Engineering Commons^™

Role Of Epidermal Growth Factor-Triggered Pi3k/Akt Signaling In The Migration Of Medulloblastoma-Derived Cells, Veronica Dudu, Richard A. Able, Jr., Veronica Rotari, Qingjun Kong, Maribel Vazquez

Publications and Research

Medulloblastoma (MB) is the most common brain cancer diagnosed among children. The cellular pathways that regulate MB invasion in response to environmental cues remain incompletely understood. Herein, we examine the migratory response of human MB-derived Daoy cells to different concentration profiles of Epidermal Growth Factor (EGF) using a microfluidic system. Our findings provide the first quantitative evidence that EGF concentration gradients modulate the chemotaxis of MB-derived cells in a dose-dependent manner via the EGF receptor (EGF-R). Data illustrates that higher concentration gradients caused increased number of cells to migrate. In addition, our results show that EGF-induced receptor phosphorylation triggered the …

Collaborative Research: North East Cyberinfrastructure Consortium, Michael Eckardt

University of Maine Office of Research Administration: Grant Reports

EPS-0918284, University of Vermont & State Agricultural College, J. L. Van Houten, linked to EPS-0918033 (University of New Hampshire), EPS-0918078 (University of Delaware), EPS-0918018 (University of Maine), EPS-0918061 (University of Rhode Island)
Collaborative Research: North East Cyberinfrastructure Consortium

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

The North East Cyberinfrastructure Consortium (NECC) unites Maine (ME), New Hampshire (NH), Vermont (VT), Rhode Island (RI), and Delaware (DE) to support cyber-enabled research that requires analyses of large datasets. The project is organized around sharing resources, expertise and facilities in order to make cyber-enabled collaborative …

Complex Of Myoglobin With Phenol Bound In A Proximal Cavity, Xiao Huang, Chunxue Wang, Lesa R. Celeste, Leslie L. Lovelace, Shengfang Sun, John H. Dawson, Lukasz Lebioda

Faculty Publications

Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with C and C of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It …

Inactivation Of Bacterial Opportunistic Skin Pathogens By Nonthermal Dc-Operated Afterglow Atmospheric Plasma, L. C. Heller, C. M. Edelblute, A. M. Mattson, X. Hao, J. F. Kolb

Bioelectrics Publications

AIMS: Multidrug-resistant opportunistic pathogens are clinically significant and require the development of new antimicrobial methods. In this study, Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus cells were exposed to atmospheric plasma on agar plates and in vitro on porcine skin for the purpose of testing bacterial inactivation.

METHODS AND RESULTS: Microbial inactivation at varying exposure durations was tested using a nonthermal plasma jet generated with a DC voltage from ambient air. The observed reduction in colony forming units was quantified as log₁₀ reductions.

CONCLUSIONS: Direct plasma exposure significantly inactivated seeded bacterial cells by approx. 6 log_{10 …}

Lonomics Atlas: A Tool To Explore Interconnected Ionomic, Genomic And Environmental Data, Eduard Dragut, Amgad Madkour, Mohamed Nabeel, Peter Baker, Mourad Ouzzani, David Salt

Cyber Center Publications

Ionomics Atlas facilitates access, analysis and interpretation of an existing large-scale heterogeneous dataset consisting of ionomic (elemental composition of an organism), ge- netic (heritable changes in the DNA of an organism) and ge- ographic information (geographic location, altitude, climate, soil properties, etc). Ionomics Atlas allows connections to be made between the genetic regulation of the ionome of plant populations and their landscape distribution, allowing scientists to investigate the role of natural ionomic variation in adaptation of populations to varied environmental conditions in the landscape. The goal of the Ionomics Atlas is twofold: (1) to allow both novice and expert users …

Computational Model Of Neuron-Astrocyte Interputational Model Of Neuron-Astrocyte Interactions During Focal Seizure Generationactions During Focal Seizure Generation, Davide Reato, Mario Cammarota, Lucas C. Parra, Giorgio Carmignoto

