Engineering Commons^™

Selective Biochlorination Of Hydroxyquinolines By A Flavin-Dependent Halogenase, Fuchao Xu, Amanda Merkley, Dayu Yu, Jixun Zhan

Biological Engineering Faculty Publications

Rdc2 is a flavin-dependent halogenase from Pochonia chlamydosporia. Through the introduction of a His₆-tag to both the N- and C-termini, the isolation yield of Rdc2 from Escherichia coli using Ni-NTA affinity chromatography was increased by three-fold. In vitro reaction of Rdc2 and a flavin reductase (Fre) with seven different hydroxyquinolines revealed that 3-hydroxyquinoline (3), 5-hydroxyquinoline (5), 6-hydroxyquinoline (6), and 7-hydroxyquinoline (7) can be specifically halogenated. These products were prepared by incubating the corresponding substrates with IPTG-induced E. coli BL21(DE3)/Rdc2. They were respectively characterized as 3-hydroxy-4-chloroquinoline (3a), 5-hydroxy-6-chloroquinoline (5a), 5-chloro-6-hydroxyquinoline (6a), and 7-hydroxy-8-chloroquinoline (7a) by NMR and MS …

Alterations In Multiple Measures Of White Matter Integrity In Normal Women At High Risk For Alzheimer's Disease, Brian T. Gold, David K. Powell, Anders H. Andersen, Charles D. Smith

Neuroscience Faculty Publications

There is evidence that disruption of white matter (WM) microstructure is an early event in the course of Alzheimer's disease (AD). However, the neurobiological bases of WM microstructural declines in presymptomatic AD are unknown. In the present study we address this issue using a multimodal imaging approach to the study of presymptomatic AD. Participants were 37 high-risk (both family history of dementia and one or more APOE4 alleles) women and 20 low-risk (neither family history nor APOE4) women. Groups were matched for age, education, neuropsychological performance, and vascular factors that could affect white matter. Whole-brain analyses of diffusion tensor imaging …

Dispersion Of Cytotoxic Properties Of Multi-Walled Carbon Nanotubes Suspended In Biological Solutions With Tween 80: Their Role In Enhancing Killing Effects Of Nanosecond Pulse Electric Fields On Tumor Cell Lines, Bhargava S. Kalluri

Biological Sciences Theses & Dissertations

The objective of this study was to determine whether multi-walled carbon nanotubes (MWCNTs) suspended in the surfactant Tween 80 give an additive killing effect on tumor cells when exposed to nsPEFs. In this study, MWCNTs were suspended in DMEM and RPMI with or without T80 (surfactant). The size distribution of MWCNTs suspended in these solutions was evaluated with a Delsa™ Nano Zeta potential and sub micro particle Size Analyzer and confirmed with microscopy. The cytotoxicity of MWCNTs dispersed in different concentrations of T80 was evaluated in PANC1 (Human pancreatic cancer cell line) and Jurkat cell lines (Human T-cell lymphoblast cell …

Balancing Limiting Factors & Economic Drivers For Sustainable Midwestern Us Agricultural Residue Feedstock Supplies, Wally W. Wilhelm, J. Richard Hess, Douglas L. Karlen, Jane M. F. Johnson, David J. Muth Jr., John M. Baker, Hero T. Gollany, Jeff M. Novak, Diane E. Scott, Gary E. Varvel

Douglas L Karlen

Advanced biofuels will be developed using cellulosic feedstock rather than grain or oilseed crops that can also be used for food and feed. To be sustainable, these new agronomic production systems must be economically viable without degrading the soil and other natural resources. This review examines six agronomic factors that collectively define many of the limits and opportunities for harvesting crop residue for biofuel feedstock in the midwestern United States. The limiting factors include soil organic carbon, wind and water erosion, plant nutrient balance, soil water and temperature dynamics, soil compaction, and off-site environmental impacts. These are discussed in relationship …

Identification Of An Archaeal Presenilin-Like Intramembrane Protease, Celia Torres-Arancivia, Carolyn M. Ross, Jose Chavez, Zahra Assur, Georgia Dolios, Filippo Mancia, Iban Ubarretxena-Belandia

Publications and Research

Background: The GXGD-type diaspartyl intramembrane protease, presenilin, constitutes the catalytic core of the c-secretase multi-protein complex responsible for activating critical signaling cascades during development and for the production of b-amyloid peptides (Ab) implicated in Alzheimer’s disease. The only other known GXGD-type diaspartyl intramembrane proteases are the eukaryotic signal peptide peptidases (SPPs). The presence of presenilin-like enzymes outside eukaryots has not been demonstrated. Here we report the existence of presenilin-like GXGD-type diaspartyl intramembrane proteases in archaea.

