Biotechnology Commons^™

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.

Enhanced Hydrocarbon Biodegradation Using Bioaugmentation With Biowish™-Aqua Fog, Michael Robert Lehrer

Master's Theses

This study was done to determine the effectiveness of a commercially available bioaugmentation product, BiOWiSH^TM-Aqua FOG, for remediating petroleum-contaminated sandy soil. Biodegradation enhancement by BiOWiSH^TM-Aqua FOG was evaluated in laboratory microcosms by directly measuring total petroleum hydrocarbon (TPH) and indirectly using respirometry. Attempts were made to enrich hydrocarbon-degrading bacteria in BiOWiSH^TM-Aqua FOG, and the resulting enrichment cultures were screened using respirometry as well. Potential hydrocarbon-degrading bacteria in BiOWiSH^TM-Aqua FOG were isolated. Experiments were performed at bench-scale using microcosm bottles containing sand contaminated with either motor oil or No. 2 diesel fuel. The …

Urinary Copper Elevation In A Mouse Model Of Wilson’S Disease Is A Regulated Process To Specifically Decrease The Hepatic Copper Load, Lawrence W. Gray, Fangyu Peng, Shannon A. Molloy, Venkata S. Pendyala, Abigael Muchenditsi, Otto Muzik, Jaekwon Lee, Jack H. Kaplan, Svetlana Lutsenko

Department of Biochemistry: Faculty Publications

Body copper homeostasis is regulated by the liver, which removes excess copper via bile. In Wilson’s disease (WD), this function is disrupted due to inactivation of the copper transporter ATP7B resulting in hepatic copper overload. High urinary copper is a diagnostic feature of WD linked to liver malfunction; the mechanism behind urinary copper elevation is not fully understood. Using Positron Emission Tomography-Computed Tomography (PET-CT) imaging of live Atp7b^‒/^‒ mice at different stages of disease, a longitudinal metal analysis, and characterization of copper-binding molecules, we show that urinary copper elevation is a specific regulatory process mediated …

Energy-Saving Hypothermia Reduces Flight Ability In Mourning Doves, Jennie M. Carr, Steven L. Lima

Symposium 2012

Overwintering birds are frequently exposed to thermal challenges that can quickly decrease energy reserves, thus leading to an increase in the risk of starvation. During these periods of energetic hardship, many avian species use nocturnal hypothermia to conserve energy that would otherwise be lost remaining warm throughout the night (McKechnie & Lovegrove 2002). However, a cool body temperature (Tb) may limit a bird’s ability to monitor the environment and may slow their response to a potential threat. Thus, birds likely trade-off between the benefits of energy-saving hypothermia and the potential costs of reduced behavioral responsiveness to predators (Welton et al. …

Conservation Of Oxidative Protein Stabilization In An Insect Homologue Of The Parkinsonism-Associated Protein Dj-1, Jiusheng Lin, Janani Prahlad, Mark A. Wilson

Department of Biochemistry: Faculty Publications

DJ-1 is a conserved, disease-associated protein that protects against oxidative stress and mitochondrial damage in multiple organisms. Human DJ-1 contains a functionally essential cysteine residue (Cys106) whose oxidation is important for regulating protein function by an unknown mechanism. This residue is well conserved in other DJ-1 homologues, including two (DJ-1α and DJ-1β) in Drosophila melanogaster. Because D. melanogaster is a powerful model system for studying DJ-1 function, we have determined the crystal structure and impact of cysteine oxidation on Drosophila DJ-1β. The structure of D. melanogaster DJ-1β is similar to that of human DJ-1, although two important residues in …

Dcm Methylation Is Detrimental To Plasmid Transformation In Clostridium Thermocellum, Adam M. Guss, Daniel G. Olson, Nicky C. Caiazza, Lee R. Lynd

Dartmouth Scholarship

Background: Industrial production of biofuels and other products by cellulolytic microorganisms is of interest but hindered by the nascent state of genetic tools. Although a genetic system for Clostridium thermocellum DSM1313 has recently been developed, available methods achieve relatively low efficiency and similar plasmids can transform C. thermocellum at dramatically different efficiencies. Results: We report an increase in transformation efficiency of C. thermocellum for a variety of plasmids by using DNA that has been methylated by Escherichia coli Dam but not Dcm methylases. When isolated from a dam + dcm + E. coli strain, pAMG206 transforms C. thermocellum 100-fold better …

