S. Han, Isaac Ho, Luis F. Larrondo, Alfredo Lopez De Leon, Jon K. Magnuson, Sandy Merino, Monica Misra, Beth Nelson, Nicholas Putnam, Barbara Robbertse, Asaf A. Salamov, Monika Schmoll, Astrid Terry, Nina Thayer, Ann Westerholm-Parvinen, Conrad L. Schoch, Jian Yao, Ravi Barabote, Mary Anne Nelson, Chris Detter, David Bruce, Cheryl R. Kuske, Gary Xie, Paul Richardson, Daniel S. Rokhsar, Susan M. Lucas, Edward M. Rubin, Nigel Dunn-Coleman, Michael Ward, Thomas Brettin

US Department of Energy Publications

Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in …

Implementing Mass Nutrient Balance Procedures On Swine Production Facilities, Richard Koelsch, Alan Sutton

Biological Systems Engineering: Papers and Publications

Whole Farm Nutrient Balance (WFNB) approaches have been used to provide a measure of environmental performance (Aarts et al., 1992; Lanyon and Beegle, 1993; Klausner, 1995). Whole farm balance concepts are used as part of the Netherlands Mineral Accounting System public policy that includes compulsory mineral input and output reports from livestock farms and levies for excess imbalances (Jongbloed and Lenis, 1998). Procedures for measuring WFNB will be followed in measurements made on commercial swine facilities for 2006 and 2007. The conclusions developed based upon data from 13 for 2006 include:

• On average, the participating swine producers import 1.5 units …

Modeling The Effects Of Value-Added Processing And Logistics Using Arena, Kurt A. Rosentrater, Elif Kongar

Kurt A. Rosentrater

Scarcity and cost of nonrenewable fossil fuels have been a growing focus of many energy-dependent nations, including the U.S., for the past couple of decades. There are mainly two ways to approach these problems: (1) reducing the energy dependency and/or (2) developing alternative means of energy production. Utilizing biofuels, which are renewable sources of energy, is a promising way to produce energy. But, as this industry grows, so too does the quantity of byproducts, which are known as DDGS. This paper discusses a model that has been developed to analyze the economic viability of DDGS processing, and includes both deterministic …

Diseño Y Construcción De Un Prototipo Piloto Para Un Sistema De Supervisión Y Control Semiautomático En La Fertiirrigación De Claveles En Cultivos Hidropónicos, Carlos Andrés Ostos Ramos, Omar Leonardo Vanegas Bernal

Ingeniería en Automatización

En los cultivos hidropónicos las unidades de producción como las plantas, en este caso, los claveles, se desarrollan al permanecer bajo condiciones óptimas, basándose en la utilización del agua y fertilizantes químicos para su nutrición. Existe un problema en cuanto a la fertiirrigación, por el suministro inadecuado de agua y nutrientes, lo que causa deshidratación o saturación en el sistema radicular del cultivo, debido a la ausencia de un método que mantenga y controle los niveles de abastecimiento en un punto ideal viéndose reflejado en pérdidas de la producción y a nivel económico. El prototipo piloto plantea una solución en …

Electric Motor Efficiency Under Variable Frequencies And Loads, Charles M. Burt, Xianshu Piao, Franklin Gaudi, Bryan Busch, N. F. N. Taufik

BioResource and Agricultural Engineering

This paper details a study performed by the Irrigation Training and Research Center to determine motor performances under varying speeds [induced by a variable frequency drives (VFD) controller] and loads. A further goal of the study was to provide sufficient information to designers so that they could estimate total pumping plant power usage with a VFD-controlled installation. Motors were tested with a VFD as well as across-the-line. On average, the relative efficiency of the electrical system with a VFD may be approximately 8% lower than the relative efficiency of a properly designed, full-load across-the-line system. If one considers actual field …

