Engineering Commons^™

Dechlorinating And Iron Reducing Bacteria Distribution In A Trichloroethene Contaminated Aquifer, Carmen Lourdes Yupanqui Zaa

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Operable Unit 5 (OU 5) area of Hill Air Force Base currently has two trichloroethene-contaminated groundwater plumes underneath residential areas in Sunset and Clinton, Utah. Bioremediation by biological reductive dechlorination can be an important mechanism for the removal of chlorinated compounds from the plumes. The presence of suitable bacteria to carry on reductive dechlorination is the key in the bioremediation process. The goal of this study was to determine the distribution and population density of the 16S rRNA genes of Bacteria, Dehalococcoides ethenogenes, Desulfuromonas michiganensis, Geobacter spp and Rhodoferax ferrireducens-like bacteria, as well as the functional genes trichloroethene reductive …

Transcriptome Analysis Identifies Novel Responses And Potential Regulatory Genes Involved In Seasonal Dormancy Transitions Of Leafy Spurge (Euphorbia Esula L.), David P. Horvath, Wun S. Chao, Jeffrey C. Suttle, Jyothi Thimmapuram, James V. Anderson

Cyber Center Publications

Dormancy of buds is a critical developmental process that allows perennial plants to survive extreme seasonal variations in climate. Dormancy transitions in underground crown buds of the model herbaceous perennial weed leafy spurge were investigated using a 23 K element cDNA microarray. These data represent the first large-scale transcriptome analysis of dormancy in underground buds of an herbaceous perennial species. Crown buds collected monthly from August through December, over a five year period, were used to monitor the changes in the transcriptome during dormancy transitions.

Multi-Break Rearrangements And Breakpoint Re-Uses: From Circular To Linear Genomes, Max A. Alekseyev

Faculty Publications

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Alekseyev and Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion …

Improving Reversal Median Computation Using Commuting Reversals And Cycle Information, William Arndt, Jijun Tang

Faculty Publications

In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods for reconstructing phylogeny from genome rearrangements include distance-based methods, MCMC methods, and direct optimization methods. The latter, pioneered by Sankoff and extended with the software suites GRAPPA and MGR, is the most accurate approach, but is very limited due to the difficulty of its scoring procedure—it must solve multiple instances of the reversal median problem to compute the score of a given tree. The reversal median problem is known to be NP-hard and all …

2008 Scholars And Artists Bibliography, Rajshehkar G. Javalgi Dr., Michael Schwartz Library, Cleveland State University, Friends Of The Michael Schwartz Library

Scholars and Artists Bibliographies

This bibliography was created for the annual Friends of the Michael Schwartz Library Scholars and Artists Reception, recognizing scholarly and creative achievements of Cleveland State University faculty, staff and emeriti. Dr. Rajshekhar Javalgi was the guest speaker.

Development And Annotation Of Perennial Triticeae Ests And Ssr Markers., B.S. Bushman, S R Larson, I W Mott, P F Cliften, R R Wang, N J Chatterton, A G Hernandez, S Ali, R W Kim, Jyothi Thimmapuram, G Gong, L Liu, M A Mikel

Cyber Center Publications

Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata, a mixture of both Elymus wawawaiensis and E. lanceolatus, and a Leymus cinereus x L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for …

Santa Clara Magazine, Volume 50 Number 2, Fall 2008, Santa Clara University

Santa Clara Magazine

10 - MEET MOUNTAIN By Lisa Taggart. A Q&A with SCU women's basketball coach Jennifer Mountain.

12 - KATRINA AT THREE By Pat Semansky '06. A New Orleans photo essay.

16 - THE MEDDLING PRIEST FROM OZ By Emily Elrod '05. An interview with Australian Jesuit John Brennan, S.J.-lauded as a "national treasure" and an "ethical burr."

18 - 20/20 VISION By Robert M. Senkewicz. How has the presidency of Paul Locatelli, S.J., transformed the University-as a place-and as an idea?

28 - GO WITH YOUR HEART By Francisco Jimenez. An exclusive excerpt from his new memoir, Reaching Out.