Design And Implementation Of A Shoulder Simulator, Chelsea Lynn Kowal

Renée Crown University Honors Thesis Projects - All

The main objective of this thesis project is to build a shoulder simulator to be able to understand the mechanics of the shoulder, specifically the rotator cuff and deltoid muscles. The shoulder simulator should be able to mimic the important motions of the human shoulder by pulling on tendons of cadaver shoulders and moving the shoulder in various specified motions. In my thesis project, I worked on creating a shoulder simulator that would control the rotator cuff muscles along with the three deltoid muscles. In order to do this, I needed to design and test the shoulder simulator using cadaver …

Biomass Assisted Synthesis Of Antibacterial Gold Nanoparticles And Commentary On Its Future Potential And Applications In Medicine, Chad Willis

Mahurin Honors College Capstone Experience/Thesis Projects

Xylose is a natural monosaccharide found in biomass such as straw, pecan shells, cottonseed hulls, and corncobs. Using this monosaccharide, we report the green synthesis and characterization of biocompatible, biodegradable xylose encapsulated gold nanoparticles (Xyl-GNPs) with potential antibacterial activity. GNPs were synthesized using the bioreduction property of xylose on the chloroaurate anions in an aqueous solution at room temperature and at atmospheric pressure. The characterization of synthesized GNPs was examined by UV-vis spectroscopy; transmission electron microscopy (TEM), energy-dispersive x-ray spectroscopy (EDS) and fourier transform infrared spectroscopy (FTIR). Results indicate that the particles were stable; near spherical in shape with an …

Fluorescence-Based Reporter For Gauging Cyclic Di-Gmp Levels In Pseudomonas Aeruginosa, Morten T. Rybtke, Bradley R. Borlee, Keiji Murakami, Yasuhiko Irie, Morten Hentzer, Thomas E. Nielsen, Michael Givskov, Matthew R. Parsek, Tim Tolker-Nielsen

Biology Faculty Publications

The increased tolerance toward the host immune system and antibiotics displayed by biofilm-forming Pseudomonas aeruginosa and other bacteria in chronic infections such as cystic fibrosis bronchopneumonia is of major concern. Targeting of biofilm formation is believed to be a key aspect in the development of novel antipathogenic drugs that can augment the effect of classic antibiotics by decreasing antimicrobial tolerance. The second messenger cyclic di-GMP is a positive regulator of biofilm formation, and cyclic di-GMP signaling is now regarded as a potential target for the development of antipathogenic compounds. Here we describe the development of fluorescent monitors that can gauge …

Automation Of Tangential Flow Filtration For Purification Of Biosynthetic Spider Silk, Candace N. Clark

Undergraduate Honors Capstone Projects

The objective of this project is to create a user-friendly, automated flow regulation system for a tangential flow filtration (TFF) process. These filtration units are crucial for the initial stages of extracting the spider silk proteins from transgenic goat milk. Automated flow regulation systems do exist, but not at an appropriate scale for this application. This system will allow bench-top studies to be conducted with automated efficiency. Spider silk is an amazing material and if commercially available, it could be used in hundreds of applications. Currently, cost effective production is the most significant issue stopping large-scale production and use of …

Optimization Of A Novel Two-Stage Whole-Cell Enzyme Production And Lignocellulose Hydrolysis Reactor Design, Brian Daniel Deis

Boise State University Theses and Dissertations

Production of lignocellulosic biofuels is one mechanism by which we can reduce our dependence on fossil fuels and enhance the carbon neutrality of transportation fuels. Current biochemical platforms for lignocellulosic biofuel production are not economically viable due to the high costs of hydrolytic enzymes for the conversion of lignocellulose to fermentable sugars. One solution to reducing these costs is the incorporation of on-site enzyme production for consolidated bioprocessing of lignocellulose to fermentable sugars. I have optimized and incorporated a whole-cell encapsulation approach into a novel two-stage fed-batch bioreactor consisting of a nursery reactor and hydrolysis reactor. This design spatially separates …

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 …

Assesment Of Social And Economic Impacts Of Biogas Digesters In Rural Kenya, Alison Hamlin