Publications and Research

Empirical research in the last decade revealed that astrocytes can respond to neurotransmitters with Ca2+ elevations and generate feedback signals to neurons which modulate synaptic transmission and neuronal excitability. This discovery changed our basic understanding of brain function and provided new perspectives for how astrocytes can participate not only to information processing, but also to the genesis of brain disorders, such as epilepsy. Epilepsy is a neurological disorder characterized by recurrent seizures that can arise focally at restricted areas and propagate throughout the brain. Studies in brain slice models suggest that astrocytes contribute to epileptiform activity by increasing neuronal excitability …

Prelude To A Master Plan: Ware, Massachusetts, Belen Alfaro, Bruno Carneiro, Margaret Engesser, Kathryn E. Fox, Evadne R. Friedman, Timothy Inacio, Anita Lockesmith, Christina Mills, Stephanie Molden, Meagen Mulherin, Russell Pandres, Vinicius Pereira, Brian Reid, Pedro Soto, Jennifer Stromsten

Landscape Architecture & Regional Planning Studio and Student Research and Creative Activity

Prelude to a Master Plan offers ideas, recommendations, and a toolkit to help the town chart its own path towards that future. While the teams and individual students worked to ‘drill down’ into specific topic areas, the Studio defined three basic areas in order to think about how the various assets, challenges and ideas undermine or reinforce one another. The report is loosely organized in those terms: addressing the outlying rural areas and issues specific to these places, considering one of the key growth areas that has extended from town and the conflicts that arise from the many uses occurring …

Developing A Restorable Wetland Index For Rainwater Basin Wetlands In South-Central Nebraska: A Multi-Criteria Spatial Analysis, Zhenghong Tang, Xu Li, Nan Zhao, Ruopu Li, F. Edwin Harvey

Community and Regional Planning Program: Faculty Scholarly and Creative Activity

It is always challenging for decision makers to prioritize wetland conservation programs at the landscape scale. This study employed a GIS-based multi-criteria spatial decision support tool that identified locations with the highest restoration potential for wetland conservation programs in the Rainwater Basin in south-central Nebraska. Five indicators were considered to assess wetland restoration potential: (1) Vegetation characteristics; (2) Soil characteristics; (3) Water volume released from hydrological modification of agricultural irrigation pits; (4) Topographical depression status; and (5) Habitat condition. The results suggested 192 (1.6% of the total) hydric soil footprints as the highest prioritized locations for future wetland restoration programs. …

Initial Changes In Species Cover Following Savanna Restoration Treatments In Western Iowa, David A. Mckenzie, Thomas B. Bragg, David M. Sutherland

Great Plains Research: A Journal of Natural and Social Sciences

Study areas in the Iowa Loess Hills were used to evaluate short-term responses of understory species to three treatment methods designed to facilitate restoration of Quercus macrocarpa savanna. Treatments included burning alone, burning with thinning, and burning with clear-cutting. Plant abundance and diversity were compared before treatment and one year after treatment. Ninety-nine plant species were identified during the study, of which 40 were new following treatment, although most of these were forest associates. Increases in diversity of understory species were observed after treatment, particularly in plots with combined burning and thinning. The forb group was most consistent in response …

Rapid Temporal Changes In The Expression Of A Set Of Neuromodulatory Genes During Alcohol Withdrawal In The Dorsal Vagal Complex: Molecular Evidence Of Homeostatic Disturbance., Kate Freeman, Mary M. Staehle, Zeynep H Gümüş, Rajanikanth Vadigepalli, Gregory E Gonye, Carmen N Nichols, Babatunde A Ogunnaike, Jan B Hoek, James S Schwaber

Faculty Scholarship for the College of Science & Mathematics

BACKGROUND: Chronic alcohol exposure produces neuroadaptation, which increases the risk of cellular excitotoxicity and autonomic dysfunction during withdrawal. The temporal progression and regulation of the gene expression that contributes to this physiologic and behavioral phenotype is poorly understood early in the withdrawal period. Further, it is unexplored in the dorsal vagal complex (DVC), a brainstem autonomic regulatory structure.