32 …

Metabolic Engineering Of A Thermophilic Bacterium To Produce Ethanol At High Yield, A. Joe Shaw, Kara K. Podkaminer, Sunil G. Desai, John S. Bardsley, Stephen R. Rogers, Philip G. Thorne, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

We report engineering Thermoanaerobacterium saccharolyticum, a thermophilic anaerobic bacterium that ferments xylan and biomass-derived sugars, to produce ethanol at high yield. Knockout of genes involved in organic acid formation (acetate kinase, phosphate acetyltransferase, and L-lactate dehydrogenase) resulted in a strain able to produce ethanol as the only detectable organic product and substantial changes in electron flow relative to the wild type. Ethanol formation in the engineered strain (ALK2) utilizes pyruvate:ferredoxin oxidoreductase with electrons transferred from ferredoxin to NAD(P), a pathway different from that in previously described microbes with a homoethanol fermentation. The homoethanologenic phenotype was stable for >150 generations …

Web-Based Information Management System For The Long Term Ecological Research Program In Kenting, Taiwan, Yang-Chi Chang, Meng-Tsung Lee, Kun-Chi Lai

Journal of Marine Science and Technology–Taiwan

This paper introduces a web-based information management system which has been set up as a collaborative facility to allow key environmental and ecological information access for the Long Term Ecological Research (LTER) in Kenting, Taiwan. The coral reef ecosystem degradation in Kenting has concerned both public and private sectors, for which a LTER team was formed to investigate the problem. A multi-functional web-based system integrates diverse data collections and analyses efforts of team members during the project span. It also provides authorities with effective information and knowledge for sustainable coral reef management. Three information technologies, web Database Management System (DBMS), …

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

Faculty Publications

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

Santa Clara Magazine, Volume 50 Number 1, Summer 2008, Santa Clara University

Santa Clara Magazine

10 - SPEED RACERS An interview by Gwen Knapp. Cycling legend Greg LeMond talks ethics and doping in sports.

14 - MEET THE NEW FATHER GENERAL By Steven Boyd Saum. Introducing Adolfo Nicols, S.J., the new Superior General of the Society of Jesus.

16 - NO SIMPLE HIGHWAY By Juan Velasco. The Casa de la Solidaridad is less a place than a journey—one that offers a new understanding of solidarity. And a new meaning of home.

22 - EXILES By Ron Hansen. A tale of a shipwreck, a priest, and a poet. Hansen tells the story behind his new novel, …

Nanoengineered Templates For Controlled Delivery Of Bioactive Compounds, Nalinkanth Ghone Veerabadran

Doctoral Dissertations

The significance of any drugs, therapeutic proteins, or any bioactive compounds, is based not only on their effects on diseases but also on how specifically, how readily, how controllable and how prolonged their effects on the disease without having any side effects. Thus the techniques involved in the drug encapsulation and its controlled release for a longer duration of time form one of the important processes of drug reformulation. In recent years nanoparticles have created overwhelming attention for delivering drugs by nanoencapsulation. The smaller size of nanoparticles has longer circulation time and higher cellular uptake when compared with larger size …

Development Of A Technique To Diagnose Subtalar Joint Instability, Ajaya Dhakal

Mechanical & Aerospace Engineering Theses & Dissertations

Most patients escape diagnosis of subtalar joint instability for years before treatment. Therefore, a clinically relevant technique to diagnose subtalar joint instability will improve its management. Towards this goal, a six degree of freedom positioning and loading device was developed to apply physiologic loads to the hindfoot. Because the ideal loading configuration to detect subtalar joint instability is unknown, the device was designed to apply rotational and translational forces simultaneously. Specifically, plantarflexion/dorsiflexion, inversion/eversion, and internal/external rotation can be applied individually or as coupled motions along with an anterior/posterior drawer. Kinematic data were collected from calcaneus, talus and tibia using a …

Experimental Analysis And Modeling Validation Of A Knee Brace In Shock Mitigation, Manish Prakash Dhekane

Mechanical & Aerospace Engineering Theses & Dissertations

An experimental setup simulating the dynamic environment in a high sea state is developed for the lower extremities to study the mitigation of shock impact. A single degree of freedom machine is equipped with six linear induction motors to produce impact acceleration ranging from 0.5G to 4G. The experiments are carried out along the dummy leg by using two configurations, one without a knee brace and one with a knee brace. Force and acceleration data is collected using a data acquisition system.

To develop the analytical model of the same experimental setup, the knee brace and dummy leg were scanned …

Neural Network Models For Solving The Maximum Flow Problem, S. Effati, M. Ranjbar

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, two new neural network models for solving the maximum flow problem are presented. The maximum flow problem in networks is formulated as a special type of linear programming problem and it is solved by appropriately defined neural networks. The nonlinear neural networks are able to generate optimal solution for maximum flow problem. We solve neural network models by one of the numerical method. Finally, some numerical examples are provided for the sake of illustration.