Effect Of Ddgs, Moisture Content, And Screw Speed On Physical Properties Of Extrudates In Single-Screw Extrusion, Nehru Chevanan, Kurt A. Rosentrater, Kasiviswanathan Muthukumarappan

Kurt A. Rosentrater

Three isocaloric (3.5 kcal/g) ingredient blends containing 20, 30, and 40% (wb) distillers dried grains with solubles (DDGS) along with soy flour, corn flour, fish meal, and mineral and vitamin mix, with net protein adjusted to 28% (wb) for all blends, were extruded in a single-screw laboratory-scale extruder at screw speeds of 100, 130, and 160 rpm, and 15, 20, and 25% (wb) moisture content. Increasing DDGS content from 20 to 40% resulted in a 37.1, 3.1, and 8.4% decrease in extrudate durability, specific gravity, and porosity, respectively, but a 7.5% increase in bulk density. Increasing screw speed from 100 …

Mycotoxins In Corn Distillers Grains: A Concern In Ruminants?, Alvaro Garcia, Kenneth Kalscheur, Arnold Hippen, David Schingoethe, Kurt A. Rosentrater

Kurt A. Rosentrater

Themain fungi that produce toxins during storage belong to three genera: Aspergillus, Fusarium, and Penicillium. When dealing with cattle diets, it is not easy to correlate the presence of mycotoxins to that of molds. The same types of molds can produce different types of toxins, and different types ofmolds can produce the samemycotoxin.

The Genome Of Laccaria Bicolor Provides Insights Into Mycorrhizal Symbiosis, F. Martin, A. Aerts, D. Ahren, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buee, P. Brokstein, B. Canback, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. Difazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbe, Y. C. Lin, V. Legue, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kues, S. Lucas, Y. Van De Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouze, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev

US Department of Energy Publications

Mycorrhizal symbioses—the union of roots and soil fungi—are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains ~20,000 …

A Preliminary Assessment Of The State Of Harvest And Collection Technology For Forest Residues, Erin G. Wilkerson, D. Brad Blackwelder, Robert D. Perlack, David J. Muth, J. Richard Hess

David J. Muth

To meet the “Twenty in Ten Initiative” goals set in the 2007 State of the Union address, forest resources will be needed as feedstocks for lignocellulosic ethanol production. It has been estimated that 368 million dry tons can be produced annually in the U.S. from logging residues and fuel treatment thinnings. Currently, very little of this woody biomass is used for energy production due to the costs and difficulty in collecting and transporting this material. However, minimizing biomass costs (including harvest, handling, transport, storage, and processing costs) delivered to the refinery is necessary to develop a sustainable cellulosic ethanol industry. …

Biofuel Feedstock Assessment For Selected Countries, Keith L. Kline, Gbadebo A. Oladosu, Amy K. Wolfe, Robert D. Perlack, Virginia H. Dale, Matthew J. Mcmahon

Economics & Finance Faculty Publications

Findings from biofuel feedstock production assessments and projections of future supply are presented and discussed. The report aims to improve capabilities to assess the degree to which imported biofuel could contribute to meeting future U.S. targets to reduce dependence on imported oil. The study scope was focused to meet time and resource requirements. A screening process identified Argentina, Brazil, Canada, China, Colombia, India, Mexico, and the Caribbean Basin Initiative (CBI) region for initial analysis, given their likely role in future feedstock supply relevant to U.S. markets. Supply curves for selected feedstocks in these countries are projected for 2012, 2017 and …

Effects Of Climate Change On Energy Production And Use In The United States, Thomas Wilbanks, Vatsal Bhatt, Daniel Bilello, Stanley Bull, James Ekmann, William Horak, Y. Joe Huang, Mark D. Levine, Michael J. Sale, David Schmalzer, Michael J. Scott