METHODS: We use a quantitative polymerase chain reaction platform to precisely and simultaneously measure the expression of 145 neuromodulatory genes in more than 100 rat DVC samples from control, chronically alcohol-exposed, and withdrawn rats. To gain insight into the dynamic progression and …

Rat Brain Pro-Oxidant Effects Of Peripherally Administered 5 Nm Ceria 30 Days After Exposure, Sarita S. Hardas, Rukhsana Sultana, Govind Warrier, Mo Dan, Rebecca L. Florence, Peng Wu, Eric A. Grulke, Michael T. Tseng, Jason M. Unrine, Uschi M. Graham, Robert A. Yokel, D. Allan Butterfield

Chemistry Faculty Publications

The objective of this study was to determine the residual pro-or anti-oxidant effects in rat brain 30 days after systemic administration of a 5 nm citrate-stabilized ceria dispersion. A ∼4% aqueous ceria dispersion was iv-infused (0 or 85 mg/kg) into rats which were terminated 30 days later. Ceria concentration, localization, and chemical speciation in the brain was assessed by inductively coupled plasma mass spectrometry (ICP-MS), light and electron microscopy (EM), and electron energy loss spectroscopy (EELS), respectively. Pro- or anti-oxidant effects were evaluated by measuring levels of protein carbonyls (PC), 3-nitrotyrosine (3NT), and protein-bound-4-hydroxy-2-trans-nonenal (HNE) in the hippocampus, cortex, and …

Characterization Of Xylan Utilization And Discovery Of A New Endoxylanase In Thermoanaerobacterium Saccharolyticum Through Targeted Gene Deletions, Kara K. Podkaminer, Adam M. Guss, Heather L. Trajano, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

The economical production of fuels and commodity chemicals from lignocellulose requires the utilization of both the cellulose and hemicellulose fractions. Xylanase enzymes allow greater utilization of hemicellulose while also increasing cellulose hydrolysis. Recent metabolic engineering efforts have resulted in a strain of Thermoanaerobacterium saccharolyticum that can convert C5 and C6 sugars, as well as insoluble xylan, into ethanol at high yield. To better understand the process of xylan solubilization in this organism, a series of targeted deletions were constructed in the homoethanologenic T. saccharolyticum strain M0355 to characterize xylan hydrolysis and xylose utilization in this organism. While the deletion of …

The Bench Scientist's Guide To Statistical Analysis Of Rna-Seq Data, Craig R. Yendrek, Elizabeth A. Ainsworth, Jyothi Thimmapuram

Cyber Center Publications

RNA sequencing (RNA-Seq) is emerging as a highly accurate method to quantify transcript abundance. However, analyses of the large data sets obtained by sequencing the entire transcriptome of organisms have generally been performed by bioinformatics specialists. Here we provide a step-by-step guide and outline a strategy using currently available statistical tools that results in a conservative list of differentially expressed genes. We also discuss potential sources of error in RNA-Seq analysis that could alter interpretation of global changes in gene expression.

2012 Tsu Undergraduate Research Program, David Owerbach

Office of Research Institutional Research and Scholarship

No abstract provided.

Ogden College Of Science & Engineering Newsletter (Fall 2012), Cheryl Stevens, Dean

Ogden College of Science & Engineering Publications

No abstract provided.

Changes In In Vivo Knee Contact Forces Through Gait Modification, Allison Kinney, Thor F. Besier, Amy Slider, Scott L. Delp, Darryl D. D'Lima, Benjamin J. Fregly

Mechanical and Aerospace Engineering Faculty Publications

Gait modification represents a non-invasive method for reducing knee joint loading in patients with knee osteoarthritis. Previous studies have shown that a variety of gait modifications are effective in reducing the external knee adduction moment. The external knee adduction moment is often used as a surrogate measure of medial compartment force. However, a recent study showed that reductions in the external knee adduction moment do not guarantee reductions in medial compartment loads. Therefore, direct measurement of changes in knee contact force is important for determining the effectiveness of gait modifications. A previous study found that medial thrust gait and walking …

Classification Of Genomic Sequences By Latent Semantic Analysis, Samuel F. Way

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

Evolutionary distance measures provide a means of identifying and organizing related organisms by comparing their genomic sequences. As such, techniques that quantify the level of similarity between DNA sequences are essential in our efforts to decipher the genetic code in which they are written.

Traditional methods for estimating the evolutionary distance separating two genomic sequences often require that the sequences first be aligned before they are compared. Unfortunately, this preliminary step imposes great computational burden, making this class of techniques impractical for applications involving a large number of sequences. Instead, we desire new methods for differentiating genomic sequences that eliminate …

Recovery Of Sensitive Watersheds In The Northeastern United States From Chronic Acidification: The Role Of Soil Chemistry, Chris E. Johnson

Civil and Environmental Engineering

No abstract provided.