Methodology and Principal Findings: We have employed in vitro activity assays to show that MCMJR1, a polytopic membrane protein from the archaeon Methanoculleus marisnigri JR1, …

Biological Computation, Melanie Mitchell

Computer Science Faculty Publications and Presentations

In this article, the term biological computation refers to the proposal that living organisms themselves perform computations, and, more specifically, that the abstract ideas of information and computation may be key to understanding biology in a more unified manner. It is important to point out that the study of biological computation is typically not the focus of the field of computational biology, which applies computing tools to the solution of specific biological problems. Likewise, biological computation is distinct from the field of biologically-inspired computing, which borrows ideas from biological systems such as the brain, insect colonies, and the immune system …

Physical And Chemical Characterization Of Fuel Ethanol Coproducts Relevant To Value-Added Uses, Rumela Bhadra, Kurt A. Rosentrater, Kasiviswanathan Muthukumarappan

Kurt A. Rosentrater

One of the fastest growing industries in the United States is the fuel ethanol industry. In terms of ethanol production capability, the industry has grown by more than 600% since the year 2000. The major coproducts from corn-based ethanol include distillers dried grains with solubles (DDGS) and carbon dioxide. DDGS is used as a livestock feed because it contains high quantities of protein, fiber, amino acids, and other nutrients. The goal of this study was to quantify various chemical and physical properties of DDGS, distillers wet grains (DWG), and distillers dried grain (DDG) from several plants in South Dakota. Chemical …

Negative Dielectrophoretic Capture Of Bacterial Spores In Food Matrices, Mehti Koklu, Seungkyung Park, Suresh D. Pillai, Ali Beskok

Mechanical & Aerospace Engineering Faculty Publications

A microfluidic device with planar square electrodes is developed for capturing particles from high conductivity media using negative dielectrophoresis (n-DEP). Specifically, Bacillus subtilis and Clostridium sporogenes spores, and polystyrene particles are tested in NaCl solution (0.05 and 0.225 S/m), apple juice (0.225 S/m), and milk (0.525 S/m). Depending on the conductivity of the medium, the Joule heating produces electrothermal flow (ETF), which continuously circulates and transports the particles to the DEP capture sites. Combination of the ETF and n-DEP results in different particle capture efficiencies as a function of the conductivity. Utilizing 20 μm height DEP chambers, “almost complete” and …

Development Of Pyrf-Based Genetic System For Targeted Gene Deletion In Clostridium Thermocellum And Creation Of A Pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. Mccool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

We report development of a genetic system for making targeted gene knockouts in Clostridium thermocellum, a thermophilic anaerobic bacterium that rapidly solubilizes cellulose. A toxic uracil analog, 5-fluoroorotic acid (5-FOA), was used to select for deletion of the pyrF gene. The ΔpyrF strain is a uracil auxotroph that could be restored to a prototroph via ectopic expression of pyrF from a plasmid, providing a positive genetic selection. Furthermore, 5-FOA was used to select against plasmid-expressed pyrF, creating a negative selection for plasmid loss. This technology was used to delete a gene involved in organic acid production, namely pta, which encodes …

3d Micro-Mr And Micro-Ct Models For Determining In-Vivo Function In The Guinea Pig Knee Model Of Osteoarthritis (Oa), Kristoffer W. Dean

Undergraduate Research Opportunities Program (UROP)

Osteoarthritis (OA) is a debilitating disease that affects an estimated 27 million adults in the United States. OA causes damage to cartilage in the joints resulting in bones that rub together. This creates pain, swelling, loss of motion of the joint, and bone spurs. As the number of adults above 65 grows (an estimated 72 million people by 2030) even more people will be at high risk for OA. It is the most common type of arthritis by far yet very little is known about it including relationships between joint structure and function. In 2004, the NIH created the Osteoarthritis …

Birdstrike Mitigation - Beyond The Airport, Paul Eschenfelder, Russ Defusco

Paul F. Eschenfelder

No abstract provided.