Independent Study Project (ISP) Collection

Although biogas technology has been in Kenya for over fifty years, it is only recently that the technology has begun to increase in popularity due to a new subsidy program. In this study, twenty-one households with fixed dome biogas digesters were visited and interviews with plant owners were carried out in order to gauge the social and economic impacts of digester use in addition to understand current challenges relating to biogas technology and the future of the industry. Of the homes visited in Kiambu County and Ngong, the greatest impact of using biogas was deemed financial, due to the monthly …

Neurodegeneration - A Means To An End, Amit Singh

Biology Faculty Publications

Cell death, a global phenomenon found throughout the animal kingdom, is a mechanism to maintain tissue homeostasis and for adaptation to changes in the environment [1,2]. Millions of cells die in our body daily- they succumb to stress and commit suicide by a mechanism referred to as cell death or apoptosis [2-4]. Under normal conditions cells are continuously replaced by new cells from the stemor progenitor- cells. For example, an optimum balance in shedding of dead cells from the skin and their replenishment by new ones maintain our health and hygiene. In this context, apoptosis is a mechanism to eliminate …

Investigation Of Bacillus Subtilis As A Biopesticide Against Botrytis Cinerea, Kenneth K. Ng

Master's Theses

The objective of this thesis was to investigate BiOWiSH^TM-Aqua, a commercial dry solid formulation containing a consortium of bacteria and yeast, as a biopesticide for treatment of Botrytis cinerea, a gray mold that affects strawberries. BiOWiSH^TM-Aqua was compared with another commercial product specifically used as a fungicide and bacteriocide, Serenade® Garden Disease Control Spray (concentrated Bacillus subtilis strain QST 713). Both laboratory tests as well as in vivo lab tests were conducted. BiOWiSH^TM-Aqua results varied widely from plate to plate, regardless of experimental conditions. In some of these plates, inhibition zones were observed …

Composition And Evolution Of The Vertebrate And Mammalian Selenoproteomes, Marco Mariotti, Perry G. Ridge, Yan Zhang, Alexei V. Lobanov, Thomas H. Pringle, Roderic Guigo, Dolph L. Hatfield, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Background: Selenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec). Human genome codes for 25 Sec-containing protein genes, and mouse and rat genomes for 24.

Methodology/Principal Findings: We characterized the selenoproteomes of 44 sequenced vertebrates by applying gene prediction and phylogenetic reconstruction methods, supplemented with the analyses of gene structures, alternative splicing isoforms, untranslated regions, SECIS elements, and pseudogenes. In total, we detected 45 selenoprotein subfamilies. 28 of them were found in mammals, and 41 in bony fishes. We define the ancestral vertebrate (28 proteins) and mammalian …

Connections Between Sphingosine Kinase And Phospholipase D In The Abscisic Acid Signaling Pathway In Arabidopsis, Liang Guo, Girish Mishra, Jennifer E. Markham, Maoyin Li, Amanda Tawfall, Ruth Welti, Xuemin Wang

Department of Biochemistry: Faculty Publications

Background: Sphingosine kinase (SPHK) and phospholipaseD(PLD) produce different lipid mediators involved in abscisic acid (ABA) response.

Results: Ablation of SPHKs and PLDα1 attenuates ABA-induced production of LCBPs and PA. Phyto-S1P closes stomata in sphk1, sphk2, but not in pldα1, whereas PA closes stomata in all mutants.

Conclusion: SPHK acts upstream of PLDα1, whereas PLDα1 promotes SPHK.

Significance: The roles of lipid messengers in the ABA signaling pathway are clarified.

Tumor Suppression By Cell Competition Through Regulation Of The Hippo Pathway, Chiao-Lin Chen, Molly C. Schroeder, Madhuri Kango-Singh, Chunyao Tao, Georg Halder

Biology Faculty Publications

Homeostatic mechanisms can eliminate abnormal cells to prevent diseases such as cancer. However, the underlying mechanisms of this surveillance are poorly understood. Here we investigated how clones of cells mutant for the neoplastic tumor suppressor gene scribble (scrib) are eliminated from Drosophila imaginal discs. When all cells in imaginal discs are mutant for scrib, they hyperactivate the Hippo pathway effector Yorkie (Yki), which drives growth of the discs into large neoplastic masses. Strikingly, when discs also contain normal cells, the scrib− cells do not overproliferate and eventually undergo apoptosis through JNK-dependent mechanisms. However, induction of apoptosis does …

Out Of Sight, But Not Out Of Mind: A Look At Nanoparticles In The Marine Environment, Evan Ward, John J. Doyle

Wrack Lines

Nanoparticles exist in many products used by humans, such as sunscreens. medications, cosmetics, paints and electronics. But what is the effect of these tiny particles on the ocean or estuarine environment when the sunscreen washes off? This article looks at that question and at shellfish in particular. Evan Ward and John Doyle are marine scientists at UConn.

