Engineering Commons^™

Gene Order Phylogeny Of The Genus Prochlorococcus, Haiwei Luo, Jian Shi, William Arndt, Jijun Tang, Robert Friedman

Faculty Publications

Background
Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria.

Methodology/Principal Findings
Orthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based …

Comparison Of Electrically Mediated And Liposome-Complexed Plasmid Dna Delivery To The Skin, Loree C. Heller, Mark J. Jaroszeski, Domenico Coppola, Richard Heller

Bioelectrics Publications

BACKGROUND: Electroporation is an established technique for enhancing plasmid delivery to many tissues in vivo, including the skin. We have previously demonstrated efficient delivery of plasmid DNA to the skin utilizing a custom-built four-plate electrode. The experiments described here further evaluate cutaneous plasmid delivery using in vivo electroporation. Plasmid expression levels are compared to those after liposome mediated delivery.

METHODS: Enhanced electrically-mediated delivery, and less extensively, liposome complexed delivery, of a plasmid encoding the reporter luciferase was tested in rodent skin. Expression kinetics and tissue damage were explored as well as testing in a second rodent model.

RESULTS: Experiments …

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 …

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 …

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 …

Genes Controlling Plant Growth Habit In Leymus (Triticeae): Maize Barren Stalk1 (Ba1), Rice Lax Panicle, And Wheat Tiller Inhibition (Tin3) Genes As Possible Candidates., Paraminder Kaur, Steven R. Larson, B.S. Bushman, Richard R. Wang, Ivan W. Mott, Jyothi Thimmapuram, George Gong, Lei Liu

Cyber Center Publications

Leymus cinereus and L. triticoides are large caespitose and rhizomatous perennial grasses, respectively. Previous studies detected quantitative trait loci (QTL) controlling rhizome spreading near the viviparous1 (vp1) gene markers on linkage groups LG3a and LG3b in two families, TTC1 and TTC2, derived from Leymus triticoides x Leymus cinereus hybrids. The wheat tiller inhibition gene (tin3) is located on Triticum monococcum chromosome 3 A(m)L near vp1. Triticeae group 3 is reportedly collinear with rice chromosome 1, which also contains the maize barren stalk1 and rice lax branching orthogene near vp1. However, previous studies lacked cross-species markers for comparative mapping and showed …

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 …

Development And Assessment Of Role-Play Scenarios For Teaching Rcr, Michael C. Loui, Bradley J. Brummel, C. K. Gunsalus, Kerri L. Kristich

Ethics in Science and Engineering National Clearinghouse

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 …

Data Management And Whistle-Blowing, Michael C. Loui

Ethics in Science and Engineering National Clearinghouse

No abstract provided.

In Situ Measurement Of Three-Dimensional Ion Densities In Focused Femtosecond Pulses, James Strohaber, Cornelis J. Uiterwaal

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

We image spatial distribution of xenon ions in the focus of a laser beam of ultrashort, intense pulses in all three dimensions, with a resolution of three by twelve microns in the two transverse directions. This allows for studying ionization processes without spatially averaging ion yields. Our in situ ion imaging is also useful to analyze focal intensity profiles and to investigate the transverse modal purity of tightly focused beams of complex light. As an example, the intensity profile of a Hermite-Gaussian beam mode HG recorded with ions is found to be in good agreement with optical images.

The Highly Similar Arabidopsis Homologs Of Trithorax Atx1 And Atx2 Encode Proteins With Divergent Biochemical Functions, Abdelaty Saleh, Raul Alvarez-Venegas, Mehtap Yilmaz, Oahn-Le, Guichuan Hou, Monther Sadder, Ayed Al-Abdallat, Yuannan Xia, Guoqinq Lu, Istvan Ladunga, Zoya Avramova

Nebraska Center for Biotechnology: Faculty and Staff Publications

Gene duplication followed by functional specialization is a potent force in the evolution of biological diversity. A comparative study of two highly conserved duplicated genes, ARABIDOPSIS TRITHORAX-LIKE PROTEIN1 (ATX1) and ATX2, revealed features of both partial redundancy and of functional divergence. Although structurally similar, their regulatory sequences have diverged, resulting in distinct temporal and spatial patterns of expression of the ATX1 and ATX2 genes. We found that ATX2 methylates only a limited fraction of nucleosomes and that ATX1 and ATX2 influence the expression of largely nonoverlapping gene sets. Even when coregulating shared targets, ATX1 and ATX2 may employ different …