Insect-Damaged Corn Stalks Decompose At Rates Similar To Bt-Protected, Non-Damaged Corn Stalks, R. Michael Lehman, Shannon L. Osborne, Deirdre A. Prischmann-Voldseth, Kurt A. Rosentrater

Kurt A. Rosentrater

The relative decomposability of corn (Zea mays L.) residues from insect (Bt)-protected hybrids and conventional hybrids cultivated under insect pressure was investigated in two studies. Above-ground biomass, residue macromolecular composition, and stalk physical strength were also measured. In the first decomposition study, chopped residues (stalks and leaves) were used from a corn rootworm-protected (Cry3Bb1) hybrid and its non-Bt near isoline that were grown in replicated plots infested with corn rootworms (Diabrotica spp.). In the second study, residue (intact stalk sections) was used from three European corn borer (ECB, Ostrinia nubilalis Hübner)-resistant (Cry1Ab) hybrids representing different seed manufacturer/maturity date series, their …

Pre-Swing Deficits In Forward Propulsion, Swing Initiation And Power Generation By Individual Muscles In Hemiparetic Walking, Carrie L. Peterson, Allison Kinney, Steven A. Kautz, Richard R. Neptune

Mechanical and Aerospace Engineering Faculty Publications

Clinical studies of hemiparetic walking have shown pre-swing abnormalities in the paretic leg suggesting that paretic muscle contributions to important biomechanical walking subtasks are different than those of non-disabled individuals. Three-dimensional forward dynamics simulations of two representative hemiparetic subjects with different levels of walking function classified by self-selected walking speed (i.e., limited community=0.4–0.8 m/s and community walkers=>0.8 m/s) and a speed-matched control were generated to quantify individual muscle contributions to forward propulsion, swing initiation and power generation during the pre-swing phase (i.e., double support phase proceeding toe-off). Simulation analyses identified decreased paretic soleus and gastrocnemius contributions to forward propulsion …

Relationships Between Muscle Contributions To Walking Subtasks And Functional Walking Status In Persons With Post-Stroke Hemiparesis, Allison Kinney, Carrie L. Peterson, Steven A. Kautz, Richard R. Neptune

Mechanical and Aerospace Engineering Faculty Publications

Walking speed is commonly used to predict stroke severity and assess functional walking status (i.e., household, limited community and community walking status) post-stroke. The underlying mechanisms that limit walking speed (and functional walking status by extension) need to be understood to improve post-stroke rehabilitation. Previous experimental studies have shown correlations between paretic plantarflexor output during the pre-swing phase and walking speed and suggest that the paretic hip flexors can compensate in some hemiparetic subjects. Modeling and simulation studies of healthy walking have shown that the ankle plantarflexors, soleus (SOL) and gastrocnemius (GAS), and uniarticular hip flexors (IL) are essential contributors …

Graph Algorithms For Machine Learning: A Case-Control Study Based On Prostate Cancer Populations And High Throughput Transcriptomic Data, Gary L. Rogers, Pablo Moscato, Michael A. Langston

Faculty Publications and Other Works -- EECS

Background

The continuing proliferation of high-throughput biological data promises to revolutionize personalized medicine. Confirming the presence or absence of disease is an important goal. In this study, we seek to identify genes, gene products and biological pathways that are crucial to human health, with prostate cancer chosen as the target disease.

Materials and methods

Using case-control transcriptomic data, we devise a graph theoretical toolkit for this task. It employs both innovative algorithms and novel two-way correlations to pinpoint putative biomarkers that classify unknown samples as cancerous or normal.

Results and conclusion

Observed accuracy on real data suggests that we are …

Hydroxyl-Terminated Poly(Urethane Acrylate) As A Soft Liner In Dental Applications: Synthesis And Characterization, Selda Keskin

ABSTRACT: Hydroxyl-terminated poly(urethane acrylate) s were synthesized for use in biomedical applications. Acrylate end capping via an interesterification reaction was successfully achieved with methacryloyl chloride addition to the hydroxyl ends of the polyurethane at low temperatures. 2,4-Toluene diisocyanate, 1,6-hexane diisocyanate, and methylene diphenyl diisocyanate were used as diisocyanates for urethane synthesis, and they were end-capped with methyl methacrylate and hydroxyethyl methacrylate. The nature of the monomers that we used had an effect on the thermal and morphological properties that were interpreted in terms of the level of hydrogen bonding and the degree of phase separation. The synthesized polymers were characterized …

Experimental Investigation Of A Non-Thermal Atmospheric Pressure Plasma Jet, Asma Begum

Electrical & Computer Engineering Theses & Dissertations

The main objective of this dissertation is to understand the formation of the plasma jet from the plasma pencil, and the propagation of the plasma jet in the ambient atmosphere where the effect of the external electric field is almost zero. Before investigating the formation and propagation phenomenon of the plasma jet, common physical properties of plasma jets are determined by using the imaging technique and optical emission spectroscopy. The first goal of this dissertation is to establish the laminar helium gas flow channel through a plasma pencil.