Isolation And Characterization Of Galactinol Synthases From Hybrid Poplar, Faride Unda, Thomas Canam, Lindsay Preston, Shawn D. Mansfield

Faculty Research & Creative Activity

The raffinose family of oligosaccharides (RFOs) serve as transport carbohydrates in the phloem, storage compounds in sink tissues, and putative biological agents to combat both abiotic and biotic stress in several plant species. To investigate further the functional roles of this class of compounds in trees, two cDNAs encoding galactinol synthase (GolS, EC 2.4.1.123), which catalyses the first step in the biosynthesis of RFOs, were identified and cloned from hybrid poplar (Populus alba3grandidentata). Phylogenetic analyses of the Populus GolS isoforms with other known GolS proteins suggested a putative role for these enzymes during biotic or abiotic stress in hybrid poplar. …

Tgd1, -2, And -3 Proteins Involved In Lipid Trafficking Form Atp-Binding Cassette (Abc) Transporter With Multiple Substrate-Binding Proteins, Rebecca Roston, Jinpeng Gao, Monika W. Murcha, James Whelan, Christoph Benning

Department of Biochemistry: Faculty Publications

Background: ATP-binding cassette transporters exist in all life forms and usually require only one substrate-binding domain.

Results: The TRIGALACTOSYLDIACYLGLYCEROL (TGD) complex contains 8–12 substrate-binding proteins.

Conclusion: Multiple substrate-binding proteins may be needed by the TGD complex to enhance its putative lipid transport activity.

Significance: Knowing the subunit stoichiometry of the TGD complex furthers understanding of lipid transfer between chloroplast membranes.

Isolation And Characterization Of Galactinol Synthases From Hybrid Poplar, Faride Unda, Thomas Canam, Lindsay Preston, Shawn Mansfield

Faculty Research & Creative Activity

The raffinose family of oligosaccharides (RFOs) serve as transport carbohydrates in the phloem, storage compounds in sink tissues, and putative biological agents to combat both abiotic and biotic stress in several plant species. To investigate further the functional roles of this class of compounds in trees, two cDNAs encoding galactinol synthase (GolS, EC 2.4.1.123), which catalyses the first step in the biosynthesis of RFOs, were identified and cloned from hybrid poplar (Populus alba3grandidentata). Phylogenetic analyses of the Populus GolS isoforms with other known GolS proteins suggested a putative role for these enzymes during biotic or abiotic stress in hybrid poplar. …

Nutraceutical Antioxidants And Their Therapeutic Potential In Neurodegeneration, Erika Kristine Ross

Electronic Theses and Dissertations

Amyotrophic lateral sclerosis (ALS) is a fatal neuromuscular disease that affects motor neurons of the brain and spinal cord. Many studies indicate that mitochondrial oxidative stress (MOS) is a principal mechanism underlying the pathophysiology of this and other devastating neurodegenerative diseases. Here, we investigated a unique whey protein supplement (Immunocal®) to determine its neuroprotective efficacy in several in vitro models of MOS and in an in vivo mouse model of ALS. This non-denatured whey supplement contains cystine which is an oxidized form of cysteine, an essential precursor for synthesis of the endogenous antioxidant, glutathione (GSH). In primary cultured rat cerebellar …

A Novel Link Between Akt1 And Twist1 In Ovarian Tumor Cell Motility And Invasiveness, Nirav Shah

Electronic Theses and Dissertations

Ovarian cancer results in more deaths per year than any other cancer of the female reproductive system. The low survival rate is partly due to the lack of early detection and the susceptibility to relapse. The AKT serine threonine kinase plays a pivotal role in hallmark cellular processes for the progression of ovarian cancer, including tumor cell growth and migration. Therapeutic targeting of pan-AKT has been problematic, in part due to feedback mechanisms and crosstalk with other pathways. The hypothesis for this study is that AKT 1, -2 and -3 isoforms may have different roles and regulate cell processes in …

Wall_1.6 — Acknowledgements, Allison Marsh

Section 1: Introduction

No abstract provided.