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 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 …

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 …

Il-21 Limits Peripheral Lymphocyte Numbers Through T Cell Homeostatic Mechanisms., Shrimati Datta, Nora E. Sarvetnick

Journal Articles: Regenerative Medicine

BACKGROUND: IL-21, a member of the common gamma-chain utilizing family of cytokines, participates in immune and inflammatory processes. In addition, the cytokine has been linked to autoimmunity in humans and rodents.

METHODOLOGY/PRINCIPAL FINDINGS: To investigate the mechanism whereby IL-21 affects the immune system, we investigated its role in T cell homeostasis and autoimmunity in both non-autoimmune C57BL/6 and autoimmune NOD mice. Our data indicate that IL-21R knockout C57BL/6 and NOD mice show increased size of their lymphocyte population and decreased homeostatic proliferation. In addition, our experimental results demonstrate that IL-21 inhibits T cell survival. These data suggest that IL-21 acts …

Text As Property / Property As Text, Christopher Kelty, Alfred Housman, Scott Mcgill

Ethics in Science and Engineering National Clearinghouse

Ownership, authorship, plagiarism, intellectual property, parody, critique, re-use, credit, reputation, allusion, imitation, patronage, payment, piracy, creativity, originality, borrowing, lending, stealing, quoting, citing, lifting, re-writing, translating, acting, performing, impersonating, collaborating, re-creating, editing, sampling, sharing.

If you can distinguish between all these activities, legally, morally, culturally and historically, then you don't need our class. If on the other hand, you want to know why ancient Romans sampled Virgil so often, or why some plagiarism is art and some is crime, or what could happen to manuscripts in antiquity when they circulated, or why the RIAA is suing thousands of college students, or …

How To Get The Mentoring You Want: A Guide For Graduate Students At A Diverse University, Rackham Graduate School - University Of Michigan

Ethics in Science and Engineering National Clearinghouse

No abstract provided.

Agricultural Systems: Agroecology And Rural Innovations For Development [Book Review], Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

To welcome yet another book on sustainable development, a reviewer must look for what is unique and what adds value to the volumes already published. In Agricultural Systems, editors Sieglinde Snapp and Barry Pound have assembled a collection of chapters that goes beyond the usual praise and criticism of the green revolution and the focus on economic development. Their book provides a first-hand story by people with lengthy experiences in the field, especially in Africa, who have developed and tested grassroots, participatory development approaches. The result is a valuable set of principles, strategies and case studies that paint a new …

An Efficient Algorithm For Biomarker Identification, Jiang Li, Rick Mckenzie, Lisa Cazares, Richard Drake, John Semmens

Electrical & Computer Engineering Faculty Publications

No abstract provided.

Polyaniline Nanofiber-Based Gas Sensors, Zhe-Fei Li, Frank D. Blum, Massimo F. Bertino, Chang-Soo Kim

Chemistry Faculty Research & Creative Works

There has been recent interest in conducting polymers that have very promising chemical and electrical applications. Some of these polymers have shown great potential for use in sensors.1 Polyaniline is one particular example of a prospective material. In our laboratory, we have studied the synthesis of polyaniline nanofibers. We have carried out one-pot syntheses to obtain polyaniline nanofibers in aqueous solutions where the polymerization was influenced by γ-radiation2 or UV-radiation.3 This polymer can also be patterned with an appropriate photo mask. In our present report, polyaniline nanofiber thin film sensors have been fabricated in one step by employing UV-irradiation and …

Kentucky Water Resources Research Institute Annual Technical Report Fy 2007, Kentucky Water Resources Research Institute, University Of Kentucky

KWRRI Annual Technical Reports (USGS’s 104b Grant Program)

The 2007 Annual Technical Report for Kentucky consolidates reporting requirements of the Section 104(b) base grant award into a single document that includes: 1) a synopsis of each student research enhancement project conducted during the period, 2) citations for related publications, reports, and presentations, 3) a description of information transfer activities, 4) a summary of student support during the reporting period, and 5) notable awards and achievements during the year.