The formation position, formation time, and the criterion of the plasma jet …

Letter To Faa Administrator Re: Usair 1549 Crash, Paul F. Eschenfelder, Russell P. Defusco Phd, Richard Sowden

Paul F. Eschenfelder

No abstract provided.

A Review Of Alternatives To Wheat Flour, Shirin Pourafshar, Kurt A. Rosentrater, Padmanaban Krishnan

Kurt A. Rosentrater

For centuries, cereals have been major food stuffs used all around the world; because of that, there are many different kinds of breads produced from different types of flours. Despite the variety of flours available, there are still many challenges to produce ingredients which maximize nutrient components, and with which healthier breads and other products can be produced. As studies have shown, traditional wheat flour has some nutritional deficiencies (although this is a matter of perspective), which depend on the level of consumption. Additionally, gluten intolerance and Celiac disease are growing problems. The nutritional value of breads can be enhanced …

Malnutrition, A Global Problem, Shirin Pourafshar, Kurt A. Rosentrater, Padmanaban Krishnan

Kurt A. Rosentrater

Malnutrition is a general term for medical conditions caused by an inadequate diet and poor nutrition. Hunger and malnutrition are among the major difficulties confronting many countries around the world. Malnutrition can be caused by several factors, such as the sharp increase in population (current world population is approximately 6,800,000,000), poor distribution of foods, lack of access to highly nutritious foods, and most important, lack of knowledge about healthy diets. Malnutrition can lead to other problems, such as reduced school attendance, learning capacity, spread of HIV/AIDS, malaria and other diseases, and it can have a negative effect on a nation’s …

Effects Of Varying Cds, Drying And Cooling Temperatures On Glass Transition Temperature Of Ddgs, Rumela Bhadra, Kurt A. Rosentrater, Kasiviswanathan Muthukumarappan

Kurt A. Rosentrater

Distillers dried grains with solubles (DDGS), a co product of the corn-based fuel ethanol industry, is used widely as an animal feed. Due to increased demand for DDGS in livestock markets it has become essential to transport DDGS over long distances. Flowability problems in DDGS, due to particle caking, often create nuisance in storage and transportation. Materials above the glass transition temperature (Tg) can exist in a “rubbery state,” this condition can often be responsible for structural collapse, particle agglomeration, and caking of materials. This study investigated the effects of varying CDS (10, 15, and 20%, wb), drying (100, 200, …

Twin-Screw Extrusion Processing Of Distillers Dried Grains With Solubles (Ddgs)-Based Yellow Perch (Perca Flavescens) Feeds, Ferouz Y. Ayadi, Kurt A. Rosentrater, Kasiviswanathan Muthukumarappan, Michael L. Brown

Kurt A. Rosentrater

Due to tremendous increases in global aquaculture production, compounded with limited availabilities of fish meal for fish feed, the need for alternative protein sources cannot be disregarded. Toward that end, twin-screw extrusion studies were performed to investigate the production of nutritionally-balanced feeds for juvenile yellow perch (Perca flavescens). Five isocaloric (~ 3.06 kcal/g) ingredient blends, adjusted to a similar protein content of 36.7% db, were formulated with 0, 10, 20, 30, and 40% distillers dried grains with solubles (DDGS) at an initial moisture content of 5-7% db, with appropriate amounts of fish meal, fish oil, whole wheat flour, corn gluten …

Twin-Screw Extrusion Processing Of Distillers Dried Grains With Solubles (Ddgs)-Based Rainbow Trout (Oncorhynchus Mykiss) Feeds, Ferouz Y. Ayadi, Kasiviswanathan Muthukumarappan, Kurt A. Rosentrater, Michael L. Brown

Kurt A. Rosentrater

The world’s increasing demand for seafood products has resulted in rising demands for fish meal for fish feed, which must be compensated for by searching for effective alternative protein sources. In this study, twin-screw extrusion trials were conducted to study the production of nutritionally-balanced feeds for rainbow trout fingerlings (Oncorhynchus mykiss). Six isocaloric (~ 4.61 kcal/g) ingredient blends with a similar protein content of 52.8% db were formulated with 0, 10, 20, 30, 40 and 50% distillers dried grains with solubles (DDGS) and other ingredients (i.e. fish meal, fish oil, whole wheat flour, corn gluten meal, and vitamin and mineral …

Some Middle Eastern Breads, Their Characteristics And Their Production, Shirin Pourafshar, Padmanaban Krishnan, Kurt A. Rosentrater