Constraints On Acoustic Signaling Among Birds Breeding In Secondary Cavities: The Effects Of Weather, Cavity Material, And Noise On Sound Propagation, John P. Swaddle, Caitlin R. Kight, Saji Perera, Eduardo Davila-Reyes, Shena Sikora

Arts & Sciences Articles

Increasing evidence suggests that anthropogenic noise from urbanization affects animal acoustic communication. We investigated whether the begging calls of nestling Eastern Bluebirds (Sialia sialis) varied along a disturbance gradient of ambient noise. Contrary to our prediction and the results of a previous study of nestling Tree Swallows (Tachycineta bicolor), we found that nestling Eastern Bluebirds did not increase the amplitude or structural characteristics—including frequency, rate, and duration—of their vocalizations in response to ambient noise. However, we found that prevalent temperature and humidity conditions attenuated begging calls. Specifically, in warmer, more humid weather, vocalizations of nestling Eastern …

Life Cycle Boundaries And Greenhouse Gas Emissions From Beef Cattle, Quentin M. Dudley

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Beef cattle are estimated to directly contribute 26% of U.S. agricultural greenhouse gas (GHG) emissions, and future climate change policy may target reducing these emissions. Life cycle assessment (LCA) of GHG emissions from U.S. feedlot beef cattle was conducted to compare methods of the U.S. Environmental Protection Agency (EPA) with a more complete evaluation of emissions. The inclusion of emissions from crop production for feed, associated land use change, and other minor factors nearly doubled GHG emissions associated with beef feedlots from the EPA Annual Inventory estimate of 1611 kgCO₂e hd^-1 yr^-1 to 3182 ± 167 …

Ethanol And Anaerobic Conditions Reversibly Inhibit Commercial Cellulase Activity In Thermophilic Simultaneous Saccharification And Fermentation (Tssf), Kara K. Podkaminer, William R. Kenealy, Christopher D. Herring, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

A previously developed mathematical model of low solids thermophilic simultaneous saccharification and fermentation (tSSF) with Avicel was unable to predict performance at high solids using a commercial cellulase preparation (Spezyme CP) and the high ethanol yield Thermoanaerobacterium saccharolyticum strain ALK2. The observed hydrolysis proceeded more slowly than predicted at solids concentrations greater than 50 g/L Avicel. Factors responsible for this inaccuracy were investigated in this study.

Agenda: A Low-Carbon Energy Blueprint For The American West, University Of Colorado Boulder. Natural Resources Law Center, University Of Colorado Boulder. Renewable And Sustainable Energy Institute, Western Resource Advocates, Rocky Mountain Research Station (Fort Collins, Colo.)

A Low-Carbon Energy Blueprint for the American West (Martz Summer Conference, June 6-8)

The future of the planet may depend upon our ability to increase energy supplies even as we reduce carbon emissions. This conference will address how a low-carbon energy program might evolve with a particular focus on the American West. It will focus on the future of energy in the West--on a “managed transition” to a different energy mix, on the need to nest this effort in a framework that acknowledges interconnections, and on identifying the most salient opportunities to consider the legal, political, financial, and technical challenges.

Resting-State Connectivity Identifies Distinct Functional Networks In Macaque Cingulate Cortex., R Matthew Hutchison, Thilo Womelsdorf, Joseph S Gati, L Stan Leung, Ravi S Menon, Stefan Everling

Physiology and Pharmacology Publications

Subregions of the cingulate cortex represent prominent intersections in the structural networks of the primate brain. The relevance of the cingulate to the structure and dynamics of large-scale networks ultimately requires a link to functional connectivity. Here, we map fine-grained functional connectivity across the complete extent of the macaque (Macaca fascicularis) cingulate cortex and delineate subdivisions pertaining to distinct identifiable networks. In particular, we identified 4 primary networks representing the functional spectrum of the cingulate: somatomotor, attention-orienting, executive, and limbic. The cingulate nodes of these networks originated from separable subfields along the rostral-to-caudal axis and were characterized by positive and …