Mechanisms Of T Helper Cell Modulation In A Simulated Space Radiation Environment, Asma Rizvi

Loma Linda University Electronic Theses, Dissertations & Projects

Exposure to solar particle events (SPEs) poses the most serious threat to astronaut health. Due to this radiation environment, exploration of the solar system beyond Earth’s orbit entails many risks for the crew on these deep space missions. Depression or dysfunction of the immune system is a major concern due to its high radio-sensitivity; potential consequences include overwhelming infection, development of cancer, fibrosis, and poor wound healing. Astronauts are also exposed to low dose/low dose rate (LDR) radiation. A three month stay at the international space station exposes them to ~ 0.05 Gy of radiation.

C57BL/6 mice received LDR gamma-radiation …

The Draft Genome Of The Transgenic Tropical Fruit Tree Papaya ( Carica Papaya Linnaeus), Ray Ming, Shaobin Hou, Yun Feng, Qinguyi Yu, Jyothi Thimmapuram

Cyber Center Publications

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3 draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree¹ to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far may account for the smaller papaya gene number in …

2008 - The Thirteenth Annual Symposium Of Student Scholars

Symposium of Student Scholars Program Books

The full program book from the Thirteenth Annual Symposium of Student Scholars, held on April 14, 2008. Includes abstracts from the presentations and posters.

Santa Clara Magazine, Volume 49 Number 4, Spring 2008, Santa Clara University

Santa Clara Magazine

14 - LET THE SUN SHINE IN By Steven Boyd Saum. In the international Solar Decathlon competition, a team from Santa Clara blazed a dazzling trail from almost-ran to third in the world.

20 - VISIONS FROM THE SIXTIES By Lisa Taggart. It was art that broke all the rules. And now an exhibit at the de Saisset Museum, curated by Santa Clara scholar Andrea Pappas, captures the sense of optimism and energy when the only limits were imagination itself.

26 - JORMA'S JOURNEY By Mark Purdy. With Jefferson Airplane, he helped define the San Francisco sound. With Hot Tuna …

Stochastic Calculations For Computation Of Radiation Effects And Cell Survivability Under Voltage Pulsing, Madhuri Ganapathiraju

Electrical & Computer Engineering Theses & Dissertations

Statistical computations are an important tool for the analysis of stochastic phenomena and processes that are characterized by variability. Biological systems (e.g., cells, tissues etc.) are perfect examples wherein response to a given external stimulus can be varied and needs to be adequately considered. The Monte Carlo method of analysis has now been recognized as the most effective way of treating stochastic variability.

This thesis uses Monte Carlo based simulations to probe two problems that require the quantification and modeling of effects caused by energy deposition onto biological matter from external sources. One problem involves the probabilistic study of the …

Modeling Electric Fields In Microfluidic Devices, Micah Fincher

Honors Capstones

No abstract provided.

Gene Rearrangement Analysis And Ancestral Order Inference From Chloroplast Genomes With Inverted Repeat, Feng Yue, Liying Cui, Claude W. Depamphilis, Bernard M.E. Moret, Jijun Tang

Faculty Publications

Background
Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction.

Results
We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR …

Poster Session, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Kentucky Water Awareness Month Packet, Ashley Osborne, UK Cooperative Extension Service, ENRI Task Force
• Recent Enhancements to the Kentucky Groundwater-Quality Data Search Engine, Bart Davidson and R. Stephen Fisher, KGS
• Diatom Colonization Patterns and Carbon Stable Isotopic Ratios in Developing Periphyton at Springs of Differing Geologic Origin in Land-Between-the-Lakes, Courtney Snapp and Susan Hendricks, Water Sciences Program, Murray State University
• Seasonal Changes in Stratification and Oxygen Content of a Eutrophic Lake, Wilgreen Lake, Madison County, Kentucky, Jill Hunter and Walter Borowski, Dept of Geography and Geology, EKU
• Water Pioneers Water Quality Program 2007, Stephanie Jenkins, …

Session 2d: Pathogen Transport, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Assessment of Nonpoint Source Impacts on Groundwater Quality in South Elkhorn Creek Basin, Central Kentucky, Robert J. Blair and others, Kentucky Division of Water, Frankfort
• Karst Groundwater Infiltration of the Sanitary Sewer within the Beargrass Creek Watershed, Jefferson County, Kentucky, Joseph Ray and others, Kentucky Division of Water
• Illicit Discharge into Town Branch in Lexington, Kentucky, Jim Buckles and others, Tetra Tech, Lexington
• Assessment of Water Quality Trends in the Upper Forks of the Kentucky River Basin: Focus on Pathogen Impairment, Chandramouli Viswanathan, Kentucky Water Resources Research Institute, UK