US Department of Energy Publications

Climate change is expected to have noticeable effects in the United States: a rise in average temperatures in most regions, changes in precipitation amounts and seasonal patterns in many regions, changes in the intensity and pattern of extreme weather events, and sea level rise. Some of these effects have clear implications for energy production and use. For instance, average warming can be expected to increase energy requirements for cooling and reduce energy requirements for warming. Changes in precipitation could affect prospects for hydropower, positively or negatively. Increases in storm intensity could threaten further disruptions of the sorts experienced in 2005 …

Genomics: Gtl 2008 Strategic Plan, Sharlene Weatherwax

US Department of Energy Publications

Table of Contents:
Mission-Inspired Science
GTL Concept and History
National Academy of Sciences Evaluation of GTL Program
GTL’s Fundamental Research Approach to Its Mission
Hallmarks of the GTL Research Approach
Multiscale Explorations
Office of Biological and Environmental Research User Facilities
Metamethods: Metagenomics and Metaproteomics
Robust Computational Framework for GTL Research
GTL Information and Data Sharing Policy
Elaboration of GTL Science for DOE Missions
Systems Biology for Energy Solutions
Systems Biology for Understanding the Carbon Cycle
Planet-Transforming Microbes
Systems Biology for Understanding Contaminant Transport in the Environment
Microbe-Mineral Interface in Contaminated Environments
DOE Office of Science
DOE Office of Biological and …

Small Angle Neutron Scattering Study Of Conformation Of Oligo(Ethylene Glycol)-Grafted Polystyrene In Dilute Solutions: Effect Of The Backbone Length, Gang Cheng, Yuri B. Melnichenko, George D. Wignall, Fengjun Hua, Kunlun Hong, Jimmy W. Mays

US Department of Energy Publications

The conformation and clusterization of comblike polymers of polystyrene densely grafted with oligo(ethylene glycol) (OEG) side chains in 1.0 wt % solutions of D₂O, toluene-d₈, and methanol-d₄ was investigated as a function of the degree of polymerization (DP) of the backbone by small angle neutron scattering (SANS). Each side chain had four EG repeat units, and the DP of the polystyrene backbone varied from 8 to 85. The global conformation of the polymers in toluene and methanol was shown to assume ellipsoidal, rigid cylindrical, or wormlike morphologies with increasing DP of the polystyrene …

Construcción De Un Aeromodelo Aplicado En La Fumigación De Cultivos, Fredy Lievano Gutierrez

Ingeniería en Automatización

No abstract provided.

Diseño Y Simulación De Un Aeromodelo Aplicado En La Fumigación De Cultivos, Darío Mejía López, Karen Alicia Palomá Montaña

Ingeniería en Automatización

No abstract provided.

Simulated Effects Of Dynamic Row Spacing On Energy And Water Conservation In Semi-Arid Central California Greenhouses, A. Moya, T. Mehlitz, Ilhami Yildiz, S. F. Kelly, C. Hardin

BioResource and Agricultural Engineering

Considerable effort is expended to conserve energy and water in current greenhouse systems, and look for alternative energy sources, especially passive heating and cooling strategies. Proper environmental management systems can significantly change the energy and moisture dynamics of greenhouse production systems. In this study, specifically, influences of dynamic row spacing on energy and water conservation were investigated. A dynamic computer simulation model was used to compare different row spacings, plant heights, and leaf dimensions to draw a conclusion about energy and water conservation. The results showed that using smaller spacings between cucumber crop rows (for instance, 0.5 m instead of …

Simulated Performance Of A Renewable Energy Technology – Heat Pump Systems In Semi-Arid California Greenhouses, C. Hardin, T. Mehlitz, Ilhami Yildiz, S. F. Kelly

BioResource and Agricultural Engineering

In addition to the labor, energy and water consumption are the two main cost drivers in current greenhouse systems. Consequently, considerable effort is expended to conserve energy and water, and look for alternative energy sources, especially environmentally friendly renewable energy sources and technologies. Greenhouses in hot and arid regions also require large quantities of water for irrigation. Using proper technologies and environmental management systems can significantly change the energy and moisture dynamics of greenhouse production systems. This study aims to focus on reducing natural gas, electricity, and water consumption in semi-arid California greenhouses introducing renewable energy heat pump technologies to …