Observations Of Localised Effects Of The Busselton Compensating Basins On Surface Water, Groundwater And Soil Salinity, D L. Bennett, Richard J. George Dr

Resource management technical reports

Between 2001 and 2009 the Water Corporation constructed three flood-compensating basins on farmland in the Vasse and Sabina river catchments, upstream of in the city of Busselton. The basins are designed to reduce the risk of flooding in urban areas of Busselton by temporarily storing and then regulating runoff during flood events. This report fulfils the reporting requirements of a contract between the Water Corporation and the Department of Agriculture and Food. Data relating to the local groundwater and surface-water dynamics, salinity, nutrients and pH, plus changes to shallow and deep-soil salinity (from repeat ground-based electromagnetic induction [EM] surveying), was …

Computational Design And Characterization Of A Temperature-Sensitive Plasmid Replicon For Gram Positive Thermophiles, Daniel G. Olson, Lee R. Lynd

Dartmouth Scholarship

Temperature-sensitive (Ts) plasmids are useful tools for genetic engineering, but there are currently none compatible with the gram positive, thermophilic, obligate anaerobe, Clostridium thermocellum. Traditional mutagenesis techniques yield Ts mutants at a low frequency, and therefore requires the development of high-throughput screening protocols, which are also not available for this organism. Recently there has been progress in the development of computer algorithms which can predict Ts mutations. Most plasmids currently used for genetic modification of C. thermocellum are based on the replicon of plasmid pNW33N, which replicates using the RepB replication protein. To address this problem, we set out …

9th Annual Symposium Of School Of Science, Engineering And Health, Messiah College

School of Science, Engineering & Health (SEH) Symposium

No abstract provided.

The Use Of High-Solids Loadings In Biomass Pretreatment – A Review, Alicia A. Modenbach, Sue E. Nokes

Biosystems and Agricultural Engineering Faculty Publications

The use of high‐solids loadings (≥ 15% solids, w/w) in the unit operations of lignocellulose conversion processes potentially offers many advantages over lower‐solids loadings, including increased sugar and ethanol concentrations and decreased production and capital costs. Since the term lignocellulosic materials refers to a wide range of feedstocks (agricultural and forestry residues, distillery by‐products, and dedicated energy crops like grasses), the term “solids loading” here is defined by the amount of dry material that enters the process divided by the total mass of material and water added to the material. The goal of this study is to provide a consolidated …

Scholar Week, Gregg A. Chenoweth

Scholar Week Archives (2011-2015)

ONU Scholar Week #2.

Living In An Age Of Technology: College Students' Perception Of The Role Of Genetic Engineering And Reproductive Technology In Today's Society, Kayla Quadros

Honors Projects

This study examines attitudes about prevalent issues in genetics and reproduction among the college population. Eighteen interviews were conducted with students at Rhode Island College. Respondents were asked questions about their moral standpoints concerning utilizing genetic engineering for disease control and aesthetic purposes, employing assisted reproductive technologies (ARTs), regulation of such procedures, and also about media sources for which they have heard of these topics. Findings suggest that, generally, participants felt that genetic engineering for health issues is permissible, yet reprehensible for the purpose of aesthetically "designing" a baby, though four students (three of which were female) found the enhancement …

Whole-Genome Resequencing Of Two Elite Sires For The Detection Of Haplotypes Under Selection In Dairy Cattle Supporting Information, Denis M. Larkin, Hans D. Daetwyler, Alvaro G. Hernandez, Chris L. Wright, Lorie A. Hetrick, Lisa Boucek, Sharon Bachman, Jyothi Thimmapuram

Cyber Center Publications

Using a combination of whole-genome resequencing and high-density genotyping arrays, genome-wide haplotypes were reconstructed for two of the most important bulls in the history of the dairy cattle industry, Pawnee Farm Arlinda Chief (“Chief”) and his son Walkway Chief Mark (“Mark”), each accounting for ∼7% of all current genomes. We aligned 20.5 Gbp (∼7.3× coverage) and 37.9 Gbp (∼13.5× coverage) of the Chief and Mark genomic sequences, respectively. More than 1.3 million high-quality SNPs were detected in Chief and Mark sequences. The genome-wide haplotypes inherited by Mark from Chief were reconstructed using ∼1 million informative SNPs. Comparison of a set …