Session 2c: Water Quality, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Determinations of Bioavailable Fractions in the Assessment of Metals in Big and Little Bayou Creeks……, McCracken County, Kentucky, David J. Price, Dept Biology, UK
• Creation of a Catalog of Environmental Mercury Databases in Kentucky, Caroline Chan and others, School of Public Health and Information Sciences, U of L
• Using Nitrogen Isotopes to Trace Nutrient Inputs to a Eutrophic Lake, Wilgreen Lake, Madison County, Kentucky, Walter Borowski and Theresa Aguiar, Dept of Geography and Geology, EKU
• Using Microbial Distribution and Abundance in a Eutrophic Lake as a Tracer for Nutrient Inputs, Wilgreen Lake, Madison County Kentucky, Theresa …

Session 2b: Variety, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Mud, Horses and Clean Water – A BMP Demonstration Project for Suburban Horse Owners, Steve Higgins and others, Biosystems and Ag Engineering, UK
• A Topological Model of Open Channel Flows, Brian Belcher and Jimmy Fox, Dept of Civil Engineering, UK
• Rain Gardens: Restoring a Waste Water to a Priceless Treasure, H. David Gabbard, LFUCG, Richard Walker, Tetra Tech, and Sandy Camargo, CDP Engineers
• Kentucky Erosion Prevention and Sediment Control (KESPSC) – An Answer to the Question “What is a Qualified Inspector?” Shelby Jett, Kentucky Transportation Cabinet, Kevin Gibson and John Ricketts, Stantec Consulting Services, Lexington

Session 2a: Groundwater, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• How Close Do We Need to Sample for Appropriate Solute Transport Characterization Through the Vadose Zone? Ole Wendroth and others, Dept of Plant and Soil Sciences, UK
• Efficiently Locating and Repairing Damaged Sewer Lines in a Karst Terrane, Kevin Lyne, LFUCG and Robert Blair, KDOW
• Hydrogeologic Investigations of Pavement Subsidence in the Cumberland Gap Tunnel, Jim Dinger and others, KGS

Session 1d: Land Use, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Mountaintop Mining and Sustainable Development Opportunities for Appalachia, J. Stephen Gardner, Engineering Consulting Services, Inc., Lexington
• Spatial Characterization of Kentucky’s 2005-2001 Land Cover Change, A Kentucky Landscape Census Product, Demetrio Zourarakis and others, Kentucky Division of Geographic Information
• Feasibility Study of Cover-Collapse Rate in the Western Pennyroyal Karst of Kentucky, James Currens and Randall Paylor, KGS
• Kentucky SPARROW Model and its Applications to Understanding Nutrient Loads, Tanja N. Williamson, USGS Kentucky Water Science Center

Session 1c: Student Research Projects, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• A 3-D Computational Fluid Dynamics Code for Simulation of Pump Stations with Vertical Plunging Jet and Air Bubble Transport, Tien Mun Yee and Scott Yost, Dept of Civil Engineering, UK
• Chemical Evolution of Groundwater in the Wilcox Aquifer of the Mississippi Embayment, Estifanos Haile and Alan Fryar, Dept of Earth and Environmental Sciences, UK
• Sediment Organic Matter Degradation within Storage Zones Deposited In-Stream, Charles Davis and Jimmy Fox, Dept of Civil Engineering, UK
• Effectiveness of Improved Skid Trail Headwater Stream Crossings, Jeffrey Stringer and Christopher Reeves, Dept of Forestry, UK

Session 1b: Education, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Community Based Science, Water Quality and Nonpoint Source Pollution, Carol Hanley and others, Tracy Farmer Center for the Environment, UK
• A Stormwater Education Program to Assist Kentucky’s MS4 Phase II Communities, Yvonne Meichtry and Julie Gee, Kentucky Transportation Cabinet, Frankfort
• Water/Wastewater Technician Training Institute: A Holistic Approach to Developing a Professional Water and Wastewater Workforce, Andrew Ernest, Center for Water Resource Studies, WKU
• Geology for Everyone, New Map Products from the Kentucky Geological Survey, Daniel Carey, KGS