Simulated Effects Of Reflective Mulch On Energy And Water Conservation In Semi-Arid Central California Greenhouses, T. Mehlitz, Ilhami Yildiz, S. Rahman, C. Hardin

BioResource and Agricultural Engineering

In addition to the labor, energy and water consumption are the two main cost drivers in current greenhouse systems. Consequently, considerable effort is expended to conserve energy and water, and look for alternative energy sources. Greenhouses in hot and arid regions also require large quantities of water for irrigation. Proper environmental management systems can significantly change the energy and moisture dynamics of greenhouse production systems. This study aims to focus on reducing energy and water consumption in semi-arid California greenhouses. Influences of mulch (having different reflectivities) on energy and water conservation were investigated. The reflectivity of mulch used as a …

Design And Evaluation Of A Greenhouse Interface For Climate Control Programming And Networking, G. Diaz, S. F. Kelly, Ilhami Yildiz

BioResource and Agricultural Engineering

At Cal Poly the motto is “Learn by Doing”. In the College of Agriculture, this is especially true and many of the labs provide an opportunity for students to implement this philosophy. Updated climate controls were installed in a series of greenhouses on the top floor of the Agricultural Science building that are used for student and faculty research projects. A Programmable Logic Controller (PLC) was installed to actuate the various vents, shading, heating, cooling and irrigation. A control program was developed to control and log temperatures and other operating parameters to monitor the greenhouse. An easy to use computer …

Simulated Effects Of Various Environmental Management Practices On Energy Consumption In Open And Confined Greenhouse Systems, Ilhami Yildiz, D. P. Stombaugh

BioResource and Agricultural Engineering

The objective of this study was to evaluate the effects of relative humidity, light management levels, minimum ventilation rates, CO₂ enrichment and canopy size on energy consumption in three different greenhouse systems (conventional, open-loop heat pump, and confined heat pump) in winter, spring, and summer months. No difference was observed in energy consumption with relative humidity set point levels in winter due to the already low relative humidity levels. Some differences were observed in spring and summer due to extra dehumidification required to maintain the inside relative humidity at lower levels. Energy consumption in summer was reduced up to …

Simulated Effects Of Various Environmental Management Practices On Water Consumption In Open And Confined Greenhouse Systems, Ilhami Yildiz, D. P. Stombaugh

BioResource and Agricultural Engineering

The objective of this study was to evaluate the effects of relative humidity, light management, minimum ventilation rates, CO₂ enrichment and canopy size on water consumption in three different greenhouse systems (conventional, open heat pump, and confined heat pump) in winter, spring, and summer months. Using different relative humidity set points resulted in almost the same relative humidity regimes within the confined greenhouse system, resulting in similar transpiration rates. No difference was observed in transpiration rates in the open system in winter either, because the inside relative humidity levels never reached the 70% and 80% set points. Some differences …

Irrigation District Energy Survey, Charles M. Burt, Daniel J. Howes

BioResource and Agricultural Engineering

This survey was completed by ITRC on behalf of the California Energy Commission Public Interest Energy Research (PIER) Program. The purpose of the survey was to establish a benchmark for the present status of the pumping systems used by agricultural water districts in California and to determine the districts' needs. The needs discussed involve technical assistance, research grant and low-interest loan funding, and district-related policy issues. Thirty agricultural water districts were selected for the survey. These districts were selected based on energy use per acre of irrigated area, size, geographic location, and distribution infrastructure.

Carbon Conversion During Bubbling Fluidized Bed Gasification Of Biomass, Kevin Timmer

Faculty Work Comprehensive List

Gasification is one means of transforming biomass so that it can be more easily utilized as a renewable source of thermal energy, transportation fuel, and chemicals. Under typical gasification conditions it is not uncommon that a portion of the carbon entering with the biomass leaves the reactor unconverted as char. Understanding and improving carbon conversion during biomass gasification in an atmospheric bubbling fluidized bed reactor is the focus of this study.