Proline Dehydrogenase Is Essential For Proline Protection Against Hydrogen Peroxide Induced Cell Death, Sathish Kumar Natarajan, Weidong Zhu, Xinwen Liang, Lu Zhang, Andrew Demers, Matthew C. Zimmerman, Melanie A. Simpson, Donald F. Becker

Department of Biochemistry: Faculty Publications

Proline metabolism has an underlying role in apoptotic signaling that impacts tumorigenesis. Proline is oxidized to glutamate in the mitochondria with the rate limiting step catalyzed by proline dehydrogenase (PRODH). PRODH expression is inducible by p53 leading to increased proline oxidation, reactive oxygen species (ROS) formation, and induction of apoptosis. Paradoxical to its role in apoptosis, proline also protects cells against oxidative stress. Here we explore the mechanism of proline protection against hydrogen peroxide stress in melanoma WM35 cells. Treatment of WM35 cells with proline significantly increased cell viability, diminished oxidative damage of cellular lipids and proteins, and retained ATP …

Influence Of Peptide Dipoles And Hydrogen Bonds On Reactive Cysteine PkA Values In Fission Yeast Dj-1, Peter Madzelan, Tetyana Labunksa, Mark A. Wilson

Department of Biochemistry: Faculty Publications

Cysteine residues with depressed pK_a values are critical for the functions of many proteins. Several types of interactions can stabilize cysteine thiolate anions, including hydrogen bonds between thiol(ate)s and nearby residues as well as electrostatic interactions involving charged residues or dipoles. Dipolar stabilization of thiolates by peptide groups has been suggested to play a particularly important role near the N-termini of α-helices. Using a combination of X-ray crystallography, site-directed mutagenesis, and spectroscopic methods, we show that the reactive cysteine residue (Cys111) in Schizosaccharomyces pombe DJ-1 experiences a 0.6 unit depression of its thiol pK_a as a consequence of …

Structure, Function, And Assembly Of Heme Centers In Mitochondrial Respiratory Complexes, Hyung J. Kim, Oleh Khalimonchuk, Pamela M. Smith, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The sequential flow of electrons in the respiratory chain, from a low reduction potential substrate to O₂, is mediated by protein-bound redox cofactors. In mitochondria, hemes—together with flavin, iron–sulfur, and copper cofactors—mediate this multi-electron transfer. Hemes, in three different forms, are used as a protein-bound prosthetic group in succinate dehydrogenase (complex II), in bc₁ complex (complex III) and in cytochrome c oxidase (complex IV). The exact function of heme b in complex II is still unclear, and lags behind in operational detail that is available for the hemes of complex III and IV. The two b hemes …

Modeling An Improvement In Phosphorus Utilization In Tropical Agriculture, David Edelstein, David J. Tonjes

Technology & Society Faculty Publications

Studies of Terra Preta soils have generated interest in recreating their fertility elsewhere. Much of the research has focused on soil amendment charcoal (“biochar”). Terra Preta also contains bone fragments, producing a high concentration of phosphorus. Some forecast worldwide declines in phosphorus supplies, and better agricultural system management is required to improve phosphorus use efficiency. A conceptual model is offered to consider the influence of charcoal on bioavailability of phosphorus. The model describes a system where improvements in the chemical and biological condition of the soil result in increased phosphorus availability and cycling. Mechanisms of phosphorus/charcoal interaction are considered, and …

Bio-Logic Builder: A Non-Technical Tool For Building Dynamical, Qualitative Models, Tomáš Helikar, Bryan Kowal, Alex Madrahimov, Manish Shrestha, Jay Pedersen, Kahani Limbu, Ishwor Thapa, Thaine Rowley, Rahul Satalkar, Naomi Kochi, John Konvalina, Jim A. Rogers

Department of Biochemistry: Faculty Publications

Computational modeling of biological processes is a promising tool in biomedical research. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. To help address this issue, we have developed a web-based tool, Bio- Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) of biological regulatory mechanisms in a modular and non-technical fashion. As part of the user interface, generalized ‘‘biologic’’ modules have been defined to provide users with the building blocks for …