Kurt A. Rosentrater

In Middle Eastern countries, there are many traditional products which are made from wheat; bread is the most important one, and it is eaten with almost every kind of food. The goals of this study are to 1) in general, review major types of breads in the Middle East, and 2) specifically discuss Iranian breads. There are four major Iranian flat breads; all of these are fundamentally the same, and the dough in all of them consists of water, yeast, baking powder, and wheat flour, but they also have some ingredients which are specific to each product. The first of …

Effects Of Varying Cds Levels And Drying And Cooling Temperatures On Flowability Properties Of Ddgs, Rumela Bhadra, Kasiviswanathan Muthukumarappan, Kurt A. Rosentrater

Kurt A. Rosentrater

Demand for alternative fuels and the need to reduce dependence on fossil fuels, have triggered the growth of corn-based ethanol production, and this is expected to rise in future years. Transportation of the co-product distillers dried grains with solubles (DDGS) from this industry occurs under various environmental conditions. It is often problematic, since caking between the particles can lead to flow problems. In this study we have prepared DDGS by combining condensed distillers solubles (CDS) with distillers wet grains (DWG) and then drying. We investigated the effects of CDS (10, 15, and 20% wb), drying temperature (100, 200, and 300°C), …

Turning Packaging Into Profit, Rihaz Z. Chughatta

Rihaz Z Chughatta

Packaging can be an expensive function to maintain, but it doesn’t have to be. In fact, Packaging can be a source of income for a company. More accurately, what if you took a look at your company’s Profit and Loss and saw Packaging as a negative expense? That’s right, you can turn packaging into profit for your company. How do you accomplish this feat? Glad you asked … read on to find three simple ways to start this process (and satisfy your curiosity) …

A Synthetic Biological Engineering Approach To Secretion- Based Recovery Of Polyhydroxyalkanoates And Other Cellular Products, Elisabeth Linton

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The costs associated with cellular product recovery commonly account for as much as 80% of the total production expense. As a specific example, significant recovery costs limit commercial use of polyhydroxyalkanoates (PHA), which comprise a class of microbially-accumulated polyesters. PHAs are biodegradable compounds that are of interest as a sustainable alternative to petrochemically-derived plastics. Secretion-based recovery of PHAs was studied to decrease PHA production costs. Type I and II secretory pathways are commonly used for the translocation of recombinant proteins out of the cytoplasm of E. coli. Proteins were targeted for translocation using four signal peptides (HlyA, TorA, GeneIII, …

The Hypericum Perforatum Herb As An Antimycobacterial Agent And Its Implications As An Additional Tuberculosis Medication, Trent W. Mortensen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

An immediate demand exists for new tuberculosis (TB) antibiotics due to the ever-increasing spread of drug-resistant strains. The drug-development process goes through four phases, the first (Phase 0) of which is to demonstrate and investigate drug effectiveness and toxicity. This research investigated the effectiveness of the Hypericum perforatum herb (commonly St. John's wort (SJW)) in its growth inhibition of mycobacteria and its viability effect on human lung cells.

Organic-solvent SJW extracts were effective at inhibiting every nonpathogenic genetically sequenced Mycobacterium isolate currently available (six isolates) in preliminary studies. Quantitative studies of five Mycobacterium isolates showed an order of concentration sensitivity …

Rapid Diagnosis Of Tuberculosis In A Peripheral Setting, Elsje Pienaar

Department of Chemical and Biomolecular Engineering: Theses and Student Research

Tuberculosis is an ancient and worldwide epidemic affecting millions of people in mainly the developing world, killing almost 2 million people in 2008. Current diagnostic techniques are outdated and have proven insufficient to control the disease. Smear microscopy has poor sensitivity and culture is slow to yield results. Modern diagnostic techniques are making great strides in shortening time to result but are restricted by two qualities: 1) prohibitively high costs prevent implementation in resource poor areas, and 2) equipment and technician requirements limit application to centralized laboratories. There exists a divide between new technologies and the people that need them …

Developing Chitosan-Based Biomaterials For Brain Repair And Neuroprosthetics, Zheng Cao

Masters Theses

Chitosan is widely investigated for biomedical applications due to its excellent properties, such as biocompatibility, biodegradability, bioadhesivity, antibacterial, etc. In the field of neural engineering, it has been extensively studied in forms of film and hydrogel, and has been used as scaffolds for nerve regeneration in the peripheral nervous system and spinal cord. One of the main issues in neural engineering is the incapability of neuron to attach on biomaterials. The present study, from a new aspect, aims to take advantage of the bio-adhesive property of chitosan to develop chitosan-based materials for neural engineering, specifically in the fields of brain …