To better understand the intricacies of biomass gasification a carbon conversion analytic methodology was developed. The methodology is based on a mass balance of the fixed carbon entering and …

Packing Factors Of Feed Products In Storage Structures, Samuel G. Mcneill, Michael D. Montross, Sidney A. Thompson, I. Joseph Ross, Thomas C. Bridges

Biosystems and Agricultural Engineering Faculty Publications

Experiments were conducted to measure the changes in bulk density of cracked corn, corn meal, soybean meal, cotton seed meal, and distillers dried grain (without solubles) when subjected to simulated overburden pressures. All materials were tested at two moisture content levels (approximately 8% and 12% w.b.) and seven pressures between 0 and 69 kPa (0 and 10 psi). A mathematical model was fitted to the data to predict the bulk density of each feed ingredient as a function of pressure and moisture content. These relationships were inserted into a previously developed computer model to predict ingredient packing within conventional storage …

Airflow Resistance Of Wheat Bedding As Influenced By The Filling Method, J. Łukaszuk, M. Molenda, J. Horabik, B. Szot, Michael D. Montross

Biosystems and Agricultural Engineering Faculty Publications

A study was conducted to estimate the degree of variability of the airflow resistance in wheat caused by the filling method, compaction of the sample, and airflow direction. Two types of grain chambers were used: a cylindrical column 0.95 m high and 0.196 m in diameter, and a cubical box of 0.35 m side. All factors examined were found to influence considerably the airflow resistance. Gravitational axial filling of the grain column from three heights (0.0, 0.95 and 1.8 m) resulted in the pressure drops of 1.0, 1.3, and 1.5 kPa at the airflow velocity of 0.3 m/s. Consolidation of …

Yield And Growth Characteristics For Cotton Under Various Irrigation Regimes On Sandy Soil, William R. Detar

William R DeTar

Over-watering cotton wastes a valuable and scarce resource; it can also lead to rank growth, nutrient leaching, and contaminated groundwater. Since under-watering can decrease yields, the question becomes one of finding the optimum application regime. An irrigation experiment was set up to apply water at six different application rates, ranging from 33% to 144% of normal, with hopes of identifying the regime that produces maximum yield. Two cultivars, Acala Maxxa and Acala PhytoGen-72 (Gossypium hirsutum L.), were planted on sandy soil and irrigated daily with a highly efficient subsurface drip irrigation system for four seasons. The results showed that on …

Physical And Chemical Properties Of Corn Distillers Wet Grains, Kurt A. Rosentrater, R. Michael Lehman

Kurt A. Rosentrater

The production of corn-based ethanol in the United States is dramatically increasing, and consequently, so is the quantity of generated coproducts, all of which are currently fed to livestock. Distillers Wet Grain (DWG) is one of these coproduct feeds. Many studies have investigated the nutritional properties of DWG and the response of livestock (primarily beef and dairy) to inclusion of these ingredients in their diets. To date, physical properties have been largely ignored, but they are needed for the design of storage facilities and equipment. The objective of this research was to quantify physical and chemical property values for typical …

Concentration Of Key Elements In North American Meat & Bone Meal, Rafael A. Garcia, Kurt A. Rosentrater

Kurt A. Rosentrater

Meat & bone meal (MBM) and related rendered protein commodities have potential for use in applications other than animal feed, including use as a fuel or a phosphorus fertilizer. In order to develop these applications, data on the elemental composition are required; the currently available elemental composition data have important limitations. To generate more appropriate and reliable data, MBM samples were collected from 17 North American rendering plants, carefully prepared and analyzed for 20 elements. Preliminary studies showed that the sample preparation process artificially increased levels of sulfur and nickel in a manner that was correctable. Concentrations of many elements …